Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
JalviewModel	396	26	20	0.8461538684.6%	Show methods
JalviewModel.FeatureSettings	731	6	4	1.0100%	Show methods
JalviewModel.FeatureSettings.Group	812	4	4	1.0100%	Show methods
JalviewModel.FeatureSettings.Setting	906	31	29	0.967741996.8%	Show methods
JalviewModel.JGroup	1328	51	46	0.941176594.1%	Show methods
JalviewModel.JSeq	1992	24	20	0.979166797.9%	Show methods
JalviewModel.JSeq.Pdbids	2291	3	2	1.0100%	Show methods
JalviewModel.JSeq.Pdbids.StructureState	2352	28	25	0.821428682.1%	Show methods
JalviewModel.JSeq.RnaViewer	2704	19	18	0.00%	Show methods
JalviewModel.JSeq.RnaViewer.SecondaryStructure	2969	8	8	0.00%	Show methods
JalviewModel.PcaViewer	3144	46	44	1.0100%	Show methods
JalviewModel.PcaViewer.Axis	3741	6	6	1.0100%	Show methods
JalviewModel.PcaViewer.SeqPointMax	3840	6	6	1.0100%	Show methods
JalviewModel.PcaViewer.SeqPointMin	3939	6	6	1.0100%	Show methods
JalviewModel.PcaViewer.SequencePoint	4040	8	8	1.0100%	Show methods
JalviewModel.Tree	4194	42	40	0.904761990.5%	Show methods
JalviewModel.UserColours	4730	4	4	0.00%	Show methods
JalviewModel.Viewport	4930	138	123	0.913043591.3%	Show methods
JalviewModel.Viewport.CalcIdParam	6485	8	7	0.00%	Show methods
JalviewModel.Viewport.HiddenColumns	6589	4	4	1.0100%	Show methods
JalviewModel.Viewport.Overview	6670	18	18	1.0100%	Show methods

Class JalviewModel

Class JalviewModel	Line # 396	Total Statements 26	Complexity 20	TOTAL Coverage 0.8461538684.6%
getCreationDate() : XMLGregorianCalendar   getCreationDate() : XMLGregorianCalendar	435435	1.01	1.01	0.0 0.00%
setCreationDate(XMLGregorianCalendar) : void   setCreationDate(XMLGregorianCalendar) : void	447447	1.01	1.01	1.0 1.0100%
getVersion() : String   getVersion() : String	458458	1.01	1.01	1.0 1.0100%
setVersion(String) : void   setVersion(String) : void	470470	1.01	1.01	1.0 1.0100%
getVamsasModel() : VAMSAS   getVamsasModel() : VAMSAS	481481	1.01	1.01	1.0 1.0100%
setVamsasModel(VAMSAS) : void   setVamsasModel(VAMSAS) : void	493493	1.01	1.01	1.0 1.0100%
getJSeq() : List<JalviewModel.JSeq>   getJSeq() : List<JalviewModel.JSeq>	515515	3.03	2.02	1.0 1.0100%
getJGroup() : List<JalviewModel.JGroup>   getJGroup() : List<JalviewModel.JGroup>	541541	3.03	2.02	1.0 1.0100%
getViewport() : List<JalviewModel.Viewport>   getViewport() : List<JalviewModel.Viewport>	567567	3.03	2.02	1.0 1.0100%
getUserColours() : List<JalviewModel.UserColours>   getUserColours() : List<JalviewModel.UserColours>	593593	3.03	2.02	0.0 0.00%
getTree() : List<JalviewModel.Tree>   getTree() : List<JalviewModel.Tree>	619619	3.03	2.02	1.0 1.0100%
getPcaViewer() : List<JalviewModel.PcaViewer>   getPcaViewer() : List<JalviewModel.PcaViewer>	645645	3.03	2.02	1.0 1.0100%
getFeatureSettings() : JalviewModel.FeatureSettings   getFeatureSettings() : JalviewModel.FeatureSettings	660660	1.01	1.01	1.0 1.0100%
setFeatureSettings(JalviewModel.FeatureSettings) : void   setFeatureSettings(JalviewModel.FeatureSettings) : void	672672	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.FeatureSettings

Class JalviewModel.FeatureSettings	Line # 731	Total Statements 6	Complexity 4	TOTAL Coverage 1.0100%
getSetting() : List<JalviewModel.FeatureSettings.Setting>   getSetting() : List<JalviewModel.FeatureSettings.Setting>	757757	3.03	2.02	1.0 1.0100%
getGroup() : List<JalviewModel.FeatureSettings.Group>   getGroup() : List<JalviewModel.FeatureSettings.Group>	783783	3.03	2.02	1.0 1.0100%

 

Class JalviewModel.FeatureSettings.Group

Class JalviewModel.FeatureSettings.Group	Line # 812	Total Statements 4	Complexity 4	TOTAL Coverage 1.0100%
getName() : String   getName() : String	827827	1.01	1.01	1.0 1.0100%
setName(String) : void   setName(String) : void	839839	1.01	1.01	1.0 1.0100%
isDisplay() : boolean   isDisplay() : boolean	848848	1.01	1.01	1.0 1.0100%
setDisplay(boolean) : void   setDisplay(boolean) : void	857857	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.FeatureSettings.Setting

Class JalviewModel.FeatureSettings.Setting	Line # 906	Total Statements 31	Complexity 29	TOTAL Coverage 0.967741996.8%
getAttributeName() : List<String>   getAttributeName() : List<String>	968968	3.03	2.02	1.0 1.0100%
getMatcherSet() : FeatureMatcherSet   getMatcherSet() : FeatureMatcherSet	983983	1.01	1.01	1.0 1.0100%
setMatcherSet(FeatureMatcherSet) : void   setMatcherSet(FeatureMatcherSet) : void	995995	1.01	1.01	1.0 1.0100%
getType() : String   getType() : String	10061006	1.01	1.01	1.0 1.0100%
setType(String) : void   setType(String) : void	10181018	1.01	1.01	1.0 1.0100%
getColour() : int   getColour() : int	10271027	1.01	1.01	1.0 1.0100%
setColour(int) : void   setColour(int) : void	10361036	1.01	1.01	1.0 1.0100%
isDisplay() : boolean   isDisplay() : boolean	10451045	1.01	1.01	1.0 1.0100%
setDisplay(boolean) : void   setDisplay(boolean) : void	10541054	1.01	1.01	1.0 1.0100%
getOrder() : Float   getOrder() : Float	10651065	1.01	1.01	1.0 1.0100%
setOrder(Float) : void   setOrder(Float) : void	10771077	1.01	1.01	1.0 1.0100%
getMincolour() : Integer   getMincolour() : Integer	10881088	1.01	1.01	1.0 1.0100%
setMincolour(Integer) : void   setMincolour(Integer) : void	11001100	1.01	1.01	1.0 1.0100%
getNoValueColour() : NoValueColour   getNoValueColour() : NoValueColour	11111111	3.03	2.02	0.6 0.660%
setNoValueColour(NoValueColour) : void   setNoValueColour(NoValueColour) : void	11301130	1.01	1.01	1.0 1.0100%
getThreshold() : Float   getThreshold() : Float	11411141	1.01	1.01	1.0 1.0100%
setThreshold(Float) : void   setThreshold(Float) : void	11531153	1.01	1.01	1.0 1.0100%
getThreshstate() : Integer   getThreshstate() : Integer	11641164	1.01	1.01	1.0 1.0100%
setThreshstate(Integer) : void   setThreshstate(Integer) : void	11761176	1.01	1.01	1.0 1.0100%
getMax() : Float   getMax() : Float	11871187	1.01	1.01	1.0 1.0100%
setMax(Float) : void   setMax(Float) : void	11991199	1.01	1.01	1.0 1.0100%
getMin() : Float   getMin() : Float	12101210	1.01	1.01	1.0 1.0100%
setMin(Float) : void   setMin(Float) : void	12221222	1.01	1.01	1.0 1.0100%
isColourByLabel() : Boolean   isColourByLabel() : Boolean	12331233	1.01	1.01	1.0 1.0100%
setColourByLabel(Boolean) : void   setColourByLabel(Boolean) : void	12451245	1.01	1.01	1.0 1.0100%
isAutoScale() : Boolean   isAutoScale() : Boolean	12561256	1.01	1.01	1.0 1.0100%
setAutoScale(Boolean) : void   setAutoScale(Boolean) : void	12681268	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.JGroup

