Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
JalviewModel	415	26	20	0.8461538684.6%	Show methods
JalviewModel.FeatureSettings	784	6	4	1.0100%	Show methods
JalviewModel.FeatureSettings.Group	876	4	4	1.0100%	Show methods
JalviewModel.FeatureSettings.Setting	963	31	29	0.967741996.8%	Show methods
JalviewModel.JGroup	1411	69	61	0.891304489.1%	Show methods
JalviewModel.JSeq	2307	26	22	0.980769298.1%	Show methods
JalviewModel.JSeq.Pdbids	2675	3	2	1.0100%	Show methods
JalviewModel.JSeq.Pdbids.StructureState	2742	28	25	0.821428682.1%	Show methods
JalviewModel.JSeq.RnaViewer	3368	19	18	0.00%	Show methods
JalviewModel.JSeq.RnaViewer.SecondaryStructure	3659	8	8	0.00%	Show methods
JalviewModel.PcaViewer	3909	46	44	1.0100%	Show methods
JalviewModel.PcaViewer.Axis	4526	6	6	1.0100%	Show methods
JalviewModel.PcaViewer.SeqPointMax	4629	6	6	1.0100%	Show methods
JalviewModel.PcaViewer.SeqPointMin	4732	6	6	1.0100%	Show methods
JalviewModel.PcaViewer.SequencePoint	4836	8	8	1.0100%	Show methods
JalviewModel.Tree	5010	52	48	0.9038461490.4%	Show methods
JalviewModel.Tree.TreeColorMap	5668	3	2	1.0100%	Show methods
JalviewModel.Tree.TreeColorMap.ColorEntry	5726	4	4	1.0100%	Show methods
JalviewModel.UserColours	5804	4	4	0.00%	Show methods
JalviewModel.Viewport	5968	155	136	0.896774289.7%	Show methods
JalviewModel.Viewport.CalcIdParam	7697	8	7	0.00%	Show methods
JalviewModel.Viewport.HiddenColumns	7819	4	4	1.0100%	Show methods
JalviewModel.Viewport.Overview	7901	18	18	1.0100%	Show methods

Class JalviewModel

Class JalviewModel	Line # 415	Total Statements 26	Complexity 20	TOTAL Coverage 0.8461538684.6%
getCreationDate() : XMLGregorianCalendar   getCreationDate() : XMLGregorianCalendar	446446	1.01	1.01	0.0 0.00%
setCreationDate(XMLGregorianCalendar) : void   setCreationDate(XMLGregorianCalendar) : void	458458	1.01	1.01	1.0 1.0100%
getVersion() : String   getVersion() : String	470470	1.01	1.01	1.0 1.0100%
setVersion(String) : void   setVersion(String) : void	482482	1.01	1.01	1.0 1.0100%
getVamsasModel() : VAMSAS   getVamsasModel() : VAMSAS	494494	1.01	1.01	1.0 1.0100%
setVamsasModel(VAMSAS) : void   setVamsasModel(VAMSAS) : void	506506	1.01	1.01	1.0 1.0100%
getJSeq() : List<JalviewModel.JSeq>   getJSeq() : List<JalviewModel.JSeq>	535535	3.03	2.02	1.0 1.0100%
getJGroup() : List<JalviewModel.JGroup>   getJGroup() : List<JalviewModel.JGroup>	567567	3.03	2.02	1.0 1.0100%
getViewport() : List<JalviewModel.Viewport>   getViewport() : List<JalviewModel.Viewport>	599599	3.03	2.02	1.0 1.0100%
getUserColours() : List<JalviewModel.UserColours>   getUserColours() : List<JalviewModel.UserColours>	631631	3.03	2.02	0.0 0.00%
getTree() : List<JalviewModel.Tree>   getTree() : List<JalviewModel.Tree>	663663	3.03	2.02	1.0 1.0100%
getPcaViewer() : List<JalviewModel.PcaViewer>   getPcaViewer() : List<JalviewModel.PcaViewer>	695695	3.03	2.02	1.0 1.0100%
getFeatureSettings() : JalviewModel.FeatureSettings   getFeatureSettings() : JalviewModel.FeatureSettings	710710	1.01	1.01	1.0 1.0100%
setFeatureSettings(JalviewModel.FeatureSettings) : void   setFeatureSettings(JalviewModel.FeatureSettings) : void	722722	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.FeatureSettings

Class JalviewModel.FeatureSettings	Line # 784	Total Statements 6	Complexity 4	TOTAL Coverage 1.0100%
getSetting() : List<JalviewModel.FeatureSettings.Setting>   getSetting() : List<JalviewModel.FeatureSettings.Setting>	816816	3.03	2.02	1.0 1.0100%
getGroup() : List<JalviewModel.FeatureSettings.Group>   getGroup() : List<JalviewModel.FeatureSettings.Group>	848848	3.03	2.02	1.0 1.0100%

 

Class JalviewModel.FeatureSettings.Group

Class JalviewModel.FeatureSettings.Group	Line # 876	Total Statements 4	Complexity 4	TOTAL Coverage 1.0100%
getName() : String   getName() : String	891891	1.01	1.01	1.0 1.0100%
setName(String) : void   setName(String) : void	903903	1.01	1.01	1.0 1.0100%
isDisplay() : boolean   isDisplay() : boolean	911911	1.01	1.01	1.0 1.0100%
setDisplay(boolean) : void   setDisplay(boolean) : void	919919	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.FeatureSettings.Setting

Class JalviewModel.FeatureSettings.Setting	Line # 963	Total Statements 31	Complexity 29	TOTAL Coverage 0.967741996.8%
getAttributeName() : List<String>   getAttributeName() : List<String>	10461046	3.03	2.02	1.0 1.0100%
getMatcherSet() : FeatureMatcherSet   getMatcherSet() : FeatureMatcherSet	10611061	1.01	1.01	1.0 1.0100%
setMatcherSet(FeatureMatcherSet) : void   setMatcherSet(FeatureMatcherSet) : void	10741074	1.01	1.01	1.0 1.0100%
getType() : String   getType() : String	10861086	1.01	1.01	1.0 1.0100%
setType(String) : void   setType(String) : void	10981098	1.01	1.01	1.0 1.0100%
getColour() : int   getColour() : int	11061106	1.01	1.01	1.0 1.0100%
setColour(int) : void   setColour(int) : void	11141114	1.01	1.01	1.0 1.0100%
isDisplay() : boolean   isDisplay() : boolean	11221122	1.01	1.01	1.0 1.0100%
setDisplay(boolean) : void   setDisplay(boolean) : void	11301130	1.01	1.01	1.0 1.0100%
getOrder() : Float   getOrder() : Float	11421142	1.01	1.01	1.0 1.0100%
setOrder(Float) : void   setOrder(Float) : void	11541154	1.01	1.01	1.0 1.0100%
getMincolour() : Integer   getMincolour() : Integer	11691169	1.01	1.01	1.0 1.0100%
setMincolour(Integer) : void   setMincolour(Integer) : void	11821182	1.01	1.01	1.0 1.0100%
getNoValueColour() : NoValueColour   getNoValueColour() : NoValueColour	11941194	3.03	2.02	0.6 0.660%
setNoValueColour(NoValueColour) : void   setNoValueColour(NoValueColour) : void	12101210	1.01	1.01	1.0 1.0100%
getThreshold() : Float   getThreshold() : Float	12231223	1.01	1.01	1.0 1.0100%
setThreshold(Float) : void   setThreshold(Float) : void	12361236	1.01	1.01	1.0 1.0100%
getThreshstate() : Integer   getThreshstate() : Integer	12491249	1.01	1.01	1.0 1.0100%
setThreshstate(Integer) : void   setThreshstate(Integer) : void	12621262	1.01	1.01	1.0 1.0100%
getMax() : Float   getMax() : Float	12741274	1.01	1.01	1.0 1.0100%
setMax(Float) : void   setMax(Float) : void	12861286	1.01	1.01	1.0 1.0100%
getMin() : Float   getMin() : Float	12981298	1.01	1.01	1.0 1.0100%
setMin(Float) : void   setMin(Float) : void	13101310	1.01	1.01	1.0 1.0100%
isColourByLabel() : Boolean   isColourByLabel() : Boolean	13221322	1.01	1.01	1.0 1.0100%
setColourByLabel(Boolean) : void   setColourByLabel(Boolean) : void	13341334	1.01	1.01	1.0 1.0100%
isAutoScale() : Boolean   isAutoScale() : Boolean	13461346	1.01	1.01	1.0 1.0100%
setAutoScale(Boolean) : void   setAutoScale(Boolean) : void	13581358	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.JGroup

Class JalviewModel.JGroup	Line # 1411	Total Statements 69	Complexity 61	TOTAL Coverage 0.891304489.1%
getSeq() : List<String>   getSeq() : List<String>	15181518	3.03	2.02	1.0 1.0100%
getAnnotationColours() : AnnotationColourScheme   getAnnotationColours() : AnnotationColourScheme	15331533	1.01	1.01	1.0 1.0100%
setAnnotationColours(AnnotationColourScheme) : void   setAnnotationColours(AnnotationColourScheme) : void	15451545	1.01	1.01	1.0 1.0100%
getAnnotationFromTree() : List<String>   getAnnotationFromTree() : List<String>	15741574	3.03	2.02	1.0 1.0100%
getSecStrProvider() : List<String>   getSecStrProvider() : List<String>	16061606	3.03	2.02	0.8 0.880%
getStart() : Integer   getStart() : Integer	16211621	1.01	1.01	1.0 1.0100%
setStart(Integer) : void   setStart(Integer) : void	16331633	1.01	1.01	1.0 1.0100%
getEnd() : Integer   getEnd() : Integer	16451645	1.01	1.01	1.0 1.0100%
setEnd(Integer) : void   setEnd(Integer) : void	16571657	1.01	1.01	1.0 1.0100%
getName() : String   getName() : String	16691669	1.01	1.01	1.0 1.0100%
setName(String) : void   setName(String) : void	16811681	1.01	1.01	1.0 1.0100%
getColour() : String   getColour() : String	16931693	1.01	1.01	1.0 1.0100%
setColour(String) : void   setColour(String) : void	17051705	1.01	1.01	1.0 1.0100%
getIdColour() : Integer   getIdColour() : Integer	17171717	1.01	1.01	1.0 1.0100%
setIdColour(Integer) : void   setIdColour(Integer) : void	17291729	1.01	1.01	1.0 1.0100%
getOutlineColour() : Integer   getOutlineColour() : Integer	17411741	1.01	1.01	1.0 1.0100%
setOutlineColour(Integer) : void   setOutlineColour(Integer) : void	17531753	1.01	1.01	1.0 1.0100%
isDisplayBoxes() : Boolean   isDisplayBoxes() : Boolean	17651765	1.01	1.01	1.0 1.0100%
setDisplayBoxes(Boolean) : void   setDisplayBoxes(Boolean) : void	17771777	1.01	1.01	1.0 1.0100%
isDisplayText() : Boolean   isDisplayText() : Boolean	17891789	1.01	1.01	1.0 1.0100%
setDisplayText(Boolean) : void   setDisplayText(Boolean) : void	18011801	1.01	1.01	1.0 1.0100%
isColourText() : Boolean   isColourText() : Boolean	18131813	1.01	1.01	1.0 1.0100%
setColourText(Boolean) : void   setColourText(Boolean) : void	18251825	1.01	1.01	1.0 1.0100%
getTextCol1() : Integer   getTextCol1() : Integer	18371837	1.01	1.01	1.0 1.0100%
setTextCol1(Integer) : void   setTextCol1(Integer) : void	18491849	1.01	1.01	1.0 1.0100%
getTextCol2() : Integer   getTextCol2() : Integer	18611861	1.01	1.01	1.0 1.0100%
setTextCol2(Integer) : void   setTextCol2(Integer) : void	18731873	1.01	1.01	1.0 1.0100%
getTextColThreshold() : Integer   getTextColThreshold() : Integer	18851885	1.01	1.01	1.0 1.0100%
setTextColThreshold(Integer) : void   setTextColThreshold(Integer) : void	18971897	1.01	1.01	1.0 1.0100%
isShowUnconserved() : Boolean   isShowUnconserved() : Boolean	19091909	1.01	1.01	1.0 1.0100%
setShowUnconserved(Boolean) : void   setShowUnconserved(Boolean) : void	19211921	1.01	1.01	1.0 1.0100%
getId() : String   getId() : String	19361936	1.01	1.01	1.0 1.0100%
setId(String) : void   setId(String) : void	19491949	1.01	1.01	1.0 1.0100%
isConservationSelected() : Boolean   isConservationSelected() : Boolean	19611961	1.01	1.01	0.0 0.00%
setConservationSelected(Boolean) : void   setConservationSelected(Boolean) : void	19731973	1.01	1.01	0.0 0.00%
getConsThreshold() : Integer   getConsThreshold() : Integer	19851985	1.01	1.01	1.0 1.0100%
setConsThreshold(Integer) : void   setConsThreshold(Integer) : void	19981998	1.01	1.01	1.0 1.0100%
isPidSelected() : Boolean   isPidSelected() : Boolean	20102010	1.01	1.01	0.0 0.00%
setPidSelected(Boolean) : void   setPidSelected(Boolean) : void	20222022	1.01	1.01	0.0 0.00%
getPidThreshold() : Integer   getPidThreshold() : Integer	20342034	1.01	1.01	1.0 1.0100%
setPidThreshold(Integer) : void   setPidThreshold(Integer) : void	20472047	1.01	1.01	1.0 1.0100%
isSecstrSelected() : boolean   isSecstrSelected() : boolean	20592059	3.03	2.02	1.0 1.0100%
setSecstrSelected(Boolean) : void   setSecstrSelected(Boolean) : void	20762076	1.01	1.01	1.0 1.0100%
getSecstrThreshold() : Integer   getSecstrThreshold() : Integer	20882088	1.01	1.01	1.0 1.0100%
setSecstrThreshold(Integer) : void   setSecstrThreshold(Integer) : void	21012101	1.01	1.01	1.0 1.0100%
isShowConsensusHistogram() : boolean   isShowConsensusHistogram() : boolean	21132113	3.03	2.02	0.6 0.660%
setShowConsensusHistogram(Boolean) : void   setShowConsensusHistogram(Boolean) : void	21292129	1.01	1.01	1.0 1.0100%
isShowSequenceLogo() : boolean   isShowSequenceLogo() : boolean	21412141	3.03	2.02	0.6 0.660%
setShowSequenceLogo(Boolean) : void   setShowSequenceLogo(Boolean) : void	21572157	1.01	1.01	1.0 1.0100%
isNormaliseSequenceLogo() : boolean   isNormaliseSequenceLogo() : boolean	21692169	3.03	2.02	1.0 1.0100%
setNormaliseSequenceLogo(Boolean) : void   setNormaliseSequenceLogo(Boolean) : void	21852185	1.01	1.01	1.0 1.0100%
isIgnoreGapsinConsensus() : boolean   isIgnoreGapsinConsensus() : boolean	21972197	3.03	2.02	0.6 0.660%
setIgnoreGapsinConsensus(Boolean) : void   setIgnoreGapsinConsensus(Boolean) : void	22132213	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.JSeq

Class JalviewModel.JSeq	Line # 2307	Total Statements 26	Complexity 22	TOTAL Coverage 0.980769298.1%
getFeatures() : List<Feature>   getFeatures() : List<Feature>	23722372	3.03	2.02	1.0 1.0100%
getPdbids() : List<JalviewModel.JSeq.Pdbids>   getPdbids() : List<JalviewModel.JSeq.Pdbids>	24042404	3.03	2.02	1.0 1.0100%
getHiddenSequences() : List<Integer>   getHiddenSequences() : List<Integer>	24362436	3.03	2.02	1.0 1.0100%
getRnaViewer() : List<JalviewModel.JSeq.RnaViewer>   getRnaViewer() : List<JalviewModel.JSeq.RnaViewer>	24772477	3.03	2.02	0.8 0.880%
getHmmerProfile() : String   getHmmerProfile() : String	24922492	1.01	1.01	1.0 1.0100%
setHmmerProfile(String) : void   setHmmerProfile(String) : void	25052505	1.01	1.01	1.0 1.0100%
getColour() : Integer   getColour() : Integer	25172517	1.01	1.01	1.0 1.0100%
setColour(Integer) : void   setColour(Integer) : void	25292529	1.01	1.01	1.0 1.0100%
getStart() : int   getStart() : int	25372537	1.01	1.01	1.0 1.0100%
setStart(int) : void   setStart(int) : void	25452545	1.01	1.01	1.0 1.0100%
getEnd() : int   getEnd() : int	25532553	1.01	1.01	1.0 1.0100%
setEnd(int) : void   setEnd(int) : void	25612561	1.01	1.01	1.0 1.0100%
getId() : String   getId() : String	25732573	1.01	1.01	1.0 1.0100%
setId(String) : void   setId(String) : void	25852585	1.01	1.01	1.0 1.0100%
isHidden() : Boolean   isHidden() : Boolean	25972597	1.01	1.01	1.0 1.0100%
setHidden(Boolean) : void   setHidden(Boolean) : void	26092609	1.01	1.01	1.0 1.0100%
isViewreference() : Boolean   isViewreference() : Boolean	26212621	1.01	1.01	1.0 1.0100%
setViewreference(Boolean) : void   setViewreference(Boolean) : void	26332633	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.JSeq.Pdbids

Class JalviewModel.JSeq.Pdbids	Line # 2675	Total Statements 3	Complexity 2	TOTAL Coverage 1.0100%
getStructureState() : List<JalviewModel.JSeq.Pdbids.StructureState>   getStructureState() : List<JalviewModel.JSeq.Pdbids.StructureState>	27072707	3.03	2.02	1.0 1.0100%

 

Class JalviewModel.JSeq.Pdbids.StructureState

Class JalviewModel.JSeq.Pdbids.StructureState	Line # 2742	Total Statements 28	Complexity 25	TOTAL Coverage 0.821428682.1%
getValue() : String   getValue() : String	29232923	1.01	1.01	1.0 1.0100%
setValue(String) : void   setValue(String) : void	29352935	1.01	1.01	0.0 0.00%
isVisible() : Boolean   isVisible() : Boolean	29472947	1.01	1.01	0.0 0.00%
setVisible(Boolean) : void   setVisible(Boolean) : void	29592959	1.01	1.01	1.0 1.0100%
getViewId() : String   getViewId() : String	30233023	1.01	1.01	1.0 1.0100%
setViewId(String) : void   setViewId(String) : void	30363036	1.01	1.01	1.0 1.0100%
isAlignwithAlignPanel() : boolean   isAlignwithAlignPanel() : boolean	30703070	3.03	2.02	0.6 0.660%
setAlignwithAlignPanel(Boolean) : void   setAlignwithAlignPanel(Boolean) : void	30873087	1.01	1.01	1.0 1.0100%
isColourwithAlignPanel() : boolean   isColourwithAlignPanel() : boolean	31233123	3.03	2.02	0.6 0.660%
setColourwithAlignPanel(Boolean) : void   setColourwithAlignPanel(Boolean) : void	31403140	1.01	1.01	1.0 1.0100%
isColourByJmol() : boolean   isColourByJmol() : boolean	31723172	3.03	2.02	0.6 0.660%
setColourByJmol(Boolean) : void   setColourByJmol(Boolean) : void	31893189	1.01	1.01	1.0 1.0100%
getType() : String   getType() : String	32113211	1.01	1.01	1.0 1.0100%
setType(String) : void   setType(String) : void	32243224	1.01	1.01	1.0 1.0100%
getWidth() : Integer   getWidth() : Integer	32363236	1.01	1.01	1.0 1.0100%
setWidth(Integer) : void   setWidth(Integer) : void	32483248	1.01	1.01	1.0 1.0100%
getHeight() : Integer   getHeight() : Integer	32603260	1.01	1.01	1.0 1.0100%
setHeight(Integer) : void   setHeight(Integer) : void	32723272	1.01	1.01	1.0 1.0100%
getXpos() : Integer   getXpos() : Integer	32843284	1.01	1.01	1.0 1.0100%
setXpos(Integer) : void   setXpos(Integer) : void	32963296	1.01	1.01	1.0 1.0100%
getYpos() : Integer   getYpos() : Integer	33083308	1.01	1.01	1.0 1.0100%
setYpos(Integer) : void   setYpos(Integer) : void	33203320	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.JSeq.RnaViewer

Class JalviewModel.JSeq.RnaViewer	Line # 3368	Total Statements 19	Complexity 18	TOTAL Coverage 0.00%
getSecondaryStructure() : List<JalviewModel.JSeq.RnaViewer.SecondaryStructure>   getSecondaryStructure() : List<JalviewModel.JSeq.RnaViewer.SecondaryStructure>	34303430	3.03	2.02	0.0 0.00%
getTitle() : String   getTitle() : String	34453445	1.01	1.01	0.0 0.00%
setTitle(String) : void   setTitle(String) : void	34573457	1.01	1.01	0.0 0.00%
getViewId() : String   getViewId() : String	34703470	1.01	1.01	0.0 0.00%
setViewId(String) : void   setViewId(String) : void	34833483	1.01	1.01	0.0 0.00%
getDividerLocation() : Integer   getDividerLocation() : Integer	34963496	1.01	1.01	0.0 0.00%
setDividerLocation(Integer) : void   setDividerLocation(Integer) : void	35093509	1.01	1.01	0.0 0.00%
getSelectedRna() : Integer   getSelectedRna() : Integer	35233523	1.01	1.01	0.0 0.00%
setSelectedRna(Integer) : void   setSelectedRna(Integer) : void	35363536	1.01	1.01	0.0 0.00%
getWidth() : Integer   getWidth() : Integer	35483548	1.01	1.01	0.0 0.00%
setWidth(Integer) : void   setWidth(Integer) : void	35603560	1.01	1.01	0.0 0.00%
getHeight() : Integer   getHeight() : Integer	35723572	1.01	1.01	0.0 0.00%
setHeight(Integer) : void   setHeight(Integer) : void	35843584	1.01	1.01	0.0 0.00%
getXpos() : Integer   getXpos() : Integer	35963596	1.01	1.01	0.0 0.00%
setXpos(Integer) : void   setXpos(Integer) : void	36083608	1.01	1.01	0.0 0.00%
getYpos() : Integer   getYpos() : Integer	36203620	1.01	1.01	0.0 0.00%
setYpos(Integer) : void   setYpos(Integer) : void	36323632	1.01	1.01	0.0 0.00%

 

Class JalviewModel.JSeq.RnaViewer.SecondaryStructure

Class JalviewModel.JSeq.RnaViewer.SecondaryStructure	Line # 3659	Total Statements 8	Complexity 8	TOTAL Coverage 0.00%
getTitle() : String   getTitle() : String	37133713	1.01	1.01	0.0 0.00%
setTitle(String) : void   setTitle(String) : void	37253725	1.01	1.01	0.0 0.00%
getAnnotationId() : String   getAnnotationId() : String	37473747	1.01	1.01	0.0 0.00%
setAnnotationId(String) : void   setAnnotationId(String) : void	37603760	1.01	1.01	0.0 0.00%
isGapped() : Boolean   isGapped() : Boolean	37783778	1.01	1.01	0.0 0.00%
setGapped(Boolean) : void   setGapped(Boolean) : void	37913791	1.01	1.01	0.0 0.00%
getViewerState() : String   getViewerState() : String	38103810	1.01	1.01	0.0 0.00%
setViewerState(String) : void   setViewerState(String) : void	38233823	1.01	1.01	0.0 0.00%

 

Class JalviewModel.PcaViewer

Class JalviewModel.PcaViewer	Line # 3909	Total Statements 46	Complexity 44	TOTAL Coverage 1.0100%
getSequencePoint() : List<JalviewModel.PcaViewer.SequencePoint>   getSequencePoint() : List<JalviewModel.PcaViewer.SequencePoint>	39853985	3.03	2.02	1.0 1.0100%
getAxis() : List<JalviewModel.PcaViewer.Axis>   getAxis() : List<JalviewModel.PcaViewer.Axis>	40194019	3.03	2.02	1.0 1.0100%
getSeqPointMin() : JalviewModel.PcaViewer.SeqPointMin   getSeqPointMin() : JalviewModel.PcaViewer.SeqPointMin	40344034	1.01	1.01	1.0 1.0100%
setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin) : void   setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin) : void	40464046	1.01	1.01	1.0 1.0100%
getSeqPointMax() : JalviewModel.PcaViewer.SeqPointMax   getSeqPointMax() : JalviewModel.PcaViewer.SeqPointMax	40584058	1.01	1.01	1.0 1.0100%
setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax) : void   setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax) : void	40704070	1.01	1.01	1.0 1.0100%
getPcaData() : PcaDataType   getPcaData() : PcaDataType	40824082	1.01	1.01	1.0 1.0100%
setPcaData(PcaDataType) : void   setPcaData(PcaDataType) : void	40944094	1.01	1.01	1.0 1.0100%
getTitle() : String   getTitle() : String	41064106	1.01	1.01	1.0 1.0100%
setTitle(String) : void   setTitle(String) : void	41184118	1.01	1.01	1.0 1.0100%
getScoreModelName() : String   getScoreModelName() : String	41304130	1.01	1.01	1.0 1.0100%
setScoreModelName(String) : void   setScoreModelName(String) : void	41424142	1.01	1.01	1.0 1.0100%
getXDim() : Integer   getXDim() : Integer	41544154	1.01	1.01	1.0 1.0100%
setXDim(Integer) : void   setXDim(Integer) : void	41664166	1.01	1.01	1.0 1.0100%
getYDim() : Integer   getYDim() : Integer	41784178	1.01	1.01	1.0 1.0100%
setYDim(Integer) : void   setYDim(Integer) : void	41904190	1.01	1.01	1.0 1.0100%
getZDim() : Integer   getZDim() : Integer	42024202	1.01	1.01	1.0 1.0100%
setZDim(Integer) : void   setZDim(Integer) : void	42144214	1.01	1.01	1.0 1.0100%
getBgColour() : Integer   getBgColour() : Integer	42264226	1.01	1.01	1.0 1.0100%
setBgColour(Integer) : void   setBgColour(Integer) : void	42384238	1.01	1.01	1.0 1.0100%
getScaleFactor() : Float   getScaleFactor() : Float	42504250	1.01	1.01	1.0 1.0100%
setScaleFactor(Float) : void   setScaleFactor(Float) : void	42624262	1.01	1.01	1.0 1.0100%
isShowLabels() : Boolean   isShowLabels() : Boolean	42744274	1.01	1.01	1.0 1.0100%
setShowLabels(Boolean) : void   setShowLabels(Boolean) : void	42864286	1.01	1.01	1.0 1.0100%
isLinkToAllViews() : Boolean   isLinkToAllViews() : Boolean	42984298	1.01	1.01	1.0 1.0100%
setLinkToAllViews(Boolean) : void   setLinkToAllViews(Boolean) : void	43104310	1.01	1.01	1.0 1.0100%
isIncludeGaps() : Boolean   isIncludeGaps() : Boolean	43224322	1.01	1.01	1.0 1.0100%
setIncludeGaps(Boolean) : void   setIncludeGaps(Boolean) : void	43344334	1.01	1.01	1.0 1.0100%
isMatchGaps() : Boolean   isMatchGaps() : Boolean	43464346	1.01	1.01	1.0 1.0100%
setMatchGaps(Boolean) : void   setMatchGaps(Boolean) : void	43584358	1.01	1.01	1.0 1.0100%
isIncludeGappedColumns() : Boolean   isIncludeGappedColumns() : Boolean	43704370	1.01	1.01	1.0 1.0100%
setIncludeGappedColumns(Boolean) : void   setIncludeGappedColumns(Boolean) : void	43824382	1.01	1.01	1.0 1.0100%
isDenominateByShortestLength() : Boolean   isDenominateByShortestLength() : Boolean	43944394	1.01	1.01	1.0 1.0100%
setDenominateByShortestLength(Boolean) : void   setDenominateByShortestLength(Boolean) : void	44064406	1.01	1.01	1.0 1.0100%
getWidth() : Integer   getWidth() : Integer	44184418	1.01	1.01	1.0 1.0100%
setWidth(Integer) : void   setWidth(Integer) : void	44304430	1.01	1.01	1.0 1.0100%
getHeight() : Integer   getHeight() : Integer	44424442	1.01	1.01	1.0 1.0100%
setHeight(Integer) : void   setHeight(Integer) : void	44544454	1.01	1.01	1.0 1.0100%
getXpos() : Integer   getXpos() : Integer	44664466	1.01	1.01	1.0 1.0100%
setXpos(Integer) : void   setXpos(Integer) : void	44784478	1.01	1.01	1.0 1.0100%
getYpos() : Integer   getYpos() : Integer	44904490	1.01	1.01	1.0 1.0100%
setYpos(Integer) : void   setYpos(Integer) : void	45024502	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.PcaViewer.Axis

Class JalviewModel.PcaViewer.Axis	Line # 4526	Total Statements 6	Complexity 6	TOTAL Coverage 1.0100%
getXPos() : Float   getXPos() : Float	45434543	1.01	1.01	1.0 1.0100%
setXPos(Float) : void   setXPos(Float) : void	45554555	1.01	1.01	1.0 1.0100%
getYPos() : Float   getYPos() : Float	45674567	1.01	1.01	1.0 1.0100%
setYPos(Float) : void   setYPos(Float) : void	45794579	1.01	1.01	1.0 1.0100%
getZPos() : Float   getZPos() : Float	45914591	1.01	1.01	1.0 1.0100%
setZPos(Float) : void   setZPos(Float) : void	46034603	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.PcaViewer.SeqPointMax

Class JalviewModel.PcaViewer.SeqPointMax	Line # 4629	Total Statements 6	Complexity 6	TOTAL Coverage 1.0100%
getXPos() : Float   getXPos() : Float	46464646	1.01	1.01	1.0 1.0100%
setXPos(Float) : void   setXPos(Float) : void	46584658	1.01	1.01	1.0 1.0100%
getYPos() : Float   getYPos() : Float	46704670	1.01	1.01	1.0 1.0100%
setYPos(Float) : void   setYPos(Float) : void	46824682	1.01	1.01	1.0 1.0100%
getZPos() : Float   getZPos() : Float	46944694	1.01	1.01	1.0 1.0100%
setZPos(Float) : void   setZPos(Float) : void	47064706	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.PcaViewer.SeqPointMin

Class JalviewModel.PcaViewer.SeqPointMin	Line # 4732	Total Statements 6	Complexity 6	TOTAL Coverage 1.0100%
getXPos() : Float   getXPos() : Float	47494749	1.01	1.01	1.0 1.0100%
setXPos(Float) : void   setXPos(Float) : void	47614761	1.01	1.01	1.0 1.0100%
getYPos() : Float   getYPos() : Float	47734773	1.01	1.01	1.0 1.0100%
setYPos(Float) : void   setYPos(Float) : void	47854785	1.01	1.01	1.0 1.0100%
getZPos() : Float   getZPos() : Float	47974797	1.01	1.01	1.0 1.0100%
setZPos(Float) : void   setZPos(Float) : void	48094809	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.PcaViewer.SequencePoint

Class JalviewModel.PcaViewer.SequencePoint	Line # 4836	Total Statements 8	Complexity 8	TOTAL Coverage 1.0100%
getSequenceRef() : String   getSequenceRef() : String	48554855	1.01	1.01	1.0 1.0100%
setSequenceRef(String) : void   setSequenceRef(String) : void	48674867	1.01	1.01	1.0 1.0100%
getXPos() : Float   getXPos() : Float	48794879	1.01	1.01	1.0 1.0100%
setXPos(Float) : void   setXPos(Float) : void	48914891	1.01	1.01	1.0 1.0100%
getYPos() : Float   getYPos() : Float	49034903	1.01	1.01	1.0 1.0100%
setYPos(Float) : void   setYPos(Float) : void	49154915	1.01	1.01	1.0 1.0100%
getZPos() : Float   getZPos() : Float	49274927	1.01	1.01	1.0 1.0100%
setZPos(Float) : void   setZPos(Float) : void	49394939	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.Tree

Class JalviewModel.Tree	Line # 5010	Total Statements 52	Complexity 48	TOTAL Coverage 0.9038461490.4%
getTitle() : String   getTitle() : String	50915091	1.01	1.01	1.0 1.0100%
setTitle(String) : void   setTitle(String) : void	51035103	1.01	1.01	1.0 1.0100%
getNewick() : String   getNewick() : String	51155115	1.01	1.01	1.0 1.0100%
setNewick(String) : void   setNewick(String) : void	51275127	1.01	1.01	1.0 1.0100%
getTreeColorMap() : JalviewModel.Tree.TreeColorMap   getTreeColorMap() : JalviewModel.Tree.TreeColorMap	51395139	1.01	1.01	1.0 1.0100%
setTreeColorMap(JalviewModel.Tree.TreeColorMap) : void   setTreeColorMap(JalviewModel.Tree.TreeColorMap) : void	51515151	1.01	1.01	1.0 1.0100%
getFontName() : String   getFontName() : String	51635163	1.01	1.01	1.0 1.0100%
setFontName(String) : void   setFontName(String) : void	51755175	1.01	1.01	1.0 1.0100%
getFontSize() : Integer   getFontSize() : Integer	51875187	1.01	1.01	1.0 1.0100%
setFontSize(Integer) : void   setFontSize(Integer) : void	51995199	1.01	1.01	1.0 1.0100%
getFontStyle() : Integer   getFontStyle() : Integer	52115211	1.01	1.01	1.0 1.0100%
setFontStyle(Integer) : void   setFontStyle(Integer) : void	52235223	1.01	1.01	1.0 1.0100%
getThreshold() : Float   getThreshold() : Float	52355235	1.01	1.01	1.0 1.0100%
setThreshold(Float) : void   setThreshold(Float) : void	52475247	1.01	1.01	1.0 1.0100%
isShowBootstrap() : Boolean   isShowBootstrap() : Boolean	52595259	1.01	1.01	1.0 1.0100%
setShowBootstrap(Boolean) : void   setShowBootstrap(Boolean) : void	52715271	1.01	1.01	1.0 1.0100%
isShowDistances() : Boolean   isShowDistances() : Boolean	52835283	1.01	1.01	1.0 1.0100%
setShowDistances(Boolean) : void   setShowDistances(Boolean) : void	52955295	1.01	1.01	1.0 1.0100%
isMarkUnlinked() : Boolean   isMarkUnlinked() : Boolean	53075307	1.01	1.01	1.0 1.0100%
setMarkUnlinked(Boolean) : void   setMarkUnlinked(Boolean) : void	53195319	1.01	1.01	1.0 1.0100%
isFitToWindow() : Boolean   isFitToWindow() : Boolean	53315331	1.01	1.01	1.0 1.0100%
setFitToWindow(Boolean) : void   setFitToWindow(Boolean) : void	53435343	1.01	1.01	1.0 1.0100%
isCurrentTree() : Boolean   isCurrentTree() : Boolean	53555355	1.01	1.01	1.0 1.0100%
setCurrentTree(Boolean) : void   setCurrentTree(Boolean) : void	53675367	1.01	1.01	1.0 1.0100%
isColumnWise() : boolean   isColumnWise() : boolean	53795379	3.03	2.02	0.6 0.660%
setColumnWise(Boolean) : void   setColumnWise(Boolean) : void	53965396	1.01	1.01	0.0 0.00%
isAnnotationBased() : boolean   isAnnotationBased() : boolean	54085408	3.03	2.02	1.0 1.0100%
setAnnotationBased(Boolean) : void   setAnnotationBased(Boolean) : void	54255425	1.01	1.01	1.0 1.0100%
getShowAnnotationAs() : String   getShowAnnotationAs() : String	54375437	3.03	2.02	0.6 0.660%
setShowAnnotationAs(String) : void   setShowAnnotationAs(String) : void	54545454	1.01	1.01	1.0 1.0100%
getColumnReference() : String   getColumnReference() : String	54665466	1.01	1.01	0.0 0.00%
setColumnReference(String) : void   setColumnReference(String) : void	54795479	1.01	1.01	0.0 0.00%
getId() : String   getId() : String	54945494	1.01	1.01	1.0 1.0100%
setId(String) : void   setId(String) : void	55075507	1.01	1.01	1.0 1.0100%
isLinkToAllViews() : boolean   isLinkToAllViews() : boolean	55195519	3.03	2.02	1.0 1.0100%
setLinkToAllViews(Boolean) : void   setLinkToAllViews(Boolean) : void	55355535	1.01	1.01	1.0 1.0100%
getWidth() : Integer   getWidth() : Integer	55475547	1.01	1.01	1.0 1.0100%
setWidth(Integer) : void   setWidth(Integer) : void	55595559	1.01	1.01	1.0 1.0100%
getHeight() : Integer   getHeight() : Integer	55715571	1.01	1.01	1.0 1.0100%
setHeight(Integer) : void   setHeight(Integer) : void	55835583	1.01	1.01	1.0 1.0100%
getXpos() : Integer   getXpos() : Integer	55955595	1.01	1.01	1.0 1.0100%
setXpos(Integer) : void   setXpos(Integer) : void	56075607	1.01	1.01	1.0 1.0100%
getYpos() : Integer   getYpos() : Integer	56195619	1.01	1.01	1.0 1.0100%
setYpos(Integer) : void   setYpos(Integer) : void	56315631	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.Tree.TreeColorMap

Class JalviewModel.Tree.TreeColorMap	Line # 5668	Total Statements 3	Complexity 2	TOTAL Coverage 1.0100%
getColorEntry() : List<JalviewModel.Tree.TreeColorMap.ColorEntry>   getColorEntry() : List<JalviewModel.Tree.TreeColorMap.ColorEntry>	56985698	3.03	2.02	1.0 1.0100%

 

Class JalviewModel.Tree.TreeColorMap.ColorEntry

Class JalviewModel.Tree.TreeColorMap.ColorEntry	Line # 5726	Total Statements 4	Complexity 4	TOTAL Coverage 1.0100%
getLabel() : String   getLabel() : String	57415741	1.01	1.01	1.0 1.0100%
setLabel(String) : void   setLabel(String) : void	57535753	1.01	1.01	1.0 1.0100%
getColor() : int   getColor() : int	57615761	1.01	1.01	1.0 1.0100%
setColor(int) : void   setColor(int) : void	57695769	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.UserColours

Class JalviewModel.UserColours	Line # 5804	Total Statements 4	Complexity 4	TOTAL Coverage 0.00%
getUserColourScheme() : JalviewUserColours   getUserColourScheme() : JalviewUserColours	58195819	1.01	1.01	0.0 0.00%
setUserColourScheme(JalviewUserColours) : void   setUserColourScheme(JalviewUserColours) : void	58315831	1.01	1.01	0.0 0.00%
getId() : String   getId() : String	58435843	1.01	1.01	0.0 0.00%
setId(String) : void   setId(String) : void	58555855	1.01	1.01	0.0 0.00%

 

Class JalviewModel.Viewport

Class JalviewModel.Viewport	Line # 5968	Total Statements 155	Complexity 136	TOTAL Coverage 0.896774289.7%
getAnnotationColours() : AnnotationColourScheme   getAnnotationColours() : AnnotationColourScheme	61426142	1.01	1.01	1.0 1.0100%
setAnnotationColours(AnnotationColourScheme) : void   setAnnotationColours(AnnotationColourScheme) : void	61546154	1.01	1.01	1.0 1.0100%
getHiddenColumns() : List<JalviewModel.Viewport.HiddenColumns>   getHiddenColumns() : List<JalviewModel.Viewport.HiddenColumns>	61836183	3.03	2.02	1.0 1.0100%
getCalcIdParam() : List<JalviewModel.Viewport.CalcIdParam>   getCalcIdParam() : List<JalviewModel.Viewport.CalcIdParam>	62156215	3.03	2.02	1.0 1.0100%
getOverview() : JalviewModel.Viewport.Overview   getOverview() : JalviewModel.Viewport.Overview	62306230	1.01	1.01	1.0 1.0100%
setOverview(JalviewModel.Viewport.Overview) : void   setOverview(JalviewModel.Viewport.Overview) : void	62426242	1.01	1.01	1.0 1.0100%
getSecStrProvider() : List<String>   getSecStrProvider() : List<String>	62716271	3.03	2.02	0.0 0.00%
getBgColour() : String   getBgColour() : String	62866286	1.01	1.01	1.0 1.0100%
setBgColour(String) : void   setBgColour(String) : void	62986298	1.01	1.01	1.0 1.0100%
getTitle() : String   getTitle() : String	63106310	1.01	1.01	1.0 1.0100%
setTitle(String) : void   setTitle(String) : void	63226322	1.01	1.01	1.0 1.0100%
isShowFullId() : Boolean   isShowFullId() : Boolean	63346334	1.01	1.01	1.0 1.0100%
setShowFullId(Boolean) : void   setShowFullId(Boolean) : void	63466346	1.01	1.01	1.0 1.0100%
isRightAlignIds() : Boolean   isRightAlignIds() : Boolean	63586358	1.01	1.01	1.0 1.0100%
setRightAlignIds(Boolean) : void   setRightAlignIds(Boolean) : void	63706370	1.01	1.01	1.0 1.0100%
isShowText() : Boolean   isShowText() : Boolean	63826382	1.01	1.01	1.0 1.0100%
setShowText(Boolean) : void   setShowText(Boolean) : void	63946394	1.01	1.01	1.0 1.0100%
isShowColourText() : Boolean   isShowColourText() : Boolean	64066406	1.01	1.01	1.0 1.0100%
setShowColourText(Boolean) : void   setShowColourText(Boolean) : void	64186418	1.01	1.01	1.0 1.0100%
isShowUnconserved() : boolean   isShowUnconserved() : boolean	64306430	3.03	2.02	0.6 0.660%
setShowUnconserved(Boolean) : void   setShowUnconserved(Boolean) : void	64466446	1.01	1.01	1.0 1.0100%
isShowBoxes() : Boolean   isShowBoxes() : Boolean	64586458	1.01	1.01	1.0 1.0100%
setShowBoxes(Boolean) : void   setShowBoxes(Boolean) : void	64706470	1.01	1.01	1.0 1.0100%
isWrapAlignment() : Boolean   isWrapAlignment() : Boolean	64826482	1.01	1.01	1.0 1.0100%
setWrapAlignment(Boolean) : void   setWrapAlignment(Boolean) : void	64946494	1.01	1.01	1.0 1.0100%
isRenderGaps() : Boolean   isRenderGaps() : Boolean	65066506	1.01	1.01	1.0 1.0100%
setRenderGaps(Boolean) : void   setRenderGaps(Boolean) : void	65186518	1.01	1.01	1.0 1.0100%
isShowSequenceFeatures() : Boolean   isShowSequenceFeatures() : Boolean	65306530	1.01	1.01	1.0 1.0100%
setShowSequenceFeatures(Boolean) : void   setShowSequenceFeatures(Boolean) : void	65426542	1.01	1.01	1.0 1.0100%
isShowNPfeatureTooltip() : Boolean   isShowNPfeatureTooltip() : Boolean	65546554	1.01	1.01	1.0 1.0100%
setShowNPfeatureTooltip(Boolean) : void   setShowNPfeatureTooltip(Boolean) : void	65666566	1.01	1.01	1.0 1.0100%
isShowDbRefTooltip() : Boolean   isShowDbRefTooltip() : Boolean	65786578	1.01	1.01	1.0 1.0100%
setShowDbRefTooltip(Boolean) : void   setShowDbRefTooltip(Boolean) : void	65906590	1.01	1.01	1.0 1.0100%
isFollowHighlight() : boolean   isFollowHighlight() : boolean	66026602	3.03	2.02	0.6 0.660%
setFollowHighlight(Boolean) : void   setFollowHighlight(Boolean) : void	66186618	1.01	1.01	1.0 1.0100%
isFollowSelection() : boolean   isFollowSelection() : boolean	66306630	3.03	2.02	0.6 0.660%
setFollowSelection(Boolean) : void   setFollowSelection(Boolean) : void	66466646	1.01	1.01	1.0 1.0100%
isShowAnnotation() : Boolean   isShowAnnotation() : Boolean	66586658	1.01	1.01	1.0 1.0100%
setShowAnnotation(Boolean) : void   setShowAnnotation(Boolean) : void	66706670	1.01	1.01	1.0 1.0100%
isShowStructureProviders() : boolean   isShowStructureProviders() : boolean	66826682	3.03	2.02	1.0 1.0100%
setShowStructureProviders(Boolean) : void   setShowStructureProviders(Boolean) : void	66986698	1.01	1.01	1.0 1.0100%
isCentreColumnLabels() : boolean   isCentreColumnLabels() : boolean	67106710	3.03	2.02	0.6 0.660%
setCentreColumnLabels(Boolean) : void   setCentreColumnLabels(Boolean) : void	67266726	1.01	1.01	0.0 0.00%
isShowGroupConservation() : boolean   isShowGroupConservation() : boolean	67386738	3.03	2.02	0.6 0.660%
setShowGroupConservation(Boolean) : void   setShowGroupConservation(Boolean) : void	67556755	1.01	1.01	1.0 1.0100%
isShowGroupConsensus() : boolean   isShowGroupConsensus() : boolean	67676767	3.03	2.02	0.6 0.660%
setShowGroupConsensus(Boolean) : void   setShowGroupConsensus(Boolean) : void	67846784	1.01	1.01	1.0 1.0100%
isShowGroupSecStrConsensus() : boolean   isShowGroupSecStrConsensus() : boolean	67966796	3.03	2.02	1.0 1.0100%
setShowGroupSecStrConsensus(Boolean) : void   setShowGroupSecStrConsensus(Boolean) : void	68136813	1.01	1.01	1.0 1.0100%
getStartRes() : Integer   getStartRes() : Integer	68256825	1.01	1.01	1.0 1.0100%
setStartRes(Integer) : void   setStartRes(Integer) : void	68376837	1.01	1.01	1.0 1.0100%
getStartSeq() : Integer   getStartSeq() : Integer	68496849	1.01	1.01	0.0 0.00%
setStartSeq(Integer) : void   setStartSeq(Integer) : void	68616861	1.01	1.01	1.0 1.0100%
getCharWidth() : Integer   getCharWidth() : Integer	68736873	1.01	1.01	1.0 1.0100%
setCharWidth(Integer) : void   setCharWidth(Integer) : void	68856885	1.01	1.01	1.0 1.0100%
getCharHeight() : Integer   getCharHeight() : Integer	68976897	1.01	1.01	1.0 1.0100%
setCharHeight(Integer) : void   setCharHeight(Integer) : void	69096909	1.01	1.01	1.0 1.0100%
getFontName() : String   getFontName() : String	69216921	1.01	1.01	1.0 1.0100%
setFontName(String) : void   setFontName(String) : void	69336933	1.01	1.01	1.0 1.0100%
getFontSize() : Integer   getFontSize() : Integer	69456945	1.01	1.01	1.0 1.0100%
setFontSize(Integer) : void   setFontSize(Integer) : void	69576957	1.01	1.01	1.0 1.0100%
getFontStyle() : Integer   getFontStyle() : Integer	69696969	1.01	1.01	1.0 1.0100%
setFontStyle(Integer) : void   setFontStyle(Integer) : void	69816981	1.01	1.01	1.0 1.0100%
getIdWidth() : Integer   getIdWidth() : Integer	69936993	1.01	1.01	1.0 1.0100%
setIdWidth(Integer) : void   setIdWidth(Integer) : void	70057005	1.01	1.01	1.0 1.0100%
isIdWidthManuallyAdjusted() : Boolean   isIdWidthManuallyAdjusted() : Boolean	70177017	1.01	1.01	1.0 1.0100%
setIdWidthManuallyAdjusted(Boolean) : void   setIdWidthManuallyAdjusted(Boolean) : void	70297029	1.01	1.01	1.0 1.0100%
isScaleProteinAsCdna() : boolean   isScaleProteinAsCdna() : boolean	70417041	3.03	2.02	1.0 1.0100%
setScaleProteinAsCdna(Boolean) : void   setScaleProteinAsCdna(Boolean) : void	70577057	1.01	1.01	1.0 1.0100%
getViewName() : String   getViewName() : String	70697069	1.01	1.01	1.0 1.0100%
setViewName(String) : void   setViewName(String) : void	70817081	1.01	1.01	1.0 1.0100%
getSequenceSetId() : String   getSequenceSetId() : String	70937093	1.01	1.01	1.0 1.0100%
setSequenceSetId(String) : void   setSequenceSetId(String) : void	71057105	1.01	1.01	1.0 1.0100%
isGatheredViews() : Boolean   isGatheredViews() : Boolean	71177117	1.01	1.01	1.0 1.0100%
setGatheredViews(Boolean) : void   setGatheredViews(Boolean) : void	71297129	1.01	1.01	1.0 1.0100%
getTextCol1() : Integer   getTextCol1() : Integer	71417141	1.01	1.01	1.0 1.0100%
setTextCol1(Integer) : void   setTextCol1(Integer) : void	71537153	1.01	1.01	1.0 1.0100%
getTextCol2() : Integer   getTextCol2() : Integer	71657165	1.01	1.01	1.0 1.0100%
setTextCol2(Integer) : void   setTextCol2(Integer) : void	71777177	1.01	1.01	1.0 1.0100%
getTextColThreshold() : Integer   getTextColThreshold() : Integer	71897189	1.01	1.01	1.0 1.0100%
setTextColThreshold(Integer) : void   setTextColThreshold(Integer) : void	72017201	1.01	1.01	1.0 1.0100%
getId() : String   getId() : String	72167216	1.01	1.01	1.0 1.0100%
setId(String) : void   setId(String) : void	72297229	1.01	1.01	1.0 1.0100%
getComplementId() : String   getComplementId() : String	72427242	1.01	1.01	1.0 1.0100%
setComplementId(String) : void   setComplementId(String) : void	72557255	1.01	1.01	0.0 0.00%
isShowComplementFeatures() : boolean   isShowComplementFeatures() : boolean	72677267	3.03	2.02	1.0 1.0100%
setShowComplementFeatures(Boolean) : void   setShowComplementFeatures(Boolean) : void	72837283	1.01	1.01	1.0 1.0100%
isShowComplementFeaturesOnTop() : boolean   isShowComplementFeaturesOnTop() : boolean	72957295	3.03	2.02	1.0 1.0100%
setShowComplementFeaturesOnTop(Boolean) : void   setShowComplementFeaturesOnTop(Boolean) : void	73117311	1.01	1.01	1.0 1.0100%
isConservationSelected() : Boolean   isConservationSelected() : Boolean	73237323	1.01	1.01	1.0 1.0100%
setConservationSelected(Boolean) : void   setConservationSelected(Boolean) : void	73357335	1.01	1.01	1.0 1.0100%
getConsThreshold() : Integer   getConsThreshold() : Integer	73477347	1.01	1.01	1.0 1.0100%
setConsThreshold(Integer) : void   setConsThreshold(Integer) : void	73607360	1.01	1.01	1.0 1.0100%
isPidSelected() : Boolean   isPidSelected() : Boolean	73727372	1.01	1.01	1.0 1.0100%
setPidSelected(Boolean) : void   setPidSelected(Boolean) : void	73847384	1.01	1.01	1.0 1.0100%
getPidThreshold() : Integer   getPidThreshold() : Integer	73967396	1.01	1.01	1.0 1.0100%
setPidThreshold(Integer) : void   setPidThreshold(Integer) : void	74097409	1.01	1.01	1.0 1.0100%
isSecstrSelected() : boolean   isSecstrSelected() : boolean	74217421	3.03	2.02	1.0 1.0100%
setSecstrSelected(Boolean) : void   setSecstrSelected(Boolean) : void	74387438	1.01	1.01	1.0 1.0100%
getSecstrThreshold() : Integer   getSecstrThreshold() : Integer	74507450	1.01	1.01	1.0 1.0100%
setSecstrThreshold(Integer) : void   setSecstrThreshold(Integer) : void	74637463	1.01	1.01	0.0 0.00%
isShowConsensusHistogram() : boolean   isShowConsensusHistogram() : boolean	74757475	3.03	2.02	0.6 0.660%
setShowConsensusHistogram(Boolean) : void   setShowConsensusHistogram(Boolean) : void	74917491	1.01	1.01	1.0 1.0100%
isShowSequenceLogo() : boolean   isShowSequenceLogo() : boolean	75037503	3.03	2.02	0.6 0.660%
setShowSequenceLogo(Boolean) : void   setShowSequenceLogo(Boolean) : void	75197519	1.01	1.01	1.0 1.0100%
isNormaliseSequenceLogo() : boolean   isNormaliseSequenceLogo() : boolean	75317531	3.03	2.02	1.0 1.0100%
setNormaliseSequenceLogo(Boolean) : void   setNormaliseSequenceLogo(Boolean) : void	75477547	1.01	1.01	1.0 1.0100%
isIgnoreGapsinConsensus() : boolean   isIgnoreGapsinConsensus() : boolean	75597559	3.03	2.02	0.6 0.660%
setIgnoreGapsinConsensus(Boolean) : void   setIgnoreGapsinConsensus(Boolean) : void	75757575	1.01	1.01	1.0 1.0100%
getWidth() : Integer   getWidth() : Integer	75877587	1.01	1.01	1.0 1.0100%
setWidth(Integer) : void   setWidth(Integer) : void	75997599	1.01	1.01	1.0 1.0100%
getHeight() : Integer   getHeight() : Integer	76117611	1.01	1.01	1.0 1.0100%
setHeight(Integer) : void   setHeight(Integer) : void	76237623	1.01	1.01	1.0 1.0100%
getXpos() : Integer   getXpos() : Integer	76357635	1.01	1.01	1.0 1.0100%
setXpos(Integer) : void   setXpos(Integer) : void	76477647	1.01	1.01	1.0 1.0100%
getYpos() : Integer   getYpos() : Integer	76597659	1.01	1.01	1.0 1.0100%
setYpos(Integer) : void   setYpos(Integer) : void	76717671	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.Viewport.CalcIdParam

Class JalviewModel.Viewport.CalcIdParam	Line # 7697	Total Statements 8	Complexity 7	TOTAL Coverage 0.00%
getCalcId() : String   getCalcId() : String	77327732	1.01	1.01	0.0 0.00%
setCalcId(String) : void   setCalcId(String) : void	77457745	1.01	1.01	0.0 0.00%
isNeedsUpdate() : boolean   isNeedsUpdate() : boolean	77587758	3.03	2.02	0.0 0.00%
setNeedsUpdate(Boolean) : void   setNeedsUpdate(Boolean) : void	77757775	1.01	1.01	0.0 0.00%
isAutoUpdate() : boolean   isAutoUpdate() : boolean	77847784	1.01	1.01	0.0 0.00%
setAutoUpdate(boolean) : void   setAutoUpdate(boolean) : void	77927792	1.01	1.01	0.0 0.00%

 

Class JalviewModel.Viewport.HiddenColumns

Class JalviewModel.Viewport.HiddenColumns	Line # 7819	Total Statements 4	Complexity 4	TOTAL Coverage 1.0100%
getStart() : Integer   getStart() : Integer	78347834	1.01	1.01	1.0 1.0100%
setStart(Integer) : void   setStart(Integer) : void	78467846	1.01	1.01	1.0 1.0100%
getEnd() : Integer   getEnd() : Integer	78587858	1.01	1.01	1.0 1.0100%
setEnd(Integer) : void   setEnd(Integer) : void	78707870	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.Viewport.Overview

Class JalviewModel.Viewport.Overview	Line # 7901	Total Statements 18	Complexity 18	TOTAL Coverage 1.0100%
isShowHidden() : Boolean   isShowHidden() : Boolean	79307930	1.01	1.01	1.0 1.0100%
setShowHidden(Boolean) : void   setShowHidden(Boolean) : void	79427942	1.01	1.01	1.0 1.0100%
getResidueColour() : Integer   getResidueColour() : Integer	79547954	1.01	1.01	1.0 1.0100%
setResidueColour(Integer) : void   setResidueColour(Integer) : void	79667966	1.01	1.01	1.0 1.0100%
getGapColour() : Integer   getGapColour() : Integer	79787978	1.01	1.01	1.0 1.0100%
setGapColour(Integer) : void   setGapColour(Integer) : void	79907990	1.01	1.01	1.0 1.0100%
getHiddenColour() : Integer   getHiddenColour() : Integer	80028002	1.01	1.01	1.0 1.0100%
setHiddenColour(Integer) : void   setHiddenColour(Integer) : void	80148014	1.01	1.01	1.0 1.0100%
getTitle() : String   getTitle() : String	80268026	1.01	1.01	1.0 1.0100%
setTitle(String) : void   setTitle(String) : void	80388038	1.01	1.01	1.0 1.0100%
getWidth() : Integer   getWidth() : Integer	80508050	1.01	1.01	1.0 1.0100%
setWidth(Integer) : void   setWidth(Integer) : void	80628062	1.01	1.01	1.0 1.0100%
getHeight() : Integer   getHeight() : Integer	80748074	1.01	1.01	1.0 1.0100%
setHeight(Integer) : void   setHeight(Integer) : void	80868086	1.01	1.01	1.0 1.0100%
getXpos() : Integer   getXpos() : Integer	80988098	1.01	1.01	1.0 1.0100%
setXpos(Integer) : void   setXpos(Integer) : void	81108110	1.01	1.01	1.0 1.0100%
getYpos() : Integer   getYpos() : Integer	81228122	1.01	1.01	1.0 1.0100%
setYpos(Integer) : void   setYpos(Integer) : void	81348134	1.01	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.62222224	jalview.project.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettingsjalview.project.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettings	1PASS
	0.58518517	jalview.project.Jalview2xmlTests.testStoreAndRecoverExpandedviewsjalview.project.Jalview2xmlTests.testStoreAndRecoverExpandedviews	1PASS
	0.55277777	jalview.project.Jalview2xmlTests.testSaveAndLoadAnnotationsPropertiesjalview.project.Jalview2xmlTests.testSaveAndLoadAnnotationsProperties	1PASS
	0.54351854	jalview.project.Jalview2xmlTests.testSaveAndLoadAnnotationBasedTreejalview.project.Jalview2xmlTests.testSaveAndLoadAnnotationBasedTree	1PASS
	0.51203704	jalview.project.Jalview2xmlTests.testStoreAndRestoreIDwidthAndAnnotationHeightjalview.project.Jalview2xmlTests.testStoreAndRestoreIDwidthAndAnnotationHeight	1PASS
	0.4398148	jalview.project.Jalview2xmlTests.testPcaViewAssociationjalview.project.Jalview2xmlTests.testPcaViewAssociation	1PASS
	0.41296297	jalview.project.Jalview2xmlTests.testColourByAnnotScoresjalview.project.Jalview2xmlTests.testColourByAnnotScores	1PASS
	0.40925926	jalview.project.Jalview2xmlTests.testStoreAndRecoverColourThresholdsjalview.project.Jalview2xmlTests.testStoreAndRecoverColourThresholds	1PASS
	0.39259258	jalview.gui.AlignFrameTest.testNewView_colourThresholdsjalview.gui.AlignFrameTest.testNewView_colourThresholds	1PASS
	0.38518518	jalview.project.Jalview2xmlTests.testStoreAndRecoverPDBEntryjalview.project.Jalview2xmlTests.testStoreAndRecoverPDBEntry	1PASS
	0.3824074	jalview.project.Jalview2xmlTests.testSaveLoadFeatureColoursAndFiltersjalview.project.Jalview2xmlTests.testSaveLoadFeatureColoursAndFilters	1PASS
	0.35	jalview.io.AnnotatedPDBFileInputTest.testJalviewProjectRelocationAnnotationjalview.io.AnnotatedPDBFileInputTest.testJalviewProjectRelocationAnnotation	1PASS
	0.34444445	jalview.project.Jalview2xmlTests.viewRefPdbAnnotationjalview.project.Jalview2xmlTests.viewRefPdbAnnotation	1PASS
	0.34444445	jalview.project.Jalview2xmlTests.testCopyViewSettingsjalview.project.Jalview2xmlTests.testCopyViewSettings	1PASS
	0.34444445	jalview.project.Jalview2xmlTests.noDuplicatePdbMappingsMadejalview.project.Jalview2xmlTests.noDuplicatePdbMappingsMade	1PASS
	0.34444445	jalview.project.Jalview2xmlTests.gatherViewsHerejalview.project.Jalview2xmlTests.gatherViewsHere	1PASS
	0.3425926	jalview.project.Jalview2xmlTests.testTCoffeeScoresjalview.project.Jalview2xmlTests.testTCoffeeScores	1PASS
	0.34074074	jalview.project.Jalview2xmlTests.testStoreAndRecoverOverviewjalview.project.Jalview2xmlTests.testStoreAndRecoverOverview	1PASS
	0.31296295	jalview.project.Jalview2xmlTests.testStoreAndRecoverGroupRepSeqsjalview.project.Jalview2xmlTests.testStoreAndRecoverGroupRepSeqs	1PASS
	0.31111112	jalview.project.Jalview2xmlTests.testStoreAndRecoverAnnotationRowElementColoursjalview.project.Jalview2xmlTests.testStoreAndRecoverAnnotationRowElementColours	1PASS
	0.3074074	jalview.gui.AlignmentPanelTest.testSetOverviewTitle_automaticOverviewjalview.gui.AlignmentPanelTest.testSetOverviewTitle_automaticOverview	1PASS
	0.3074074	jalview.project.Jalview2xmlTests.testRNAStructureRecoveryjalview.project.Jalview2xmlTests.testRNAStructureRecovery	1PASS
	0.3074074	jalview.project.Jalview2xmlTests.testStoreAndRecoverHmmProfilejalview.project.Jalview2xmlTests.testStoreAndRecoverHmmProfile	1PASS
	0.3074074	jalview.gui.AlignmentPanelTest.testSetOverviewTitlejalview.gui.AlignmentPanelTest.testSetOverviewTitle	1PASS
	0.30555555	jalview.project.Jalview2xmlTests.testStoreAndRecoverGeneLocusjalview.project.Jalview2xmlTests.testStoreAndRecoverGeneLocus	1PASS
	0.30555555	jalview.project.Jalview2xmlTests.testPAEsaveRestorejalview.project.Jalview2xmlTests.testPAEsaveRestore	1PASS
	0.30555555	jalview.project.Jalview2xmlTests.testStoreAndRecoverNoOverviewjalview.project.Jalview2xmlTests.testStoreAndRecoverNoOverview	1PASS
	0.2888889	jalview.gui.AlignFrameTest.testNewView_dsRefPreservedjalview.gui.AlignFrameTest.testNewView_dsRefPreserved	1PASS
	0.2888889	jalview.gui.AlignViewportTest.testDeregisterMapping_onCloseViewjalview.gui.AlignViewportTest.testDeregisterMapping_onCloseView	1PASS
	0.28425926	jalview.project.Jalview2xmlTests.testAutoShowOverviewForLegacyProjectsjalview.project.Jalview2xmlTests.testAutoShowOverviewForLegacyProjects	1PASS
	0.24259259	jalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwicejalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwice	1PASS
	0.19907407	jalview.project.Jalview2xmlTests.testMergeDatasetsforManyViewsjalview.project.Jalview2xmlTests.testMergeDatasetsforManyViews	1PASS
	0.19444445	jalview.project.Jalview2xmlTests.testMergeDatasetsforViewsjalview.project.Jalview2xmlTests.testMergeDatasetsforViews	1PASS
	0.117592596	jalview.gui.QuitHandlerTest.testSavedProjectChangesjalview.gui.QuitHandlerTest.testSavedProjectChanges	1PASS
	0.117592596	jalview.gui.QuitHandlerTest.testWaitForSaveQuitjalview.gui.QuitHandlerTest.testWaitForSaveQuit	1PASS

 