Class JalviewModel.JGroup	Line # 1328	Total Statements 51	Complexity 46	TOTAL Coverage 0.941176594.1%
getSeq() : List<String>   getSeq() : List<String>	14111411	3.03	2.02	1.0 1.0100%
getAnnotationColours() : AnnotationColourScheme   getAnnotationColours() : AnnotationColourScheme	14261426	1.01	1.01	1.0 1.0100%
setAnnotationColours(AnnotationColourScheme) : void   setAnnotationColours(AnnotationColourScheme) : void	14381438	1.01	1.01	1.0 1.0100%
getStart() : Integer   getStart() : Integer	14491449	1.01	1.01	1.0 1.0100%
setStart(Integer) : void   setStart(Integer) : void	14611461	1.01	1.01	1.0 1.0100%
getEnd() : Integer   getEnd() : Integer	14721472	1.01	1.01	1.0 1.0100%
setEnd(Integer) : void   setEnd(Integer) : void	14841484	1.01	1.01	1.0 1.0100%
getName() : String   getName() : String	14951495	1.01	1.01	1.0 1.0100%
setName(String) : void   setName(String) : void	15071507	1.01	1.01	1.0 1.0100%
getColour() : String   getColour() : String	15181518	1.01	1.01	1.0 1.0100%
setColour(String) : void   setColour(String) : void	15301530	1.01	1.01	1.0 1.0100%
getConsThreshold() : Integer   getConsThreshold() : Integer	15411541	1.01	1.01	1.0 1.0100%
setConsThreshold(Integer) : void   setConsThreshold(Integer) : void	15531553	1.01	1.01	1.0 1.0100%
getPidThreshold() : Integer   getPidThreshold() : Integer	15641564	1.01	1.01	1.0 1.0100%
setPidThreshold(Integer) : void   setPidThreshold(Integer) : void	15761576	1.01	1.01	1.0 1.0100%
getOutlineColour() : Integer   getOutlineColour() : Integer	15871587	1.01	1.01	1.0 1.0100%
setOutlineColour(Integer) : void   setOutlineColour(Integer) : void	15991599	1.01	1.01	1.0 1.0100%
isDisplayBoxes() : Boolean   isDisplayBoxes() : Boolean	16101610	1.01	1.01	1.0 1.0100%
setDisplayBoxes(Boolean) : void   setDisplayBoxes(Boolean) : void	16221622	1.01	1.01	1.0 1.0100%
isDisplayText() : Boolean   isDisplayText() : Boolean	16331633	1.01	1.01	1.0 1.0100%
setDisplayText(Boolean) : void   setDisplayText(Boolean) : void	16451645	1.01	1.01	1.0 1.0100%
isColourText() : Boolean   isColourText() : Boolean	16561656	1.01	1.01	1.0 1.0100%
setColourText(Boolean) : void   setColourText(Boolean) : void	16681668	1.01	1.01	1.0 1.0100%
getTextCol1() : Integer   getTextCol1() : Integer	16791679	1.01	1.01	1.0 1.0100%
setTextCol1(Integer) : void   setTextCol1(Integer) : void	16911691	1.01	1.01	1.0 1.0100%
getTextCol2() : Integer   getTextCol2() : Integer	17021702	1.01	1.01	1.0 1.0100%
setTextCol2(Integer) : void   setTextCol2(Integer) : void	17141714	1.01	1.01	1.0 1.0100%
getTextColThreshold() : Integer   getTextColThreshold() : Integer	17251725	1.01	1.01	1.0 1.0100%
setTextColThreshold(Integer) : void   setTextColThreshold(Integer) : void	17371737	1.01	1.01	1.0 1.0100%
isShowUnconserved() : Boolean   isShowUnconserved() : Boolean	17481748	1.01	1.01	1.0 1.0100%
setShowUnconserved(Boolean) : void   setShowUnconserved(Boolean) : void	17601760	1.01	1.01	1.0 1.0100%
isIgnoreGapsinConsensus() : boolean   isIgnoreGapsinConsensus() : boolean	17711771	3.03	2.02	0.6 0.660%
setIgnoreGapsinConsensus(Boolean) : void   setIgnoreGapsinConsensus(Boolean) : void	17901790	1.01	1.01	1.0 1.0100%
isShowConsensusHistogram() : boolean   isShowConsensusHistogram() : boolean	18011801	3.03	2.02	0.6 0.660%
setShowConsensusHistogram(Boolean) : void   setShowConsensusHistogram(Boolean) : void	18201820	1.01	1.01	1.0 1.0100%
isShowSequenceLogo() : boolean   isShowSequenceLogo() : boolean	18311831	3.03	2.02	0.6 0.660%
setShowSequenceLogo(Boolean) : void   setShowSequenceLogo(Boolean) : void	18501850	1.01	1.01	1.0 1.0100%
isNormaliseSequenceLogo() : boolean   isNormaliseSequenceLogo() : boolean	18611861	3.03	2.02	1.0 1.0100%
setNormaliseSequenceLogo(Boolean) : void   setNormaliseSequenceLogo(Boolean) : void	18801880	1.01	1.01	1.0 1.0100%
getId() : String   getId() : String	18911891	1.01	1.01	1.0 1.0100%
setId(String) : void   setId(String) : void	19031903	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.JSeq

Class JalviewModel.JSeq	Line # 1992	Total Statements 24	Complexity 20	TOTAL Coverage 0.979166797.9%
getFeatures() : List<Feature>   getFeatures() : List<Feature>	20422042	3.03	2.02	1.0 1.0100%
getPdbids() : List<JalviewModel.JSeq.Pdbids>   getPdbids() : List<JalviewModel.JSeq.Pdbids>	20682068	3.03	2.02	1.0 1.0100%
getHiddenSequences() : List<Integer>   getHiddenSequences() : List<Integer>	20942094	3.03	2.02	1.0 1.0100%
getRnaViewer() : List<JalviewModel.JSeq.RnaViewer>   getRnaViewer() : List<JalviewModel.JSeq.RnaViewer>	21202120	3.03	2.02	0.8 0.880%
getColour() : Integer   getColour() : Integer	21352135	1.01	1.01	1.0 1.0100%
setColour(Integer) : void   setColour(Integer) : void	21472147	1.01	1.01	1.0 1.0100%
getStart() : int   getStart() : int	21562156	1.01	1.01	1.0 1.0100%
setStart(int) : void   setStart(int) : void	21652165	1.01	1.01	1.0 1.0100%
getEnd() : int   getEnd() : int	21742174	1.01	1.01	1.0 1.0100%
setEnd(int) : void   setEnd(int) : void	21832183	1.01	1.01	1.0 1.0100%
getId() : String   getId() : String	21942194	1.01	1.01	1.0 1.0100%
setId(String) : void   setId(String) : void	22062206	1.01	1.01	1.0 1.0100%
isHidden() : Boolean   isHidden() : Boolean	22172217	1.01	1.01	1.0 1.0100%
setHidden(Boolean) : void   setHidden(Boolean) : void	22292229	1.01	1.01	1.0 1.0100%
isViewreference() : Boolean   isViewreference() : Boolean	22402240	1.01	1.01	1.0 1.0100%
setViewreference(Boolean) : void   setViewreference(Boolean) : void	22522252	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.JSeq.Pdbids

Class JalviewModel.JSeq.Pdbids	Line # 2291	Total Statements 3	Complexity 2	TOTAL Coverage 1.0100%
getStructureState() : List<JalviewModel.JSeq.Pdbids.StructureState>   getStructureState() : List<JalviewModel.JSeq.Pdbids.StructureState>	23142314	3.03	2.02	1.0 1.0100%

 

Class JalviewModel.JSeq.Pdbids.StructureState

Class JalviewModel.JSeq.Pdbids.StructureState	Line # 2352	Total Statements 28	Complexity 25	TOTAL Coverage 0.821428682.1%
getValue() : String   getValue() : String	23942394	1.01	1.01	1.0 1.0100%
setValue(String) : void   setValue(String) : void	24062406	1.01	1.01	0.0 0.00%
isVisible() : Boolean   isVisible() : Boolean	24172417	1.01	1.01	0.0 0.00%
setVisible(Boolean) : void   setVisible(Boolean) : void	24292429	1.01	1.01	1.0 1.0100%
getViewId() : String   getViewId() : String	24402440	1.01	1.01	1.0 1.0100%
setViewId(String) : void   setViewId(String) : void	24522452	1.01	1.01	1.0 1.0100%
isAlignwithAlignPanel() : boolean   isAlignwithAlignPanel() : boolean	24632463	3.03	2.02	0.6 0.660%
setAlignwithAlignPanel(Boolean) : void   setAlignwithAlignPanel(Boolean) : void	24822482	1.01	1.01	1.0 1.0100%
isColourwithAlignPanel() : boolean   isColourwithAlignPanel() : boolean	24932493	3.03	2.02	0.6 0.660%
setColourwithAlignPanel(Boolean) : void   setColourwithAlignPanel(Boolean) : void	25122512	1.01	1.01	1.0 1.0100%
isColourByJmol() : boolean   isColourByJmol() : boolean	25232523	3.03	2.02	0.6 0.660%
setColourByJmol(Boolean) : void   setColourByJmol(Boolean) : void	25422542	1.01	1.01	1.0 1.0100%
getType() : String   getType() : String	25532553	1.01	1.01	1.0 1.0100%
setType(String) : void   setType(String) : void	25652565	1.01	1.01	1.0 1.0100%
getWidth() : Integer   getWidth() : Integer	25762576	1.01	1.01	1.0 1.0100%
setWidth(Integer) : void   setWidth(Integer) : void	25882588	1.01	1.01	1.0 1.0100%
getHeight() : Integer   getHeight() : Integer	25992599	1.01	1.01	1.0 1.0100%
setHeight(Integer) : void   setHeight(Integer) : void	26112611	1.01	1.01	1.0 1.0100%
getXpos() : Integer   getXpos() : Integer	26222622	1.01	1.01	1.0 1.0100%
setXpos(Integer) : void   setXpos(Integer) : void	26342634	1.01	1.01	1.0 1.0100%
getYpos() : Integer   getYpos() : Integer	26452645	1.01	1.01	1.0 1.0100%
setYpos(Integer) : void   setYpos(Integer) : void	26572657	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.JSeq.RnaViewer