Source view

1		//
2		// This file was generated by the Eclipse Implementation of JAXB, v2.3.9
3		// See https://eclipse-ee4j.github.io/jaxb-ri
4		// Any modifications to this file will be lost upon recompilation of the source schema.
5		// Generated on: 2025.08.25 at 12:52:58 PM BST
6		//
7
8
9		package jalview.xml.binding.jalview;
10
11		import java.util.ArrayList;
12		import java.util.List;
13		import javax.xml.bind.annotation.XmlAccessType;
14		import javax.xml.bind.annotation.XmlAccessorType;
15		import javax.xml.bind.annotation.XmlAttribute;
16		import javax.xml.bind.annotation.XmlElement;
17		import javax.xml.bind.annotation.XmlID;
18		import javax.xml.bind.annotation.XmlSchemaType;
19		import javax.xml.bind.annotation.XmlType;
20		import javax.xml.bind.annotation.XmlValue;
21		import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
22		import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
23		import javax.xml.datatype.XMLGregorianCalendar;
24
25
26		/**
27		* <p>Java class for JalviewModel complex type</p>.
28		*
29		* <p>The following schema fragment specifies the expected content contained within this class.</p>
30		*
31		* <pre>
32		* &lt;complexType name="JalviewModel"&gt;
33		* &lt;complexContent&gt;
34		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
35		* &lt;sequence&gt;
36		* &lt;element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/&gt;
37		* &lt;element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
38		* &lt;element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/&gt;
39		* &lt;sequence&gt;
40		* &lt;element name="JSeq" maxOccurs="unbounded" minOccurs="0"&gt;
41		* &lt;complexType&gt;
42		* &lt;complexContent&gt;
43		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
44		* &lt;sequence&gt;
45		* &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
46		* &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
47		* &lt;complexType&gt;
48		* &lt;complexContent&gt;
49		* &lt;extension base="{www.jalview.org}pdbentry"&gt;
50		* &lt;sequence&gt;
51		* &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
52		* &lt;complexType&gt;
53		* &lt;simpleContent&gt;
54		* &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
55		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
56		* &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
57		* &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
58		* &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
59		* &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
60		* &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
61		* &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
62		* &lt;/extension&gt;
63		* &lt;/simpleContent&gt;
64		* &lt;/complexType&gt;
65		* &lt;/element&gt;
66		* &lt;/sequence&gt;
67		* &lt;/extension&gt;
68		* &lt;/complexContent&gt;
69		* &lt;/complexType&gt;
70		* &lt;/element&gt;
71		* &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&gt;
72		* &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
73		* &lt;complexType&gt;
74		* &lt;complexContent&gt;
75		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
76		* &lt;sequence&gt;
77		* &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
78		* &lt;complexType&gt;
79		* &lt;complexContent&gt;
80		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
81		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
82		* &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
83		* &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
84		* &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
85		* &lt;/restriction&gt;
86		* &lt;/complexContent&gt;
87		* &lt;/complexType&gt;
88		* &lt;/element&gt;
89		* &lt;/sequence&gt;
90		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
91		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
92		* &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
93		* &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
94		* &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
95		* &lt;/restriction&gt;
96		* &lt;/complexContent&gt;
97		* &lt;/complexType&gt;
98		* &lt;/element&gt;
99		* &lt;element name="hmmerProfile" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
100		* &lt;/sequence&gt;
101		* &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
102		* &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
103		* &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
104		* &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
105		* &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
106		* &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
107		* &lt;/restriction&gt;
108		* &lt;/complexContent&gt;
109		* &lt;/complexType&gt;
110		* &lt;/element&gt;
111		* &lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0"&gt;
112		* &lt;complexType&gt;
113		* &lt;complexContent&gt;
114		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
115		* &lt;sequence&gt;
116		* &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
117		* &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
118		* &lt;element name="annotationFromTree" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
119		* &lt;element name="SecStrProvider" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt;
120		* &lt;/sequence&gt;
121		* &lt;attGroup ref="{www.jalview.org}conservationShading"/&gt;
122		* &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
123		* &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
124		* &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
125		* &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
126		* &lt;attribute name="idColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
127		* &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
128		* &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
129		* &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
130		* &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
131		* &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
132		* &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
133		* &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
134		* &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
135		* &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
136		* &lt;/restriction&gt;
137		* &lt;/complexContent&gt;
138		* &lt;/complexType&gt;
139		* &lt;/element&gt;
140		* &lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0"&gt;
141		* &lt;complexType&gt;
142		* &lt;complexContent&gt;
143		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
144		* &lt;sequence&gt;
145		* &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
146		* &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&gt;
147		* &lt;complexType&gt;
148		* &lt;complexContent&gt;
149		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
150		* &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
151		* &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
152		* &lt;/restriction&gt;
153		* &lt;/complexContent&gt;
154		* &lt;/complexType&gt;
155		* &lt;/element&gt;
156		* &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
157		* &lt;complexType&gt;
158		* &lt;complexContent&gt;
159		* &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
160		* &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
161		* &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
162		* &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
163		* &lt;/extension&gt;
164		* &lt;/complexContent&gt;
165		* &lt;/complexType&gt;
166		* &lt;/element&gt;
167		* &lt;element name="overview" minOccurs="0"&gt;
168		* &lt;complexType&gt;
169		* &lt;complexContent&gt;
170		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
171		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
172		* &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
173		* &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
174		* &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
175		* &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
176		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
177		* &lt;/restriction&gt;
178		* &lt;/complexContent&gt;
179		* &lt;/complexType&gt;
180		* &lt;/element&gt;
181		* &lt;element name="SecStrProvider" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt;
182		* &lt;/sequence&gt;
183		* &lt;attGroup ref="{www.jalview.org}conservationShading"/&gt;
184		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
185		* &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
186		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
187		* &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
188		* &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
189		* &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
190		* &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
191		* &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
192		* &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
193		* &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
194		* &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
195		* &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
196		* &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
197		* &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
198		* &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
199		* &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
200		* &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
201		* &lt;attribute name="showStructureProviders" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
202		* &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
203		* &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
204		* &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
205		* &lt;attribute name="showGroupSecStrConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
206		* &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
207		* &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
208		* &lt;attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
209		* &lt;attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
210		* &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
211		* &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
212		* &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
213		* &lt;attribute name="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
214		* &lt;attribute name="idWidthManuallyAdjusted" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
215		* &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
216		* &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
217		* &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
218		* &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
219		* &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
220		* &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
221		* &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
222		* &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
223		* &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
224		* &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
225		* &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
226		* &lt;/restriction&gt;
227		* &lt;/complexContent&gt;
228		* &lt;/complexType&gt;
229		* &lt;/element&gt;
230		* &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0"&gt;
231		* &lt;complexType&gt;
232		* &lt;complexContent&gt;
233		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
234		* &lt;sequence&gt;
235		* &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&gt;
236		* &lt;/sequence&gt;
237		* &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
238		* &lt;/restriction&gt;
239		* &lt;/complexContent&gt;
240		* &lt;/complexType&gt;
241		* &lt;/element&gt;
242		* &lt;element name="tree" maxOccurs="unbounded" minOccurs="0"&gt;
243		* &lt;complexType&gt;
244		* &lt;complexContent&gt;
245		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
246		* &lt;sequence minOccurs="0"&gt;
247		* &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
248		* &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
249		* &lt;element name="TreeColorMap" minOccurs="0"&gt;
250		* &lt;complexType&gt;
251		* &lt;complexContent&gt;
252		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
253		* &lt;sequence&gt;
254		* &lt;element name="ColorEntry" maxOccurs="unbounded" minOccurs="0"&gt;
255		* &lt;complexType&gt;
256		* &lt;complexContent&gt;
257		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
258		* &lt;attribute name="label" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
259		* &lt;attribute name="color" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
260		* &lt;/restriction&gt;
261		* &lt;/complexContent&gt;
262		* &lt;/complexType&gt;
263		* &lt;/element&gt;
264		* &lt;/sequence&gt;
265		* &lt;/restriction&gt;
266		* &lt;/complexContent&gt;
267		* &lt;/complexType&gt;
268		* &lt;/element&gt;
269		* &lt;/sequence&gt;
270		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
271		* &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
272		* &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
273		* &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
274		* &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
275		* &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
276		* &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
277		* &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
278		* &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
279		* &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
280		* &lt;attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
281		* &lt;attribute name="annotationBased" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
282		* &lt;attribute name="showAnnotationAs" type="{http://www.w3.org/2001/XMLSchema}string" default="None" /&gt;
283		* &lt;attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
284		* &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
285		* &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
286		* &lt;/restriction&gt;
287		* &lt;/complexContent&gt;
288		* &lt;/complexType&gt;
289		* &lt;/element&gt;
290		* &lt;element name="PcaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
291		* &lt;complexType&gt;
292		* &lt;complexContent&gt;
293		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
294		* &lt;sequence&gt;
295		* &lt;element name="sequencePoint" maxOccurs="unbounded"&gt;
296		* &lt;complexType&gt;
297		* &lt;complexContent&gt;
298		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
299		* &lt;attGroup ref="{www.jalview.org}position"/&gt;
300		* &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
301		* &lt;/restriction&gt;
302		* &lt;/complexContent&gt;
303		* &lt;/complexType&gt;
304		* &lt;/element&gt;
305		* &lt;element name="axis" maxOccurs="3" minOccurs="3"&gt;
306		* &lt;complexType&gt;
307		* &lt;complexContent&gt;
308		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
309		* &lt;attGroup ref="{www.jalview.org}position"/&gt;
310		* &lt;/restriction&gt;
311		* &lt;/complexContent&gt;
312		* &lt;/complexType&gt;
313		* &lt;/element&gt;
314		* &lt;element name="seqPointMin"&gt;
315		* &lt;complexType&gt;
316		* &lt;complexContent&gt;
317		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
318		* &lt;attGroup ref="{www.jalview.org}position"/&gt;
319		* &lt;/restriction&gt;
320		* &lt;/complexContent&gt;
321		* &lt;/complexType&gt;
322		* &lt;/element&gt;
323		* &lt;element name="seqPointMax"&gt;
324		* &lt;complexType&gt;
325		* &lt;complexContent&gt;
326		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
327		* &lt;attGroup ref="{www.jalview.org}position"/&gt;
328		* &lt;/restriction&gt;
329		* &lt;/complexContent&gt;
330		* &lt;/complexType&gt;
331		* &lt;/element&gt;
332		* &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&gt;
333		* &lt;/sequence&gt;
334		* &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
335		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
336		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
337		* &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
338		* &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
339		* &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
340		* &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
341		* &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
342		* &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
343		* &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
344		* &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
345		* &lt;/restriction&gt;
346		* &lt;/complexContent&gt;
347		* &lt;/complexType&gt;
348		* &lt;/element&gt;
349		* &lt;element name="FeatureSettings" minOccurs="0"&gt;
350		* &lt;complexType&gt;
351		* &lt;complexContent&gt;
352		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
353		* &lt;sequence&gt;
354		* &lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&gt;
355		* &lt;complexType&gt;
356		* &lt;complexContent&gt;
357		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
358		* &lt;sequence&gt;
359		* &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
360		* &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
361		* &lt;/sequence&gt;
362		* &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
363		* &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
364		* &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
365		* &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
366		* &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
367		* &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
368		* &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
369		* &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
370		* &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
371		* &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
372		* &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
373		* &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
374		* &lt;/restriction&gt;
375		* &lt;/complexContent&gt;
376		* &lt;/complexType&gt;
377		* &lt;/element&gt;
378		* &lt;element name="group" maxOccurs="unbounded" minOccurs="0"&gt;
379		* &lt;complexType&gt;
380		* &lt;complexContent&gt;
381		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
382		* &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
383		* &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
384		* &lt;/restriction&gt;
385		* &lt;/complexContent&gt;
386		* &lt;/complexType&gt;
387		* &lt;/element&gt;
388		* &lt;/sequence&gt;
389		* &lt;/restriction&gt;
390		* &lt;/complexContent&gt;
391		* &lt;/complexType&gt;
392		* &lt;/element&gt;
393		* &lt;/sequence&gt;
394		* &lt;/sequence&gt;
395		* &lt;/restriction&gt;
396		* &lt;/complexContent&gt;
397		* &lt;/complexType&gt;
398		* </pre>
399		*
400		*
401		*/
402		@XmlAccessorType(XmlAccessType.FIELD)
403		@XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
404		"creationDate",
405		"version",
406		"vamsasModel",
407		"jSeq",
408		"jGroup",
409		"viewport",
410		"userColours",
411		"tree",
412		"pcaViewer",
413		"featureSettings"
414		})
		84.6% Uncovered Elements: 8 (52) Complexity: 20 Complexity Density: 0.77
415		public class JalviewModel {
416
417		@XmlElement(required = true)
418		@XmlSchemaType(name = "dateTime")
419		protected XMLGregorianCalendar creationDate;
420		@XmlElement(required = true)
421		protected String version;
422		@XmlElement(required = true)
423		protected VAMSAS vamsasModel;
424		@XmlElement(name = "JSeq")
425		protected List<JalviewModel.JSeq> jSeq;
426		@XmlElement(name = "JGroup")
427		protected List<JalviewModel.JGroup> jGroup;
428		@XmlElement(name = "Viewport")
429		protected List<JalviewModel.Viewport> viewport;
430		@XmlElement(name = "UserColours")
431		protected List<JalviewModel.UserColours> userColours;
432		protected List<JalviewModel.Tree> tree;
433		@XmlElement(name = "PcaViewer")
434		protected List<JalviewModel.PcaViewer> pcaViewer;
435		@XmlElement(name = "FeatureSettings")
436		protected JalviewModel.FeatureSettings featureSettings;
437
438		/**
439		* Gets the value of the creationDate property.
440		*
441		* @return
442		* possible object is
443		* {@link XMLGregorianCalendar }
444		*
445		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
446	0	public XMLGregorianCalendar getCreationDate() {...
447	0	return creationDate;
448		}
449
450		/**
451		* Sets the value of the creationDate property.
452		*
453		* @param value
454		* allowed object is
455		* {@link XMLGregorianCalendar }
456		*
457		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
458	81	public void setCreationDate(XMLGregorianCalendar value) {...
459	81	this.creationDate = value;
460		}
461
462		/**
463		* Gets the value of the version property.
464		*
465		* @return
466		* possible object is
467		* {@link String }
468		*
469		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
470	225	public String getVersion() {...
471	225	return version;
472		}
473
474		/**
475		* Sets the value of the version property.
476		*
477		* @param value
478		* allowed object is
479		* {@link String }
480		*
481		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
482	81	public void setVersion(String value) {...
483	81	this.version = value;
484		}
485
486		/**
487		* Gets the value of the vamsasModel property.
488		*
489		* @return
490		* possible object is
491		* {@link VAMSAS }
492		*
493		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
494	223	public VAMSAS getVamsasModel() {...
495	223	return vamsasModel;
496		}
497
498		/**
499		* Sets the value of the vamsasModel property.
500		*
501		* @param value
502		* allowed object is
503		* {@link VAMSAS }
504		*
505		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
506	81	public void setVamsasModel(VAMSAS value) {...
507	81	this.vamsasModel = value;
508		}
509
510		/**
511		* Gets the value of the jSeq property.
512		*
513		* <p>This accessor method returns a reference to the live list,
514		* not a snapshot. Therefore any modification you make to the
515		* returned list will be present inside the JAXB object.
516		* This is why there is not a <CODE>set</CODE> method for the jSeq property.</p>
517		*
518		* <p>
519		* For example, to add a new item, do as follows:
520		* </p>
521		* <pre>
522		* getJSeq().add(newItem);
523		* </pre>
524		*
525		*
526		* <p>
527		* Objects of the following type(s) are allowed in the list
528		* {@link JalviewModel.JSeq }
529		* </p>
530		*
531		*
532		* @return
533		* The value of the jSeq property.
534		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
535	8526	public List<JalviewModel.JSeq> getJSeq() {...
536	8526	if (jSeq == null) {
537	81	jSeq = new ArrayList<JalviewModel.JSeq>();
538		}
539	8526	return this.jSeq;
540		}
541
542		/**
543		* Gets the value of the jGroup property.
544		*
545		* <p>This accessor method returns a reference to the live list,
546		* not a snapshot. Therefore any modification you make to the
547		* returned list will be present inside the JAXB object.
548		* This is why there is not a <CODE>set</CODE> method for the jGroup property.</p>
549		*
550		* <p>
551		* For example, to add a new item, do as follows:
552		* </p>
553		* <pre>
554		* getJGroup().add(newItem);
555		* </pre>
556		*
557		*
558		* <p>
559		* Objects of the following type(s) are allowed in the list
560		* {@link JalviewModel.JGroup }
561		* </p>
562		*
563		*
564		* @return
565		* The value of the jGroup property.
566		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
567	188	public List<JalviewModel.JGroup> getJGroup() {...
568	188	if (jGroup == null) {
569	111	jGroup = new ArrayList<JalviewModel.JGroup>();
570		}
571	188	return this.jGroup;
572		}
573
574		/**
575		* Gets the value of the viewport property.
576		*
577		* <p>This accessor method returns a reference to the live list,
578		* not a snapshot. Therefore any modification you make to the
579		* returned list will be present inside the JAXB object.
580		* This is why there is not a <CODE>set</CODE> method for the viewport property.</p>
581		*
582		* <p>
583		* For example, to add a new item, do as follows:
584		* </p>
585		* <pre>
586		* getViewport().add(newItem);
587		* </pre>
588		*
589		*
590		* <p>
591		* Objects of the following type(s) are allowed in the list
592		* {@link JalviewModel.Viewport }
593		* </p>
594		*
595		*
596		* @return
597		* The value of the viewport property.
598		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
599	476	public List<JalviewModel.Viewport> getViewport() {...
600	476	if (viewport == null) {
601	86	viewport = new ArrayList<JalviewModel.Viewport>();
602		}
603	476	return this.viewport;
604		}
605
606		/**
607		* Gets the value of the userColours property.
608		*
609		* <p>This accessor method returns a reference to the live list,
610		* not a snapshot. Therefore any modification you make to the
611		* returned list will be present inside the JAXB object.
612		* This is why there is not a <CODE>set</CODE> method for the userColours property.</p>
613		*
614		* <p>
615		* For example, to add a new item, do as follows:
616		* </p>
617		* <pre>
618		* getUserColours().add(newItem);
619		* </pre>
620		*
621		*
622		* <p>
623		* Objects of the following type(s) are allowed in the list
624		* {@link JalviewModel.UserColours }
625		* </p>
626		*
627		*
628		* @return
629		* The value of the userColours property.
630		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
631	0	public List<JalviewModel.UserColours> getUserColours() {...
632	0	if (userColours == null) {
633	0	userColours = new ArrayList<JalviewModel.UserColours>();
634		}
635	0	return this.userColours;
636		}
637
638		/**
639		* Gets the value of the tree property.
640		*
641		* <p>This accessor method returns a reference to the live list,
642		* not a snapshot. Therefore any modification you make to the
643		* returned list will be present inside the JAXB object.
644		* This is why there is not a <CODE>set</CODE> method for the tree property.</p>
645		*
646		* <p>
647		* For example, to add a new item, do as follows:
648		* </p>
649		* <pre>
650		* getTree().add(newItem);
651		* </pre>
652		*
653		*
654		* <p>
655		* Objects of the following type(s) are allowed in the list
656		* {@link JalviewModel.Tree }
657		* </p>
658		*
659		*
660		* @return
661		* The value of the tree property.
662		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
663	125	public List<JalviewModel.Tree> getTree() {...
664	125	if (tree == null) {
665	77	tree = new ArrayList<JalviewModel.Tree>();
666		}
667	125	return this.tree;
668		}
669
670		/**
671		* Gets the value of the pcaViewer property.
672		*
673		* <p>This accessor method returns a reference to the live list,
674		* not a snapshot. Therefore any modification you make to the
675		* returned list will be present inside the JAXB object.
676		* This is why there is not a <CODE>set</CODE> method for the pcaViewer property.</p>
677		*
678		* <p>
679		* For example, to add a new item, do as follows:
680		* </p>
681		* <pre>
682		* getPcaViewer().add(newItem);
683		* </pre>
684		*
685		*
686		* <p>
687		* Objects of the following type(s) are allowed in the list
688		* {@link JalviewModel.PcaViewer }
689		* </p>
690		*
691		*
692		* @return
693		* The value of the pcaViewer property.
694		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
695	89	public List<JalviewModel.PcaViewer> getPcaViewer() {...
696	89	if (pcaViewer == null) {
697	86	pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
698		}
699	89	return this.pcaViewer;
700		}
701
702		/**
703		* Gets the value of the featureSettings property.
704		*
705		* @return
706		* possible object is
707		* {@link JalviewModel.FeatureSettings }
708		*
709		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
710	2337	public JalviewModel.FeatureSettings getFeatureSettings() {...
711	2337	return featureSettings;
712		}
713
714		/**
715		* Sets the value of the featureSettings property.
716		*
717		* @param value
718		* allowed object is
719		* {@link JalviewModel.FeatureSettings }
720		*
721		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
722	13	public void setFeatureSettings(JalviewModel.FeatureSettings value) {...
723	13	this.featureSettings = value;
724		}
725
726
727		/**
728		* <p>Java class for anonymous complex type</p>.
729		*
730		* <p>The following schema fragment specifies the expected content contained within this class.</p>
731		*
732		* <pre>
733		* &lt;complexType&gt;
734		* &lt;complexContent&gt;
735		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
736		* &lt;sequence&gt;
737		* &lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&gt;
738		* &lt;complexType&gt;
739		* &lt;complexContent&gt;
740		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
741		* &lt;sequence&gt;
742		* &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
743		* &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
744		* &lt;/sequence&gt;
745		* &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
746		* &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
747		* &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
748		* &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
749		* &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
750		* &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
751		* &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
752		* &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
753		* &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
754		* &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
755		* &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
756		* &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
757		* &lt;/restriction&gt;
758		* &lt;/complexContent&gt;
759		* &lt;/complexType&gt;
760		* &lt;/element&gt;
761		* &lt;element name="group" maxOccurs="unbounded" minOccurs="0"&gt;
762		* &lt;complexType&gt;
763		* &lt;complexContent&gt;
764		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
765		* &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
766		* &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
767		* &lt;/restriction&gt;
768		* &lt;/complexContent&gt;
769		* &lt;/complexType&gt;
770		* &lt;/element&gt;
771		* &lt;/sequence&gt;
772		* &lt;/restriction&gt;
773		* &lt;/complexContent&gt;
774		* &lt;/complexType&gt;
775		* </pre>
776		*
777		*
778		*/
779		@XmlAccessorType(XmlAccessType.FIELD)
780		@XmlType(name = "", propOrder = {
781		"setting",
782		"group"
783		})
		100% Uncovered Elements: 0 (12) Complexity: 4 Complexity Density: 0.67
784		public static class FeatureSettings {
785
786		@XmlElement(namespace = "www.jalview.org")
787		protected List<JalviewModel.FeatureSettings.Setting> setting;
788		@XmlElement(namespace = "www.jalview.org")
789		protected List<JalviewModel.FeatureSettings.Group> group;
790
791		/**
792		* Gets the value of the setting property.
793		*
794		* <p>This accessor method returns a reference to the live list,
795		* not a snapshot. Therefore any modification you make to the
796		* returned list will be present inside the JAXB object.
797		* This is why there is not a <CODE>set</CODE> method for the setting property.</p>
798		*
799		* <p>
800		* For example, to add a new item, do as follows:
801		* </p>
802		* <pre>
803		* getSetting().add(newItem);
804		* </pre>
805		*
806		*
807		* <p>
808		* Objects of the following type(s) are allowed in the list
809		* {@link JalviewModel.FeatureSettings.Setting }
810		* </p>
811		*
812		*
813		* @return
814		* The value of the setting property.
815		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
816	2040	public List<JalviewModel.FeatureSettings.Setting> getSetting() {...
817	2040	if (setting == null) {
818	13	setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
819		}
820	2040	return this.setting;
821		}
822
823		/**
824		* Gets the value of the group property.
825		*
826		* <p>This accessor method returns a reference to the live list,
827		* not a snapshot. Therefore any modification you make to the
828		* returned list will be present inside the JAXB object.
829		* This is why there is not a <CODE>set</CODE> method for the group property.</p>
830		*
831		* <p>
832		* For example, to add a new item, do as follows:
833		* </p>
834		* <pre>
835		* getGroup().add(newItem);
836		* </pre>
837		*
838		*
839		* <p>
840		* Objects of the following type(s) are allowed in the list
841		* {@link JalviewModel.FeatureSettings.Group }
842		* </p>
843		*
844		*
845		* @return
846		* The value of the group property.
847		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
848	472	public List<JalviewModel.FeatureSettings.Group> getGroup() {...
849	472	if (group == null) {
850	13	group = new ArrayList<JalviewModel.FeatureSettings.Group>();
851		}
852	472	return this.group;
853		}
854
855
856		/**
857		* <p>Java class for anonymous complex type</p>.
858		*
859		* <p>The following schema fragment specifies the expected content contained within this class.</p>
860		*
861		* <pre>
862		* &lt;complexType&gt;
863		* &lt;complexContent&gt;
864		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
865		* &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
866		* &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
867		* &lt;/restriction&gt;
868		* &lt;/complexContent&gt;
869		* &lt;/complexType&gt;
870		* </pre>
871		*
872		*
873		*/
874		@XmlAccessorType(XmlAccessType.FIELD)
875		@XmlType(name = "")
		100% Uncovered Elements: 0 (8) Complexity: 4 Complexity Density: 1
876		public static class Group {
877
878		@XmlAttribute(name = "name", required = true)
879		protected String name;
880		@XmlAttribute(name = "display", required = true)
881		protected boolean display;
882
883		/**
884		* Gets the value of the name property.
885		*
886		* @return
887		* possible object is
888		* {@link String }
889		*
890		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
891	184	public String getName() {...
892	184	return name;
893		}
894
895		/**
896		* Sets the value of the name property.
897		*
898		* @param value
899		* allowed object is
900		* {@link String }
901		*
902		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
903	59	public void setName(String value) {...
904	59	this.name = value;
905		}
906
907		/**
908		* Gets the value of the display property.
909		*
910		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
911	184	public boolean isDisplay() {...
912	184	return display;
913		}
914
915		/**
916		* Sets the value of the display property.
917		*
918		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
919	59	public void setDisplay(boolean value) {...
920	59	this.display = value;
921		}
922
923		}
924
925
926		/**
927		* <p>Java class for anonymous complex type</p>.
928		*
929		* <p>The following schema fragment specifies the expected content contained within this class.</p>
930		*
931		* <pre>
932		* &lt;complexType&gt;
933		* &lt;complexContent&gt;
934		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
935		* &lt;sequence&gt;
936		* &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
937		* &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
938		* &lt;/sequence&gt;
939		* &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
940		* &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
941		* &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
942		* &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
943		* &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
944		* &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
945		* &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
946		* &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
947		* &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
948		* &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
949		* &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
950		* &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
951		* &lt;/restriction&gt;
952		* &lt;/complexContent&gt;
953		* &lt;/complexType&gt;
954		* </pre>
955		*
956		*
957		*/
958		@XmlAccessorType(XmlAccessType.FIELD)
959		@XmlType(name = "", propOrder = {
960		"attributeName",
961		"matcherSet"
962		})
		96.8% Uncovered Elements: 2 (62) Complexity: 29 Complexity Density: 0.94
963		public static class Setting {
964
965		/**
966		* name of feature attribute to colour by, or attribute and sub-attribute
967		*
968		*/
969		@XmlElement(namespace = "www.jalview.org")
970		protected List<String> attributeName;
971		/**
972		* optional filter(s) applied to the feature type
973		*
974		*/
975		@XmlElement(namespace = "www.jalview.org")
976		protected FeatureMatcherSet matcherSet;
977		@XmlAttribute(name = "type", required = true)
978		protected String type;
979		@XmlAttribute(name = "colour", required = true)
980		protected int colour;
981		@XmlAttribute(name = "display", required = true)
982		protected boolean display;
983		@XmlAttribute(name = "order")
984		protected Float order;
985		/**
986		* Optional minimum colour
987		* for graduated
988		* feature
989		* colour
990		*
991		*/
992		@XmlAttribute(name = "mincolour")
993		protected Integer mincolour;
994		@XmlAttribute(name = "noValueColour")
995		protected NoValueColour noValueColour;
996		/**
997		* threshold value for
998		* graduated feature colour
999		*
1000		*/
1001		@XmlAttribute(name = "threshold")
1002		protected Float threshold;
1003		/**
1004		* threshold type for
1005		* graduated feature colour
1006		*
1007		*/
1008		@XmlAttribute(name = "threshstate")
1009		protected Integer threshstate;
1010		@XmlAttribute(name = "max")
1011		protected Float max;
1012		@XmlAttribute(name = "min")
1013		protected Float min;
1014		@XmlAttribute(name = "colourByLabel")
1015		protected Boolean colourByLabel;
1016		@XmlAttribute(name = "autoScale")
1017		protected Boolean autoScale;
1018
1019		/**
1020		* name of feature attribute to colour by, or attribute and sub-attribute
1021		*
1022		* Gets the value of the attributeName property.
1023		*
1024		* <p>This accessor method returns a reference to the live list,
1025		* not a snapshot. Therefore any modification you make to the
1026		* returned list will be present inside the JAXB object.
1027		* This is why there is not a <CODE>set</CODE> method for the attributeName property.</p>
1028		*
1029		* <p>
1030		* For example, to add a new item, do as follows:
1031		* </p>
1032		* <pre>
1033		* getAttributeName().add(newItem);
1034		* </pre>
1035		*
1036		*
1037		* <p>
1038		* Objects of the following type(s) are allowed in the list
1039		* {@link String }
1040		* </p>
1041		*
1042		*
1043		* @return
1044		* The value of the attributeName property.
1045		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
1046	12	public List<String> getAttributeName() {...
1047	12	if (attributeName == null) {
1048	5	attributeName = new ArrayList<String>();
1049		}
1050	12	return this.attributeName;
1051		}
1052
1053		/**
1054		* optional filter(s) applied to the feature type
1055		*
1056		* @return
1057		* possible object is
1058		* {@link FeatureMatcherSet }
1059		*
1060		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1061	869	public FeatureMatcherSet getMatcherSet() {...
1062	869	return matcherSet;
1063		}
1064
1065		/**
1066		* Sets the value of the matcherSet property.
1067		*
1068		* @param value
1069		* allowed object is
1070		* {@link FeatureMatcherSet }
1071		*
1072		* @see #getMatcherSet()
1073		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1074	3	public void setMatcherSet(FeatureMatcherSet value) {...
1075	3	this.matcherSet = value;
1076		}
1077
1078		/**
1079		* Gets the value of the type property.
1080		*
1081		* @return
1082		* possible object is
1083		* {@link String }
1084		*
1085		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1086	869	public String getType() {...
1087	869	return type;
1088		}
1089
1090		/**
1091		* Sets the value of the type property.
1092		*
1093		* @param value
1094		* allowed object is
1095		* {@link String }
1096		*
1097		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1098	212	public void setType(String value) {...
1099	212	this.type = value;
1100		}
1101
1102		/**
1103		* Gets the value of the colour property.
1104		*
1105		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1106	869	public int getColour() {...
1107	869	return colour;
1108		}
1109
1110		/**
1111		* Sets the value of the colour property.
1112		*
1113		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1114	212	public void setColour(int value) {...
1115	212	this.colour = value;
1116		}
1117
1118		/**
1119		* Gets the value of the display property.
1120		*
1121		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1122	869	public boolean isDisplay() {...
1123	869	return display;
1124		}
1125
1126		/**
1127		* Sets the value of the display property.
1128		*
1129		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1130	212	public void setDisplay(boolean value) {...
1131	212	this.display = value;
1132		}
1133
1134		/**
1135		* Gets the value of the order property.
1136		*
1137		* @return
1138		* possible object is
1139		* {@link Float }
1140		*
1141		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1142	1738	public Float getOrder() {...
1143	1738	return order;
1144		}
1145
1146		/**
1147		* Sets the value of the order property.
1148		*
1149		* @param value
1150		* allowed object is
1151		* {@link Float }
1152		*
1153		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1154	212	public void setOrder(Float value) {...
1155	212	this.order = value;
1156		}
1157
1158		/**
1159		* Optional minimum colour
1160		* for graduated
1161		* feature
1162		* colour
1163		*
1164		* @return
1165		* possible object is
1166		* {@link Integer }
1167		*
1168		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1169	874	public Integer getMincolour() {...
1170	874	return mincolour;
1171		}
1172
1173		/**
1174		* Sets the value of the mincolour property.
1175		*
1176		* @param value
1177		* allowed object is
1178		* {@link Integer }
1179		*
1180		* @see #getMincolour()
1181		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1182	4	public void setMincolour(Integer value) {...
1183	4	this.mincolour = value;
1184		}
1185
1186		/**
1187		* Gets the value of the noValueColour property.
1188		*
1189		* @return
1190		* possible object is
1191		* {@link NoValueColour }
1192		*
1193		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
1194	5	public NoValueColour getNoValueColour() {...
1195	5	if (noValueColour == null) {
1196	0	return NoValueColour.MIN;
1197		} else {
1198	5	return noValueColour;
1199		}
1200		}
1201
1202		/**
1203		* Sets the value of the noValueColour property.
1204		*
1205		* @param value
1206		* allowed object is
1207		* {@link NoValueColour }
1208		*
1209		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1210	4	public void setNoValueColour(NoValueColour value) {...
1211	4	this.noValueColour = value;
1212		}
1213
1214		/**
1215		* threshold value for
1216		* graduated feature colour
1217		*
1218		* @return
1219		* possible object is
1220		* {@link Float }
1221		*
1222		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1223	10	public Float getThreshold() {...
1224	10	return threshold;
1225		}
1226
1227		/**
1228		* Sets the value of the threshold property.
1229		*
1230		* @param value
1231		* allowed object is
1232		* {@link Float }
1233		*
1234		* @see #getThreshold()
1235		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1236	4	public void setThreshold(Float value) {...
1237	4	this.threshold = value;
1238		}
1239
1240		/**
1241		* threshold type for
1242		* graduated feature colour
1243		*
1244		* @return
1245		* possible object is
1246		* {@link Integer }
1247		*
1248		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1249	5	public Integer getThreshstate() {...
1250	5	return threshstate;
1251		}
1252
1253		/**
1254		* Sets the value of the threshstate property.
1255		*
1256		* @param value
1257		* allowed object is
1258		* {@link Integer }
1259		*
1260		* @see #getThreshstate()
1261		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1262	4	public void setThreshstate(Integer value) {...
1263	4	this.threshstate = value;
1264		}
1265
1266		/**
1267		* Gets the value of the max property.
1268		*
1269		* @return
1270		* possible object is
1271		* {@link Float }
1272		*
1273		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1274	10	public Float getMax() {...
1275	10	return max;
1276		}
1277
1278		/**
1279		* Sets the value of the max property.
1280		*
1281		* @param value
1282		* allowed object is
1283		* {@link Float }
1284		*
1285		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1286	4	public void setMax(Float value) {...
1287	4	this.max = value;
1288		}
1289
1290		/**
1291		* Gets the value of the min property.
1292		*
1293		* @return
1294		* possible object is
1295		* {@link Float }
1296		*
1297		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1298	5	public Float getMin() {...
1299	5	return min;
1300		}
1301
1302		/**
1303		* Sets the value of the min property.
1304		*
1305		* @param value
1306		* allowed object is
1307		* {@link Float }
1308		*
1309		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1310	4	public void setMin(Float value) {...
1311	4	this.min = value;
1312		}
1313
1314		/**
1315		* Gets the value of the colourByLabel property.
1316		*
1317		* @return
1318		* possible object is
1319		* {@link Boolean }
1320		*
1321		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1322	10	public Boolean isColourByLabel() {...
1323	10	return colourByLabel;
1324		}
1325
1326		/**
1327		* Sets the value of the colourByLabel property.
1328		*
1329		* @param value
1330		* allowed object is
1331		* {@link Boolean }
1332		*
1333		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1334	4	public void setColourByLabel(Boolean value) {...
1335	4	this.colourByLabel = value;
1336		}
1337
1338		/**
1339		* Gets the value of the autoScale property.
1340		*
1341		* @return
1342		* possible object is
1343		* {@link Boolean }
1344		*
1345		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1346	10	public Boolean isAutoScale() {...
1347	10	return autoScale;
1348		}
1349
1350		/**
1351		* Sets the value of the autoScale property.
1352		*
1353		* @param value
1354		* allowed object is
1355		* {@link Boolean }
1356		*
1357		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1358	4	public void setAutoScale(Boolean value) {...
1359	4	this.autoScale = value;
1360		}
1361
1362		}
1363
1364		}
1365
1366
1367		/**
1368		* <p>Java class for anonymous complex type</p>.
1369		*
1370		* <p>The following schema fragment specifies the expected content contained within this class.</p>
1371		*
1372		* <pre>
1373		* &lt;complexType&gt;
1374		* &lt;complexContent&gt;
1375		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
1376		* &lt;sequence&gt;
1377		* &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
1378		* &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
1379		* &lt;element name="annotationFromTree" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
1380		* &lt;element name="SecStrProvider" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt;
1381		* &lt;/sequence&gt;
1382		* &lt;attGroup ref="{www.jalview.org}conservationShading"/&gt;
1383		* &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1384		* &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1385		* &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1386		* &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1387		* &lt;attribute name="idColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1388		* &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1389		* &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1390		* &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1391		* &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1392		* &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1393		* &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1394		* &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1395		* &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1396		* &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1397		* &lt;/restriction&gt;
1398		* &lt;/complexContent&gt;
1399		* &lt;/complexType&gt;
1400		* </pre>
1401		*
1402		*
1403		*/
1404		@XmlAccessorType(XmlAccessType.FIELD)
1405		@XmlType(name = "", propOrder = {
1406		"seq",
1407		"annotationColours",
1408		"annotationFromTree",
1409		"secStrProvider"
1410		})
		89.1% Uncovered Elements: 15 (138) Complexity: 61 Complexity Density: 0.88
1411		public static class JGroup {
1412
1413		@XmlElement(namespace = "www.jalview.org", required = true)
1414		protected List<String> seq;
1415		@XmlElement(namespace = "www.jalview.org")
1416		protected AnnotationColourScheme annotationColours;
1417		@XmlElement(namespace = "www.jalview.org", required = true)
1418		protected List<String> annotationFromTree;
1419		@XmlElement(name = "SecStrProvider", namespace = "www.jalview.org")
1420		protected List<String> secStrProvider;
1421		@XmlAttribute(name = "start")
1422		protected Integer start;
1423		@XmlAttribute(name = "end")
1424		protected Integer end;
1425		@XmlAttribute(name = "name")
1426		protected String name;
1427		@XmlAttribute(name = "colour")
1428		protected String colour;
1429		@XmlAttribute(name = "idColour")
1430		protected Integer idColour;
1431		@XmlAttribute(name = "outlineColour")
1432		protected Integer outlineColour;
1433		@XmlAttribute(name = "displayBoxes")
1434		protected Boolean displayBoxes;
1435		@XmlAttribute(name = "displayText")
1436		protected Boolean displayText;
1437		@XmlAttribute(name = "colourText")
1438		protected Boolean colourText;
1439		@XmlAttribute(name = "textCol1")
1440		protected Integer textCol1;
1441		@XmlAttribute(name = "textCol2")
1442		protected Integer textCol2;
1443		@XmlAttribute(name = "textColThreshold")
1444		protected Integer textColThreshold;
1445		@XmlAttribute(name = "showUnconserved")
1446		protected Boolean showUnconserved;
1447		/**
1448		* Optional sequence group ID (only
1449		* needs to be
1450		* unique for this
1451		* alignment)
1452		*
1453		*/
1454		@XmlAttribute(name = "id")
1455		protected String id;
1456		@XmlAttribute(name = "conservationSelected")
1457		protected Boolean conservationSelected;
1458		/**
1459		* Conservation shading increment
1460		*
1461		*/
1462		@XmlAttribute(name = "consThreshold")
1463		protected Integer consThreshold;
1464		@XmlAttribute(name = "pidSelected")
1465		protected Boolean pidSelected;
1466		/**
1467		* Percent Identity Threshold
1468		*
1469		*/
1470		@XmlAttribute(name = "pidThreshold")
1471		protected Integer pidThreshold;
1472		/**
1473		* Secondary structure consensus shading - since 2.11.4
1474		*
1475		*/
1476		@XmlAttribute(name = "secstrSelected")
1477		protected Boolean secstrSelected;
1478		/**
1479		* Secondary structure consensus increment
1480		*
1481		*/
1482		@XmlAttribute(name = "secstrThreshold")
1483		protected Integer secstrThreshold;
1484		@XmlAttribute(name = "showConsensusHistogram")
1485		protected Boolean showConsensusHistogram;
1486		@XmlAttribute(name = "showSequenceLogo")
1487		protected Boolean showSequenceLogo;
1488		@XmlAttribute(name = "normaliseSequenceLogo")
1489		protected Boolean normaliseSequenceLogo;
1490		@XmlAttribute(name = "ignoreGapsinConsensus")
1491		protected Boolean ignoreGapsinConsensus;
1492
1493		/**
1494		* Gets the value of the seq property.
1495		*
1496		* <p>This accessor method returns a reference to the live list,
1497		* not a snapshot. Therefore any modification you make to the
1498		* returned list will be present inside the JAXB object.
1499		* This is why there is not a <CODE>set</CODE> method for the seq property.</p>
1500		*
1501		* <p>
1502		* For example, to add a new item, do as follows:
1503		* </p>
1504		* <pre>
1505		* getSeq().add(newItem);
1506		* </pre>
1507		*
1508		*
1509		* <p>
1510		* Objects of the following type(s) are allowed in the list
1511		* {@link String }
1512		* </p>
1513		*
1514		*
1515		* @return
1516		* The value of the seq property.
1517		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
1518	1081	public List<String> getSeq() {...
1519	1081	if (seq == null) {
1520	22	seq = new ArrayList<String>();
1521		}
1522	1081	return this.seq;
1523		}
1524
1525		/**
1526		* Gets the value of the annotationColours property.
1527		*
1528		* @return
1529		* possible object is
1530		* {@link AnnotationColourScheme }
1531		*
1532		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1533	2	public AnnotationColourScheme getAnnotationColours() {...
1534	2	return annotationColours;
1535		}
1536
1537		/**
1538		* Sets the value of the annotationColours property.
1539		*
1540		* @param value
1541		* allowed object is
1542		* {@link AnnotationColourScheme }
1543		*
1544		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1545	1	public void setAnnotationColours(AnnotationColourScheme value) {...
1546	1	this.annotationColours = value;
1547		}
1548
1549		/**
1550		* Gets the value of the annotationFromTree property.
1551		*
1552		* <p>This accessor method returns a reference to the live list,
1553		* not a snapshot. Therefore any modification you make to the
1554		* returned list will be present inside the JAXB object.
1555		* This is why there is not a <CODE>set</CODE> method for the annotationFromTree property.</p>
1556		*
1557		* <p>
1558		* For example, to add a new item, do as follows:
1559		* </p>
1560		* <pre>
1561		* getAnnotationFromTree().add(newItem);
1562		* </pre>
1563		*
1564		*
1565		* <p>
1566		* Objects of the following type(s) are allowed in the list
1567		* {@link String }
1568		* </p>
1569		*
1570		*
1571		* @return
1572		* The value of the annotationFromTree property.
1573		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
1574	138	public List<String> getAnnotationFromTree() {...
1575	138	if (annotationFromTree == null) {
1576	55	annotationFromTree = new ArrayList<String>();
1577		}
1578	138	return this.annotationFromTree;
1579		}
1580
1581		/**
1582		* Gets the value of the secStrProvider property.
1583		*
1584		* <p>This accessor method returns a reference to the live list,
1585		* not a snapshot. Therefore any modification you make to the
1586		* returned list will be present inside the JAXB object.
1587		* This is why there is not a <CODE>set</CODE> method for the secStrProvider property.</p>
1588		*
1589		* <p>
1590		* For example, to add a new item, do as follows:
1591		* </p>
1592		* <pre>
1593		* getSecStrProvider().add(newItem);
1594		* </pre>
1595		*
1596		*
1597		* <p>
1598		* Objects of the following type(s) are allowed in the list
1599		* {@link String }
1600		* </p>
1601		*
1602		*
1603		* @return
1604		* The value of the secStrProvider property.
1605		*/
		80% Uncovered Elements: 1 (5) Complexity: 2 Complexity Density: 0.67
1606	59	public List<String> getSecStrProvider() {...
1607	59	if (secStrProvider == null) {
1608	59	secStrProvider = new ArrayList<String>();
1609		}
1610	59	return this.secStrProvider;
1611		}
1612
1613		/**
1614		* Gets the value of the start property.
1615		*
1616		* @return
1617		* possible object is
1618		* {@link Integer }
1619		*
1620		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1621	59	public Integer getStart() {...
1622	59	return start;
1623		}
1624
1625		/**
1626		* Sets the value of the start property.
1627		*
1628		* @param value
1629		* allowed object is
1630		* {@link Integer }
1631		*
1632		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1633	22	public void setStart(Integer value) {...
1634	22	this.start = value;
1635		}
1636
1637		/**
1638		* Gets the value of the end property.
1639		*
1640		* @return
1641		* possible object is
1642		* {@link Integer }
1643		*
1644		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1645	59	public Integer getEnd() {...
1646	59	return end;
1647		}
1648
1649		/**
1650		* Sets the value of the end property.
1651		*
1652		* @param value
1653		* allowed object is
1654		* {@link Integer }
1655		*
1656		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1657	22	public void setEnd(Integer value) {...
1658	22	this.end = value;
1659		}
1660
1661		/**
1662		* Gets the value of the name property.
1663		*
1664		* @return
1665		* possible object is
1666		* {@link String }
1667		*
1668		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1669	59	public String getName() {...
1670	59	return name;
1671		}
1672
1673		/**
1674		* Sets the value of the name property.
1675		*
1676		* @param value
1677		* allowed object is
1678		* {@link String }
1679		*
1680		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1681	22	public void setName(String value) {...
1682	22	this.name = value;
1683		}
1684
1685		/**
1686		* Gets the value of the colour property.
1687		*
1688		* @return
1689		* possible object is
1690		* {@link String }
1691		*
1692		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1693	157	public String getColour() {...
1694	157	return colour;
1695		}
1696
1697		/**
1698		* Sets the value of the colour property.
1699		*
1700		* @param value
1701		* allowed object is
1702		* {@link String }
1703		*
1704		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1705	14	public void setColour(String value) {...
1706	14	this.colour = value;
1707		}
1708
1709		/**
1710		* Gets the value of the idColour property.
1711		*
1712		* @return
1713		* possible object is
1714		* {@link Integer }
1715		*
1716		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1717	59	public Integer getIdColour() {...
1718	59	return idColour;
1719		}
1720
1721		/**
1722		* Sets the value of the idColour property.
1723		*
1724		* @param value
1725		* allowed object is
1726		* {@link Integer }
1727		*
1728		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1729	19	public void setIdColour(Integer value) {...
1730	19	this.idColour = value;
1731		}
1732
1733		/**
1734		* Gets the value of the outlineColour property.
1735		*
1736		* @return
1737		* possible object is
1738		* {@link Integer }
1739		*
1740		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1741	59	public Integer getOutlineColour() {...
1742	59	return outlineColour;
1743		}
1744
1745		/**
1746		* Sets the value of the outlineColour property.
1747		*
1748		* @param value
1749		* allowed object is
1750		* {@link Integer }
1751		*
1752		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1753	22	public void setOutlineColour(Integer value) {...
1754	22	this.outlineColour = value;
1755		}
1756
1757		/**
1758		* Gets the value of the displayBoxes property.
1759		*
1760		* @return
1761		* possible object is
1762		* {@link Boolean }
1763		*
1764		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1765	59	public Boolean isDisplayBoxes() {...
1766	59	return displayBoxes;
1767		}
1768
1769		/**
1770		* Sets the value of the displayBoxes property.
1771		*
1772		* @param value
1773		* allowed object is
1774		* {@link Boolean }
1775		*
1776		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1777	22	public void setDisplayBoxes(Boolean value) {...
1778	22	this.displayBoxes = value;
1779		}
1780
1781		/**
1782		* Gets the value of the displayText property.
1783		*
1784		* @return
1785		* possible object is
1786		* {@link Boolean }
1787		*
1788		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1789	59	public Boolean isDisplayText() {...
1790	59	return displayText;
1791		}
1792
1793		/**
1794		* Sets the value of the displayText property.
1795		*
1796		* @param value
1797		* allowed object is
1798		* {@link Boolean }
1799		*
1800		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1801	22	public void setDisplayText(Boolean value) {...
1802	22	this.displayText = value;
1803		}
1804
1805		/**
1806		* Gets the value of the colourText property.
1807		*
1808		* @return
1809		* possible object is
1810		* {@link Boolean }
1811		*
1812		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1813	59	public Boolean isColourText() {...
1814	59	return colourText;
1815		}
1816
1817		/**
1818		* Sets the value of the colourText property.
1819		*
1820		* @param value
1821		* allowed object is
1822		* {@link Boolean }
1823		*
1824		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1825	22	public void setColourText(Boolean value) {...
1826	22	this.colourText = value;
1827		}
1828
1829		/**
1830		* Gets the value of the textCol1 property.
1831		*
1832		* @return
1833		* possible object is
1834		* {@link Integer }
1835		*
1836		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1837	59	public Integer getTextCol1() {...
1838	59	return textCol1;
1839		}
1840
1841		/**
1842		* Sets the value of the textCol1 property.
1843		*
1844		* @param value
1845		* allowed object is
1846		* {@link Integer }
1847		*
1848		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1849	22	public void setTextCol1(Integer value) {...
1850	22	this.textCol1 = value;
1851		}
1852
1853		/**
1854		* Gets the value of the textCol2 property.
1855		*
1856		* @return
1857		* possible object is
1858		* {@link Integer }
1859		*
1860		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1861	59	public Integer getTextCol2() {...
1862	59	return textCol2;
1863		}
1864
1865		/**
1866		* Sets the value of the textCol2 property.
1867		*
1868		* @param value
1869		* allowed object is
1870		* {@link Integer }
1871		*
1872		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1873	22	public void setTextCol2(Integer value) {...
1874	22	this.textCol2 = value;
1875		}
1876
1877		/**
1878		* Gets the value of the textColThreshold property.
1879		*
1880		* @return
1881		* possible object is
1882		* {@link Integer }
1883		*
1884		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1885	59	public Integer getTextColThreshold() {...
1886	59	return textColThreshold;
1887		}
1888
1889		/**
1890		* Sets the value of the textColThreshold property.
1891		*
1892		* @param value
1893		* allowed object is
1894		* {@link Integer }
1895		*
1896		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1897	22	public void setTextColThreshold(Integer value) {...
1898	22	this.textColThreshold = value;
1899		}
1900
1901		/**
1902		* Gets the value of the showUnconserved property.
1903		*
1904		* @return
1905		* possible object is
1906		* {@link Boolean }
1907		*
1908		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1909	59	public Boolean isShowUnconserved() {...
1910	59	return showUnconserved;
1911		}
1912
1913		/**
1914		* Sets the value of the showUnconserved property.
1915		*
1916		* @param value
1917		* allowed object is
1918		* {@link Boolean }
1919		*
1920		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1921	22	public void setShowUnconserved(Boolean value) {...
1922	22	this.showUnconserved = value;
1923		}
1924
1925		/**
1926		* Optional sequence group ID (only
1927		* needs to be
1928		* unique for this
1929		* alignment)
1930		*
1931		* @return
1932		* possible object is
1933		* {@link String }
1934		*
1935		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1936	83	public String getId() {...
1937	83	return id;
1938		}
1939
1940		/**
1941		* Sets the value of the id property.
1942		*
1943		* @param value
1944		* allowed object is
1945		* {@link String }
1946		*
1947		* @see #getId()
1948		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1949	6	public void setId(String value) {...
1950	6	this.id = value;
1951		}
1952
1953		/**
1954		* Gets the value of the conservationSelected property.
1955		*
1956		* @return
1957		* possible object is
1958		* {@link Boolean }
1959		*
1960		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1961	0	public Boolean isConservationSelected() {...
1962	0	return conservationSelected;
1963		}
1964
1965		/**
1966		* Sets the value of the conservationSelected property.
1967		*
1968		* @param value
1969		* allowed object is
1970		* {@link Boolean }
1971		*
1972		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1973	0	public void setConservationSelected(Boolean value) {...
1974	0	this.conservationSelected = value;
1975		}
1976
1977		/**
1978		* Conservation shading increment
1979		*
1980		* @return
1981		* possible object is
1982		* {@link Integer }
1983		*
1984		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1985	120	public Integer getConsThreshold() {...
1986	120	return consThreshold;
1987		}
1988
1989		/**
1990		* Sets the value of the consThreshold property.
1991		*
1992		* @param value
1993		* allowed object is
1994		* {@link Integer }
1995		*
1996		* @see #getConsThreshold()
1997		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1998	2	public void setConsThreshold(Integer value) {...
1999	2	this.consThreshold = value;
2000		}
2001
2002		/**
2003		* Gets the value of the pidSelected property.
2004		*
2005		* @return
2006		* possible object is
2007		* {@link Boolean }
2008		*
2009		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2010	0	public Boolean isPidSelected() {...
2011	0	return pidSelected;
2012		}
2013
2014		/**
2015		* Sets the value of the pidSelected property.
2016		*
2017		* @param value
2018		* allowed object is
2019		* {@link Boolean }
2020		*
2021		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2022	0	public void setPidSelected(Boolean value) {...
2023	0	this.pidSelected = value;
2024		}
2025
2026		/**
2027		* Percent Identity Threshold
2028		*
2029		* @return
2030		* possible object is
2031		* {@link Integer }
2032		*
2033		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2034	59	public Integer getPidThreshold() {...
2035	59	return pidThreshold;
2036		}
2037
2038		/**
2039		* Sets the value of the pidThreshold property.
2040		*
2041		* @param value
2042		* allowed object is
2043		* {@link Integer }
2044		*
2045		* @see #getPidThreshold()
2046		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2047	14	public void setPidThreshold(Integer value) {...
2048	14	this.pidThreshold = value;
2049		}
2050
2051		/**
2052		* Secondary structure consensus shading - since 2.11.4
2053		*
2054		* @return
2055		* possible object is
2056		* {@link Boolean }
2057		*
2058		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
2059	59	public boolean isSecstrSelected() {...
2060	59	if (secstrSelected == null) {
2061	49	return false;
2062		} else {
2063	10	return secstrSelected;
2064		}
2065		}
2066
2067		/**
2068		* Sets the value of the secstrSelected property.
2069		*
2070		* @param value
2071		* allowed object is
2072		* {@link Boolean }
2073		*
2074		* @see #isSecstrSelected()
2075		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2076	5	public void setSecstrSelected(Boolean value) {...
2077	5	this.secstrSelected = value;
2078		}
2079
2080		/**
2081		* Secondary structure consensus increment
2082		*
2083		* @return
2084		* possible object is
2085		* {@link Integer }
2086		*
2087		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2088	59	public Integer getSecstrThreshold() {...
2089	59	return secstrThreshold;
2090		}
2091
2092		/**
2093		* Sets the value of the secstrThreshold property.
2094		*
2095		* @param value
2096		* allowed object is
2097		* {@link Integer }
2098		*
2099		* @see #getSecstrThreshold()
2100		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2101	5	public void setSecstrThreshold(Integer value) {...
2102	5	this.secstrThreshold = value;
2103		}
2104
2105		/**
2106		* Gets the value of the showConsensusHistogram property.
2107		*
2108		* @return
2109		* possible object is
2110		* {@link Boolean }
2111		*
2112		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
2113	59	public boolean isShowConsensusHistogram() {...
2114	59	if (showConsensusHistogram == null) {
2115	0	return true;
2116		} else {
2117	59	return showConsensusHistogram;
2118		}
2119		}
2120
2121		/**
2122		* Sets the value of the showConsensusHistogram property.
2123		*
2124		* @param value
2125		* allowed object is
2126		* {@link Boolean }
2127		*
2128		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2129	22	public void setShowConsensusHistogram(Boolean value) {...
2130	22	this.showConsensusHistogram = value;
2131		}
2132
2133		/**
2134		* Gets the value of the showSequenceLogo property.
2135		*
2136		* @return
2137		* possible object is
2138		* {@link Boolean }
2139		*
2140		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
2141	59	public boolean isShowSequenceLogo() {...
2142	59	if (showSequenceLogo == null) {
2143	0	return false;
2144		} else {
2145	59	return showSequenceLogo;
2146		}
2147		}
2148
2149		/**
2150		* Sets the value of the showSequenceLogo property.
2151		*
2152		* @param value
2153		* allowed object is
2154		* {@link Boolean }
2155		*
2156		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2157	22	public void setShowSequenceLogo(Boolean value) {...
2158	22	this.showSequenceLogo = value;
2159		}
2160
2161		/**
2162		* Gets the value of the normaliseSequenceLogo property.
2163		*
2164		* @return
2165		* possible object is
2166		* {@link Boolean }
2167		*
2168		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
2169	59	public boolean isNormaliseSequenceLogo() {...
2170	59	if (normaliseSequenceLogo == null) {
2171	30	return false;
2172		} else {
2173	29	return normaliseSequenceLogo;
2174		}
2175		}
2176
2177		/**
2178		* Sets the value of the normaliseSequenceLogo property.
2179		*
2180		* @param value
2181		* allowed object is
2182		* {@link Boolean }
2183		*
2184		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2185	22	public void setNormaliseSequenceLogo(Boolean value) {...
2186	22	this.normaliseSequenceLogo = value;
2187		}
2188
2189		/**
2190		* Gets the value of the ignoreGapsinConsensus property.
2191		*
2192		* @return
2193		* possible object is
2194		* {@link Boolean }
2195		*
2196		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
2197	59	public boolean isIgnoreGapsinConsensus() {...
2198	59	if (ignoreGapsinConsensus == null) {
2199	0	return true;
2200		} else {
2201	59	return ignoreGapsinConsensus;
2202		}
2203		}
2204
2205		/**
2206		* Sets the value of the ignoreGapsinConsensus property.
2207		*
2208		* @param value
2209		* allowed object is
2210		* {@link Boolean }
2211		*
2212		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2213	22	public void setIgnoreGapsinConsensus(Boolean value) {...
2214	22	this.ignoreGapsinConsensus = value;
2215		}
2216
2217		}
2218
2219
2220		/**
2221		* <p>Java class for anonymous complex type</p>.
2222		*
2223		* <p>The following schema fragment specifies the expected content contained within this class.</p>
2224		*
2225		* <pre>
2226		* &lt;complexType&gt;
2227		* &lt;complexContent&gt;
2228		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
2229		* &lt;sequence&gt;
2230		* &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
2231		* &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
2232		* &lt;complexType&gt;
2233		* &lt;complexContent&gt;
2234		* &lt;extension base="{www.jalview.org}pdbentry"&gt;
2235		* &lt;sequence&gt;
2236		* &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
2237		* &lt;complexType&gt;
2238		* &lt;simpleContent&gt;
2239		* &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
2240		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
2241		* &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2242		* &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2243		* &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2244		* &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
2245		* &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2246		* &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2247		* &lt;/extension&gt;
2248		* &lt;/simpleContent&gt;
2249		* &lt;/complexType&gt;
2250		* &lt;/element&gt;
2251		* &lt;/sequence&gt;
2252		* &lt;/extension&gt;
2253		* &lt;/complexContent&gt;
2254		* &lt;/complexType&gt;
2255		* &lt;/element&gt;
2256		* &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&gt;
2257		* &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
2258		* &lt;complexType&gt;
2259		* &lt;complexContent&gt;
2260		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
2261		* &lt;sequence&gt;
2262		* &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
2263		* &lt;complexType&gt;
2264		* &lt;complexContent&gt;
2265		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
2266		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2267		* &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2268		* &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2269		* &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2270		* &lt;/restriction&gt;
2271		* &lt;/complexContent&gt;
2272		* &lt;/complexType&gt;
2273		* &lt;/element&gt;
2274		* &lt;/sequence&gt;
2275		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
2276		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2277		* &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2278		* &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
2279		* &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
2280		* &lt;/restriction&gt;
2281		* &lt;/complexContent&gt;
2282		* &lt;/complexType&gt;
2283		* &lt;/element&gt;
2284		* &lt;element name="hmmerProfile" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
2285		* &lt;/sequence&gt;
2286		* &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
2287		* &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
2288		* &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
2289		* &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2290		* &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2291		* &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2292		* &lt;/restriction&gt;
2293		* &lt;/complexContent&gt;
2294		* &lt;/complexType&gt;
2295		* </pre>
2296		*
2297		*
2298		*/
2299		@XmlAccessorType(XmlAccessType.FIELD)
2300		@XmlType(name = "", propOrder = {
2301		"features",
2302		"pdbids",
2303		"hiddenSequences",
2304		"rnaViewer",
2305		"hmmerProfile"
2306		})
		98.1% Uncovered Elements: 1 (52) Complexity: 22 Complexity Density: 0.85
2307		public static class JSeq {
2308
2309		@XmlElement(namespace = "www.jalview.org")
2310		protected List<Feature> features;
2311		@XmlElement(namespace = "www.jalview.org")
2312		protected List<JalviewModel.JSeq.Pdbids> pdbids;
2313		@XmlElement(namespace = "www.jalview.org", type = Integer.class)
2314		protected List<Integer> hiddenSequences;
2315		/**
2316		* Reference to a viewer showing
2317		* RNA structure for this sequence.
2318		* Schema supports one viewer
2319		* showing multiple annotations for
2320		* multiple sequences, though
2321		* currently only one annotation
2322		* for one sequence (gapped or
2323		* trimmed) is used
2324		*
2325		*/
2326		@XmlElement(namespace = "www.jalview.org")
2327		protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
2328		/**
2329		* name of the project jar entry that holds the HMM file with the profile for the sequence
2330		*
2331		*/
2332		@XmlElement(namespace = "www.jalview.org")
2333		protected String hmmerProfile;
2334		@XmlAttribute(name = "colour")
2335		protected Integer colour;
2336		@XmlAttribute(name = "start", required = true)
2337		protected int start;
2338		@XmlAttribute(name = "end", required = true)
2339		protected int end;
2340		@XmlAttribute(name = "id", required = true)
2341		protected String id;
2342		@XmlAttribute(name = "hidden")
2343		protected Boolean hidden;
2344		@XmlAttribute(name = "viewreference")
2345		protected Boolean viewreference;
2346
2347		/**
2348		* Gets the value of the features property.
2349		*
2350		* <p>This accessor method returns a reference to the live list,
2351		* not a snapshot. Therefore any modification you make to the
2352		* returned list will be present inside the JAXB object.
2353		* This is why there is not a <CODE>set</CODE> method for the features property.</p>
2354		*
2355		* <p>
2356		* For example, to add a new item, do as follows:
2357		* </p>
2358		* <pre>
2359		* getFeatures().add(newItem);
2360		* </pre>
2361		*
2362		*
2363		* <p>
2364		* Objects of the following type(s) are allowed in the list
2365		* {@link Feature }
2366		* </p>
2367		*
2368		*
2369		* @return
2370		* The value of the features property.
2371		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
2372	32239	public List<Feature> getFeatures() {...
2373	32239	if (features == null) {
2374	15709	features = new ArrayList<Feature>();
2375		}
2376	32239	return this.features;
2377		}
2378
2379		/**
2380		* Gets the value of the pdbids property.
2381		*
2382		* <p>This accessor method returns a reference to the live list,
2383		* not a snapshot. Therefore any modification you make to the
2384		* returned list will be present inside the JAXB object.
2385		* This is why there is not a <CODE>set</CODE> method for the pdbids property.</p>
2386		*
2387		* <p>
2388		* For example, to add a new item, do as follows:
2389		* </p>
2390		* <pre>
2391		* getPdbids().add(newItem);
2392		* </pre>
2393		*
2394		*
2395		* <p>
2396		* Objects of the following type(s) are allowed in the list
2397		* {@link JalviewModel.JSeq.Pdbids }
2398		* </p>
2399		*
2400		*
2401		* @return
2402		* The value of the pdbids property.