Class JalviewModel.JSeq.RnaViewer	Line # 2704	Total Statements 19	Complexity 18	TOTAL Coverage 0.00%
getSecondaryStructure() : List<JalviewModel.JSeq.RnaViewer.SecondaryStructure>   getSecondaryStructure() : List<JalviewModel.JSeq.RnaViewer.SecondaryStructure>	27522752	3.03	2.02	0.0 0.00%
getTitle() : String   getTitle() : String	27672767	1.01	1.01	0.0 0.00%
setTitle(String) : void   setTitle(String) : void	27792779	1.01	1.01	0.0 0.00%
getViewId() : String   getViewId() : String	27902790	1.01	1.01	0.0 0.00%
setViewId(String) : void   setViewId(String) : void	28022802	1.01	1.01	0.0 0.00%
getDividerLocation() : Integer   getDividerLocation() : Integer	28132813	1.01	1.01	0.0 0.00%
setDividerLocation(Integer) : void   setDividerLocation(Integer) : void	28252825	1.01	1.01	0.0 0.00%
getSelectedRna() : Integer   getSelectedRna() : Integer	28362836	1.01	1.01	0.0 0.00%
setSelectedRna(Integer) : void   setSelectedRna(Integer) : void	28482848	1.01	1.01	0.0 0.00%
getWidth() : Integer   getWidth() : Integer	28592859	1.01	1.01	0.0 0.00%
setWidth(Integer) : void   setWidth(Integer) : void	28712871	1.01	1.01	0.0 0.00%
getHeight() : Integer   getHeight() : Integer	28822882	1.01	1.01	0.0 0.00%
setHeight(Integer) : void   setHeight(Integer) : void	28942894	1.01	1.01	0.0 0.00%
getXpos() : Integer   getXpos() : Integer	29052905	1.01	1.01	0.0 0.00%
setXpos(Integer) : void   setXpos(Integer) : void	29172917	1.01	1.01	0.0 0.00%
getYpos() : Integer   getYpos() : Integer	29282928	1.01	1.01	0.0 0.00%
setYpos(Integer) : void   setYpos(Integer) : void	29402940	1.01	1.01	0.0 0.00%

 

Class JalviewModel.JSeq.RnaViewer.SecondaryStructure

Class JalviewModel.JSeq.RnaViewer.SecondaryStructure	Line # 2969	Total Statements 8	Complexity 8	TOTAL Coverage 0.00%
getTitle() : String   getTitle() : String	29902990	1.01	1.01	0.0 0.00%
setTitle(String) : void   setTitle(String) : void	30023002	1.01	1.01	0.0 0.00%
getAnnotationId() : String   getAnnotationId() : String	30133013	1.01	1.01	0.0 0.00%
setAnnotationId(String) : void   setAnnotationId(String) : void	30253025	1.01	1.01	0.0 0.00%
isGapped() : Boolean   isGapped() : Boolean	30363036	1.01	1.01	0.0 0.00%
setGapped(Boolean) : void   setGapped(Boolean) : void	30483048	1.01	1.01	0.0 0.00%
getViewerState() : String   getViewerState() : String	30593059	1.01	1.01	0.0 0.00%
setViewerState(String) : void   setViewerState(String) : void	30713071	1.01	1.01	0.0 0.00%

 

Class JalviewModel.PcaViewer

Class JalviewModel.PcaViewer	Line # 3144	Total Statements 46	Complexity 44	TOTAL Coverage 1.0100%
getSequencePoint() : List<JalviewModel.PcaViewer.SequencePoint>   getSequencePoint() : List<JalviewModel.PcaViewer.SequencePoint>	32303230	3.03	2.02	1.0 1.0100%
getAxis() : List<JalviewModel.PcaViewer.Axis>   getAxis() : List<JalviewModel.PcaViewer.Axis>	32563256	3.03	2.02	1.0 1.0100%
getSeqPointMin() : JalviewModel.PcaViewer.SeqPointMin   getSeqPointMin() : JalviewModel.PcaViewer.SeqPointMin	32713271	1.01	1.01	1.0 1.0100%
setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin) : void   setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin) : void	32833283	1.01	1.01	1.0 1.0100%
getSeqPointMax() : JalviewModel.PcaViewer.SeqPointMax   getSeqPointMax() : JalviewModel.PcaViewer.SeqPointMax	32943294	1.01	1.01	1.0 1.0100%
setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax) : void   setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax) : void	33063306	1.01	1.01	1.0 1.0100%
getPcaData() : PcaDataType   getPcaData() : PcaDataType	33173317	1.01	1.01	1.0 1.0100%
setPcaData(PcaDataType) : void   setPcaData(PcaDataType) : void	33293329	1.01	1.01	1.0 1.0100%
getTitle() : String   getTitle() : String	33403340	1.01	1.01	1.0 1.0100%
setTitle(String) : void   setTitle(String) : void	33523352	1.01	1.01	1.0 1.0100%
getScoreModelName() : String   getScoreModelName() : String	33633363	1.01	1.01	1.0 1.0100%
setScoreModelName(String) : void   setScoreModelName(String) : void	33753375	1.01	1.01	1.0 1.0100%
getXDim() : Integer   getXDim() : Integer	33863386	1.01	1.01	1.0 1.0100%
setXDim(Integer) : void   setXDim(Integer) : void	33983398	1.01	1.01	1.0 1.0100%
getYDim() : Integer   getYDim() : Integer	34093409	1.01	1.01	1.0 1.0100%
setYDim(Integer) : void   setYDim(Integer) : void	34213421	1.01	1.01	1.0 1.0100%
getZDim() : Integer   getZDim() : Integer	34323432	1.01	1.01	1.0 1.0100%
setZDim(Integer) : void   setZDim(Integer) : void	34443444	1.01	1.01	1.0 1.0100%
getBgColour() : Integer   getBgColour() : Integer	34553455	1.01	1.01	1.0 1.0100%
setBgColour(Integer) : void   setBgColour(Integer) : void	34673467	1.01	1.01	1.0 1.0100%
getScaleFactor() : Float   getScaleFactor() : Float	34783478	1.01	1.01	1.0 1.0100%
setScaleFactor(Float) : void   setScaleFactor(Float) : void	34903490	1.01	1.01	1.0 1.0100%
isShowLabels() : Boolean   isShowLabels() : Boolean	35013501	1.01	1.01	1.0 1.0100%
setShowLabels(Boolean) : void   setShowLabels(Boolean) : void	35133513	1.01	1.01	1.0 1.0100%
isLinkToAllViews() : Boolean   isLinkToAllViews() : Boolean	35243524	1.01	1.01	1.0 1.0100%
setLinkToAllViews(Boolean) : void   setLinkToAllViews(Boolean) : void	35363536	1.01	1.01	1.0 1.0100%
isIncludeGaps() : Boolean   isIncludeGaps() : Boolean	35473547	1.01	1.01	1.0 1.0100%
setIncludeGaps(Boolean) : void   setIncludeGaps(Boolean) : void	35593559	1.01	1.01	1.0 1.0100%
isMatchGaps() : Boolean   isMatchGaps() : Boolean	35703570	1.01	1.01	1.0 1.0100%
setMatchGaps(Boolean) : void   setMatchGaps(Boolean) : void	35823582	1.01	1.01	1.0 1.0100%
isIncludeGappedColumns() : Boolean   isIncludeGappedColumns() : Boolean	35933593	1.01	1.01	1.0 1.0100%
setIncludeGappedColumns(Boolean) : void   setIncludeGappedColumns(Boolean) : void	36053605	1.01	1.01	1.0 1.0100%
isDenominateByShortestLength() : Boolean   isDenominateByShortestLength() : Boolean	36163616	1.01	1.01	1.0 1.0100%
setDenominateByShortestLength(Boolean) : void   setDenominateByShortestLength(Boolean) : void	36283628	1.01	1.01	1.0 1.0100%
getWidth() : Integer   getWidth() : Integer	36393639	1.01	1.01	1.0 1.0100%
setWidth(Integer) : void   setWidth(Integer) : void	36513651	1.01	1.01	1.0 1.0100%
getHeight() : Integer   getHeight() : Integer	36623662	1.01	1.01	1.0 1.0100%
setHeight(Integer) : void   setHeight(Integer) : void	36743674	1.01	1.01	1.0 1.0100%
getXpos() : Integer   getXpos() : Integer	36853685	1.01	1.01	1.0 1.0100%
setXpos(Integer) : void   setXpos(Integer) : void	36973697	1.01	1.01	1.0 1.0100%
getYpos() : Integer   getYpos() : Integer	37083708	1.01	1.01	1.0 1.0100%
setYpos(Integer) : void   setYpos(Integer) : void	37203720	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.PcaViewer.Axis

Class JalviewModel.PcaViewer.Axis	Line # 3741	Total Statements 6	Complexity 6	TOTAL Coverage 1.0100%
getXPos() : Float   getXPos() : Float	37593759	1.01	1.01	1.0 1.0100%
setXPos(Float) : void   setXPos(Float) : void	37713771	1.01	1.01	1.0 1.0100%
getYPos() : Float   getYPos() : Float	37823782	1.01	1.01	1.0 1.0100%
setYPos(Float) : void   setYPos(Float) : void	37943794	1.01	1.01	1.0 1.0100%
getZPos() : Float   getZPos() : Float	38053805	1.01	1.01	1.0 1.0100%
setZPos(Float) : void   setZPos(Float) : void	38173817	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.PcaViewer.SeqPointMax

Class JalviewModel.PcaViewer.SeqPointMax	Line # 3840	Total Statements 6	Complexity 6	TOTAL Coverage 1.0100%
getXPos() : Float   getXPos() : Float	38583858	1.01	1.01	1.0 1.0100%
setXPos(Float) : void   setXPos(Float) : void	38703870	1.01	1.01	1.0 1.0100%
getYPos() : Float   getYPos() : Float	38813881	1.01	1.01	1.0 1.0100%
setYPos(Float) : void   setYPos(Float) : void	38933893	1.01	1.01	1.0 1.0100%
getZPos() : Float   getZPos() : Float	39043904	1.01	1.01	1.0 1.0100%
setZPos(Float) : void   setZPos(Float) : void	39163916	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.PcaViewer.SeqPointMin

Class JalviewModel.PcaViewer.SeqPointMin	Line # 3939	Total Statements 6	Complexity 6	TOTAL Coverage 1.0100%
getXPos() : Float   getXPos() : Float	39573957	1.01	1.01	1.0 1.0100%
setXPos(Float) : void   setXPos(Float) : void	39693969	1.01	1.01	1.0 1.0100%
getYPos() : Float   getYPos() : Float	39803980	1.01	1.01	1.0 1.0100%
setYPos(Float) : void   setYPos(Float) : void	39923992	1.01	1.01	1.0 1.0100%
getZPos() : Float   getZPos() : Float	40034003	1.01	1.01	1.0 1.0100%
setZPos(Float) : void   setZPos(Float) : void	40154015	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.PcaViewer.SequencePoint

Class JalviewModel.PcaViewer.SequencePoint	Line # 4040	Total Statements 8	Complexity 8	TOTAL Coverage 1.0100%
getSequenceRef() : String   getSequenceRef() : String	40614061	1.01	1.01	1.0 1.0100%
setSequenceRef(String) : void   setSequenceRef(String) : void	40734073	1.01	1.01	1.0 1.0100%
getXPos() : Float   getXPos() : Float	40844084	1.01	1.01	1.0 1.0100%
setXPos(Float) : void   setXPos(Float) : void	40964096	1.01	1.01	1.0 1.0100%
getYPos() : Float   getYPos() : Float	41074107	1.01	1.01	1.0 1.0100%
setYPos(Float) : void   setYPos(Float) : void	41194119	1.01	1.01	1.0 1.0100%
getZPos() : Float   getZPos() : Float	41304130	1.01	1.01	1.0 1.0100%
setZPos(Float) : void   setZPos(Float) : void	41424142	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.Tree

Class JalviewModel.Tree	Line # 4194	Total Statements 42	Complexity 40	TOTAL Coverage 0.904761990.5%
getTitle() : String   getTitle() : String	42634263	1.01	1.01	1.0 1.0100%
setTitle(String) : void   setTitle(String) : void	42754275	1.01	1.01	1.0 1.0100%
getNewick() : String   getNewick() : String	42864286	1.01	1.01	1.0 1.0100%
setNewick(String) : void   setNewick(String) : void	42984298	1.01	1.01	1.0 1.0100%
getFontName() : String   getFontName() : String	43094309	1.01	1.01	1.0 1.0100%
setFontName(String) : void   setFontName(String) : void	43214321	1.01	1.01	1.0 1.0100%
getFontSize() : Integer   getFontSize() : Integer	43324332	1.01	1.01	1.0 1.0100%
setFontSize(Integer) : void   setFontSize(Integer) : void	43444344	1.01	1.01	1.0 1.0100%
getFontStyle() : Integer   getFontStyle() : Integer	43554355	1.01	1.01	1.0 1.0100%
setFontStyle(Integer) : void   setFontStyle(Integer) : void	43674367	1.01	1.01	1.0 1.0100%
getThreshold() : Float   getThreshold() : Float	43784378	1.01	1.01	1.0 1.0100%
setThreshold(Float) : void   setThreshold(Float) : void	43904390	1.01	1.01	1.0 1.0100%
isShowBootstrap() : Boolean   isShowBootstrap() : Boolean	44014401	1.01	1.01	1.0 1.0100%
setShowBootstrap(Boolean) : void   setShowBootstrap(Boolean) : void	44134413	1.01	1.01	1.0 1.0100%
isShowDistances() : Boolean   isShowDistances() : Boolean	44244424	1.01	1.01	1.0 1.0100%
setShowDistances(Boolean) : void   setShowDistances(Boolean) : void	44364436	1.01	1.01	1.0 1.0100%
isMarkUnlinked() : Boolean   isMarkUnlinked() : Boolean	44474447	1.01	1.01	1.0 1.0100%
setMarkUnlinked(Boolean) : void   setMarkUnlinked(Boolean) : void	44594459	1.01	1.01	1.0 1.0100%
isFitToWindow() : Boolean   isFitToWindow() : Boolean	44704470	1.01	1.01	1.0 1.0100%
setFitToWindow(Boolean) : void   setFitToWindow(Boolean) : void	44824482	1.01	1.01	1.0 1.0100%
isCurrentTree() : Boolean   isCurrentTree() : Boolean	44934493	1.01	1.01	1.0 1.0100%
setCurrentTree(Boolean) : void   setCurrentTree(Boolean) : void	45054505	1.01	1.01	1.0 1.0100%
isColumnWise() : boolean   isColumnWise() : boolean	45164516	3.03	2.02	0.6 0.660%
setColumnWise(Boolean) : void   setColumnWise(Boolean) : void	45354535	1.01	1.01	0.0 0.00%
getColumnReference() : String   getColumnReference() : String	45464546	1.01	1.01	0.0 0.00%
setColumnReference(String) : void   setColumnReference(String) : void	45584558	1.01	1.01	0.0 0.00%
getId() : String   getId() : String	45694569	1.01	1.01	1.0 1.0100%
setId(String) : void   setId(String) : void	45814581	1.01	1.01	1.0 1.0100%
isLinkToAllViews() : boolean   isLinkToAllViews() : boolean	45924592	3.03	2.02	1.0 1.0100%
setLinkToAllViews(Boolean) : void   setLinkToAllViews(Boolean) : void	46114611	1.01	1.01	1.0 1.0100%
getWidth() : Integer   getWidth() : Integer	46224622	1.01	1.01	1.0 1.0100%
setWidth(Integer) : void   setWidth(Integer) : void	46344634	1.01	1.01	1.0 1.0100%
getHeight() : Integer   getHeight() : Integer	46454645	1.01	1.01	1.0 1.0100%
setHeight(Integer) : void   setHeight(Integer) : void	46574657	1.01	1.01	1.0 1.0100%
getXpos() : Integer   getXpos() : Integer	46684668	1.01	1.01	1.0 1.0100%
setXpos(Integer) : void   setXpos(Integer) : void	46804680	1.01	1.01	1.0 1.0100%
getYpos() : Integer   getYpos() : Integer	46914691	1.01	1.01	1.0 1.0100%
setYpos(Integer) : void   setYpos(Integer) : void	47034703	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.UserColours

Class JalviewModel.UserColours	Line # 4730	Total Statements 4	Complexity 4	TOTAL Coverage 0.00%
getUserColourScheme() : JalviewUserColours   getUserColourScheme() : JalviewUserColours	47484748	1.01	1.01	0.0 0.00%
setUserColourScheme(JalviewUserColours) : void   setUserColourScheme(JalviewUserColours) : void	47604760	1.01	1.01	0.0 0.00%
getId() : String   getId() : String	47714771	1.01	1.01	0.0 0.00%
setId(String) : void   setId(String) : void	47834783	1.01	1.01	0.0 0.00%

 