2403		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
2404	17293	public List<JalviewModel.JSeq.Pdbids> getPdbids() {...
2405	17293	if (pdbids == null) {
2406	16270	pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
2407		}
2408	17293	return this.pdbids;
2409		}
2410
2411		/**
2412		* Gets the value of the hiddenSequences property.
2413		*
2414		* <p>This accessor method returns a reference to the live list,
2415		* not a snapshot. Therefore any modification you make to the
2416		* returned list will be present inside the JAXB object.
2417		* This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.</p>
2418		*
2419		* <p>
2420		* For example, to add a new item, do as follows:
2421		* </p>
2422		* <pre>
2423		* getHiddenSequences().add(newItem);
2424		* </pre>
2425		*
2426		*
2427		* <p>
2428		* Objects of the following type(s) are allowed in the list
2429		* {@link Integer }
2430		* </p>
2431		*
2432		*
2433		* @return
2434		* The value of the hiddenSequences property.
2435		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
2436	676	public List<Integer> getHiddenSequences() {...
2437	676	if (hiddenSequences == null) {
2438	670	hiddenSequences = new ArrayList<Integer>();
2439		}
2440	676	return this.hiddenSequences;
2441		}
2442
2443		/**
2444		* Reference to a viewer showing
2445		* RNA structure for this sequence.
2446		* Schema supports one viewer
2447		* showing multiple annotations for
2448		* multiple sequences, though
2449		* currently only one annotation
2450		* for one sequence (gapped or
2451		* trimmed) is used
2452		*
2453		* Gets the value of the rnaViewer property.
2454		*
2455		* <p>This accessor method returns a reference to the live list,
2456		* not a snapshot. Therefore any modification you make to the
2457		* returned list will be present inside the JAXB object.
2458		* This is why there is not a <CODE>set</CODE> method for the rnaViewer property.</p>
2459		*
2460		* <p>
2461		* For example, to add a new item, do as follows:
2462		* </p>
2463		* <pre>
2464		* getRnaViewer().add(newItem);
2465		* </pre>
2466		*
2467		*
2468		* <p>
2469		* Objects of the following type(s) are allowed in the list
2470		* {@link JalviewModel.JSeq.RnaViewer }
2471		* </p>
2472		*
2473		*
2474		* @return
2475		* The value of the rnaViewer property.
2476		*/
		80% Uncovered Elements: 1 (5) Complexity: 2 Complexity Density: 0.67
2477	1152	public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {...
2478	1152	if (rnaViewer == null) {
2479	1152	rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2480		}
2481	1152	return this.rnaViewer;
2482		}
2483
2484		/**
2485		* name of the project jar entry that holds the HMM file with the profile for the sequence
2486		*
2487		* @return
2488		* possible object is
2489		* {@link String }
2490		*
2491		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2492	15722	public String getHmmerProfile() {...
2493	15722	return hmmerProfile;
2494		}
2495
2496		/**
2497		* Sets the value of the hmmerProfile property.
2498		*
2499		* @param value
2500		* allowed object is
2501		* {@link String }
2502		*
2503		* @see #getHmmerProfile()
2504		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2505	2	public void setHmmerProfile(String value) {...
2506	2	this.hmmerProfile = value;
2507		}
2508
2509		/**
2510		* Gets the value of the colour property.
2511		*
2512		* @return
2513		* possible object is
2514		* {@link Integer }
2515		*
2516		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2517	1274	public Integer getColour() {...
2518	1274	return colour;
2519		}
2520
2521		/**
2522		* Sets the value of the colour property.
2523		*
2524		* @param value
2525		* allowed object is
2526		* {@link Integer }
2527		*
2528		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2529	8394	public void setColour(Integer value) {...
2530	8394	this.colour = value;
2531		}
2532
2533		/**
2534		* Gets the value of the start property.
2535		*
2536		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2537	17557	public int getStart() {...
2538	17557	return start;
2539		}
2540
2541		/**
2542		* Sets the value of the start property.
2543		*
2544		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2545	8394	public void setStart(int value) {...
2546	8394	this.start = value;
2547		}
2548
2549		/**
2550		* Gets the value of the end property.
2551		*
2552		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2553	17557	public int getEnd() {...
2554	17557	return end;
2555		}
2556
2557		/**
2558		* Sets the value of the end property.
2559		*
2560		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2561	8394	public void setEnd(int value) {...
2562	8394	this.end = value;
2563		}
2564
2565		/**
2566		* Gets the value of the id property.
2567		*
2568		* @return
2569		* possible object is
2570		* {@link String }
2571		*
2572		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2573	16467	public String getId() {...
2574	16467	return id;
2575		}
2576
2577		/**
2578		* Sets the value of the id property.
2579		*
2580		* @param value
2581		* allowed object is
2582		* {@link String }
2583		*
2584		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2585	8394	public void setId(String value) {...
2586	8394	this.id = value;
2587		}
2588
2589		/**
2590		* Gets the value of the hidden property.
2591		*
2592		* @return
2593		* possible object is
2594		* {@link Boolean }
2595		*
2596		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2597	17057	public Boolean isHidden() {...
2598	17057	return hidden;
2599		}
2600
2601		/**
2602		* Sets the value of the hidden property.
2603		*
2604		* @param value
2605		* allowed object is
2606		* {@link Boolean }
2607		*
2608		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2609	190	public void setHidden(Boolean value) {...
2610	190	this.hidden = value;
2611		}
2612
2613		/**
2614		* Gets the value of the viewreference property.
2615		*
2616		* @return
2617		* possible object is
2618		* {@link Boolean }
2619		*
2620		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2621	16387	public Boolean isViewreference() {...
2622	16387	return viewreference;
2623		}
2624
2625		/**
2626		* Sets the value of the viewreference property.
2627		*
2628		* @param value
2629		* allowed object is
2630		* {@link Boolean }
2631		*
2632		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2633	80	public void setViewreference(Boolean value) {...
2634	80	this.viewreference = value;
2635		}
2636
2637
2638		/**
2639		* <p>Java class for anonymous complex type</p>.
2640		*
2641		* <p>The following schema fragment specifies the expected content contained within this class.</p>
2642		*
2643		* <pre>
2644		* &lt;complexType&gt;
2645		* &lt;complexContent&gt;
2646		* &lt;extension base="{www.jalview.org}pdbentry"&gt;
2647		* &lt;sequence&gt;
2648		* &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
2649		* &lt;complexType&gt;
2650		* &lt;simpleContent&gt;
2651		* &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
2652		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
2653		* &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2654		* &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2655		* &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2656		* &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
2657		* &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2658		* &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2659		* &lt;/extension&gt;
2660		* &lt;/simpleContent&gt;
2661		* &lt;/complexType&gt;
2662		* &lt;/element&gt;
2663		* &lt;/sequence&gt;
2664		* &lt;/extension&gt;
2665		* &lt;/complexContent&gt;
2666		* &lt;/complexType&gt;
2667		* </pre>
2668		*
2669		*
2670		*/
2671		@XmlAccessorType(XmlAccessType.FIELD)
2672		@XmlType(name = "", propOrder = {
2673		"structureState"
2674		})
		100% Uncovered Elements: 0 (6) Complexity: 2 Complexity Density: 0.67
2675		public static class Pdbids
2676		extends Pdbentry
2677		{
2678
2679		@XmlElement(namespace = "www.jalview.org")
2680		protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2681
2682		/**
2683		* Gets the value of the structureState property.
2684		*
2685		* <p>This accessor method returns a reference to the live list,
2686		* not a snapshot. Therefore any modification you make to the
2687		* returned list will be present inside the JAXB object.
2688		* This is why there is not a <CODE>set</CODE> method for the structureState property.</p>
2689		*
2690		* <p>
2691		* For example, to add a new item, do as follows:
2692		* </p>
2693		* <pre>
2694		* getStructureState().add(newItem);
2695		* </pre>
2696		*
2697		*
2698		* <p>
2699		* Objects of the following type(s) are allowed in the list
2700		* {@link JalviewModel.JSeq.Pdbids.StructureState }
2701		* </p>
2702		*
2703		*
2704		* @return
2705		* The value of the structureState property.
2706		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
2707	371	public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {...
2708	371	if (structureState == null) {
2709	211	structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2710		}
2711	371	return this.structureState;
2712		}
2713
2714
2715		/**
2716		* <p>Java class for anonymous complex type</p>.
2717		*
2718		* <p>The following schema fragment specifies the expected content contained within this class.</p>
2719		*
2720		* <pre>
2721		* &lt;complexType&gt;
2722		* &lt;simpleContent&gt;
2723		* &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
2724		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
2725		* &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2726		* &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2727		* &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2728		* &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
2729		* &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2730		* &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2731		* &lt;/extension&gt;
2732		* &lt;/simpleContent&gt;
2733		* &lt;/complexType&gt;
2734		* </pre>
2735		*
2736		*
2737		*/
2738		@XmlAccessorType(XmlAccessType.FIELD)
2739		@XmlType(name = "", propOrder = {
2740		"value"
2741		})
		82.1% Uncovered Elements: 10 (56) Complexity: 25 Complexity Density: 0.89
2742		public static class StructureState {
2743
2744		@XmlValue
2745		protected String value;
2746		@XmlAttribute(name = "visible")
2747		protected Boolean visible;
2748		/**
2749		* additional
2750		* identifier
2751		* which
2752		* properly
2753		* disambiguates
2754		* the
2755		* structure
2756		* view
2757		* from
2758		* any
2759		* other
2760		* view
2761		* with
2762		* the
2763		* same
2764		* attributes.
2765		* This
2766		* is
2767		* not
2768		* an
2769		* ID,
2770		* because
2771		* it
2772		* is
2773		* possible
2774		* to
2775		* have
2776		* many
2777		* references
2778		* to
2779		* the
2780		* same
2781		* physical
2782		* structure
2783		* view
2784		* from
2785		* different
2786		* sequences
2787		* in
2788		* an
2789		* alignment.
2790		* A
2791		* structureState
2792		* element
2793		* citing
2794		* the
2795		* same
2796		* viewId
2797		* will
2798		* appear
2799		* for
2800		* each
2801		* instance.
2802		*
2803		*/
2804		@XmlAttribute(name = "viewId")
2805		protected String viewId;
2806		/**
2807		* Flag
2808		* set
2809		* if
2810		* the
2811		* alignment
2812		* panel
2813		* containing
2814		* this
2815		* JSeq
2816		* should
2817		* be
2818		* included
2819		* in
2820		* those
2821		* used
2822		* to
2823		* perform
2824		* a
2825		* structure
2826		* superposition
2827		* (since
2828		* Jalview
2829		* 2.7).
2830		*
2831		*/
2832		@XmlAttribute(name = "alignwithAlignPanel")
2833		protected Boolean alignwithAlignPanel;
2834		/**
2835		* Flag
2836		* set
2837		* if
2838		* the
2839		* alignment
2840		* panel
2841		* containing
2842		* this
2843		* JSeq
2844		* should
2845		* be
2846		* included
2847		* in
2848		* those
2849		* used
2850		* to
2851		* colour
2852		* its
2853		* associated
2854		* sequences
2855		* in
2856		* this
2857		* structureState(since
2858		* Jalview
2859		* 2.7).
2860		*
2861		*/
2862		@XmlAttribute(name = "colourwithAlignPanel")
2863		protected Boolean colourwithAlignPanel;
2864		/**
2865		* Flag
2866		* set
2867		* if
2868		* the
2869		* structure
2870		* display
2871		* is
2872		* coloured
2873		* by
2874		* the
2875		* Jmol
2876		* state,
2877		* rather
2878		* than
2879		* by
2880		* one
2881		* or
2882		* more
2883		* linked
2884		* alignment
2885		* views.
2886		*
2887		*/
2888		@XmlAttribute(name = "colourByJmol")
2889		protected Boolean colourByJmol;
2890		/**
2891		* An
2892		* identifier
2893		* for
2894		* the
2895		* viewer
2896		* type,
2897		* currently
2898		* either
2899		* JMOL
2900		* or
2901		* CHIMERA
2902		*
2903		*/
2904		@XmlAttribute(name = "type")
2905		protected String type;
2906		@XmlAttribute(name = "width")
2907		protected Integer width;
2908		@XmlAttribute(name = "height")
2909		protected Integer height;
2910		@XmlAttribute(name = "xpos")
2911		protected Integer xpos;
2912		@XmlAttribute(name = "ypos")
2913		protected Integer ypos;
2914
2915		/**
2916		* Gets the value of the value property.
2917		*
2918		* @return
2919		* possible object is
2920		* {@link String }
2921		*
2922		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2923	110	public String getValue() {...
2924	110	return value;
2925		}
2926
2927		/**
2928		* Sets the value of the value property.
2929		*
2930		* @param value
2931		* allowed object is
2932		* {@link String }
2933		*
2934		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2935	0	public void setValue(String value) {...
2936	0	this.value = value;
2937		}
2938
2939		/**
2940		* Gets the value of the visible property.
2941		*
2942		* @return
2943		* possible object is
2944		* {@link Boolean }
2945		*
2946		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2947	0	public Boolean isVisible() {...
2948	0	return visible;
2949		}
2950
2951		/**
2952		* Sets the value of the visible property.
2953		*
2954		* @param value
2955		* allowed object is
2956		* {@link Boolean }
2957		*
2958		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2959	20	public void setVisible(Boolean value) {...
2960	20	this.visible = value;
2961		}
2962
2963		/**
2964		* additional
2965		* identifier
2966		* which
2967		* properly
2968		* disambiguates
2969		* the
2970		* structure
2971		* view
2972		* from
2973		* any
2974		* other
2975		* view
2976		* with
2977		* the
2978		* same
2979		* attributes.
2980		* This
2981		* is
2982		* not
2983		* an
2984		* ID,
2985		* because
2986		* it
2987		* is
2988		* possible
2989		* to
2990		* have
2991		* many
2992		* references
2993		* to
2994		* the
2995		* same
2996		* physical
2997		* structure
2998		* view
2999		* from
3000		* different
3001		* sequences
3002		* in
3003		* an
3004		* alignment.
3005		* A
3006		* structureState
3007		* element
3008		* citing
3009		* the
3010		* same
3011		* viewId
3012		* will
3013		* appear
3014		* for
3015		* each
3016		* instance.
3017		*
3018		* @return
3019		* possible object is
3020		* {@link String }
3021		*
3022		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3023	200	public String getViewId() {...
3024	200	return viewId;
3025		}
3026
3027		/**
3028		* Sets the value of the viewId property.
3029		*
3030		* @param value
3031		* allowed object is
3032		* {@link String }
3033		*
3034		* @see #getViewId()
3035		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3036	20	public void setViewId(String value) {...
3037	20	this.viewId = value;
3038		}
3039
3040		/**
3041		* Flag
3042		* set
3043		* if
3044		* the
3045		* alignment
3046		* panel
3047		* containing
3048		* this
3049		* JSeq
3050		* should
3051		* be
3052		* included
3053		* in
3054		* those
3055		* used
3056		* to
3057		* perform
3058		* a
3059		* structure
3060		* superposition
3061		* (since
3062		* Jalview
3063		* 2.7).
3064		*
3065		* @return
3066		* possible object is
3067		* {@link Boolean }
3068		*
3069		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
3070	80	public boolean isAlignwithAlignPanel() {...
3071	80	if (alignwithAlignPanel == null) {
3072	0	return true;
3073		} else {
3074	80	return alignwithAlignPanel;
3075		}
3076		}
3077
3078		/**
3079		* Sets the value of the alignwithAlignPanel property.
3080		*
3081		* @param value
3082		* allowed object is
3083		* {@link Boolean }
3084		*
3085		* @see #isAlignwithAlignPanel()
3086		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3087	20	public void setAlignwithAlignPanel(Boolean value) {...
3088	20	this.alignwithAlignPanel = value;
3089		}
3090
3091		/**
3092		* Flag
3093		* set
3094		* if
3095		* the
3096		* alignment
3097		* panel
3098		* containing
3099		* this
3100		* JSeq
3101		* should
3102		* be
3103		* included
3104		* in
3105		* those
3106		* used
3107		* to
3108		* colour
3109		* its
3110		* associated
3111		* sequences
3112		* in
3113		* this
3114		* structureState(since
3115		* Jalview
3116		* 2.7).
3117		*
3118		* @return
3119		* possible object is
3120		* {@link Boolean }
3121		*
3122		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
3123	80	public boolean isColourwithAlignPanel() {...
3124	80	if (colourwithAlignPanel == null) {
3125	0	return false;
3126		} else {
3127	80	return colourwithAlignPanel;
3128		}
3129		}
3130
3131		/**
3132		* Sets the value of the colourwithAlignPanel property.
3133		*
3134		* @param value
3135		* allowed object is
3136		* {@link Boolean }
3137		*
3138		* @see #isColourwithAlignPanel()
3139		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3140	20	public void setColourwithAlignPanel(Boolean value) {...
3141	20	this.colourwithAlignPanel = value;
3142		}
3143
3144		/**
3145		* Flag
3146		* set
3147		* if
3148		* the
3149		* structure
3150		* display
3151		* is
3152		* coloured
3153		* by
3154		* the
3155		* Jmol
3156		* state,
3157		* rather
3158		* than
3159		* by
3160		* one
3161		* or
3162		* more
3163		* linked
3164		* alignment
3165		* views.
3166		*
3167		* @return
3168		* possible object is
3169		* {@link Boolean }
3170		*
3171		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
3172	80	public boolean isColourByJmol() {...
3173	80	if (colourByJmol == null) {
3174	0	return true;
3175		} else {
3176	80	return colourByJmol;
3177		}
3178		}
3179
3180		/**
3181		* Sets the value of the colourByJmol property.
3182		*
3183		* @param value
3184		* allowed object is
3185		* {@link Boolean }
3186		*
3187		* @see #isColourByJmol()
3188		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3189	20	public void setColourByJmol(Boolean value) {...
3190	20	this.colourByJmol = value;
3191		}
3192
3193		/**
3194		* An
3195		* identifier
3196		* for
3197		* the
3198		* viewer
3199		* type,
3200		* currently
3201		* either
3202		* JMOL
3203		* or
3204		* CHIMERA
3205		*
3206		* @return
3207		* possible object is
3208		* {@link String }
3209		*
3210		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3211	40	public String getType() {...
3212	40	return type;
3213		}
3214
3215		/**
3216		* Sets the value of the type property.
3217		*
3218		* @param value
3219		* allowed object is
3220		* {@link String }
3221		*
3222		* @see #getType()
3223		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3224	20	public void setType(String value) {...
3225	20	this.type = value;
3226		}
3227
3228		/**
3229		* Gets the value of the width property.
3230		*
3231		* @return
3232		* possible object is
3233		* {@link Integer }
3234		*
3235		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3236	80	public Integer getWidth() {...
3237	80	return width;
3238		}
3239
3240		/**
3241		* Sets the value of the width property.
3242		*
3243		* @param value
3244		* allowed object is
3245		* {@link Integer }
3246		*
3247		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3248	20	public void setWidth(Integer value) {...
3249	20	this.width = value;
3250		}
3251
3252		/**
3253		* Gets the value of the height property.
3254		*
3255		* @return
3256		* possible object is
3257		* {@link Integer }
3258		*
3259		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3260	80	public Integer getHeight() {...
3261	80	return height;
3262		}
3263
3264		/**
3265		* Sets the value of the height property.
3266		*
3267		* @param value
3268		* allowed object is
3269		* {@link Integer }
3270		*
3271		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3272	20	public void setHeight(Integer value) {...
3273	20	this.height = value;
3274		}
3275
3276		/**
3277		* Gets the value of the xpos property.
3278		*
3279		* @return
3280		* possible object is
3281		* {@link Integer }
3282		*
3283		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3284	80	public Integer getXpos() {...
3285	80	return xpos;
3286		}
3287
3288		/**
3289		* Sets the value of the xpos property.
3290		*
3291		* @param value
3292		* allowed object is
3293		* {@link Integer }
3294		*
3295		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3296	20	public void setXpos(Integer value) {...
3297	20	this.xpos = value;
3298		}
3299
3300		/**
3301		* Gets the value of the ypos property.
3302		*
3303		* @return
3304		* possible object is
3305		* {@link Integer }
3306		*
3307		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3308	80	public Integer getYpos() {...
3309	80	return ypos;
3310		}
3311
3312		/**
3313		* Sets the value of the ypos property.
3314		*
3315		* @param value
3316		* allowed object is
3317		* {@link Integer }
3318		*
3319		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3320	20	public void setYpos(Integer value) {...
3321	20	this.ypos = value;
3322		}
3323
3324		}
3325
3326		}
3327
3328
3329		/**
3330		* <p>Java class for anonymous complex type</p>.
3331		*
3332		* <p>The following schema fragment specifies the expected content contained within this class.</p>
3333		*
3334		* <pre>
3335		* &lt;complexType&gt;
3336		* &lt;complexContent&gt;
3337		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3338		* &lt;sequence&gt;
3339		* &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
3340		* &lt;complexType&gt;
3341		* &lt;complexContent&gt;
3342		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3343		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3344		* &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3345		* &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
3346		* &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3347		* &lt;/restriction&gt;
3348		* &lt;/complexContent&gt;
3349		* &lt;/complexType&gt;
3350		* &lt;/element&gt;
3351		* &lt;/sequence&gt;
3352		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
3353		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3354		* &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3355		* &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3356		* &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3357		* &lt;/restriction&gt;
3358		* &lt;/complexContent&gt;
3359		* &lt;/complexType&gt;
3360		* </pre>
3361		*
3362		*
3363		*/
3364		@XmlAccessorType(XmlAccessType.FIELD)
3365		@XmlType(name = "", propOrder = {
3366		"secondaryStructure"
3367		})
		0% Uncovered Elements: 38 (38) Complexity: 18 Complexity Density: 0.95
3368		public static class RnaViewer {
3369
3370		@XmlElement(namespace = "www.jalview.org", required = true)
3371		protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
3372		@XmlAttribute(name = "title")
3373		protected String title;
3374		/**
3375		* An id unique to the RNA
3376		* viewer panel
3377		*
3378		*/
3379		@XmlAttribute(name = "viewId")
3380		protected String viewId;
3381		/**
3382		* horizontal position of
3383		* split pane divider
3384		*
3385		*/
3386		@XmlAttribute(name = "dividerLocation")
3387		protected Integer dividerLocation;
3388		/**
3389		* Index of the selected
3390		* structure in the viewer
3391		* panel
3392		*
3393		*/
3394		@XmlAttribute(name = "selectedRna")
3395		protected Integer selectedRna;
3396		@XmlAttribute(name = "width")
3397		protected Integer width;
3398		@XmlAttribute(name = "height")
3399		protected Integer height;
3400		@XmlAttribute(name = "xpos")
3401		protected Integer xpos;
3402		@XmlAttribute(name = "ypos")
3403		protected Integer ypos;
3404
3405		/**
3406		* Gets the value of the secondaryStructure property.
3407		*
3408		* <p>This accessor method returns a reference to the live list,
3409		* not a snapshot. Therefore any modification you make to the
3410		* returned list will be present inside the JAXB object.
3411		* This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.</p>
3412		*
3413		* <p>
3414		* For example, to add a new item, do as follows:
3415		* </p>
3416		* <pre>
3417		* getSecondaryStructure().add(newItem);
3418		* </pre>
3419		*
3420		*
3421		* <p>
3422		* Objects of the following type(s) are allowed in the list
3423		* {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
3424		* </p>
3425		*
3426		*
3427		* @return
3428		* The value of the secondaryStructure property.
3429		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
3430	0	public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {...
3431	0	if (secondaryStructure == null) {
3432	0	secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
3433		}
3434	0	return this.secondaryStructure;
3435		}
3436
3437		/**
3438		* Gets the value of the title property.
3439		*
3440		* @return
3441		* possible object is
3442		* {@link String }
3443		*
3444		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3445	0	public String getTitle() {...
3446	0	return title;
3447		}
3448
3449		/**
3450		* Sets the value of the title property.
3451		*
3452		* @param value
3453		* allowed object is
3454		* {@link String }
3455		*
3456		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3457	0	public void setTitle(String value) {...
3458	0	this.title = value;
3459		}
3460
3461		/**
3462		* An id unique to the RNA
3463		* viewer panel
3464		*
3465		* @return
3466		* possible object is
3467		* {@link String }
3468		*
3469		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3470	0	public String getViewId() {...
3471	0	return viewId;
3472		}
3473
3474		/**
3475		* Sets the value of the viewId property.
3476		*
3477		* @param value
3478		* allowed object is
3479		* {@link String }
3480		*
3481		* @see #getViewId()
3482		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3483	0	public void setViewId(String value) {...
3484	0	this.viewId = value;
3485		}
3486
3487		/**
3488		* horizontal position of
3489		* split pane divider
3490		*
3491		* @return
3492		* possible object is
3493		* {@link Integer }
3494		*
3495		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3496	0	public Integer getDividerLocation() {...
3497	0	return dividerLocation;
3498		}
3499
3500		/**
3501		* Sets the value of the dividerLocation property.
3502		*
3503		* @param value
3504		* allowed object is
3505		* {@link Integer }
3506		*
3507		* @see #getDividerLocation()
3508		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3509	0	public void setDividerLocation(Integer value) {...
3510	0	this.dividerLocation = value;
3511		}
3512
3513		/**
3514		* Index of the selected
3515		* structure in the viewer
3516		* panel
3517		*
3518		* @return
3519		* possible object is
3520		* {@link Integer }
3521		*
3522		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3523	0	public Integer getSelectedRna() {...
3524	0	return selectedRna;
3525		}
3526
3527		/**
3528		* Sets the value of the selectedRna property.
3529		*
3530		* @param value
3531		* allowed object is
3532		* {@link Integer }
3533		*
3534		* @see #getSelectedRna()
3535		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3536	0	public void setSelectedRna(Integer value) {...
3537	0	this.selectedRna = value;
3538		}
3539
3540		/**
3541		* Gets the value of the width property.
3542		*
3543		* @return
3544		* possible object is
3545		* {@link Integer }
3546		*
3547		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3548	0	public Integer getWidth() {...
3549	0	return width;
3550		}
3551
3552		/**
3553		* Sets the value of the width property.
3554		*
3555		* @param value
3556		* allowed object is
3557		* {@link Integer }
3558		*
3559		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3560	0	public void setWidth(Integer value) {...
3561	0	this.width = value;
3562		}
3563
3564		/**
3565		* Gets the value of the height property.
3566		*
3567		* @return
3568		* possible object is
3569		* {@link Integer }
3570		*
3571		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3572	0	public Integer getHeight() {...
3573	0	return height;
3574		}
3575
3576		/**
3577		* Sets the value of the height property.
3578		*
3579		* @param value
3580		* allowed object is
3581		* {@link Integer }
3582		*
3583		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3584	0	public void setHeight(Integer value) {...
3585	0	this.height = value;
3586		}
3587
3588		/**
3589		* Gets the value of the xpos property.
3590		*
3591		* @return
3592		* possible object is
3593		* {@link Integer }
3594		*
3595		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3596	0	public Integer getXpos() {...
3597	0	return xpos;
3598		}
3599
3600		/**
3601		* Sets the value of the xpos property.
3602		*
3603		* @param value
3604		* allowed object is
3605		* {@link Integer }
3606		*
3607		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3608	0	public void setXpos(Integer value) {...
3609	0	this.xpos = value;
3610		}
3611
3612		/**
3613		* Gets the value of the ypos property.
3614		*
3615		* @return
3616		* possible object is
3617		* {@link Integer }
3618		*
3619		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3620	0	public Integer getYpos() {...
3621	0	return ypos;
3622		}
3623
3624		/**
3625		* Sets the value of the ypos property.
3626		*
3627		* @param value
3628		* allowed object is
3629		* {@link Integer }
3630		*
3631		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3632	0	public void setYpos(Integer value) {...
3633	0	this.ypos = value;
3634		}
3635
3636
3637		/**
3638		* <p>Java class for anonymous complex type</p>.
3639		*
3640		* <p>The following schema fragment specifies the expected content contained within this class.</p>
3641		*
3642		* <pre>
3643		* &lt;complexType&gt;
3644		* &lt;complexContent&gt;
3645		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3646		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3647		* &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3648		* &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
3649		* &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3650		* &lt;/restriction&gt;
3651		* &lt;/complexContent&gt;
3652		* &lt;/complexType&gt;
3653		* </pre>
3654		*
3655		*
3656		*/
3657		@XmlAccessorType(XmlAccessType.FIELD)
3658		@XmlType(name = "")
		0% Uncovered Elements: 16 (16) Complexity: 8 Complexity Density: 1
3659		public static class SecondaryStructure {
3660
3661		@XmlAttribute(name = "title")
3662		protected String title;
3663		/**
3664		* id attribute
3665		* of
3666		* Annotation
3667		* in
3668		* vamsasModel
3669		* for the
3670		* secondary
3671		* structure
3672		* annotation
3673		* shown in the
3674		* viewer
3675		*
3676		*/
3677		@XmlAttribute(name = "annotationId", required = true)
3678		protected String annotationId;
3679		/**
3680		* if true the
3681		* RNA
3682		* structure is
3683		* shown with
3684		* gaps, if
3685		* false
3686		* without
3687		*
3688		*/
3689		@XmlAttribute(name = "gapped")
3690		protected Boolean gapped;
3691		/**
3692		* name of the
3693		* project jar
3694		* entry that
3695		* holds the
3696		* VARNA viewer
3697		* state for
3698		* the
3699		* structure
3700		*
3701		*/
3702		@XmlAttribute(name = "viewerState")
3703		protected String viewerState;
3704
3705		/**
3706		* Gets the value of the title property.
3707		*
3708		* @return
3709		* possible object is
3710		* {@link String }
3711		*
3712		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3713	0	public String getTitle() {...
3714	0	return title;
3715		}
3716
3717		/**
3718		* Sets the value of the title property.
3719		*
3720		* @param value
3721		* allowed object is
3722		* {@link String }
3723		*
3724		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3725	0	public void setTitle(String value) {...
3726	0	this.title = value;
3727		}
3728
3729		/**
3730		* id attribute
3731		* of
3732		* Annotation
3733		* in
3734		* vamsasModel
3735		* for the
3736		* secondary
3737		* structure
3738		* annotation
3739		* shown in the
3740		* viewer
3741		*
3742		* @return
3743		* possible object is
3744		* {@link String }
3745		*
3746		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3747	0	public String getAnnotationId() {...
3748	0	return annotationId;
3749		}
3750
3751		/**
3752		* Sets the value of the annotationId property.
3753		*
3754		* @param value
3755		* allowed object is
3756		* {@link String }
3757		*
3758		* @see #getAnnotationId()
3759		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3760	0	public void setAnnotationId(String value) {...
3761	0	this.annotationId = value;
3762		}
3763
3764		/**
3765		* if true the
3766		* RNA
3767		* structure is
3768		* shown with
3769		* gaps, if
3770		* false
3771		* without
3772		*
3773		* @return
3774		* possible object is
3775		* {@link Boolean }
3776		*
3777		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3778	0	public Boolean isGapped() {...
3779	0	return gapped;
3780		}
3781
3782		/**
3783		* Sets the value of the gapped property.
3784		*
3785		* @param value
3786		* allowed object is
3787		* {@link Boolean }
3788		*
3789		* @see #isGapped()
3790		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3791	0	public void setGapped(Boolean value) {...
3792	0	this.gapped = value;
3793		}
3794
3795		/**
3796		* name of the
3797		* project jar
3798		* entry that
3799		* holds the
3800		* VARNA viewer
3801		* state for
3802		* the
3803		* structure
3804		*
3805		* @return
3806		* possible object is
3807		* {@link String }
3808		*
3809		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3810	0	public String getViewerState() {...
3811	0	return viewerState;
3812		}
3813
3814		/**
3815		* Sets the value of the viewerState property.
3816		*
3817		* @param value
3818		* allowed object is
3819		* {@link String }
3820		*
3821		* @see #getViewerState()
3822		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3823	0	public void setViewerState(String value) {...
3824	0	this.viewerState = value;
3825		}
3826
3827		}
3828
3829		}
3830
3831		}
3832
3833
3834		/**
3835		* <p>Java class for anonymous complex type</p>.
3836		*
3837		* <p>The following schema fragment specifies the expected content contained within this class.</p>
3838		*
3839		* <pre>
3840		* &lt;complexType&gt;
3841		* &lt;complexContent&gt;
3842		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3843		* &lt;sequence&gt;
3844		* &lt;element name="sequencePoint" maxOccurs="unbounded"&gt;
3845		* &lt;complexType&gt;
3846		* &lt;complexContent&gt;
3847		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3848		* &lt;attGroup ref="{www.jalview.org}position"/&gt;
3849		* &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3850		* &lt;/restriction&gt;
3851		* &lt;/complexContent&gt;
3852		* &lt;/complexType&gt;
3853		* &lt;/element&gt;
3854		* &lt;element name="axis" maxOccurs="3" minOccurs="3"&gt;
3855		* &lt;complexType&gt;
3856		* &lt;complexContent&gt;
3857		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3858		* &lt;attGroup ref="{www.jalview.org}position"/&gt;
3859		* &lt;/restriction&gt;
3860		* &lt;/complexContent&gt;
3861		* &lt;/complexType&gt;
3862		* &lt;/element&gt;
3863		* &lt;element name="seqPointMin"&gt;
3864		* &lt;complexType&gt;
3865		* &lt;complexContent&gt;
3866		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3867		* &lt;attGroup ref="{www.jalview.org}position"/&gt;
3868		* &lt;/restriction&gt;
3869		* &lt;/complexContent&gt;
3870		* &lt;/complexType&gt;
3871		* &lt;/element&gt;
3872		* &lt;element name="seqPointMax"&gt;
3873		* &lt;complexType&gt;
3874		* &lt;complexContent&gt;
3875		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3876		* &lt;attGroup ref="{www.jalview.org}position"/&gt;
3877		* &lt;/restriction&gt;
3878		* &lt;/complexContent&gt;
3879		* &lt;/complexType&gt;
3880		* &lt;/element&gt;
3881		* &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&gt;
3882		* &lt;/sequence&gt;
3883		* &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
3884		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
3885		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3886		* &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3887		* &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3888		* &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3889		* &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3890		* &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3891		* &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
3892		* &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
3893		* &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
3894		* &lt;/restriction&gt;
3895		* &lt;/complexContent&gt;
3896		* &lt;/complexType&gt;
3897		* </pre>
3898		*
3899		*
3900		*/
3901		@XmlAccessorType(XmlAccessType.FIELD)
3902		@XmlType(name = "", propOrder = {
3903		"sequencePoint",
3904		"axis",
3905		"seqPointMin",
3906		"seqPointMax",
3907		"pcaData"
3908		})
		100% Uncovered Elements: 0 (92) Complexity: 44 Complexity Density: 0.96
3909		public static class PcaViewer {
3910
3911		@XmlElement(namespace = "www.jalview.org", required = true)
3912		protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
3913		/**
3914		* endpoints of X, Y and Z axes in that order
3915		*
3916		*/
3917		@XmlElement(namespace = "www.jalview.org", required = true)
3918		protected List<JalviewModel.PcaViewer.Axis> axis;
3919		@XmlElement(namespace = "www.jalview.org", required = true)
3920		protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
3921		@XmlElement(namespace = "www.jalview.org", required = true)
3922		protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
3923		@XmlElement(namespace = "www.jalview.org", required = true)
3924		protected PcaDataType pcaData;
3925		@XmlAttribute(name = "title")
3926		protected String title;
3927		@XmlAttribute(name = "scoreModelName")
3928		protected String scoreModelName;
3929		@XmlAttribute(name = "xDim")
3930		protected Integer xDim;
3931		@XmlAttribute(name = "yDim")
3932		protected Integer yDim;
3933		@XmlAttribute(name = "zDim")
3934		protected Integer zDim;
3935		@XmlAttribute(name = "bgColour")