Class JalviewModel.Viewport

Class JalviewModel.Viewport	Line # 4930	Total Statements 138	Complexity 123	TOTAL Coverage 0.913043591.3%
getAnnotationColours() : AnnotationColourScheme   getAnnotationColours() : AnnotationColourScheme	51075107	1.01	1.01	1.0 1.0100%
setAnnotationColours(AnnotationColourScheme) : void   setAnnotationColours(AnnotationColourScheme) : void	51195119	1.01	1.01	1.0 1.0100%
getHiddenColumns() : List<JalviewModel.Viewport.HiddenColumns>   getHiddenColumns() : List<JalviewModel.Viewport.HiddenColumns>	51415141	3.03	2.02	1.0 1.0100%
getCalcIdParam() : List<JalviewModel.Viewport.CalcIdParam>   getCalcIdParam() : List<JalviewModel.Viewport.CalcIdParam>	51675167	3.03	2.02	1.0 1.0100%
getOverview() : JalviewModel.Viewport.Overview   getOverview() : JalviewModel.Viewport.Overview	51825182	1.01	1.01	1.0 1.0100%
setOverview(JalviewModel.Viewport.Overview) : void   setOverview(JalviewModel.Viewport.Overview) : void	51945194	1.01	1.01	1.0 1.0100%
isConservationSelected() : Boolean   isConservationSelected() : Boolean	52055205	1.01	1.01	1.0 1.0100%
setConservationSelected(Boolean) : void   setConservationSelected(Boolean) : void	52175217	1.01	1.01	1.0 1.0100%
isPidSelected() : Boolean   isPidSelected() : Boolean	52285228	1.01	1.01	1.0 1.0100%
setPidSelected(Boolean) : void   setPidSelected(Boolean) : void	52405240	1.01	1.01	1.0 1.0100%
getBgColour() : String   getBgColour() : String	52515251	1.01	1.01	1.0 1.0100%
setBgColour(String) : void   setBgColour(String) : void	52635263	1.01	1.01	1.0 1.0100%
getConsThreshold() : Integer   getConsThreshold() : Integer	52745274	1.01	1.01	1.0 1.0100%
setConsThreshold(Integer) : void   setConsThreshold(Integer) : void	52865286	1.01	1.01	1.0 1.0100%
getPidThreshold() : Integer   getPidThreshold() : Integer	52975297	1.01	1.01	1.0 1.0100%
setPidThreshold(Integer) : void   setPidThreshold(Integer) : void	53095309	1.01	1.01	1.0 1.0100%
getTitle() : String   getTitle() : String	53205320	1.01	1.01	1.0 1.0100%
setTitle(String) : void   setTitle(String) : void	53325332	1.01	1.01	1.0 1.0100%
isShowFullId() : Boolean   isShowFullId() : Boolean	53435343	1.01	1.01	1.0 1.0100%
setShowFullId(Boolean) : void   setShowFullId(Boolean) : void	53555355	1.01	1.01	1.0 1.0100%
isRightAlignIds() : Boolean   isRightAlignIds() : Boolean	53665366	1.01	1.01	1.0 1.0100%
setRightAlignIds(Boolean) : void   setRightAlignIds(Boolean) : void	53785378	1.01	1.01	1.0 1.0100%
isShowText() : Boolean   isShowText() : Boolean	53895389	1.01	1.01	1.0 1.0100%
setShowText(Boolean) : void   setShowText(Boolean) : void	54015401	1.01	1.01	1.0 1.0100%
isShowColourText() : Boolean   isShowColourText() : Boolean	54125412	1.01	1.01	1.0 1.0100%
setShowColourText(Boolean) : void   setShowColourText(Boolean) : void	54245424	1.01	1.01	1.0 1.0100%
isShowUnconserved() : boolean   isShowUnconserved() : boolean	54355435	3.03	2.02	0.6 0.660%
setShowUnconserved(Boolean) : void   setShowUnconserved(Boolean) : void	54545454	1.01	1.01	1.0 1.0100%
isShowBoxes() : Boolean   isShowBoxes() : Boolean	54655465	1.01	1.01	1.0 1.0100%
setShowBoxes(Boolean) : void   setShowBoxes(Boolean) : void	54775477	1.01	1.01	1.0 1.0100%
isWrapAlignment() : Boolean   isWrapAlignment() : Boolean	54885488	1.01	1.01	1.0 1.0100%
setWrapAlignment(Boolean) : void   setWrapAlignment(Boolean) : void	55005500	1.01	1.01	1.0 1.0100%
isRenderGaps() : Boolean   isRenderGaps() : Boolean	55115511	1.01	1.01	1.0 1.0100%
setRenderGaps(Boolean) : void   setRenderGaps(Boolean) : void	55235523	1.01	1.01	1.0 1.0100%
isShowSequenceFeatures() : Boolean   isShowSequenceFeatures() : Boolean	55345534	1.01	1.01	1.0 1.0100%
setShowSequenceFeatures(Boolean) : void   setShowSequenceFeatures(Boolean) : void	55465546	1.01	1.01	1.0 1.0100%
isShowNPfeatureTooltip() : Boolean   isShowNPfeatureTooltip() : Boolean	55575557	1.01	1.01	1.0 1.0100%
setShowNPfeatureTooltip(Boolean) : void   setShowNPfeatureTooltip(Boolean) : void	55695569	1.01	1.01	1.0 1.0100%
isShowDbRefTooltip() : Boolean   isShowDbRefTooltip() : Boolean	55805580	1.01	1.01	1.0 1.0100%
setShowDbRefTooltip(Boolean) : void   setShowDbRefTooltip(Boolean) : void	55925592	1.01	1.01	1.0 1.0100%
isFollowHighlight() : boolean   isFollowHighlight() : boolean	56035603	3.03	2.02	0.6 0.660%
setFollowHighlight(Boolean) : void   setFollowHighlight(Boolean) : void	56225622	1.01	1.01	1.0 1.0100%
isFollowSelection() : boolean   isFollowSelection() : boolean	56335633	3.03	2.02	0.6 0.660%
setFollowSelection(Boolean) : void   setFollowSelection(Boolean) : void	56525652	1.01	1.01	1.0 1.0100%
isShowAnnotation() : Boolean   isShowAnnotation() : Boolean	56635663	1.01	1.01	1.0 1.0100%
setShowAnnotation(Boolean) : void   setShowAnnotation(Boolean) : void	56755675	1.01	1.01	1.0 1.0100%
isCentreColumnLabels() : boolean   isCentreColumnLabels() : boolean	56865686	3.03	2.02	0.6 0.660%
setCentreColumnLabels(Boolean) : void   setCentreColumnLabels(Boolean) : void	57055705	1.01	1.01	0.0 0.00%
isShowGroupConservation() : boolean   isShowGroupConservation() : boolean	57165716	3.03	2.02	0.6 0.660%
setShowGroupConservation(Boolean) : void   setShowGroupConservation(Boolean) : void	57355735	1.01	1.01	1.0 1.0100%
isShowGroupConsensus() : boolean   isShowGroupConsensus() : boolean	57465746	3.03	2.02	0.6 0.660%
setShowGroupConsensus(Boolean) : void   setShowGroupConsensus(Boolean) : void	57655765	1.01	1.01	1.0 1.0100%
isShowConsensusHistogram() : boolean   isShowConsensusHistogram() : boolean	57765776	3.03	2.02	0.6 0.660%
setShowConsensusHistogram(Boolean) : void   setShowConsensusHistogram(Boolean) : void	57955795	1.01	1.01	1.0 1.0100%
isShowSequenceLogo() : boolean   isShowSequenceLogo() : boolean	58065806	3.03	2.02	0.6 0.660%
setShowSequenceLogo(Boolean) : void   setShowSequenceLogo(Boolean) : void	58255825	1.01	1.01	1.0 1.0100%
isNormaliseSequenceLogo() : boolean   isNormaliseSequenceLogo() : boolean	58365836	3.03	2.02	1.0 1.0100%
setNormaliseSequenceLogo(Boolean) : void   setNormaliseSequenceLogo(Boolean) : void	58555855	1.01	1.01	1.0 1.0100%
isIgnoreGapsinConsensus() : boolean   isIgnoreGapsinConsensus() : boolean	58665866	3.03	2.02	0.6 0.660%
setIgnoreGapsinConsensus(Boolean) : void   setIgnoreGapsinConsensus(Boolean) : void	58855885	1.01	1.01	1.0 1.0100%
getStartRes() : Integer   getStartRes() : Integer	58965896	1.01	1.01	1.0 1.0100%
setStartRes(Integer) : void   setStartRes(Integer) : void	59085908	1.01	1.01	1.0 1.0100%
getStartSeq() : Integer   getStartSeq() : Integer	59195919	1.01	1.01	0.0 0.00%
setStartSeq(Integer) : void   setStartSeq(Integer) : void	59315931	1.01	1.01	1.0 1.0100%
getCharWidth() : Integer   getCharWidth() : Integer	59425942	1.01	1.01	1.0 1.0100%
setCharWidth(Integer) : void   setCharWidth(Integer) : void	59545954	1.01	1.01	1.0 1.0100%
getCharHeight() : Integer   getCharHeight() : Integer	59655965	1.01	1.01	1.0 1.0100%
setCharHeight(Integer) : void   setCharHeight(Integer) : void	59775977	1.01	1.01	1.0 1.0100%
getFontName() : String   getFontName() : String	59885988	1.01	1.01	1.0 1.0100%
setFontName(String) : void   setFontName(String) : void	60006000	1.01	1.01	1.0 1.0100%
getFontSize() : Integer   getFontSize() : Integer	60116011	1.01	1.01	1.0 1.0100%
setFontSize(Integer) : void   setFontSize(Integer) : void	60236023	1.01	1.01	1.0 1.0100%
getFontStyle() : Integer   getFontStyle() : Integer	60346034	1.01	1.01	1.0 1.0100%
setFontStyle(Integer) : void   setFontStyle(Integer) : void	60466046	1.01	1.01	1.0 1.0100%
getIdWidth() : Integer   getIdWidth() : Integer	60576057	1.01	1.01	1.0 1.0100%
setIdWidth(Integer) : void   setIdWidth(Integer) : void	60696069	1.01	1.01	1.0 1.0100%
isIdWidthManuallyAdjusted() : Boolean   isIdWidthManuallyAdjusted() : Boolean	60806080	1.01	1.01	1.0 1.0100%
setIdWidthManuallyAdjusted(Boolean) : void   setIdWidthManuallyAdjusted(Boolean) : void	60926092	1.01	1.01	1.0 1.0100%
isScaleProteinAsCdna() : boolean   isScaleProteinAsCdna() : boolean	61036103	3.03	2.02	1.0 1.0100%
setScaleProteinAsCdna(Boolean) : void   setScaleProteinAsCdna(Boolean) : void	61226122	1.01	1.01	1.0 1.0100%
getViewName() : String   getViewName() : String	61336133	1.01	1.01	1.0 1.0100%
setViewName(String) : void   setViewName(String) : void	61456145	1.01	1.01	1.0 1.0100%
getSequenceSetId() : String   getSequenceSetId() : String	61566156	1.01	1.01	1.0 1.0100%
setSequenceSetId(String) : void   setSequenceSetId(String) : void	61686168	1.01	1.01	1.0 1.0100%
isGatheredViews() : Boolean   isGatheredViews() : Boolean	61796179	1.01	1.01	1.0 1.0100%
setGatheredViews(Boolean) : void   setGatheredViews(Boolean) : void	61916191	1.01	1.01	1.0 1.0100%
getTextCol1() : Integer   getTextCol1() : Integer	62026202	1.01	1.01	1.0 1.0100%
setTextCol1(Integer) : void   setTextCol1(Integer) : void	62146214	1.01	1.01	1.0 1.0100%
getTextCol2() : Integer   getTextCol2() : Integer	62256225	1.01	1.01	1.0 1.0100%
setTextCol2(Integer) : void   setTextCol2(Integer) : void	62376237	1.01	1.01	1.0 1.0100%
getTextColThreshold() : Integer   getTextColThreshold() : Integer	62486248	1.01	1.01	1.0 1.0100%
setTextColThreshold(Integer) : void   setTextColThreshold(Integer) : void	62606260	1.01	1.01	1.0 1.0100%
getId() : String   getId() : String	62716271	1.01	1.01	1.0 1.0100%
setId(String) : void   setId(String) : void	62836283	1.01	1.01	1.0 1.0100%
getComplementId() : String   getComplementId() : String	62946294	1.01	1.01	1.0 1.0100%
setComplementId(String) : void   setComplementId(String) : void	63066306	1.01	1.01	0.0 0.00%
isShowComplementFeatures() : boolean   isShowComplementFeatures() : boolean	63176317	3.03	2.02	1.0 1.0100%
setShowComplementFeatures(Boolean) : void   setShowComplementFeatures(Boolean) : void	63366336	1.01	1.01	1.0 1.0100%
isShowComplementFeaturesOnTop() : boolean   isShowComplementFeaturesOnTop() : boolean	63476347	3.03	2.02	1.0 1.0100%
setShowComplementFeaturesOnTop(Boolean) : void   setShowComplementFeaturesOnTop(Boolean) : void	63666366	1.01	1.01	1.0 1.0100%
getWidth() : Integer   getWidth() : Integer	63776377	1.01	1.01	1.0 1.0100%
setWidth(Integer) : void   setWidth(Integer) : void	63896389	1.01	1.01	1.0 1.0100%
getHeight() : Integer   getHeight() : Integer	64006400	1.01	1.01	1.0 1.0100%
setHeight(Integer) : void   setHeight(Integer) : void	64126412	1.01	1.01	1.0 1.0100%
getXpos() : Integer   getXpos() : Integer	64236423	1.01	1.01	1.0 1.0100%
setXpos(Integer) : void   setXpos(Integer) : void	64356435	1.01	1.01	1.0 1.0100%
getYpos() : Integer   getYpos() : Integer	64466446	1.01	1.01	1.0 1.0100%
setYpos(Integer) : void   setYpos(Integer) : void	64586458	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.Viewport.CalcIdParam