3936		protected Integer bgColour;
3937		@XmlAttribute(name = "scaleFactor")
3938		protected Float scaleFactor;
3939		@XmlAttribute(name = "showLabels")
3940		protected Boolean showLabels;
3941		@XmlAttribute(name = "linkToAllViews")
3942		protected Boolean linkToAllViews;
3943		@XmlAttribute(name = "includeGaps")
3944		protected Boolean includeGaps;
3945		@XmlAttribute(name = "matchGaps")
3946		protected Boolean matchGaps;
3947		@XmlAttribute(name = "includeGappedColumns")
3948		protected Boolean includeGappedColumns;
3949		@XmlAttribute(name = "denominateByShortestLength")
3950		protected Boolean denominateByShortestLength;
3951		@XmlAttribute(name = "width")
3952		protected Integer width;
3953		@XmlAttribute(name = "height")
3954		protected Integer height;
3955		@XmlAttribute(name = "xpos")
3956		protected Integer xpos;
3957		@XmlAttribute(name = "ypos")
3958		protected Integer ypos;
3959
3960		/**
3961		* Gets the value of the sequencePoint property.
3962		*
3963		* <p>This accessor method returns a reference to the live list,
3964		* not a snapshot. Therefore any modification you make to the
3965		* returned list will be present inside the JAXB object.
3966		* This is why there is not a <CODE>set</CODE> method for the sequencePoint property.</p>
3967		*
3968		* <p>
3969		* For example, to add a new item, do as follows:
3970		* </p>
3971		* <pre>
3972		* getSequencePoint().add(newItem);
3973		* </pre>
3974		*
3975		*
3976		* <p>
3977		* Objects of the following type(s) are allowed in the list
3978		* {@link JalviewModel.PcaViewer.SequencePoint }
3979		* </p>
3980		*
3981		*
3982		* @return
3983		* The value of the sequencePoint property.
3984		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
3985	16	public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {...
3986	16	if (sequencePoint == null) {
3987	1	sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
3988		}
3989	16	return this.sequencePoint;
3990		}
3991
3992		/**
3993		* endpoints of X, Y and Z axes in that order
3994		*
3995		* Gets the value of the axis property.
3996		*
3997		* <p>This accessor method returns a reference to the live list,
3998		* not a snapshot. Therefore any modification you make to the
3999		* returned list will be present inside the JAXB object.
4000		* This is why there is not a <CODE>set</CODE> method for the axis property.</p>
4001		*
4002		* <p>
4003		* For example, to add a new item, do as follows:
4004		* </p>
4005		* <pre>
4006		* getAxis().add(newItem);
4007		* </pre>
4008		*
4009		*
4010		* <p>
4011		* Objects of the following type(s) are allowed in the list
4012		* {@link JalviewModel.PcaViewer.Axis }
4013		* </p>
4014		*
4015		*
4016		* @return
4017		* The value of the axis property.
4018		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
4019	6	public List<JalviewModel.PcaViewer.Axis> getAxis() {...
4020	6	if (axis == null) {
4021	1	axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
4022		}
4023	6	return this.axis;
4024		}
4025
4026		/**
4027		* Gets the value of the seqPointMin property.
4028		*
4029		* @return
4030		* possible object is
4031		* {@link JalviewModel.PcaViewer.SeqPointMin }
4032		*
4033		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4034	1	public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {...
4035	1	return seqPointMin;
4036		}
4037
4038		/**
4039		* Sets the value of the seqPointMin property.
4040		*
4041		* @param value
4042		* allowed object is
4043		* {@link JalviewModel.PcaViewer.SeqPointMin }
4044		*
4045		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4046	1	public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {...
4047	1	this.seqPointMin = value;
4048		}
4049
4050		/**
4051		* Gets the value of the seqPointMax property.
4052		*
4053		* @return
4054		* possible object is
4055		* {@link JalviewModel.PcaViewer.SeqPointMax }
4056		*
4057		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4058	1	public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {...
4059	1	return seqPointMax;
4060		}
4061
4062		/**
4063		* Sets the value of the seqPointMax property.
4064		*
4065		* @param value
4066		* allowed object is
4067		* {@link JalviewModel.PcaViewer.SeqPointMax }
4068		*
4069		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4070	1	public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {...
4071	1	this.seqPointMax = value;
4072		}
4073
4074		/**
4075		* Gets the value of the pcaData property.
4076		*
4077		* @return
4078		* possible object is
4079		* {@link PcaDataType }
4080		*
4081		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4082	1	public PcaDataType getPcaData() {...
4083	1	return pcaData;
4084		}
4085
4086		/**
4087		* Sets the value of the pcaData property.
4088		*
4089		* @param value
4090		* allowed object is
4091		* {@link PcaDataType }
4092		*
4093		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4094	1	public void setPcaData(PcaDataType value) {...
4095	1	this.pcaData = value;
4096		}
4097
4098		/**
4099		* Gets the value of the title property.
4100		*
4101		* @return
4102		* possible object is
4103		* {@link String }
4104		*
4105		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4106	3	public String getTitle() {...
4107	3	return title;
4108		}
4109
4110		/**
4111		* Sets the value of the title property.
4112		*
4113		* @param value
4114		* allowed object is
4115		* {@link String }
4116		*
4117		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4118	1	public void setTitle(String value) {...
4119	1	this.title = value;
4120		}
4121
4122		/**
4123		* Gets the value of the scoreModelName property.
4124		*
4125		* @return
4126		* possible object is
4127		* {@link String }
4128		*
4129		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4130	1	public String getScoreModelName() {...
4131	1	return scoreModelName;
4132		}
4133
4134		/**
4135		* Sets the value of the scoreModelName property.
4136		*
4137		* @param value
4138		* allowed object is
4139		* {@link String }
4140		*
4141		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4142	1	public void setScoreModelName(String value) {...
4143	1	this.scoreModelName = value;
4144		}
4145
4146		/**
4147		* Gets the value of the xDim property.
4148		*
4149		* @return
4150		* possible object is
4151		* {@link Integer }
4152		*
4153		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4154	1	public Integer getXDim() {...
4155	1	return xDim;
4156		}
4157
4158		/**
4159		* Sets the value of the xDim property.
4160		*
4161		* @param value
4162		* allowed object is
4163		* {@link Integer }
4164		*
4165		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4166	1	public void setXDim(Integer value) {...
4167	1	this.xDim = value;
4168		}
4169
4170		/**
4171		* Gets the value of the yDim property.
4172		*
4173		* @return
4174		* possible object is
4175		* {@link Integer }
4176		*
4177		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4178	1	public Integer getYDim() {...
4179	1	return yDim;
4180		}
4181
4182		/**
4183		* Sets the value of the yDim property.
4184		*
4185		* @param value
4186		* allowed object is
4187		* {@link Integer }
4188		*
4189		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4190	1	public void setYDim(Integer value) {...
4191	1	this.yDim = value;
4192		}
4193
4194		/**
4195		* Gets the value of the zDim property.
4196		*
4197		* @return
4198		* possible object is
4199		* {@link Integer }
4200		*
4201		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4202	1	public Integer getZDim() {...
4203	1	return zDim;
4204		}
4205
4206		/**
4207		* Sets the value of the zDim property.
4208		*
4209		* @param value
4210		* allowed object is
4211		* {@link Integer }
4212		*
4213		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4214	1	public void setZDim(Integer value) {...
4215	1	this.zDim = value;
4216		}
4217
4218		/**
4219		* Gets the value of the bgColour property.
4220		*
4221		* @return
4222		* possible object is
4223		* {@link Integer }
4224		*
4225		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4226	1	public Integer getBgColour() {...
4227	1	return bgColour;
4228		}
4229
4230		/**
4231		* Sets the value of the bgColour property.
4232		*
4233		* @param value
4234		* allowed object is
4235		* {@link Integer }
4236		*
4237		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4238	1	public void setBgColour(Integer value) {...
4239	1	this.bgColour = value;
4240		}
4241
4242		/**
4243		* Gets the value of the scaleFactor property.
4244		*
4245		* @return
4246		* possible object is
4247		* {@link Float }
4248		*
4249		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4250	1	public Float getScaleFactor() {...
4251	1	return scaleFactor;
4252		}
4253
4254		/**
4255		* Sets the value of the scaleFactor property.
4256		*
4257		* @param value
4258		* allowed object is
4259		* {@link Float }
4260		*
4261		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4262	1	public void setScaleFactor(Float value) {...
4263	1	this.scaleFactor = value;
4264		}
4265
4266		/**
4267		* Gets the value of the showLabels property.
4268		*
4269		* @return
4270		* possible object is
4271		* {@link Boolean }
4272		*
4273		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4274	1	public Boolean isShowLabels() {...
4275	1	return showLabels;
4276		}
4277
4278		/**
4279		* Sets the value of the showLabels property.
4280		*
4281		* @param value
4282		* allowed object is
4283		* {@link Boolean }
4284		*
4285		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4286	1	public void setShowLabels(Boolean value) {...
4287	1	this.showLabels = value;
4288		}
4289
4290		/**
4291		* Gets the value of the linkToAllViews property.
4292		*
4293		* @return
4294		* possible object is
4295		* {@link Boolean }
4296		*
4297		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4298	1	public Boolean isLinkToAllViews() {...
4299	1	return linkToAllViews;
4300		}
4301
4302		/**
4303		* Sets the value of the linkToAllViews property.
4304		*
4305		* @param value
4306		* allowed object is
4307		* {@link Boolean }
4308		*
4309		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4310	1	public void setLinkToAllViews(Boolean value) {...
4311	1	this.linkToAllViews = value;
4312		}
4313
4314		/**
4315		* Gets the value of the includeGaps property.
4316		*
4317		* @return
4318		* possible object is
4319		* {@link Boolean }
4320		*
4321		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4322	1	public Boolean isIncludeGaps() {...
4323	1	return includeGaps;
4324		}
4325
4326		/**
4327		* Sets the value of the includeGaps property.
4328		*
4329		* @param value
4330		* allowed object is
4331		* {@link Boolean }
4332		*
4333		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4334	1	public void setIncludeGaps(Boolean value) {...
4335	1	this.includeGaps = value;
4336		}
4337
4338		/**
4339		* Gets the value of the matchGaps property.
4340		*
4341		* @return
4342		* possible object is
4343		* {@link Boolean }
4344		*
4345		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4346	1	public Boolean isMatchGaps() {...
4347	1	return matchGaps;
4348		}
4349
4350		/**
4351		* Sets the value of the matchGaps property.
4352		*
4353		* @param value
4354		* allowed object is
4355		* {@link Boolean }
4356		*
4357		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4358	1	public void setMatchGaps(Boolean value) {...
4359	1	this.matchGaps = value;
4360		}
4361
4362		/**
4363		* Gets the value of the includeGappedColumns property.
4364		*
4365		* @return
4366		* possible object is
4367		* {@link Boolean }
4368		*
4369		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4370	1	public Boolean isIncludeGappedColumns() {...
4371	1	return includeGappedColumns;
4372		}
4373
4374		/**
4375		* Sets the value of the includeGappedColumns property.
4376		*
4377		* @param value
4378		* allowed object is
4379		* {@link Boolean }
4380		*
4381		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4382	1	public void setIncludeGappedColumns(Boolean value) {...
4383	1	this.includeGappedColumns = value;
4384		}
4385
4386		/**
4387		* Gets the value of the denominateByShortestLength property.
4388		*
4389		* @return
4390		* possible object is
4391		* {@link Boolean }
4392		*
4393		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4394	1	public Boolean isDenominateByShortestLength() {...
4395	1	return denominateByShortestLength;
4396		}
4397
4398		/**
4399		* Sets the value of the denominateByShortestLength property.
4400		*
4401		* @param value
4402		* allowed object is
4403		* {@link Boolean }
4404		*
4405		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4406	1	public void setDenominateByShortestLength(Boolean value) {...
4407	1	this.denominateByShortestLength = value;
4408		}
4409
4410		/**
4411		* Gets the value of the width property.
4412		*
4413		* @return
4414		* possible object is
4415		* {@link Integer }
4416		*
4417		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4418	1	public Integer getWidth() {...
4419	1	return width;
4420		}
4421
4422		/**
4423		* Sets the value of the width property.
4424		*
4425		* @param value
4426		* allowed object is
4427		* {@link Integer }
4428		*
4429		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4430	1	public void setWidth(Integer value) {...
4431	1	this.width = value;
4432		}
4433
4434		/**
4435		* Gets the value of the height property.
4436		*
4437		* @return
4438		* possible object is
4439		* {@link Integer }
4440		*
4441		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4442	1	public Integer getHeight() {...
4443	1	return height;
4444		}
4445
4446		/**
4447		* Sets the value of the height property.
4448		*
4449		* @param value
4450		* allowed object is
4451		* {@link Integer }
4452		*
4453		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4454	1	public void setHeight(Integer value) {...
4455	1	this.height = value;
4456		}
4457
4458		/**
4459		* Gets the value of the xpos property.
4460		*
4461		* @return
4462		* possible object is
4463		* {@link Integer }
4464		*
4465		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4466	1	public Integer getXpos() {...
4467	1	return xpos;
4468		}
4469
4470		/**
4471		* Sets the value of the xpos property.
4472		*
4473		* @param value
4474		* allowed object is
4475		* {@link Integer }
4476		*
4477		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4478	1	public void setXpos(Integer value) {...
4479	1	this.xpos = value;
4480		}
4481
4482		/**
4483		* Gets the value of the ypos property.
4484		*
4485		* @return
4486		* possible object is
4487		* {@link Integer }
4488		*
4489		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4490	1	public Integer getYpos() {...
4491	1	return ypos;
4492		}
4493
4494		/**
4495		* Sets the value of the ypos property.
4496		*
4497		* @param value
4498		* allowed object is
4499		* {@link Integer }
4500		*
4501		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4502	1	public void setYpos(Integer value) {...
4503	1	this.ypos = value;
4504		}
4505
4506
4507		/**
4508		* <p>Java class for anonymous complex type</p>.
4509		*
4510		* <p>The following schema fragment specifies the expected content contained within this class.</p>
4511		*
4512		* <pre>
4513		* &lt;complexType&gt;
4514		* &lt;complexContent&gt;
4515		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4516		* &lt;attGroup ref="{www.jalview.org}position"/&gt;
4517		* &lt;/restriction&gt;
4518		* &lt;/complexContent&gt;
4519		* &lt;/complexType&gt;
4520		* </pre>
4521		*
4522		*
4523		*/
4524		@XmlAccessorType(XmlAccessType.FIELD)
4525		@XmlType(name = "")
		100% Uncovered Elements: 0 (12) Complexity: 6 Complexity Density: 1
4526		public static class Axis {
4527
4528		@XmlAttribute(name = "xPos")
4529		protected Float xPos;
4530		@XmlAttribute(name = "yPos")
4531		protected Float yPos;
4532		@XmlAttribute(name = "zPos")
4533		protected Float zPos;
4534
4535		/**
4536		* Gets the value of the xPos property.
4537		*
4538		* @return
4539		* possible object is
4540		* {@link Float }
4541		*
4542		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4543	3	public Float getXPos() {...
4544	3	return xPos;
4545		}
4546
4547		/**
4548		* Sets the value of the xPos property.
4549		*
4550		* @param value
4551		* allowed object is
4552		* {@link Float }
4553		*
4554		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4555	3	public void setXPos(Float value) {...
4556	3	this.xPos = value;
4557		}
4558
4559		/**
4560		* Gets the value of the yPos property.
4561		*
4562		* @return
4563		* possible object is
4564		* {@link Float }
4565		*
4566		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4567	3	public Float getYPos() {...
4568	3	return yPos;
4569		}
4570
4571		/**
4572		* Sets the value of the yPos property.
4573		*
4574		* @param value
4575		* allowed object is
4576		* {@link Float }
4577		*
4578		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4579	3	public void setYPos(Float value) {...
4580	3	this.yPos = value;
4581		}
4582
4583		/**
4584		* Gets the value of the zPos property.
4585		*
4586		* @return
4587		* possible object is
4588		* {@link Float }
4589		*
4590		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4591	3	public Float getZPos() {...
4592	3	return zPos;
4593		}
4594
4595		/**
4596		* Sets the value of the zPos property.
4597		*
4598		* @param value
4599		* allowed object is
4600		* {@link Float }
4601		*
4602		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4603	3	public void setZPos(Float value) {...
4604	3	this.zPos = value;
4605		}
4606
4607		}
4608
4609
4610		/**
4611		* <p>Java class for anonymous complex type</p>.
4612		*
4613		* <p>The following schema fragment specifies the expected content contained within this class.</p>
4614		*
4615		* <pre>
4616		* &lt;complexType&gt;
4617		* &lt;complexContent&gt;
4618		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4619		* &lt;attGroup ref="{www.jalview.org}position"/&gt;
4620		* &lt;/restriction&gt;
4621		* &lt;/complexContent&gt;
4622		* &lt;/complexType&gt;
4623		* </pre>
4624		*
4625		*
4626		*/
4627		@XmlAccessorType(XmlAccessType.FIELD)
4628		@XmlType(name = "")
		100% Uncovered Elements: 0 (12) Complexity: 6 Complexity Density: 1
4629		public static class SeqPointMax {
4630
4631		@XmlAttribute(name = "xPos")
4632		protected Float xPos;
4633		@XmlAttribute(name = "yPos")
4634		protected Float yPos;
4635		@XmlAttribute(name = "zPos")
4636		protected Float zPos;
4637
4638		/**
4639		* Gets the value of the xPos property.
4640		*
4641		* @return
4642		* possible object is
4643		* {@link Float }
4644		*
4645		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4646	1	public Float getXPos() {...
4647	1	return xPos;
4648		}
4649
4650		/**
4651		* Sets the value of the xPos property.
4652		*
4653		* @param value
4654		* allowed object is
4655		* {@link Float }
4656		*
4657		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4658	1	public void setXPos(Float value) {...
4659	1	this.xPos = value;
4660		}
4661
4662		/**
4663		* Gets the value of the yPos property.
4664		*
4665		* @return
4666		* possible object is
4667		* {@link Float }
4668		*
4669		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4670	1	public Float getYPos() {...
4671	1	return yPos;
4672		}
4673
4674		/**
4675		* Sets the value of the yPos property.
4676		*
4677		* @param value
4678		* allowed object is
4679		* {@link Float }
4680		*
4681		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4682	1	public void setYPos(Float value) {...
4683	1	this.yPos = value;
4684		}
4685
4686		/**
4687		* Gets the value of the zPos property.
4688		*
4689		* @return
4690		* possible object is
4691		* {@link Float }
4692		*
4693		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4694	1	public Float getZPos() {...
4695	1	return zPos;
4696		}
4697
4698		/**
4699		* Sets the value of the zPos property.
4700		*
4701		* @param value
4702		* allowed object is
4703		* {@link Float }
4704		*
4705		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4706	1	public void setZPos(Float value) {...
4707	1	this.zPos = value;
4708		}
4709
4710		}
4711
4712
4713		/**
4714		* <p>Java class for anonymous complex type</p>.
4715		*
4716		* <p>The following schema fragment specifies the expected content contained within this class.</p>
4717		*
4718		* <pre>
4719		* &lt;complexType&gt;
4720		* &lt;complexContent&gt;
4721		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4722		* &lt;attGroup ref="{www.jalview.org}position"/&gt;
4723		* &lt;/restriction&gt;
4724		* &lt;/complexContent&gt;
4725		* &lt;/complexType&gt;
4726		* </pre>
4727		*
4728		*
4729		*/
4730		@XmlAccessorType(XmlAccessType.FIELD)
4731		@XmlType(name = "")
		100% Uncovered Elements: 0 (12) Complexity: 6 Complexity Density: 1
4732		public static class SeqPointMin {
4733
4734		@XmlAttribute(name = "xPos")
4735		protected Float xPos;
4736		@XmlAttribute(name = "yPos")
4737		protected Float yPos;
4738		@XmlAttribute(name = "zPos")
4739		protected Float zPos;
4740
4741		/**
4742		* Gets the value of the xPos property.
4743		*
4744		* @return
4745		* possible object is
4746		* {@link Float }
4747		*
4748		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4749	1	public Float getXPos() {...
4750	1	return xPos;
4751		}
4752
4753		/**
4754		* Sets the value of the xPos property.
4755		*
4756		* @param value
4757		* allowed object is
4758		* {@link Float }
4759		*
4760		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4761	1	public void setXPos(Float value) {...
4762	1	this.xPos = value;
4763		}
4764
4765		/**
4766		* Gets the value of the yPos property.
4767		*
4768		* @return
4769		* possible object is
4770		* {@link Float }
4771		*
4772		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4773	1	public Float getYPos() {...
4774	1	return yPos;
4775		}
4776
4777		/**
4778		* Sets the value of the yPos property.
4779		*
4780		* @param value
4781		* allowed object is
4782		* {@link Float }
4783		*
4784		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4785	1	public void setYPos(Float value) {...
4786	1	this.yPos = value;
4787		}
4788
4789		/**
4790		* Gets the value of the zPos property.
4791		*
4792		* @return
4793		* possible object is
4794		* {@link Float }
4795		*
4796		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4797	1	public Float getZPos() {...
4798	1	return zPos;
4799		}
4800
4801		/**
4802		* Sets the value of the zPos property.
4803		*
4804		* @param value
4805		* allowed object is
4806		* {@link Float }
4807		*
4808		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4809	1	public void setZPos(Float value) {...
4810	1	this.zPos = value;
4811		}
4812
4813		}
4814
4815
4816		/**
4817		* <p>Java class for anonymous complex type</p>.
4818		*
4819		* <p>The following schema fragment specifies the expected content contained within this class.</p>
4820		*
4821		* <pre>
4822		* &lt;complexType&gt;
4823		* &lt;complexContent&gt;
4824		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4825		* &lt;attGroup ref="{www.jalview.org}position"/&gt;
4826		* &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4827		* &lt;/restriction&gt;
4828		* &lt;/complexContent&gt;
4829		* &lt;/complexType&gt;
4830		* </pre>
4831		*
4832		*
4833		*/
4834		@XmlAccessorType(XmlAccessType.FIELD)
4835		@XmlType(name = "")
		100% Uncovered Elements: 0 (16) Complexity: 8 Complexity Density: 1
4836		public static class SequencePoint {
4837
4838		@XmlAttribute(name = "sequenceRef")
4839		protected String sequenceRef;
4840		@XmlAttribute(name = "xPos")
4841		protected Float xPos;
4842		@XmlAttribute(name = "yPos")
4843		protected Float yPos;
4844		@XmlAttribute(name = "zPos")
4845		protected Float zPos;
4846
4847		/**
4848		* Gets the value of the sequenceRef property.
4849		*
4850		* @return
4851		* possible object is
4852		* {@link String }
4853		*
4854		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4855	15	public String getSequenceRef() {...
4856	15	return sequenceRef;
4857		}
4858
4859		/**
4860		* Sets the value of the sequenceRef property.
4861		*
4862		* @param value
4863		* allowed object is
4864		* {@link String }
4865		*
4866		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4867	15	public void setSequenceRef(String value) {...
4868	15	this.sequenceRef = value;
4869		}
4870
4871		/**
4872		* Gets the value of the xPos property.
4873		*
4874		* @return
4875		* possible object is
4876		* {@link Float }
4877		*
4878		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4879	15	public Float getXPos() {...
4880	15	return xPos;
4881		}
4882
4883		/**
4884		* Sets the value of the xPos property.
4885		*
4886		* @param value
4887		* allowed object is
4888		* {@link Float }
4889		*
4890		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4891	15	public void setXPos(Float value) {...
4892	15	this.xPos = value;
4893		}
4894
4895		/**
4896		* Gets the value of the yPos property.
4897		*
4898		* @return
4899		* possible object is
4900		* {@link Float }
4901		*
4902		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4903	15	public Float getYPos() {...
4904	15	return yPos;
4905		}
4906
4907		/**
4908		* Sets the value of the yPos property.
4909		*
4910		* @param value
4911		* allowed object is
4912		* {@link Float }
4913		*
4914		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4915	15	public void setYPos(Float value) {...
4916	15	this.yPos = value;
4917		}
4918
4919		/**
4920		* Gets the value of the zPos property.
4921		*
4922		* @return
4923		* possible object is
4924		* {@link Float }
4925		*
4926		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4927	15	public Float getZPos() {...
4928	15	return zPos;
4929		}
4930
4931		/**
4932		* Sets the value of the zPos property.
4933		*
4934		* @param value
4935		* allowed object is
4936		* {@link Float }
4937		*
4938		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4939	15	public void setZPos(Float value) {...
4940	15	this.zPos = value;
4941		}
4942
4943		}
4944
4945		}
4946
4947
4948		/**
4949		* <p>Java class for anonymous complex type</p>.
4950		*
4951		* <p>The following schema fragment specifies the expected content contained within this class.</p>
4952		*
4953		* <pre>
4954		* &lt;complexType&gt;
4955		* &lt;complexContent&gt;
4956		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4957		* &lt;sequence minOccurs="0"&gt;
4958		* &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
4959		* &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
4960		* &lt;element name="TreeColorMap" minOccurs="0"&gt;
4961		* &lt;complexType&gt;
4962		* &lt;complexContent&gt;
4963		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4964		* &lt;sequence&gt;
4965		* &lt;element name="ColorEntry" maxOccurs="unbounded" minOccurs="0"&gt;
4966		* &lt;complexType&gt;
4967		* &lt;complexContent&gt;
4968		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4969		* &lt;attribute name="label" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4970		* &lt;attribute name="color" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4971		* &lt;/restriction&gt;
4972		* &lt;/complexContent&gt;
4973		* &lt;/complexType&gt;
4974		* &lt;/element&gt;
4975		* &lt;/sequence&gt;
4976		* &lt;/restriction&gt;
4977		* &lt;/complexContent&gt;
4978		* &lt;/complexType&gt;
4979		* &lt;/element&gt;
4980		* &lt;/sequence&gt;
4981		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
4982		* &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4983		* &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4984		* &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4985		* &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
4986		* &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4987		* &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4988		* &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4989		* &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4990		* &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4991		* &lt;attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4992		* &lt;attribute name="annotationBased" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4993		* &lt;attribute name="showAnnotationAs" type="{http://www.w3.org/2001/XMLSchema}string" default="None" /&gt;
4994		* &lt;attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4995		* &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
4996		* &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4997		* &lt;/restriction&gt;
4998		* &lt;/complexContent&gt;
4999		* &lt;/complexType&gt;
5000		* </pre>
5001		*
5002		*
5003		*/
5004		@XmlAccessorType(XmlAccessType.FIELD)
5005		@XmlType(name = "", propOrder = {
5006		"title",
5007		"newick",
5008		"treeColorMap"
5009		})
		90.4% Uncovered Elements: 10 (104) Complexity: 48 Complexity Density: 0.92
5010		public static class Tree {
5011
5012		@XmlElement(namespace = "www.jalview.org")
5013		protected String title;
5014		@XmlElement(namespace = "www.jalview.org")
5015		protected String newick;
5016		@XmlElement(name = "TreeColorMap", namespace = "www.jalview.org")
5017		protected JalviewModel.Tree.TreeColorMap treeColorMap;
5018		@XmlAttribute(name = "fontName")
5019		protected String fontName;
5020		@XmlAttribute(name = "fontSize")
5021		protected Integer fontSize;
5022		@XmlAttribute(name = "fontStyle")
5023		protected Integer fontStyle;
5024		@XmlAttribute(name = "threshold")
5025		protected Float threshold;
5026		@XmlAttribute(name = "showBootstrap")
5027		protected Boolean showBootstrap;
5028		@XmlAttribute(name = "showDistances")
5029		protected Boolean showDistances;
5030		@XmlAttribute(name = "markUnlinked")
5031		protected Boolean markUnlinked;
5032		@XmlAttribute(name = "fitToWindow")
5033		protected Boolean fitToWindow;
5034		@XmlAttribute(name = "currentTree")
5035		protected Boolean currentTree;
5036		/**
5037		* Set for trees associated with columns of an alignment, sequence or annotation row
5038		*
5039		*/
5040		@XmlAttribute(name = "columnWise")
5041		protected Boolean columnWise;
5042		/**
5043		* Set for trees associated with annotations
5044		*
5045		*/
5046		@XmlAttribute(name = "annotationBased")
5047		protected Boolean annotationBased;
5048		/**
5049		* The view selected for trees, associated with annotations
5050		*
5051		*/
5052		@XmlAttribute(name = "showAnnotationAs")
5053		protected String showAnnotationAs;
5054		/**
5055		* Refers to annotation row the tree is provided by
5056		*
5057		*/
5058		@XmlAttribute(name = "columnReference")
5059		protected String columnReference;
5060		/**
5061		* Tree ID added for binding tree
5062		* visualization
5063		* settings to vamsas
5064		* document trees in jalview 2.4.1
5065		*
5066		*/
5067		@XmlAttribute(name = "id")
5068		@XmlJavaTypeAdapter(CollapsedStringAdapter.class)
5069		@XmlID
5070		@XmlSchemaType(name = "ID")
5071		protected String id;
5072		@XmlAttribute(name = "linkToAllViews")
5073		protected Boolean linkToAllViews;
5074		@XmlAttribute(name = "width")
5075		protected Integer width;
5076		@XmlAttribute(name = "height")
5077		protected Integer height;
5078		@XmlAttribute(name = "xpos")
5079		protected Integer xpos;
5080		@XmlAttribute(name = "ypos")
5081		protected Integer ypos;
5082
5083		/**
5084		* Gets the value of the title property.
5085		*
5086		* @return
5087		* possible object is
5088		* {@link String }
5089		*
5090		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5091	15	public String getTitle() {...
5092	15	return title;
5093		}
5094
5095		/**
5096		* Sets the value of the title property.
5097		*
5098		* @param value
5099		* allowed object is
5100		* {@link String }
5101		*
5102		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5103	6	public void setTitle(String value) {...
5104	6	this.title = value;
5105		}
5106
5107		/**
5108		* Gets the value of the newick property.
5109		*
5110		* @return
5111		* possible object is
5112		* {@link String }
5113		*
5114		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5115	15	public String getNewick() {...
5116	15	return newick;
5117		}
5118
5119		/**
5120		* Sets the value of the newick property.
5121		*
5122		* @param value
5123		* allowed object is
5124		* {@link String }
5125		*
5126		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5127	6	public void setNewick(String value) {...
5128	6	this.newick = value;
5129		}
5130
5131		/**
5132		* Gets the value of the treeColorMap property.
5133		*
5134		* @return
5135		* possible object is
5136		* {@link JalviewModel.Tree.TreeColorMap }
5137		*
5138		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5139	18	public JalviewModel.Tree.TreeColorMap getTreeColorMap() {...
5140	18	return treeColorMap;
5141		}
5142
5143		/**
5144		* Sets the value of the treeColorMap property.
5145		*
5146		* @param value
5147		* allowed object is
5148		* {@link JalviewModel.Tree.TreeColorMap }
5149		*
5150		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5151	2	public void setTreeColorMap(JalviewModel.Tree.TreeColorMap value) {...
5152	2	this.treeColorMap = value;
5153		}
5154
5155		/**
5156		* Gets the value of the fontName property.
5157		*
5158		* @return
5159		* possible object is
5160		* {@link String }
5161		*
5162		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5163	6	public String getFontName() {...
5164	6	return fontName;
5165		}
5166
5167		/**
5168		* Sets the value of the fontName property.
5169		*
5170		* @param value
5171		* allowed object is
5172		* {@link String }
5173		*
5174		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5175	6	public void setFontName(String value) {...
5176	6	this.fontName = value;
5177		}
5178
5179		/**
5180		* Gets the value of the fontSize property.
5181		*
5182		* @return
5183		* possible object is
5184		* {@link Integer }
5185		*
5186		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5187	3	public Integer getFontSize() {...
5188	3	return fontSize;
5189		}
5190
5191		/**
5192		* Sets the value of the fontSize property.
5193		*
5194		* @param value
5195		* allowed object is
5196		* {@link Integer }
5197		*
5198		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5199	6	public void setFontSize(Integer value) {...
5200	6	this.fontSize = value;
5201		}
5202
5203		/**
5204		* Gets the value of the fontStyle property.
5205		*
5206		* @return
5207		* possible object is
5208		* {@link Integer }
5209		*
5210		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5211	3	public Integer getFontStyle() {...
5212	3	return fontStyle;
5213		}
5214
5215		/**
5216		* Sets the value of the fontStyle property.
5217		*
5218		* @param value
5219		* allowed object is
5220		* {@link Integer }
5221		*
5222		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5223	6	public void setFontStyle(Integer value) {...
5224	6	this.fontStyle = value;
5225		}
5226
5227		/**
5228		* Gets the value of the threshold property.
5229		*
5230		* @return
5231		* possible object is
5232		* {@link Float }
5233		*
5234		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5235	3	public Float getThreshold() {...
5236	3	return threshold;
5237		}
5238
5239		/**
5240		* Sets the value of the threshold property.
5241		*
5242		* @param value
5243		* allowed object is
5244		* {@link Float }
5245		*
5246		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5247	6	public void setThreshold(Float value) {...
5248	6	this.threshold = value;
5249		}
5250
5251		/**
5252		* Gets the value of the showBootstrap property.
5253		*
5254		* @return
5255		* possible object is
5256		* {@link Boolean }
5257		*
5258		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5259	3	public Boolean isShowBootstrap() {...
5260	3	return showBootstrap;
5261		}
5262
5263		/**
5264		* Sets the value of the showBootstrap property.
5265		*
5266		* @param value
5267		* allowed object is
5268		* {@link Boolean }
5269		*
5270		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5271	6	public void setShowBootstrap(Boolean value) {...
5272	6	this.showBootstrap = value;
5273		}
5274
5275		/**
5276		* Gets the value of the showDistances property.
5277		*
5278		* @return
5279		* possible object is
5280		* {@link Boolean }
5281		*
5282		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5283	3	public Boolean isShowDistances() {...
5284	3	return showDistances;
5285		}
5286
5287		/**
5288		* Sets the value of the showDistances property.
5289		*
5290		* @param value
5291		* allowed object is
5292		* {@link Boolean }
5293		*
5294		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5295	6	public void setShowDistances(Boolean value) {...
5296	6	this.showDistances = value;
5297		}
5298
5299		/**
5300		* Gets the value of the markUnlinked property.
5301		*
5302		* @return
5303		* possible object is
5304		* {@link Boolean }
5305		*
5306		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5307	3	public Boolean isMarkUnlinked() {...
5308	3	return markUnlinked;
5309		}
5310
5311		/**
5312		* Sets the value of the markUnlinked property.
5313		*
5314		* @param value
5315		* allowed object is
5316		* {@link Boolean }
5317		*
5318		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5319	6	public void setMarkUnlinked(Boolean value) {...
5320	6	this.markUnlinked = value;
5321		}
5322
5323		/**
5324		* Gets the value of the fitToWindow property.
5325		*
5326		* @return
5327		* possible object is
5328		* {@link Boolean }
5329		*
5330		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5331	3	public Boolean isFitToWindow() {...
5332	3	return fitToWindow;
5333		}
5334
5335		/**
5336		* Sets the value of the fitToWindow property.
5337		*
5338		* @param value
5339		* allowed object is
5340		* {@link Boolean }
5341		*
5342		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5343	6	public void setFitToWindow(Boolean value) {...
5344	6	this.fitToWindow = value;
5345		}
5346
5347		/**
5348		* Gets the value of the currentTree property.
5349		*
5350		* @return
5351		* possible object is
5352		* {@link Boolean }
5353		*
5354		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5355	3	public Boolean isCurrentTree() {...
5356	3	return currentTree;
5357		}
5358
5359		/**
5360		* Sets the value of the currentTree property.
5361		*
5362		* @param value
5363		* allowed object is
5364		* {@link Boolean }
5365		*
5366		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5367	6	public void setCurrentTree(Boolean value) {...
5368	6	this.currentTree = value;
5369		}
5370
5371		/**
5372		* Set for trees associated with columns of an alignment, sequence or annotation row
5373		*
5374		* @return
5375		* possible object is
5376		* {@link Boolean }
5377		*