Class JalviewModel.Viewport.CalcIdParam	Line # 6485	Total Statements 8	Complexity 7	TOTAL Coverage 0.00%
getCalcId() : String   getCalcId() : String	65036503	1.01	1.01	0.0 0.00%
setCalcId(String) : void   setCalcId(String) : void	65156515	1.01	1.01	0.0 0.00%
isNeedsUpdate() : boolean   isNeedsUpdate() : boolean	65266526	3.03	2.02	0.0 0.00%
setNeedsUpdate(Boolean) : void   setNeedsUpdate(Boolean) : void	65456545	1.01	1.01	0.0 0.00%
isAutoUpdate() : boolean   isAutoUpdate() : boolean	65546554	1.01	1.01	0.0 0.00%
setAutoUpdate(boolean) : void   setAutoUpdate(boolean) : void	65636563	1.01	1.01	0.0 0.00%

 

Class JalviewModel.Viewport.HiddenColumns

Class JalviewModel.Viewport.HiddenColumns	Line # 6589	Total Statements 4	Complexity 4	TOTAL Coverage 1.0100%
getStart() : Integer   getStart() : Integer	66046604	1.01	1.01	1.0 1.0100%
setStart(Integer) : void   setStart(Integer) : void	66166616	1.01	1.01	1.0 1.0100%
getEnd() : Integer   getEnd() : Integer	66276627	1.01	1.01	1.0 1.0100%
setEnd(Integer) : void   setEnd(Integer) : void	66396639	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.Viewport.Overview

Class JalviewModel.Viewport.Overview	Line # 6670	Total Statements 18	Complexity 18	TOTAL Coverage 1.0100%
isShowHidden() : Boolean   isShowHidden() : Boolean	67066706	1.01	1.01	1.0 1.0100%
setShowHidden(Boolean) : void   setShowHidden(Boolean) : void	67186718	1.01	1.01	1.0 1.0100%
getResidueColour() : Integer   getResidueColour() : Integer	67296729	1.01	1.01	1.0 1.0100%
setResidueColour(Integer) : void   setResidueColour(Integer) : void	67416741	1.01	1.01	1.0 1.0100%
getGapColour() : Integer   getGapColour() : Integer	67526752	1.01	1.01	1.0 1.0100%
setGapColour(Integer) : void   setGapColour(Integer) : void	67646764	1.01	1.01	1.0 1.0100%
getHiddenColour() : Integer   getHiddenColour() : Integer	67756775	1.01	1.01	1.0 1.0100%
setHiddenColour(Integer) : void   setHiddenColour(Integer) : void	67876787	1.01	1.01	1.0 1.0100%
getTitle() : String   getTitle() : String	67986798	1.01	1.01	1.0 1.0100%
setTitle(String) : void   setTitle(String) : void	68106810	1.01	1.01	1.0 1.0100%
getWidth() : Integer   getWidth() : Integer	68216821	1.01	1.01	1.0 1.0100%
setWidth(Integer) : void   setWidth(Integer) : void	68336833	1.01	1.01	1.0 1.0100%
getHeight() : Integer   getHeight() : Integer	68446844	1.01	1.01	1.0 1.0100%
setHeight(Integer) : void   setHeight(Integer) : void	68566856	1.01	1.01	1.0 1.0100%
getXpos() : Integer   getXpos() : Integer	68676867	1.01	1.01	1.0 1.0100%
setXpos(Integer) : void   setXpos(Integer) : void	68796879	1.01	1.01	1.0 1.0100%
getYpos() : Integer   getYpos() : Integer	68906890	1.01	1.01	1.0 1.0100%
setYpos(Integer) : void   setYpos(Integer) : void	69026902	1.01	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.654321	jalview.project.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettingsjalview.project.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettings	1PASS
	0.6131687	jalview.project.Jalview2xmlTests.testStoreAndRecoverExpandedviewsjalview.project.Jalview2xmlTests.testStoreAndRecoverExpandedviews	1PASS
	0.531893	jalview.project.Jalview2xmlTests.testStoreAndRestoreIDwidthAndAnnotationHeightjalview.project.Jalview2xmlTests.testStoreAndRestoreIDwidthAndAnnotationHeight	1PASS
	0.46604937	jalview.project.Jalview2xmlTests.testPcaViewAssociationjalview.project.Jalview2xmlTests.testPcaViewAssociation	1PASS
	0.41769546	jalview.project.Jalview2xmlTests.testColourByAnnotScoresjalview.project.Jalview2xmlTests.testColourByAnnotScores	1PASS
	0.41358024	jalview.project.Jalview2xmlTests.testStoreAndRecoverColourThresholdsjalview.project.Jalview2xmlTests.testStoreAndRecoverColourThresholds	1PASS
	0.4063786	jalview.project.Jalview2xmlTests.testStoreAndRecoverPDBEntryjalview.project.Jalview2xmlTests.testStoreAndRecoverPDBEntry	1PASS
	0.40329218	jalview.project.Jalview2xmlTests.testSaveLoadFeatureColoursAndFiltersjalview.project.Jalview2xmlTests.testSaveLoadFeatureColoursAndFilters	1PASS
	0.39403293	jalview.gui.AlignFrameTest.testNewView_colourThresholdsjalview.gui.AlignFrameTest.testNewView_colourThresholds	1PASS
	0.36728394	jalview.io.AnnotatedPDBFileInputTest.testJalviewProjectRelocationAnnotationjalview.io.AnnotatedPDBFileInputTest.testJalviewProjectRelocationAnnotation	1PASS
	0.3600823	jalview.project.Jalview2xmlTests.testCopyViewSettingsjalview.project.Jalview2xmlTests.testCopyViewSettings	1PASS
	0.3600823	jalview.project.Jalview2xmlTests.viewRefPdbAnnotationjalview.project.Jalview2xmlTests.viewRefPdbAnnotation	1PASS
	0.3600823	jalview.project.Jalview2xmlTests.gatherViewsHerejalview.project.Jalview2xmlTests.gatherViewsHere	1PASS
	0.3600823	jalview.project.Jalview2xmlTests.noDuplicatePdbMappingsMadejalview.project.Jalview2xmlTests.noDuplicatePdbMappingsMade	1PASS
	0.3590535	jalview.project.Jalview2xmlTests.testTCoffeeScoresjalview.project.Jalview2xmlTests.testTCoffeeScores	1PASS
	0.35699588	jalview.project.Jalview2xmlTests.testStoreAndRecoverOverviewjalview.project.Jalview2xmlTests.testStoreAndRecoverOverview	1PASS
	0.3261317	jalview.project.Jalview2xmlTests.testStoreAndRecoverGroupRepSeqsjalview.project.Jalview2xmlTests.testStoreAndRecoverGroupRepSeqs	1PASS
	0.32407406	jalview.project.Jalview2xmlTests.testStoreAndRecoverAnnotationRowElementColoursjalview.project.Jalview2xmlTests.testStoreAndRecoverAnnotationRowElementColours	1PASS
	0.31995884	jalview.project.Jalview2xmlTests.testRNAStructureRecoveryjalview.project.Jalview2xmlTests.testRNAStructureRecovery	1PASS
	0.31893003	jalview.gui.AlignmentPanelTest.testSetOverviewTitle_automaticOverviewjalview.gui.AlignmentPanelTest.testSetOverviewTitle_automaticOverview	1PASS
	0.31893003	jalview.gui.AlignmentPanelTest.testSetOverviewTitlejalview.gui.AlignmentPanelTest.testSetOverviewTitle	1PASS
	0.31790122	jalview.project.Jalview2xmlTests.testStoreAndRecoverGeneLocusjalview.project.Jalview2xmlTests.testStoreAndRecoverGeneLocus	1PASS
	0.31790122	jalview.project.Jalview2xmlTests.testStoreAndRecoverNoOverviewjalview.project.Jalview2xmlTests.testStoreAndRecoverNoOverview	1PASS
	0.31790122	jalview.project.Jalview2xmlTests.testPAEsaveRestorejalview.project.Jalview2xmlTests.testPAEsaveRestore	1PASS
	0.2983539	jalview.gui.AlignViewportTest.testDeregisterMapping_onCloseViewjalview.gui.AlignViewportTest.testDeregisterMapping_onCloseView	1PASS
	0.2983539	jalview.gui.AlignFrameTest.testNewView_dsRefPreservedjalview.gui.AlignFrameTest.testNewView_dsRefPreserved	1PASS
	0.29320988	jalview.project.Jalview2xmlTests.testAutoShowOverviewForLegacyProjectsjalview.project.Jalview2xmlTests.testAutoShowOverviewForLegacyProjects	1PASS
	0.25411522	jalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwicejalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwice	1PASS
	0.20576131	jalview.project.Jalview2xmlTests.testMergeDatasetsforManyViewsjalview.project.Jalview2xmlTests.testMergeDatasetsforManyViews	1PASS
	0.20061728	jalview.project.Jalview2xmlTests.testMergeDatasetsforViewsjalview.project.Jalview2xmlTests.testMergeDatasetsforViews	1PASS
	0.1244856	jalview.gui.QuitHandlerTest.testSavedProjectChangesjalview.gui.QuitHandlerTest.testSavedProjectChanges	1PASS
	0.1244856	jalview.gui.QuitHandlerTest.testWaitForSaveQuitjalview.gui.QuitHandlerTest.testWaitForSaveQuit	1PASS