5378		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
5379	15	public boolean isColumnWise() {...
5380	15	if (columnWise == null) {
5381	15	return false;
5382		} else {
5383	0	return columnWise;
5384		}
5385		}
5386
5387		/**
5388		* Sets the value of the columnWise property.
5389		*
5390		* @param value
5391		* allowed object is
5392		* {@link Boolean }
5393		*
5394		* @see #isColumnWise()
5395		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
5396	0	public void setColumnWise(Boolean value) {...
5397	0	this.columnWise = value;
5398		}
5399
5400		/**
5401		* Set for trees associated with annotations
5402		*
5403		* @return
5404		* possible object is
5405		* {@link Boolean }
5406		*
5407		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
5408	30	public boolean isAnnotationBased() {...
5409	30	if (annotationBased == null) {
5410	24	return false;
5411		} else {
5412	6	return annotationBased;
5413		}
5414		}
5415
5416		/**
5417		* Sets the value of the annotationBased property.
5418		*
5419		* @param value
5420		* allowed object is
5421		* {@link Boolean }
5422		*
5423		* @see #isAnnotationBased()
5424		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5425	2	public void setAnnotationBased(Boolean value) {...
5426	2	this.annotationBased = value;
5427		}
5428
5429		/**
5430		* The view selected for trees, associated with annotations
5431		*
5432		* @return
5433		* possible object is
5434		* {@link String }
5435		*
5436		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
5437	3	public String getShowAnnotationAs() {...
5438	3	if (showAnnotationAs == null) {
5439	0	return "None";
5440		} else {
5441	3	return showAnnotationAs;
5442		}
5443		}
5444
5445		/**
5446		* Sets the value of the showAnnotationAs property.
5447		*
5448		* @param value
5449		* allowed object is
5450		* {@link String }
5451		*
5452		* @see #getShowAnnotationAs()
5453		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5454	2	public void setShowAnnotationAs(String value) {...
5455	2	this.showAnnotationAs = value;
5456		}
5457
5458		/**
5459		* Refers to annotation row the tree is provided by
5460		*
5461		* @return
5462		* possible object is
5463		* {@link String }
5464		*
5465		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
5466	0	public String getColumnReference() {...
5467	0	return columnReference;
5468		}
5469
5470		/**
5471		* Sets the value of the columnReference property.
5472		*
5473		* @param value
5474		* allowed object is
5475		* {@link String }
5476		*
5477		* @see #getColumnReference()
5478		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
5479	0	public void setColumnReference(String value) {...
5480	0	this.columnReference = value;
5481		}
5482
5483		/**
5484		* Tree ID added for binding tree
5485		* visualization
5486		* settings to vamsas
5487		* document trees in jalview 2.4.1
5488		*
5489		* @return
5490		* possible object is
5491		* {@link String }
5492		*
5493		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5494	30	public String getId() {...
5495	30	return id;
5496		}
5497
5498		/**
5499		* Sets the value of the id property.
5500		*
5501		* @param value
5502		* allowed object is
5503		* {@link String }
5504		*
5505		* @see #getId()
5506		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5507	6	public void setId(String value) {...
5508	6	this.id = value;
5509		}
5510
5511		/**
5512		* Gets the value of the linkToAllViews property.
5513		*
5514		* @return
5515		* possible object is
5516		* {@link Boolean }
5517		*
5518		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
5519	15	public boolean isLinkToAllViews() {...
5520	15	if (linkToAllViews == null) {
5521	8	return false;
5522		} else {
5523	7	return linkToAllViews;
5524		}
5525		}
5526
5527		/**
5528		* Sets the value of the linkToAllViews property.
5529		*
5530		* @param value
5531		* allowed object is
5532		* {@link Boolean }
5533		*
5534		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5535	6	public void setLinkToAllViews(Boolean value) {...
5536	6	this.linkToAllViews = value;
5537		}
5538
5539		/**
5540		* Gets the value of the width property.
5541		*
5542		* @return
5543		* possible object is
5544		* {@link Integer }
5545		*
5546		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5547	15	public Integer getWidth() {...
5548	15	return width;
5549		}
5550
5551		/**
5552		* Sets the value of the width property.
5553		*
5554		* @param value
5555		* allowed object is
5556		* {@link Integer }
5557		*
5558		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5559	6	public void setWidth(Integer value) {...
5560	6	this.width = value;
5561		}
5562
5563		/**
5564		* Gets the value of the height property.
5565		*
5566		* @return
5567		* possible object is
5568		* {@link Integer }
5569		*
5570		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5571	15	public Integer getHeight() {...
5572	15	return height;
5573		}
5574
5575		/**
5576		* Sets the value of the height property.
5577		*
5578		* @param value
5579		* allowed object is
5580		* {@link Integer }
5581		*
5582		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5583	6	public void setHeight(Integer value) {...
5584	6	this.height = value;
5585		}
5586
5587		/**
5588		* Gets the value of the xpos property.
5589		*
5590		* @return
5591		* possible object is
5592		* {@link Integer }
5593		*
5594		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5595	15	public Integer getXpos() {...
5596	15	return xpos;
5597		}
5598
5599		/**
5600		* Sets the value of the xpos property.
5601		*
5602		* @param value
5603		* allowed object is
5604		* {@link Integer }
5605		*
5606		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5607	6	public void setXpos(Integer value) {...
5608	6	this.xpos = value;
5609		}
5610
5611		/**
5612		* Gets the value of the ypos property.
5613		*
5614		* @return
5615		* possible object is
5616		* {@link Integer }
5617		*
5618		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5619	15	public Integer getYpos() {...
5620	15	return ypos;
5621		}
5622
5623		/**
5624		* Sets the value of the ypos property.
5625		*
5626		* @param value
5627		* allowed object is
5628		* {@link Integer }
5629		*
5630		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5631	6	public void setYpos(Integer value) {...
5632	6	this.ypos = value;
5633		}
5634
5635
5636		/**
5637		* <p>Java class for anonymous complex type</p>.
5638		*
5639		* <p>The following schema fragment specifies the expected content contained within this class.</p>
5640		*
5641		* <pre>
5642		* &lt;complexType&gt;
5643		* &lt;complexContent&gt;
5644		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
5645		* &lt;sequence&gt;
5646		* &lt;element name="ColorEntry" maxOccurs="unbounded" minOccurs="0"&gt;
5647		* &lt;complexType&gt;
5648		* &lt;complexContent&gt;
5649		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
5650		* &lt;attribute name="label" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
5651		* &lt;attribute name="color" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5652		* &lt;/restriction&gt;
5653		* &lt;/complexContent&gt;
5654		* &lt;/complexType&gt;
5655		* &lt;/element&gt;
5656		* &lt;/sequence&gt;
5657		* &lt;/restriction&gt;
5658		* &lt;/complexContent&gt;
5659		* &lt;/complexType&gt;
5660		* </pre>
5661		*
5662		*
5663		*/
5664		@XmlAccessorType(XmlAccessType.FIELD)
5665		@XmlType(name = "", propOrder = {
5666		"colorEntry"
5667		})
		100% Uncovered Elements: 0 (6) Complexity: 2 Complexity Density: 0.67
5668		public static class TreeColorMap {
5669
5670		@XmlElement(name = "ColorEntry", namespace = "www.jalview.org")
5671		protected List<JalviewModel.Tree.TreeColorMap.ColorEntry> colorEntry;
5672
5673		/**
5674		* Gets the value of the colorEntry property.
5675		*
5676		* <p>This accessor method returns a reference to the live list,
5677		* not a snapshot. Therefore any modification you make to the
5678		* returned list will be present inside the JAXB object.
5679		* This is why there is not a <CODE>set</CODE> method for the colorEntry property.</p>
5680		*
5681		* <p>
5682		* For example, to add a new item, do as follows:
5683		* </p>
5684		* <pre>
5685		* getColorEntry().add(newItem);
5686		* </pre>
5687		*
5688		*
5689		* <p>
5690		* Objects of the following type(s) are allowed in the list
5691		* {@link JalviewModel.Tree.TreeColorMap.ColorEntry }
5692		* </p>
5693		*
5694		*
5695		* @return
5696		* The value of the colorEntry property.
5697		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
5698	10	public List<JalviewModel.Tree.TreeColorMap.ColorEntry> getColorEntry() {...
5699	10	if (colorEntry == null) {
5700	2	colorEntry = new ArrayList<JalviewModel.Tree.TreeColorMap.ColorEntry>();
5701		}
5702	10	return this.colorEntry;
5703		}
5704
5705
5706		/**
5707		* <p>Java class for anonymous complex type</p>.
5708		*
5709		* <p>The following schema fragment specifies the expected content contained within this class.</p>
5710		*
5711		* <pre>
5712		* &lt;complexType&gt;
5713		* &lt;complexContent&gt;
5714		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
5715		* &lt;attribute name="label" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
5716		* &lt;attribute name="color" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5717		* &lt;/restriction&gt;
5718		* &lt;/complexContent&gt;
5719		* &lt;/complexType&gt;
5720		* </pre>
5721		*
5722		*
5723		*/
5724		@XmlAccessorType(XmlAccessType.FIELD)
5725		@XmlType(name = "")
		100% Uncovered Elements: 0 (8) Complexity: 4 Complexity Density: 1
5726		public static class ColorEntry {
5727
5728		@XmlAttribute(name = "label", required = true)
5729		protected String label;
5730		@XmlAttribute(name = "color", required = true)
5731		protected int color;
5732
5733		/**
5734		* Gets the value of the label property.
5735		*
5736		* @return
5737		* possible object is
5738		* {@link String }
5739		*
5740		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5741	12	public String getLabel() {...
5742	12	return label;
5743		}
5744
5745		/**
5746		* Sets the value of the label property.
5747		*
5748		* @param value
5749		* allowed object is
5750		* {@link String }
5751		*
5752		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5753	7	public void setLabel(String value) {...
5754	7	this.label = value;
5755		}
5756
5757		/**
5758		* Gets the value of the color property.
5759		*
5760		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5761	12	public int getColor() {...
5762	12	return color;
5763		}
5764
5765		/**
5766		* Sets the value of the color property.
5767		*
5768		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5769	7	public void setColor(int value) {...
5770	7	this.color = value;
5771		}
5772
5773		}
5774
5775		}
5776
5777		}
5778
5779
5780		/**
5781		* <p>Java class for anonymous complex type</p>.
5782		*
5783		* <p>The following schema fragment specifies the expected content contained within this class.</p>
5784		*
5785		* <pre>
5786		* &lt;complexType&gt;
5787		* &lt;complexContent&gt;
5788		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
5789		* &lt;sequence&gt;
5790		* &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&gt;
5791		* &lt;/sequence&gt;
5792		* &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
5793		* &lt;/restriction&gt;
5794		* &lt;/complexContent&gt;
5795		* &lt;/complexType&gt;
5796		* </pre>
5797		*
5798		*
5799		*/
5800		@XmlAccessorType(XmlAccessType.FIELD)
5801		@XmlType(name = "", propOrder = {
5802		"userColourScheme"
5803		})
		0% Uncovered Elements: 8 (8) Complexity: 4 Complexity Density: 1
5804		public static class UserColours {
5805
5806		@XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
5807		protected JalviewUserColours userColourScheme;
5808		@XmlAttribute(name = "id")
5809		protected String id;
5810
5811		/**
5812		* Gets the value of the userColourScheme property.
5813		*
5814		* @return
5815		* possible object is
5816		* {@link JalviewUserColours }
5817		*
5818		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
5819	0	public JalviewUserColours getUserColourScheme() {...
5820	0	return userColourScheme;
5821		}
5822
5823		/**
5824		* Sets the value of the userColourScheme property.
5825		*
5826		* @param value
5827		* allowed object is
5828		* {@link JalviewUserColours }
5829		*
5830		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
5831	0	public void setUserColourScheme(JalviewUserColours value) {...
5832	0	this.userColourScheme = value;
5833		}
5834
5835		/**
5836		* Gets the value of the id property.
5837		*
5838		* @return
5839		* possible object is
5840		* {@link String }
5841		*
5842		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
5843	0	public String getId() {...
5844	0	return id;
5845		}
5846
5847		/**
5848		* Sets the value of the id property.
5849		*
5850		* @param value
5851		* allowed object is
5852		* {@link String }
5853		*
5854		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
5855	0	public void setId(String value) {...
5856	0	this.id = value;
5857		}
5858
5859		}
5860
5861
5862		/**
5863		* <p>Java class for anonymous complex type</p>.
5864		*
5865		* <p>The following schema fragment specifies the expected content contained within this class.</p>
5866		*
5867		* <pre>
5868		* &lt;complexType&gt;
5869		* &lt;complexContent&gt;
5870		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
5871		* &lt;sequence&gt;
5872		* &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
5873		* &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&gt;
5874		* &lt;complexType&gt;
5875		* &lt;complexContent&gt;
5876		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
5877		* &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5878		* &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5879		* &lt;/restriction&gt;
5880		* &lt;/complexContent&gt;
5881		* &lt;/complexType&gt;
5882		* &lt;/element&gt;
5883		* &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
5884		* &lt;complexType&gt;
5885		* &lt;complexContent&gt;
5886		* &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
5887		* &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
5888		* &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
5889		* &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5890		* &lt;/extension&gt;
5891		* &lt;/complexContent&gt;
5892		* &lt;/complexType&gt;
5893		* &lt;/element&gt;
5894		* &lt;element name="overview" minOccurs="0"&gt;
5895		* &lt;complexType&gt;
5896		* &lt;complexContent&gt;
5897		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
5898		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
5899		* &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5900		* &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5901		* &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5902		* &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5903		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
5904		* &lt;/restriction&gt;
5905		* &lt;/complexContent&gt;
5906		* &lt;/complexType&gt;
5907		* &lt;/element&gt;
5908		* &lt;element name="SecStrProvider" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt;
5909		* &lt;/sequence&gt;
5910		* &lt;attGroup ref="{www.jalview.org}conservationShading"/&gt;
5911		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
5912		* &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
5913		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
5914		* &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5915		* &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5916		* &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5917		* &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5918		* &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
5919		* &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5920		* &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5921		* &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5922		* &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5923		* &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5924		* &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5925		* &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
5926		* &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
5927		* &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5928		* &lt;attribute name="showStructureProviders" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
5929		* &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
5930		* &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
5931		* &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
5932		* &lt;attribute name="showGroupSecStrConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
5933		* &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5934		* &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5935		* &lt;attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5936		* &lt;attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5937		* &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
5938		* &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5939		* &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5940		* &lt;attribute name="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5941		* &lt;attribute name="idWidthManuallyAdjusted" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5942		* &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
5943		* &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
5944		* &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
5945		* &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5946		* &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5947		* &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5948		* &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5949		* &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
5950		* &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
5951		* &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
5952		* &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
5953		* &lt;/restriction&gt;
5954		* &lt;/complexContent&gt;
5955		* &lt;/complexType&gt;
5956		* </pre>
5957		*
5958		*
5959		*/
5960		@XmlAccessorType(XmlAccessType.FIELD)
5961		@XmlType(name = "", propOrder = {
5962		"annotationColours",
5963		"hiddenColumns",
5964		"calcIdParam",
5965		"overview",
5966		"secStrProvider"
5967		})
		89.7% Uncovered Elements: 32 (310) Complexity: 136 Complexity Density: 0.88
5968		public static class Viewport {
5969
5970		@XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
5971		protected AnnotationColourScheme annotationColours;
5972		@XmlElement(namespace = "www.jalview.org")
5973		protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
5974		@XmlElement(namespace = "www.jalview.org")
5975		protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
5976		@XmlElement(namespace = "www.jalview.org")
5977		protected JalviewModel.Viewport.Overview overview;
5978		@XmlElement(name = "SecStrProvider", namespace = "www.jalview.org")
5979		protected List<String> secStrProvider;
5980		@XmlAttribute(name = "bgColour")
5981		protected String bgColour;
5982		@XmlAttribute(name = "title")
5983		protected String title;
5984		@XmlAttribute(name = "showFullId")
5985		protected Boolean showFullId;
5986		@XmlAttribute(name = "rightAlignIds")
5987		protected Boolean rightAlignIds;
5988		@XmlAttribute(name = "showText")
5989		protected Boolean showText;
5990		@XmlAttribute(name = "showColourText")
5991		protected Boolean showColourText;
5992		@XmlAttribute(name = "showUnconserved")
5993		protected Boolean showUnconserved;
5994		@XmlAttribute(name = "showBoxes")
5995		protected Boolean showBoxes;
5996		@XmlAttribute(name = "wrapAlignment")
5997		protected Boolean wrapAlignment;
5998		@XmlAttribute(name = "renderGaps")
5999		protected Boolean renderGaps;
6000		@XmlAttribute(name = "showSequenceFeatures")
6001		protected Boolean showSequenceFeatures;
6002		@XmlAttribute(name = "showNPfeatureTooltip")
6003		protected Boolean showNPfeatureTooltip;
6004		@XmlAttribute(name = "showDbRefTooltip")
6005		protected Boolean showDbRefTooltip;
6006		@XmlAttribute(name = "followHighlight")
6007		protected Boolean followHighlight;
6008		@XmlAttribute(name = "followSelection")
6009		protected Boolean followSelection;
6010		@XmlAttribute(name = "showAnnotation")
6011		protected Boolean showAnnotation;
6012		@XmlAttribute(name = "showStructureProviders")
6013		protected Boolean showStructureProviders;
6014		@XmlAttribute(name = "centreColumnLabels")
6015		protected Boolean centreColumnLabels;
6016		/**
6017		* whether a new group has conservation displayed by default
6018		*
6019		*/
6020		@XmlAttribute(name = "showGroupConservation")
6021		protected Boolean showGroupConservation;
6022		/**
6023		* whether a new group has consensus displayed by default
6024		*
6025		*/
6026		@XmlAttribute(name = "showGroupConsensus")
6027		protected Boolean showGroupConsensus;
6028		/**
6029		* whether a new group has secondary structure consensus displayed by default
6030		*
6031		*/
6032		@XmlAttribute(name = "showGroupSecStrConsensus")
6033		protected Boolean showGroupSecStrConsensus;
6034		@XmlAttribute(name = "startRes")
6035		protected Integer startRes;
6036		@XmlAttribute(name = "startSeq")
6037		protected Integer startSeq;
6038		@XmlAttribute(name = "charWidth")
6039		protected Integer charWidth;
6040		@XmlAttribute(name = "charHeight")
6041		protected Integer charHeight;
6042		@XmlAttribute(name = "fontName")
6043		protected String fontName;
6044		@XmlAttribute(name = "fontSize")
6045		protected Integer fontSize;
6046		@XmlAttribute(name = "fontStyle")
6047		protected Integer fontStyle;
6048		@XmlAttribute(name = "idWidth")
6049		protected Integer idWidth;
6050		@XmlAttribute(name = "idWidthManuallyAdjusted")
6051		protected Boolean idWidthManuallyAdjusted;
6052		@XmlAttribute(name = "scaleProteinAsCdna")
6053		protected Boolean scaleProteinAsCdna;
6054		@XmlAttribute(name = "viewName")
6055		protected String viewName;
6056		@XmlAttribute(name = "sequenceSetId")
6057		protected String sequenceSetId;
6058		@XmlAttribute(name = "gatheredViews")
6059		protected Boolean gatheredViews;
6060		@XmlAttribute(name = "textCol1")
6061		protected Integer textCol1;
6062		@XmlAttribute(name = "textCol2")
6063		protected Integer textCol2;
6064		@XmlAttribute(name = "textColThreshold")
6065		protected Integer textColThreshold;
6066		/**
6067		* unique id used by jalview to
6068		* synchronize
6069		* between stored and
6070		* instantiated views
6071		*
6072		*/
6073		@XmlAttribute(name = "id")
6074		@XmlJavaTypeAdapter(CollapsedStringAdapter.class)
6075		@XmlID
6076		@XmlSchemaType(name = "ID")
6077		protected String id;
6078		/**
6079		* The viewport id of this viewport's
6080		* (cdna/protein) coding complement, if any
6081		*
6082		*/
6083		@XmlAttribute(name = "complementId")
6084		protected String complementId;
6085		@XmlAttribute(name = "showComplementFeatures")
6086		protected Boolean showComplementFeatures;
6087		@XmlAttribute(name = "showComplementFeaturesOnTop")
6088		protected Boolean showComplementFeaturesOnTop;
6089		@XmlAttribute(name = "conservationSelected")
6090		protected Boolean conservationSelected;
6091		/**
6092		* Conservation shading increment
6093		*
6094		*/
6095		@XmlAttribute(name = "consThreshold")
6096		protected Integer consThreshold;
6097		@XmlAttribute(name = "pidSelected")
6098		protected Boolean pidSelected;
6099		/**
6100		* Percent Identity Threshold
6101		*
6102		*/
6103		@XmlAttribute(name = "pidThreshold")
6104		protected Integer pidThreshold;
6105		/**
6106		* Secondary structure consensus shading - since 2.11.4
6107		*
6108		*/
6109		@XmlAttribute(name = "secstrSelected")
6110		protected Boolean secstrSelected;
6111		/**
6112		* Secondary structure consensus increment
6113		*
6114		*/
6115		@XmlAttribute(name = "secstrThreshold")
6116		protected Integer secstrThreshold;
6117		@XmlAttribute(name = "showConsensusHistogram")
6118		protected Boolean showConsensusHistogram;
6119		@XmlAttribute(name = "showSequenceLogo")
6120		protected Boolean showSequenceLogo;
6121		@XmlAttribute(name = "normaliseSequenceLogo")
6122		protected Boolean normaliseSequenceLogo;
6123		@XmlAttribute(name = "ignoreGapsinConsensus")
6124		protected Boolean ignoreGapsinConsensus;
6125		@XmlAttribute(name = "width")
6126		protected Integer width;
6127		@XmlAttribute(name = "height")
6128		protected Integer height;
6129		@XmlAttribute(name = "xpos")
6130		protected Integer xpos;
6131		@XmlAttribute(name = "ypos")
6132		protected Integer ypos;
6133
6134		/**
6135		* Gets the value of the annotationColours property.
6136		*
6137		* @return
6138		* possible object is
6139		* {@link AnnotationColourScheme }
6140		*
6141		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6142	2	public AnnotationColourScheme getAnnotationColours() {...
6143	2	return annotationColours;
6144		}
6145
6146		/**
6147		* Sets the value of the annotationColours property.
6148		*
6149		* @param value
6150		* allowed object is
6151		* {@link AnnotationColourScheme }
6152		*
6153		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6154	2	public void setAnnotationColours(AnnotationColourScheme value) {...
6155	2	this.annotationColours = value;
6156		}
6157
6158		/**
6159		* Gets the value of the hiddenColumns property.
6160		*
6161		* <p>This accessor method returns a reference to the live list,
6162		* not a snapshot. Therefore any modification you make to the
6163		* returned list will be present inside the JAXB object.
6164		* This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.</p>
6165		*
6166		* <p>
6167		* For example, to add a new item, do as follows:
6168		* </p>
6169		* <pre>
6170		* getHiddenColumns().add(newItem);
6171		* </pre>
6172		*
6173		*
6174		* <p>
6175		* Objects of the following type(s) are allowed in the list
6176		* {@link JalviewModel.Viewport.HiddenColumns }
6177		* </p>
6178		*
6179		*
6180		* @return
6181		* The value of the hiddenColumns property.
6182		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
6183	232	public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {...
6184	232	if (hiddenColumns == null) {
6185	78	hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
6186		}
6187	232	return this.hiddenColumns;
6188		}
6189
6190		/**
6191		* Gets the value of the calcIdParam property.
6192		*
6193		* <p>This accessor method returns a reference to the live list,
6194		* not a snapshot. Therefore any modification you make to the
6195		* returned list will be present inside the JAXB object.
6196		* This is why there is not a <CODE>set</CODE> method for the calcIdParam property.</p>
6197		*
6198		* <p>
6199		* For example, to add a new item, do as follows:
6200		* </p>
6201		* <pre>
6202		* getCalcIdParam().add(newItem);
6203		* </pre>
6204		*
6205		*
6206		* <p>
6207		* Objects of the following type(s) are allowed in the list
6208		* {@link JalviewModel.Viewport.CalcIdParam }
6209		* </p>
6210		*
6211		*
6212		* @return
6213		* The value of the calcIdParam property.
6214		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
6215	192	public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {...
6216	192	if (calcIdParam == null) {
6217	96	calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
6218		}
6219	192	return this.calcIdParam;
6220		}
6221
6222		/**
6223		* Gets the value of the overview property.
6224		*
6225		* @return
6226		* possible object is
6227		* {@link JalviewModel.Viewport.Overview }
6228		*
6229		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6230	86	public JalviewModel.Viewport.Overview getOverview() {...
6231	86	return overview;
6232		}
6233
6234		/**
6235		* Sets the value of the overview property.
6236		*
6237		* @param value
6238		* allowed object is
6239		* {@link JalviewModel.Viewport.Overview }
6240		*
6241		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6242	14	public void setOverview(JalviewModel.Viewport.Overview value) {...
6243	14	this.overview = value;
6244		}
6245
6246		/**
6247		* Gets the value of the secStrProvider property.
6248		*
6249		* <p>This accessor method returns a reference to the live list,
6250		* not a snapshot. Therefore any modification you make to the
6251		* returned list will be present inside the JAXB object.
6252		* This is why there is not a <CODE>set</CODE> method for the secStrProvider property.</p>
6253		*
6254		* <p>
6255		* For example, to add a new item, do as follows:
6256		* </p>
6257		* <pre>
6258		* getSecStrProvider().add(newItem);
6259		* </pre>
6260		*
6261		*
6262		* <p>
6263		* Objects of the following type(s) are allowed in the list
6264		* {@link String }
6265		* </p>
6266		*
6267		*
6268		* @return
6269		* The value of the secStrProvider property.
6270		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
6271	0	public List<String> getSecStrProvider() {...
6272	0	if (secStrProvider == null) {
6273	0	secStrProvider = new ArrayList<String>();
6274		}
6275	0	return this.secStrProvider;
6276		}
6277
6278		/**
6279		* Gets the value of the bgColour property.
6280		*
6281		* @return
6282		* possible object is
6283		* {@link String }
6284		*
6285		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6286	382	public String getBgColour() {...
6287	382	return bgColour;
6288		}
6289
6290		/**
6291		* Sets the value of the bgColour property.
6292		*
6293		* @param value
6294		* allowed object is
6295		* {@link String }
6296		*
6297		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6298	50	public void setBgColour(String value) {...
6299	50	this.bgColour = value;
6300		}
6301
6302		/**
6303		* Gets the value of the title property.
6304		*
6305		* @return
6306		* possible object is
6307		* {@link String }
6308		*
6309		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6310	192	public String getTitle() {...
6311	192	return title;
6312		}
6313
6314		/**
6315		* Sets the value of the title property.
6316		*
6317		* @param value
6318		* allowed object is
6319		* {@link String }
6320		*
6321		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6322	50	public void setTitle(String value) {...
6323	50	this.title = value;
6324		}
6325
6326		/**
6327		* Gets the value of the showFullId property.
6328		*
6329		* @return
6330		* possible object is
6331		* {@link Boolean }
6332		*
6333		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6334	96	public Boolean isShowFullId() {...
6335	96	return showFullId;
6336		}
6337
6338		/**
6339		* Sets the value of the showFullId property.
6340		*
6341		* @param value
6342		* allowed object is
6343		* {@link Boolean }
6344		*
6345		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6346	50	public void setShowFullId(Boolean value) {...
6347	50	this.showFullId = value;
6348		}
6349
6350		/**
6351		* Gets the value of the rightAlignIds property.
6352		*
6353		* @return
6354		* possible object is
6355		* {@link Boolean }
6356		*
6357		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6358	96	public Boolean isRightAlignIds() {...
6359	96	return rightAlignIds;
6360		}
6361
6362		/**
6363		* Sets the value of the rightAlignIds property.
6364		*
6365		* @param value
6366		* allowed object is
6367		* {@link Boolean }
6368		*
6369		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6370	50	public void setRightAlignIds(Boolean value) {...
6371	50	this.rightAlignIds = value;
6372		}
6373
6374		/**
6375		* Gets the value of the showText property.
6376		*
6377		* @return
6378		* possible object is
6379		* {@link Boolean }
6380		*
6381		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6382	96	public Boolean isShowText() {...
6383	96	return showText;
6384		}
6385
6386		/**
6387		* Sets the value of the showText property.
6388		*
6389		* @param value
6390		* allowed object is
6391		* {@link Boolean }
6392		*
6393		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6394	50	public void setShowText(Boolean value) {...
6395	50	this.showText = value;
6396		}
6397
6398		/**
6399		* Gets the value of the showColourText property.
6400		*
6401		* @return
6402		* possible object is
6403		* {@link Boolean }
6404		*
6405		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6406	96	public Boolean isShowColourText() {...
6407	96	return showColourText;
6408		}
6409
6410		/**
6411		* Sets the value of the showColourText property.
6412		*
6413		* @param value
6414		* allowed object is
6415		* {@link Boolean }
6416		*
6417		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6418	50	public void setShowColourText(Boolean value) {...
6419	50	this.showColourText = value;
6420		}
6421
6422		/**
6423		* Gets the value of the showUnconserved property.
6424		*
6425		* @return
6426		* possible object is
6427		* {@link Boolean }
6428		*
6429		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
6430	96	public boolean isShowUnconserved() {...
6431	96	if (showUnconserved == null) {
6432	0	return false;
6433		} else {
6434	96	return showUnconserved;
6435		}
6436		}
6437
6438		/**
6439		* Sets the value of the showUnconserved property.
6440		*
6441		* @param value
6442		* allowed object is
6443		* {@link Boolean }
6444		*
6445		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6446	50	public void setShowUnconserved(Boolean value) {...
6447	50	this.showUnconserved = value;
6448		}
6449
6450		/**
6451		* Gets the value of the showBoxes property.
6452		*
6453		* @return
6454		* possible object is
6455		* {@link Boolean }
6456		*
6457		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6458	96	public Boolean isShowBoxes() {...
6459	96	return showBoxes;
6460		}
6461
6462		/**
6463		* Sets the value of the showBoxes property.
6464		*
6465		* @param value
6466		* allowed object is
6467		* {@link Boolean }
6468		*
6469		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6470	50	public void setShowBoxes(Boolean value) {...
6471	50	this.showBoxes = value;
6472		}
6473
6474		/**
6475		* Gets the value of the wrapAlignment property.
6476		*
6477		* @return
6478		* possible object is
6479		* {@link Boolean }
6480		*
6481		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6482	96	public Boolean isWrapAlignment() {...
6483	96	return wrapAlignment;
6484		}
6485
6486		/**
6487		* Sets the value of the wrapAlignment property.
6488		*
6489		* @param value
6490		* allowed object is
6491		* {@link Boolean }
6492		*
6493		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6494	50	public void setWrapAlignment(Boolean value) {...
6495	50	this.wrapAlignment = value;
6496		}
6497
6498		/**
6499		* Gets the value of the renderGaps property.
6500		*
6501		* @return
6502		* possible object is
6503		* {@link Boolean }
6504		*
6505		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6506	96	public Boolean isRenderGaps() {...
6507	96	return renderGaps;
6508		}
6509
6510		/**
6511		* Sets the value of the renderGaps property.
6512		*
6513		* @param value
6514		* allowed object is
6515		* {@link Boolean }
6516		*
6517		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6518	50	public void setRenderGaps(Boolean value) {...
6519	50	this.renderGaps = value;
6520		}
6521
6522		/**
6523		* Gets the value of the showSequenceFeatures property.
6524		*
6525		* @return
6526		* possible object is
6527		* {@link Boolean }
6528		*
6529		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6530	96	public Boolean isShowSequenceFeatures() {...
6531	96	return showSequenceFeatures;
6532		}
6533
6534		/**
6535		* Sets the value of the showSequenceFeatures property.
6536		*
6537		* @param value
6538		* allowed object is
6539		* {@link Boolean }
6540		*
6541		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6542	50	public void setShowSequenceFeatures(Boolean value) {...
6543	50	this.showSequenceFeatures = value;
6544		}
6545
6546		/**
6547		* Gets the value of the showNPfeatureTooltip property.
6548		*
6549		* @return
6550		* possible object is
6551		* {@link Boolean }
6552		*
6553		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6554	96	public Boolean isShowNPfeatureTooltip() {...
6555	96	return showNPfeatureTooltip;
6556		}
6557
6558		/**
6559		* Sets the value of the showNPfeatureTooltip property.
6560		*
6561		* @param value
6562		* allowed object is
6563		* {@link Boolean }
6564		*
6565		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6566	50	public void setShowNPfeatureTooltip(Boolean value) {...
6567	50	this.showNPfeatureTooltip = value;
6568		}
6569
6570		/**
6571		* Gets the value of the showDbRefTooltip property.
6572		*
6573		* @return
6574		* possible object is
6575		* {@link Boolean }
6576		*
6577		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6578	96	public Boolean isShowDbRefTooltip() {...
6579	96	return showDbRefTooltip;
6580		}
6581
6582		/**
6583		* Sets the value of the showDbRefTooltip property.
6584		*
6585		* @param value
6586		* allowed object is
6587		* {@link Boolean }
6588		*
6589		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6590	50	public void setShowDbRefTooltip(Boolean value) {...
6591	50	this.showDbRefTooltip = value;
6592		}
6593
6594		/**
6595		* Gets the value of the followHighlight property.
6596		*
6597		* @return
6598		* possible object is
6599		* {@link Boolean }
6600		*
6601		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
6602	96	public boolean isFollowHighlight() {...
6603	96	if (followHighlight == null) {
6604	0	return true;
6605		} else {
6606	96	return followHighlight;
6607		}
6608		}
6609
6610		/**
6611		* Sets the value of the followHighlight property.
6612		*
6613		* @param value
6614		* allowed object is
6615		* {@link Boolean }
6616		*
6617		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6618	50	public void setFollowHighlight(Boolean value) {...
6619	50	this.followHighlight = value;
6620		}
6621
6622		/**
6623		* Gets the value of the followSelection property.
6624		*
6625		* @return
6626		* possible object is
6627		* {@link Boolean }
6628		*
6629		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
6630	96	public boolean isFollowSelection() {...
6631	96	if (followSelection == null) {
6632	0	return true;
6633		} else {
6634	96	return followSelection;
6635		}
6636		}
6637
6638		/**
6639		* Sets the value of the followSelection property.
6640		*
6641		* @param value
6642		* allowed object is
6643		* {@link Boolean }
6644		*
6645		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6646	50	public void setFollowSelection(Boolean value) {...
6647	50	this.followSelection = value;
6648		}
6649
6650		/**
6651		* Gets the value of the showAnnotation property.
6652		*