 

Source view

1		//
2		// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
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: 2023.11.01 at 07:03:09 PM GMT
6		//
7
8		package jalview.xml.binding.jalview;
9
10		import java.util.ArrayList;
11		import java.util.List;
12		import javax.xml.bind.annotation.XmlAccessType;
13		import javax.xml.bind.annotation.XmlAccessorType;
14		import javax.xml.bind.annotation.XmlAttribute;
15		import javax.xml.bind.annotation.XmlElement;
16		import javax.xml.bind.annotation.XmlID;
17		import javax.xml.bind.annotation.XmlSchemaType;
18		import javax.xml.bind.annotation.XmlType;
19		import javax.xml.bind.annotation.XmlValue;
20		import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
21		import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
22		import javax.xml.datatype.XMLGregorianCalendar;
23
24		/**
25		* <p>Java class for JalviewModel complex type.
26		*
27		* <p>The following schema fragment specifies the expected content
28		* contained within this class.
29		*
30		* <pre> <complexType name="JalviewModel">
31		* <complexContent> <restriction
32		* base="{http://www.w3.org/2001/XMLSchema}anyType">
33		* <sequence> <element name="creationDate"
34		* type="{http://www.w3.org/2001/XMLSchema}dateTime"/> <element
35		* name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
36		* <element name="vamsasModel"
37		* type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
38		* <sequence> <element name="JSeq" maxOccurs="unbounded"
39		* minOccurs="0"> <complexType>
40		* <complexContent> <restriction
41		* base="{http://www.w3.org/2001/XMLSchema}anyType">
42		* <sequence> <element name="features"
43		* type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
44		* <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
45		* <complexType> <complexContent> <extension
46		* base="{www.jalview.org}pdbentry"> <sequence>
47		* <element name="structureState" maxOccurs="unbounded"
48		* minOccurs="0"> <complexType>
49		* <simpleContent> <extension
50		* base="<http://www.w3.org/2001/XMLSchema>string">
51		* <attGroup ref="{www.jalview.org}swingwindow"/>
52		* <attribute name="visible"
53		* type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
54		* name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
55		* <attribute name="alignwithAlignPanel"
56		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
57		* <attribute name="colourwithAlignPanel"
58		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
59		* <attribute name="colourByJmol"
60		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
61		* <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string"
62		* /> </extension> </simpleContent>
63		* </complexType> </element>
64		* </sequence> </extension>
65		* </complexContent> </complexType>
66		* </element> <element name="hiddenSequences"
67		* type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded"
68		* minOccurs="0"/> <element name="rnaViewer" maxOccurs="unbounded"
69		* minOccurs="0"> <complexType>
70		* <complexContent> <restriction
71		* base="{http://www.w3.org/2001/XMLSchema}anyType">
72		* <sequence> <element name="secondaryStructure"
73		* maxOccurs="unbounded"> <complexType>
74		* <complexContent> <restriction
75		* base="{http://www.w3.org/2001/XMLSchema}anyType"> <attribute
76		* name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
77		* <attribute name="annotationId" use="required"
78		* type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
79		* name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
80		* <attribute name="viewerState"
81		* type="{http://www.w3.org/2001/XMLSchema}string" />
82		* </restriction> </complexContent>
83		* </complexType> </element>
84		* </sequence> <attGroup
85		* ref="{www.jalview.org}swingwindow"/> <attribute name="title"
86		* type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
87		* name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
88		* <attribute name="dividerLocation"
89		* type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
90		* name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
91		* </restriction> </complexContent>
92		* </complexType> </element>
93		* </sequence> <attribute name="colour"
94		* type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
95		* name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
96		* /> <attribute name="end" use="required"
97		* type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
98		* name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
99		* /> <attribute name="hidden"
100		* type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
101		* name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean"
102		* /> </restriction> </complexContent>
103		* </complexType> </element> <element
104		* name="JGroup" maxOccurs="unbounded" minOccurs="0">
105		* <complexType> <complexContent>
106		* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
107		* <sequence> <element name="seq"
108		* type="{http://www.w3.org/2001/XMLSchema}string"
109		* maxOccurs="unbounded"/> <element name="annotationColours"
110		* type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
111		* </sequence> <attribute name="start"
112		* type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
113		* name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
114		* <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string"
115		* /> <attribute name="colour"
116		* type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
117		* name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
118		* <attribute name="pidThreshold"
119		* type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
120		* name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
121		* <attribute name="displayBoxes"
122		* type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
123		* name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
124		* <attribute name="colourText"
125		* type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
126		* name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
127		* <attribute name="textCol2"
128		* type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
129		* name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int"
130		* /> <attribute name="showUnconserved"
131		* type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
132		* name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean"
133		* default="true" /> <attribute name="showConsensusHistogram"
134		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
135		* <attribute name="showSequenceLogo"
136		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
137		* <attribute name="normaliseSequenceLogo"
138		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
139		* <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string"
140		* /> </restriction> </complexContent>
141		* </complexType> </element> <element
142		* name="Viewport" maxOccurs="unbounded" minOccurs="0">
143		* <complexType> <complexContent>
144		* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
145		* <sequence> <element name="AnnotationColours"
146		* type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
147		* <element name="hiddenColumns" maxOccurs="unbounded"
148		* minOccurs="0"> <complexType>
149		* <complexContent> <restriction
150		* base="{http://www.w3.org/2001/XMLSchema}anyType"> <attribute
151		* name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
152		* <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int"
153		* /> </restriction> </complexContent>
154		* </complexType> </element> <element
155		* name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
156		* <complexType> <complexContent> <extension
157		* base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
158		* <attribute name="calcId" use="required"
159		* type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
160		* name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean"
161		* default="false" /> <attribute name="autoUpdate" use="required"
162		* type="{http://www.w3.org/2001/XMLSchema}boolean" />
163		* </extension> </complexContent>
164		* </complexType> </element> <element
165		* name="overview" minOccurs="0"> <complexType>
166		* <complexContent> <restriction
167		* base="{http://www.w3.org/2001/XMLSchema}anyType"> <attGroup
168		* ref="{www.jalview.org}swingwindow"/> <attribute
169		* name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
170		* <attribute name="residueColour"
171		* type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
172		* name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
173		* <attribute name="hiddenColour"
174		* type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
175		* name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
176		* </restriction> </complexContent>
177		* </complexType> </element>
178		* </sequence> <attGroup
179		* ref="{www.jalview.org}swingwindow"/> <attribute
180		* name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean"
181		* /> <attribute name="pidSelected"
182		* type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
183		* name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
184		* <attribute name="consThreshold"
185		* type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
186		* name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
187		* <attribute name="title"
188		* type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
189		* name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
190		* <attribute name="rightAlignIds"
191		* type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
192		* name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
193		* <attribute name="showColourText"
194		* type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
195		* name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean"
196		* default="false" /> <attribute name="showBoxes"
197		* type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
198		* name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean"
199		* /> <attribute name="renderGaps"
200		* type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
201		* name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean"
202		* /> <attribute name="showNPfeatureTooltip"
203		* type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
204		* name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean"
205		* /> <attribute name="followHighlight"
206		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
207		* <attribute name="followSelection"
208		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
209		* <attribute name="showAnnotation"
210		* type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
211		* name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean"
212		* default="false" /> <attribute name="showGroupConservation"