6653		* @return
6654		* possible object is
6655		* {@link Boolean }
6656		*
6657		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6658	192	public Boolean isShowAnnotation() {...
6659	192	return showAnnotation;
6660		}
6661
6662		/**
6663		* Sets the value of the showAnnotation property.
6664		*
6665		* @param value
6666		* allowed object is
6667		* {@link Boolean }
6668		*
6669		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6670	50	public void setShowAnnotation(Boolean value) {...
6671	50	this.showAnnotation = value;
6672		}
6673
6674		/**
6675		* Gets the value of the showStructureProviders property.
6676		*
6677		* @return
6678		* possible object is
6679		* {@link Boolean }
6680		*
6681		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
6682	96	public boolean isShowStructureProviders() {...
6683	96	if (showStructureProviders == null) {
6684	43	return false;
6685		} else {
6686	53	return showStructureProviders;
6687		}
6688		}
6689
6690		/**
6691		* Sets the value of the showStructureProviders property.
6692		*
6693		* @param value
6694		* allowed object is
6695		* {@link Boolean }
6696		*
6697		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6698	50	public void setShowStructureProviders(Boolean value) {...
6699	50	this.showStructureProviders = value;
6700		}
6701
6702		/**
6703		* Gets the value of the centreColumnLabels property.
6704		*
6705		* @return
6706		* possible object is
6707		* {@link Boolean }
6708		*
6709		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
6710	96	public boolean isCentreColumnLabels() {...
6711	96	if (centreColumnLabels == null) {
6712	96	return false;
6713		} else {
6714	0	return centreColumnLabels;
6715		}
6716		}
6717
6718		/**
6719		* Sets the value of the centreColumnLabels property.
6720		*
6721		* @param value
6722		* allowed object is
6723		* {@link Boolean }
6724		*
6725		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
6726	0	public void setCentreColumnLabels(Boolean value) {...
6727	0	this.centreColumnLabels = value;
6728		}
6729
6730		/**
6731		* whether a new group has conservation displayed by default
6732		*
6733		* @return
6734		* possible object is
6735		* {@link Boolean }
6736		*
6737		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
6738	96	public boolean isShowGroupConservation() {...
6739	96	if (showGroupConservation == null) {
6740	0	return false;
6741		} else {
6742	96	return showGroupConservation;
6743		}
6744		}
6745
6746		/**
6747		* Sets the value of the showGroupConservation property.
6748		*
6749		* @param value
6750		* allowed object is
6751		* {@link Boolean }
6752		*
6753		* @see #isShowGroupConservation()
6754		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6755	50	public void setShowGroupConservation(Boolean value) {...
6756	50	this.showGroupConservation = value;
6757		}
6758
6759		/**
6760		* whether a new group has consensus displayed by default
6761		*
6762		* @return
6763		* possible object is
6764		* {@link Boolean }
6765		*
6766		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
6767	96	public boolean isShowGroupConsensus() {...
6768	96	if (showGroupConsensus == null) {
6769	0	return false;
6770		} else {
6771	96	return showGroupConsensus;
6772		}
6773		}
6774
6775		/**
6776		* Sets the value of the showGroupConsensus property.
6777		*
6778		* @param value
6779		* allowed object is
6780		* {@link Boolean }
6781		*
6782		* @see #isShowGroupConsensus()
6783		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6784	50	public void setShowGroupConsensus(Boolean value) {...
6785	50	this.showGroupConsensus = value;
6786		}
6787
6788		/**
6789		* whether a new group has secondary structure consensus displayed by default
6790		*
6791		* @return
6792		* possible object is
6793		* {@link Boolean }
6794		*
6795		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
6796	96	public boolean isShowGroupSecStrConsensus() {...
6797	96	if (showGroupSecStrConsensus == null) {
6798	43	return false;
6799		} else {
6800	53	return showGroupSecStrConsensus;
6801		}
6802		}
6803
6804		/**
6805		* Sets the value of the showGroupSecStrConsensus property.
6806		*
6807		* @param value
6808		* allowed object is
6809		* {@link Boolean }
6810		*
6811		* @see #isShowGroupSecStrConsensus()
6812		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6813	50	public void setShowGroupSecStrConsensus(Boolean value) {...
6814	50	this.showGroupSecStrConsensus = value;
6815		}
6816
6817		/**
6818		* Gets the value of the startRes property.
6819		*
6820		* @return
6821		* possible object is
6822		* {@link Integer }
6823		*
6824		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6825	96	public Integer getStartRes() {...
6826	96	return startRes;
6827		}
6828
6829		/**
6830		* Sets the value of the startRes property.
6831		*
6832		* @param value
6833		* allowed object is
6834		* {@link Integer }
6835		*
6836		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6837	50	public void setStartRes(Integer value) {...
6838	50	this.startRes = value;
6839		}
6840
6841		/**
6842		* Gets the value of the startSeq property.
6843		*
6844		* @return
6845		* possible object is
6846		* {@link Integer }
6847		*
6848		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
6849	0	public Integer getStartSeq() {...
6850	0	return startSeq;
6851		}
6852
6853		/**
6854		* Sets the value of the startSeq property.
6855		*
6856		* @param value
6857		* allowed object is
6858		* {@link Integer }
6859		*
6860		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6861	50	public void setStartSeq(Integer value) {...
6862	50	this.startSeq = value;
6863		}
6864
6865		/**
6866		* Gets the value of the charWidth property.
6867		*
6868		* @return
6869		* possible object is
6870		* {@link Integer }
6871		*
6872		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6873	245	public Integer getCharWidth() {...
6874	245	return charWidth;
6875		}
6876
6877		/**
6878		* Sets the value of the charWidth property.
6879		*
6880		* @param value
6881		* allowed object is
6882		* {@link Integer }
6883		*
6884		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6885	50	public void setCharWidth(Integer value) {...
6886	50	this.charWidth = value;
6887		}
6888
6889		/**
6890		* Gets the value of the charHeight property.
6891		*
6892		* @return
6893		* possible object is
6894		* {@link Integer }
6895		*
6896		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6897	53	public Integer getCharHeight() {...
6898	53	return charHeight;
6899		}
6900
6901		/**
6902		* Sets the value of the charHeight property.
6903		*
6904		* @param value
6905		* allowed object is
6906		* {@link Integer }
6907		*
6908		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6909	50	public void setCharHeight(Integer value) {...
6910	50	this.charHeight = value;
6911		}
6912
6913		/**
6914		* Gets the value of the fontName property.
6915		*
6916		* @return
6917		* possible object is
6918		* {@link String }
6919		*
6920		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6921	96	public String getFontName() {...
6922	96	return fontName;
6923		}
6924
6925		/**
6926		* Sets the value of the fontName property.
6927		*
6928		* @param value
6929		* allowed object is
6930		* {@link String }
6931		*
6932		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6933	50	public void setFontName(String value) {...
6934	50	this.fontName = value;
6935		}
6936
6937		/**
6938		* Gets the value of the fontSize property.
6939		*
6940		* @return
6941		* possible object is
6942		* {@link Integer }
6943		*
6944		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6945	96	public Integer getFontSize() {...
6946	96	return fontSize;
6947		}
6948
6949		/**
6950		* Sets the value of the fontSize property.
6951		*
6952		* @param value
6953		* allowed object is
6954		* {@link Integer }
6955		*
6956		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6957	50	public void setFontSize(Integer value) {...
6958	50	this.fontSize = value;
6959		}
6960
6961		/**
6962		* Gets the value of the fontStyle property.
6963		*
6964		* @return
6965		* possible object is
6966		* {@link Integer }
6967		*
6968		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6969	96	public Integer getFontStyle() {...
6970	96	return fontStyle;
6971		}
6972
6973		/**
6974		* Sets the value of the fontStyle property.
6975		*
6976		* @param value
6977		* allowed object is
6978		* {@link Integer }
6979		*
6980		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6981	50	public void setFontStyle(Integer value) {...
6982	50	this.fontStyle = value;
6983		}
6984
6985		/**
6986		* Gets the value of the idWidth property.
6987		*
6988		* @return
6989		* possible object is
6990		* {@link Integer }
6991		*
6992		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6993	149	public Integer getIdWidth() {...
6994	149	return idWidth;
6995		}
6996
6997		/**
6998		* Sets the value of the idWidth property.
6999		*
7000		* @param value
7001		* allowed object is
7002		* {@link Integer }
7003		*
7004		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7005	50	public void setIdWidth(Integer value) {...
7006	50	this.idWidth = value;
7007		}
7008
7009		/**
7010		* Gets the value of the idWidthManuallyAdjusted property.
7011		*
7012		* @return
7013		* possible object is
7014		* {@link Boolean }
7015		*
7016		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7017	53	public Boolean isIdWidthManuallyAdjusted() {...
7018	53	return idWidthManuallyAdjusted;
7019		}
7020
7021		/**
7022		* Sets the value of the idWidthManuallyAdjusted property.
7023		*
7024		* @param value
7025		* allowed object is
7026		* {@link Boolean }
7027		*
7028		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7029	50	public void setIdWidthManuallyAdjusted(Boolean value) {...
7030	50	this.idWidthManuallyAdjusted = value;
7031		}
7032
7033		/**
7034		* Gets the value of the scaleProteinAsCdna property.
7035		*
7036		* @return
7037		* possible object is
7038		* {@link Boolean }
7039		*
7040		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
7041	96	public boolean isScaleProteinAsCdna() {...
7042	96	if (scaleProteinAsCdna == null) {
7043	30	return true;
7044		} else {
7045	66	return scaleProteinAsCdna;
7046		}
7047		}
7048
7049		/**
7050		* Sets the value of the scaleProteinAsCdna property.
7051		*
7052		* @param value
7053		* allowed object is
7054		* {@link Boolean }
7055		*
7056		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7057	50	public void setScaleProteinAsCdna(Boolean value) {...
7058	50	this.scaleProteinAsCdna = value;
7059		}
7060
7061		/**
7062		* Gets the value of the viewName property.
7063		*
7064		* @return
7065		* possible object is
7066		* {@link String }
7067		*
7068		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7069	155	public String getViewName() {...
7070	155	return viewName;
7071		}
7072
7073		/**
7074		* Sets the value of the viewName property.
7075		*
7076		* @param value
7077		* allowed object is
7078		* {@link String }
7079		*
7080		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7081	50	public void setViewName(String value) {...
7082	50	this.viewName = value;
7083		}
7084
7085		/**
7086		* Gets the value of the sequenceSetId property.
7087		*
7088		* @return
7089		* possible object is
7090		* {@link String }
7091		*
7092		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7093	192	public String getSequenceSetId() {...
7094	192	return sequenceSetId;
7095		}
7096
7097		/**
7098		* Sets the value of the sequenceSetId property.
7099		*
7100		* @param value
7101		* allowed object is
7102		* {@link String }
7103		*
7104		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7105	50	public void setSequenceSetId(String value) {...
7106	50	this.sequenceSetId = value;
7107		}
7108
7109		/**
7110		* Gets the value of the gatheredViews property.
7111		*
7112		* @return
7113		* possible object is
7114		* {@link Boolean }
7115		*
7116		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7117	96	public Boolean isGatheredViews() {...
7118	96	return gatheredViews;
7119		}
7120
7121		/**
7122		* Sets the value of the gatheredViews property.
7123		*
7124		* @param value
7125		* allowed object is
7126		* {@link Boolean }
7127		*
7128		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7129	50	public void setGatheredViews(Boolean value) {...
7130	50	this.gatheredViews = value;
7131		}
7132
7133		/**
7134		* Gets the value of the textCol1 property.
7135		*
7136		* @return
7137		* possible object is
7138		* {@link Integer }
7139		*
7140		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7141	96	public Integer getTextCol1() {...
7142	96	return textCol1;
7143		}
7144
7145		/**
7146		* Sets the value of the textCol1 property.
7147		*
7148		* @param value
7149		* allowed object is
7150		* {@link Integer }
7151		*
7152		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7153	50	public void setTextCol1(Integer value) {...
7154	50	this.textCol1 = value;
7155		}
7156
7157		/**
7158		* Gets the value of the textCol2 property.
7159		*
7160		* @return
7161		* possible object is
7162		* {@link Integer }
7163		*
7164		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7165	96	public Integer getTextCol2() {...
7166	96	return textCol2;
7167		}
7168
7169		/**
7170		* Sets the value of the textCol2 property.
7171		*
7172		* @param value
7173		* allowed object is
7174		* {@link Integer }
7175		*
7176		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7177	50	public void setTextCol2(Integer value) {...
7178	50	this.textCol2 = value;
7179		}
7180
7181		/**
7182		* Gets the value of the textColThreshold property.
7183		*
7184		* @return
7185		* possible object is
7186		* {@link Integer }
7187		*
7188		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7189	96	public Integer getTextColThreshold() {...
7190	96	return textColThreshold;
7191		}
7192
7193		/**
7194		* Sets the value of the textColThreshold property.
7195		*
7196		* @param value
7197		* allowed object is
7198		* {@link Integer }
7199		*
7200		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7201	50	public void setTextColThreshold(Integer value) {...
7202	50	this.textColThreshold = value;
7203		}
7204
7205		/**
7206		* unique id used by jalview to
7207		* synchronize
7208		* between stored and
7209		* instantiated views
7210		*
7211		* @return
7212		* possible object is
7213		* {@link String }
7214		*
7215		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7216	182	public String getId() {...
7217	182	return id;
7218		}
7219
7220		/**
7221		* Sets the value of the id property.
7222		*
7223		* @param value
7224		* allowed object is
7225		* {@link String }
7226		*
7227		* @see #getId()
7228		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7229	60	public void setId(String value) {...
7230	60	this.id = value;
7231		}
7232
7233		/**
7234		* The viewport id of this viewport's
7235		* (cdna/protein) coding complement, if any
7236		*
7237		* @return
7238		* possible object is
7239		* {@link String }
7240		*
7241		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7242	96	public String getComplementId() {...
7243	96	return complementId;
7244		}
7245
7246		/**
7247		* Sets the value of the complementId property.
7248		*
7249		* @param value
7250		* allowed object is
7251		* {@link String }
7252		*
7253		* @see #getComplementId()
7254		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
7255	0	public void setComplementId(String value) {...
7256	0	this.complementId = value;
7257		}
7258
7259		/**
7260		* Gets the value of the showComplementFeatures property.
7261		*
7262		* @return
7263		* possible object is
7264		* {@link Boolean }
7265		*
7266		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
7267	96	public boolean isShowComplementFeatures() {...
7268	96	if (showComplementFeatures == null) {
7269	43	return false;
7270		} else {
7271	53	return showComplementFeatures;
7272		}
7273		}
7274
7275		/**
7276		* Sets the value of the showComplementFeatures property.
7277		*
7278		* @param value
7279		* allowed object is
7280		* {@link Boolean }
7281		*
7282		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7283	50	public void setShowComplementFeatures(Boolean value) {...
7284	50	this.showComplementFeatures = value;
7285		}
7286
7287		/**
7288		* Gets the value of the showComplementFeaturesOnTop property.
7289		*
7290		* @return
7291		* possible object is
7292		* {@link Boolean }
7293		*
7294		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
7295	96	public boolean isShowComplementFeaturesOnTop() {...
7296	96	if (showComplementFeaturesOnTop == null) {
7297	43	return false;
7298		} else {
7299	53	return showComplementFeaturesOnTop;
7300		}
7301		}
7302
7303		/**
7304		* Sets the value of the showComplementFeaturesOnTop property.
7305		*
7306		* @param value
7307		* allowed object is
7308		* {@link Boolean }
7309		*
7310		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7311	50	public void setShowComplementFeaturesOnTop(Boolean value) {...
7312	50	this.showComplementFeaturesOnTop = value;
7313		}
7314
7315		/**
7316		* Gets the value of the conservationSelected property.
7317		*
7318		* @return
7319		* possible object is
7320		* {@link Boolean }
7321		*
7322		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7323	192	public Boolean isConservationSelected() {...
7324	192	return conservationSelected;
7325		}
7326
7327		/**
7328		* Sets the value of the conservationSelected property.
7329		*
7330		* @param value
7331		* allowed object is
7332		* {@link Boolean }
7333		*
7334		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7335	50	public void setConservationSelected(Boolean value) {...
7336	50	this.conservationSelected = value;
7337		}
7338
7339		/**
7340		* Conservation shading increment
7341		*
7342		* @return
7343		* possible object is
7344		* {@link Integer }
7345		*
7346		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7347	98	public Integer getConsThreshold() {...
7348	98	return consThreshold;
7349		}
7350
7351		/**
7352		* Sets the value of the consThreshold property.
7353		*
7354		* @param value
7355		* allowed object is
7356		* {@link Integer }
7357		*
7358		* @see #getConsThreshold()
7359		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7360	2	public void setConsThreshold(Integer value) {...
7361	2	this.consThreshold = value;
7362		}
7363
7364		/**
7365		* Gets the value of the pidSelected property.
7366		*
7367		* @return
7368		* possible object is
7369		* {@link Boolean }
7370		*
7371		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7372	96	public Boolean isPidSelected() {...
7373	96	return pidSelected;
7374		}
7375
7376		/**
7377		* Sets the value of the pidSelected property.
7378		*
7379		* @param value
7380		* allowed object is
7381		* {@link Boolean }
7382		*
7383		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7384	50	public void setPidSelected(Boolean value) {...
7385	50	this.pidSelected = value;
7386		}
7387
7388		/**
7389		* Percent Identity Threshold
7390		*
7391		* @return
7392		* possible object is
7393		* {@link Integer }
7394		*
7395		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7396	96	public Integer getPidThreshold() {...
7397	96	return pidThreshold;
7398		}
7399
7400		/**
7401		* Sets the value of the pidThreshold property.
7402		*
7403		* @param value
7404		* allowed object is
7405		* {@link Integer }
7406		*
7407		* @see #getPidThreshold()
7408		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7409	9	public void setPidThreshold(Integer value) {...
7410	9	this.pidThreshold = value;
7411		}
7412
7413		/**
7414		* Secondary structure consensus shading - since 2.11.4
7415		*
7416		* @return
7417		* possible object is
7418		* {@link Boolean }
7419		*
7420		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
7421	192	public boolean isSecstrSelected() {...
7422	192	if (secstrSelected == null) {
7423	86	return false;
7424		} else {
7425	106	return secstrSelected;
7426		}
7427		}
7428
7429		/**
7430		* Sets the value of the secstrSelected property.
7431		*
7432		* @param value
7433		* allowed object is
7434		* {@link Boolean }
7435		*
7436		* @see #isSecstrSelected()
7437		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7438	50	public void setSecstrSelected(Boolean value) {...
7439	50	this.secstrSelected = value;
7440		}
7441
7442		/**
7443		* Secondary structure consensus increment
7444		*
7445		* @return
7446		* possible object is
7447		* {@link Integer }
7448		*
7449		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7450	98	public Integer getSecstrThreshold() {...
7451	98	return secstrThreshold;
7452		}
7453
7454		/**
7455		* Sets the value of the secstrThreshold property.
7456		*
7457		* @param value
7458		* allowed object is
7459		* {@link Integer }
7460		*
7461		* @see #getSecstrThreshold()
7462		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
7463	0	public void setSecstrThreshold(Integer value) {...
7464	0	this.secstrThreshold = value;
7465		}
7466
7467		/**
7468		* Gets the value of the showConsensusHistogram property.
7469		*
7470		* @return
7471		* possible object is
7472		* {@link Boolean }
7473		*
7474		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
7475	96	public boolean isShowConsensusHistogram() {...
7476	96	if (showConsensusHistogram == null) {
7477	0	return true;
7478		} else {
7479	96	return showConsensusHistogram;
7480		}
7481		}
7482
7483		/**
7484		* Sets the value of the showConsensusHistogram property.
7485		*
7486		* @param value
7487		* allowed object is
7488		* {@link Boolean }
7489		*
7490		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7491	50	public void setShowConsensusHistogram(Boolean value) {...
7492	50	this.showConsensusHistogram = value;
7493		}
7494
7495		/**
7496		* Gets the value of the showSequenceLogo property.
7497		*
7498		* @return
7499		* possible object is
7500		* {@link Boolean }
7501		*
7502		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
7503	96	public boolean isShowSequenceLogo() {...
7504	96	if (showSequenceLogo == null) {
7505	0	return false;
7506		} else {
7507	96	return showSequenceLogo;
7508		}
7509		}
7510
7511		/**
7512		* Sets the value of the showSequenceLogo property.
7513		*
7514		* @param value
7515		* allowed object is
7516		* {@link Boolean }
7517		*
7518		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7519	50	public void setShowSequenceLogo(Boolean value) {...
7520	50	this.showSequenceLogo = value;
7521		}
7522
7523		/**
7524		* Gets the value of the normaliseSequenceLogo property.
7525		*
7526		* @return
7527		* possible object is
7528		* {@link Boolean }
7529		*
7530		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
7531	96	public boolean isNormaliseSequenceLogo() {...
7532	96	if (normaliseSequenceLogo == null) {
7533	30	return false;
7534		} else {
7535	66	return normaliseSequenceLogo;
7536		}
7537		}
7538
7539		/**
7540		* Sets the value of the normaliseSequenceLogo property.
7541		*
7542		* @param value
7543		* allowed object is
7544		* {@link Boolean }
7545		*
7546		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7547	50	public void setNormaliseSequenceLogo(Boolean value) {...
7548	50	this.normaliseSequenceLogo = value;
7549		}
7550
7551		/**
7552		* Gets the value of the ignoreGapsinConsensus property.
7553		*
7554		* @return
7555		* possible object is
7556		* {@link Boolean }
7557		*
7558		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
7559	192	public boolean isIgnoreGapsinConsensus() {...
7560	192	if (ignoreGapsinConsensus == null) {
7561	0	return true;
7562		} else {
7563	192	return ignoreGapsinConsensus;
7564		}
7565		}
7566
7567		/**
7568		* Sets the value of the ignoreGapsinConsensus property.
7569		*
7570		* @param value
7571		* allowed object is
7572		* {@link Boolean }
7573		*
7574		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7575	50	public void setIgnoreGapsinConsensus(Boolean value) {...
7576	50	this.ignoreGapsinConsensus = value;
7577		}
7578
7579		/**
7580		* Gets the value of the width property.
7581		*
7582		* @return
7583		* possible object is
7584		* {@link Integer }
7585		*
7586		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7587	288	public Integer getWidth() {...
7588	288	return width;
7589		}
7590
7591		/**
7592		* Sets the value of the width property.
7593		*
7594		* @param value
7595		* allowed object is
7596		* {@link Integer }
7597		*
7598		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7599	50	public void setWidth(Integer value) {...
7600	50	this.width = value;
7601		}
7602
7603		/**
7604		* Gets the value of the height property.
7605		*
7606		* @return
7607		* possible object is
7608		* {@link Integer }
7609		*
7610		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7611	288	public Integer getHeight() {...
7612	288	return height;
7613		}
7614
7615		/**
7616		* Sets the value of the height property.
7617		*
7618		* @param value
7619		* allowed object is
7620		* {@link Integer }
7621		*
7622		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7623	50	public void setHeight(Integer value) {...
7624	50	this.height = value;
7625		}
7626
7627		/**
7628		* Gets the value of the xpos property.
7629		*
7630		* @return
7631		* possible object is
7632		* {@link Integer }
7633		*
7634		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7635	96	public Integer getXpos() {...
7636	96	return xpos;
7637		}
7638
7639		/**
7640		* Sets the value of the xpos property.
7641		*
7642		* @param value
7643		* allowed object is
7644		* {@link Integer }
7645		*
7646		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7647	50	public void setXpos(Integer value) {...
7648	50	this.xpos = value;
7649		}
7650
7651		/**
7652		* Gets the value of the ypos property.
7653		*
7654		* @return
7655		* possible object is
7656		* {@link Integer }
7657		*
7658		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7659	96	public Integer getYpos() {...
7660	96	return ypos;
7661		}
7662
7663		/**
7664		* Sets the value of the ypos property.
7665		*
7666		* @param value
7667		* allowed object is
7668		* {@link Integer }
7669		*
7670		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7671	50	public void setYpos(Integer value) {...
7672	50	this.ypos = value;
7673		}
7674
7675
7676		/**
7677		* <p>Java class for anonymous complex type</p>.
7678		*
7679		* <p>The following schema fragment specifies the expected content contained within this class.</p>
7680		*
7681		* <pre>
7682		* &lt;complexType&gt;
7683		* &lt;complexContent&gt;
7684		* &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
7685		* &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
7686		* &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
7687		* &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
7688		* &lt;/extension&gt;
7689		* &lt;/complexContent&gt;
7690		* &lt;/complexType&gt;
7691		* </pre>
7692		*
7693		*
7694		*/
7695		@XmlAccessorType(XmlAccessType.FIELD)
7696		@XmlType(name = "")
		0% Uncovered Elements: 16 (16) Complexity: 7 Complexity Density: 0.88
7697		public static class CalcIdParam
7698		extends WebServiceParameterSet
7699		{
7700
7701		/**
7702		* handle for the calculation which uses
7703		* this parameter set
7704		*
7705		*/
7706		@XmlAttribute(name = "calcId", required = true)
7707		protected String calcId;
7708		/**
7709		* should the calculation be performed
7710		* immediately after loading in order to refresh results
7711		*
7712		*/
7713		@XmlAttribute(name = "needsUpdate")
7714		protected Boolean needsUpdate;
7715		/**
7716		* should the calculation be automatically
7717		* performed on edits
7718		*
7719		*/
7720		@XmlAttribute(name = "autoUpdate", required = true)
7721		protected boolean autoUpdate;
7722
7723		/**
7724		* handle for the calculation which uses
7725		* this parameter set
7726		*
7727		* @return
7728		* possible object is
7729		* {@link String }
7730		*
7731		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
7732	0	public String getCalcId() {...
7733	0	return calcId;
7734		}
7735
7736		/**
7737		* Sets the value of the calcId property.
7738		*
7739		* @param value
7740		* allowed object is
7741		* {@link String }
7742		*
7743		* @see #getCalcId()
7744		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
7745	0	public void setCalcId(String value) {...
7746	0	this.calcId = value;
7747		}
7748
7749		/**
7750		* should the calculation be performed
7751		* immediately after loading in order to refresh results
7752		*
7753		* @return
7754		* possible object is
7755		* {@link Boolean }
7756		*
7757		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
7758	0	public boolean isNeedsUpdate() {...
7759	0	if (needsUpdate == null) {
7760	0	return false;
7761		} else {
7762	0	return needsUpdate;
7763		}
7764		}
7765
7766		/**
7767		* Sets the value of the needsUpdate property.
7768		*
7769		* @param value
7770		* allowed object is
7771		* {@link Boolean }
7772		*
7773		* @see #isNeedsUpdate()
7774		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
7775	0	public void setNeedsUpdate(Boolean value) {...
7776	0	this.needsUpdate = value;
7777		}
7778
7779		/**
7780		* should the calculation be automatically
7781		* performed on edits
7782		*
7783		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
7784	0	public boolean isAutoUpdate() {...
7785	0	return autoUpdate;
7786		}
7787
7788		/**
7789		* Sets the value of the autoUpdate property.
7790		*
7791		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
7792	0	public void setAutoUpdate(boolean value) {...
7793	0	this.autoUpdate = value;
7794		}
7795
7796		}
7797
7798
7799		/**
7800		* <p>Java class for anonymous complex type</p>.
7801		*
7802		* <p>The following schema fragment specifies the expected content contained within this class.</p>
7803		*
7804		* <pre>
7805		* &lt;complexType&gt;
7806		* &lt;complexContent&gt;
7807		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
7808		* &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
7809		* &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
7810		* &lt;/restriction&gt;
7811		* &lt;/complexContent&gt;
7812		* &lt;/complexType&gt;
7813		* </pre>
7814		*
7815		*
7816		*/
7817		@XmlAccessorType(XmlAccessType.FIELD)
7818		@XmlType(name = "")
		100% Uncovered Elements: 0 (8) Complexity: 4 Complexity Density: 1
7819		public static class HiddenColumns {
7820
7821		@XmlAttribute(name = "start")
7822		protected Integer start;
7823		@XmlAttribute(name = "end")
7824		protected Integer end;
7825
7826		/**
7827		* Gets the value of the start property.
7828		*
7829		* @return
7830		* possible object is
7831		* {@link Integer }
7832		*
7833		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7834	54	public Integer getStart() {...
7835	54	return start;
7836		}
7837
7838		/**
7839		* Sets the value of the start property.
7840		*
7841		* @param value
7842		* allowed object is
7843		* {@link Integer }
7844		*
7845		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7846	6	public void setStart(Integer value) {...
7847	6	this.start = value;
7848		}
7849
7850		/**
7851		* Gets the value of the end property.
7852		*
7853		* @return
7854		* possible object is
7855		* {@link Integer }
7856		*
7857		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7858	54	public Integer getEnd() {...
7859	54	return end;
7860		}
7861
7862		/**
7863		* Sets the value of the end property.
7864		*
7865		* @param value
7866		* allowed object is
7867		* {@link Integer }
7868		*
7869		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7870	6	public void setEnd(Integer value) {...
7871	6	this.end = value;
7872		}
7873
7874		}
7875
7876
7877		/**
7878		* <p>Java class for anonymous complex type</p>.
7879		*
7880		* <p>The following schema fragment specifies the expected content contained within this class.</p>
7881		*
7882		* <pre>
7883		* &lt;complexType&gt;
7884		* &lt;complexContent&gt;
7885		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
7886		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
7887		* &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
7888		* &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
7889		* &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
7890		* &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
7891		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
7892		* &lt;/restriction&gt;
7893		* &lt;/complexContent&gt;
7894		* &lt;/complexType&gt;
7895		* </pre>
7896		*
7897		*
7898		*/
7899		@XmlAccessorType(XmlAccessType.FIELD)
7900		@XmlType(name = "")
		100% Uncovered Elements: 0 (36) Complexity: 18 Complexity Density: 1
7901		public static class Overview {
7902
7903		@XmlAttribute(name = "showHidden")
7904		protected Boolean showHidden;
7905		@XmlAttribute(name = "residueColour")
7906		protected Integer residueColour;
7907		@XmlAttribute(name = "gapColour")
7908		protected Integer gapColour;
7909		@XmlAttribute(name = "hiddenColour")
7910		protected Integer hiddenColour;
7911		@XmlAttribute(name = "title")
7912		protected String title;
7913		@XmlAttribute(name = "width")
7914		protected Integer width;
7915		@XmlAttribute(name = "height")
7916		protected Integer height;
7917		@XmlAttribute(name = "xpos")
7918		protected Integer xpos;
7919		@XmlAttribute(name = "ypos")
7920		protected Integer ypos;
7921
7922		/**
7923		* Gets the value of the showHidden property.
7924		*
7925		* @return
7926		* possible object is
7927		* {@link Boolean }
7928		*
7929		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7930	11	public Boolean isShowHidden() {...
7931	11	return showHidden;
7932		}
7933
7934		/**
7935		* Sets the value of the showHidden property.
7936		*
7937		* @param value
7938		* allowed object is
7939		* {@link Boolean }
7940		*
7941		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7942	14	public void setShowHidden(Boolean value) {...
7943	14	this.showHidden = value;
7944		}
7945
7946		/**
7947		* Gets the value of the residueColour property.
7948		*
7949		* @return
7950		* possible object is
7951		* {@link Integer }
7952		*
7953		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7954	11	public Integer getResidueColour() {...
7955	11	return residueColour;
7956		}
7957
7958		/**
7959		* Sets the value of the residueColour property.
7960		*
7961		* @param value
7962		* allowed object is
7963		* {@link Integer }
7964		*
7965		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7966	14	public void setResidueColour(Integer value) {...
7967	14	this.residueColour = value;
7968		}
7969
7970		/**
7971		* Gets the value of the gapColour property.
7972		*
7973		* @return
7974		* possible object is
7975		* {@link Integer }
7976		*
7977		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7978	11	public Integer getGapColour() {...
7979	11	return gapColour;
7980		}
7981
7982		/**
7983		* Sets the value of the gapColour property.
7984		*
7985		* @param value
7986		* allowed object is
7987		* {@link Integer }
7988		*
7989		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7990	14	public void setGapColour(Integer value) {...
7991	14	this.gapColour = value;
7992		}
7993
7994		/**
7995		* Gets the value of the hiddenColour property.
7996		*
7997		* @return
7998		* possible object is
7999		* {@link Integer }
8000		*
8001		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
8002	11	public Integer getHiddenColour() {...
8003	11	return hiddenColour;
8004		}
8005
8006		/**
8007		* Sets the value of the hiddenColour property.
8008		*
8009		* @param value
8010		* allowed object is
8011		* {@link Integer }
8012		*
8013		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
8014	14	public void setHiddenColour(Integer value) {...
8015	14	this.hiddenColour = value;
8016		}
8017
8018		/**
8019		* Gets the value of the title property.
8020		*
8021		* @return
8022		* possible object is
8023		* {@link String }
8024		*
8025		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
8026	11	public String getTitle() {...
8027	11	return title;
8028		}
8029
8030		/**
8031		* Sets the value of the title property.
8032		*
8033		* @param value
8034		* allowed object is
8035		* {@link String }
8036		*
8037		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
8038	14	public void setTitle(String value) {...
8039	14	this.title = value;
8040		}
8041
8042		/**
8043		* Gets the value of the width property.
8044		*
8045		* @return
8046		* possible object is
8047		* {@link Integer }
8048		*
8049		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
8050	11	public Integer getWidth() {...
8051	11	return width;
8052		}
8053
8054		/**
8055		* Sets the value of the width property.
8056		*
8057		* @param value
8058		* allowed object is
8059		* {@link Integer }
8060		*
8061		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
8062	14	public void setWidth(Integer value) {...
8063	14	this.width = value;
8064		}
8065
8066		/**
8067		* Gets the value of the height property.
8068		*
8069		* @return
8070		* possible object is
8071		* {@link Integer }
8072		*
8073		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
8074	11	public Integer getHeight() {...
8075	11	return height;
8076		}
8077
8078		/**
8079		* Sets the value of the height property.
8080		*
8081		* @param value
8082		* allowed object is
8083		* {@link Integer }
8084		*
8085		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
8086	14	public void setHeight(Integer value) {...
8087	14	this.height = value;
8088		}
8089
8090		/**
8091		* Gets the value of the xpos property.
8092		*
8093		* @return
8094		* possible object is
8095		* {@link Integer }
8096		*
8097		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
8098	11	public Integer getXpos() {...
8099	11	return xpos;
8100		}
8101
8102		/**
8103		* Sets the value of the xpos property.
8104		*
8105		* @param value
8106		* allowed object is
8107		* {@link Integer }
8108		*
8109		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
8110	14	public void setXpos(Integer value) {...
8111	14	this.xpos = value;
8112		}
8113
8114		/**
8115		* Gets the value of the ypos property.
8116		*
8117		* @return
8118		* possible object is
8119		* {@link Integer }
8120		*
8121		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
8122	11	public Integer getYpos() {...
8123	11	return ypos;
8124		}
8125
8126		/**
8127		* Sets the value of the ypos property.
8128		*
8129		* @param value
8130		* allowed object is
8131		* {@link Integer }
8132		*
8133		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
8134	14	public void setYpos(Integer value) {...
8135	14	this.ypos = value;
8136		}
8137
8138		}
8139
8140		}
8141
8142		}