213		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
214		* <attribute name="showGroupConsensus"
215		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
216		* <attribute name="showConsensusHistogram"
217		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
218		* <attribute name="showSequenceLogo"
219		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
220		* <attribute name="normaliseSequenceLogo"
221		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
222		* <attribute name="ignoreGapsinConsensus"
223		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
224		* <attribute name="startRes"
225		* type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
226		* name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
227		* <attribute name="charWidth"
228		* type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
229		* name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
230		* <attribute name="fontName"
231		* type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
232		* name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
233		* <attribute name="fontStyle"
234		* type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
235		* name="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
236		* <attribute name="idWidthManuallyAdjusted"
237		* type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
238		* name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean"
239		* default="true" /> <attribute name="viewName"
240		* type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
241		* name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string"
242		* /> <attribute name="gatheredViews"
243		* type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
244		* name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
245		* <attribute name="textCol2"
246		* type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
247		* name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int"
248		* /> <attribute name="id"
249		* type="{http://www.w3.org/2001/XMLSchema}ID" /> <attribute
250		* name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
251		* <attribute name="showComplementFeatures"
252		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
253		* <attribute name="showComplementFeaturesOnTop"
254		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
255		* </restriction> </complexContent>
256		* </complexType> </element> <element
257		* name="UserColours" maxOccurs="unbounded" minOccurs="0">
258		* <complexType> <complexContent>
259		* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
260		* <sequence> <element name="UserColourScheme"
261		* type="{www.jalview.org/colours}JalviewUserColours"/>
262		* </sequence> <attribute name="id"
263		* type="{http://www.w3.org/2001/XMLSchema}string" />
264		* </restriction> </complexContent>
265		* </complexType> </element> <element
266		* name="tree" maxOccurs="unbounded" minOccurs="0">
267		* <complexType> <complexContent>
268		* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
269		* <sequence minOccurs="0"> <element name="title"
270		* type="{http://www.w3.org/2001/XMLSchema}string"/> <element
271		* name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
272		* </sequence> <attGroup
273		* ref="{www.jalview.org}swingwindow"/> <attribute name="fontName"
274		* type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
275		* name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
276		* <attribute name="fontStyle"
277		* type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
278		* name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
279		* <attribute name="showBootstrap"
280		* type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
281		* name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean"
282		* /> <attribute name="markUnlinked"
283		* type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
284		* name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
285		* <attribute name="currentTree"
286		* type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
287		* name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean"
288		* default="false" /> <attribute name="columnReference"
289		* type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
290		* name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
291		* <attribute name="linkToAllViews"
292		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
293		* </restriction> </complexContent>
294		* </complexType> </element> <element
295		* name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
296		* <complexType> <complexContent>
297		* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
298		* <sequence> <element name="sequencePoint"
299		* maxOccurs="unbounded"> <complexType>
300		* <complexContent> <restriction
301		* base="{http://www.w3.org/2001/XMLSchema}anyType"> <attGroup
302		* ref="{www.jalview.org}position"/> <attribute name="sequenceRef"
303		* type="{http://www.w3.org/2001/XMLSchema}string" />
304		* </restriction> </complexContent>
305		* </complexType> </element> <element
306		* name="axis" maxOccurs="3" minOccurs="3"> <complexType>
307		* <complexContent> <restriction
308		* base="{http://www.w3.org/2001/XMLSchema}anyType"> <attGroup
309		* ref="{www.jalview.org}position"/> </restriction>
310		* </complexContent> </complexType>
311		* </element> <element name="seqPointMin">
312		* <complexType> <complexContent>
313		* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
314		* <attGroup ref="{www.jalview.org}position"/>
315		* </restriction> </complexContent>
316		* </complexType> </element> <element
317		* name="seqPointMax"> <complexType>
318		* <complexContent> <restriction
319		* base="{http://www.w3.org/2001/XMLSchema}anyType"> <attGroup
320		* ref="{www.jalview.org}position"/> </restriction>
321		* </complexContent> </complexType>
322		* </element> <element name="pcaData"
323		* type="{www.jalview.org}PcaDataType"/> </sequence>
324		* <attGroup ref="{www.jalview.org}SimilarityParams"/>
325		* <attGroup ref="{www.jalview.org}swingwindow"/>
326		* <attribute name="title"
327		* type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
328		* name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string"
329		* /> <attribute name="xDim"
330		* type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
331		* name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
332		* <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int"
333		* /> <attribute name="bgColour"
334		* type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
335		* name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
336		* <attribute name="showLabels"
337		* type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
338		* name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean"
339		* /> </restriction> </complexContent>
340		* </complexType> </element> <element
341		* name="FeatureSettings" minOccurs="0"> <complexType>
342		* <complexContent> <restriction
343		* base="{http://www.w3.org/2001/XMLSchema}anyType">
344		* <sequence> <element name="setting" maxOccurs="unbounded"
345		* minOccurs="0"> <complexType>
346		* <complexContent> <restriction
347		* base="{http://www.w3.org/2001/XMLSchema}anyType">
348		* <sequence> <element name="attributeName"
349		* type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
350		* minOccurs="0"/> <element name="matcherSet"
351		* type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
352		* </sequence> <attribute name="type" use="required"
353		* type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
354		* name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
355		* /> <attribute name="display" use="required"
356		* type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
357		* name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
358		* <attribute name="mincolour"
359		* type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
360		* name="noValueColour" type="{www.jalview.org/colours}NoValueColour"
361		* default="Min" /> <attribute name="threshold"
362		* type="{http://www.w3.org/2001/XMLSchema}float" /> <attribute
363		* name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
364		* <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
365		* /> <attribute name="min"
366		* type="{http://www.w3.org/2001/XMLSchema}float" /> <attribute
367		* name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
368		* /> <attribute name="autoScale"
369		* type="{http://www.w3.org/2001/XMLSchema}boolean" />
370		* </restriction> </complexContent>
371		* </complexType> </element> <element
372		* name="group" maxOccurs="unbounded" minOccurs="0">
373		* <complexType> <complexContent>
374		* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
375		* <attribute name="name" use="required"
376		* type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
377		* name="display" use="required"
378		* type="{http://www.w3.org/2001/XMLSchema}boolean" />
379		* </restriction> </complexContent>
380		* </complexType> </element>
381		* </sequence> </restriction>
382		* </complexContent> </complexType>
383		* </element> </sequence> </sequence>
384		* </restriction> </complexContent>
385		* </complexType> </pre>
386		*
387		*
388		*/
389		@XmlAccessorType(XmlAccessType.FIELD)
390		@XmlType(
391		name = "JalviewModel",
392		namespace = "www.jalview.org",
393		propOrder =
394		{ "creationDate", "version", "vamsasModel", "jSeq", "jGroup", "viewport",
395		"userColours", "tree", "pcaViewer", "featureSettings" })
		84.6% Uncovered Elements: 8 (52) Complexity: 20 Complexity Density: 0.77
396		public class JalviewModel
397		{
398
399		@XmlElement(required = true)
400		@XmlSchemaType(name = "dateTime")
401		protected XMLGregorianCalendar creationDate;
402
403		@XmlElement(required = true)
404		protected String version;
405
406		@XmlElement(required = true)
407		protected VAMSAS vamsasModel;
408
409		@XmlElement(name = "JSeq")
410		protected List<JalviewModel.JSeq> jSeq;
411
412		@XmlElement(name = "JGroup")
413		protected List<JalviewModel.JGroup> jGroup;
414
415		@XmlElement(name = "Viewport")
416		protected List<JalviewModel.Viewport> viewport;
417
418		@XmlElement(name = "UserColours")
419		protected List<JalviewModel.UserColours> userColours;
420
421		protected List<JalviewModel.Tree> tree;
422
423		@XmlElement(name = "PcaViewer")
424		protected List<JalviewModel.PcaViewer> pcaViewer;
425
426		@XmlElement(name = "FeatureSettings")
427		protected JalviewModel.FeatureSettings featureSettings;
428
429		/**
430		* Gets the value of the creationDate property.
431		*
432		* @return possible object is {@link XMLGregorianCalendar }
433		*
434		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
435	0	public XMLGregorianCalendar getCreationDate()...
436		{
437	0	return creationDate;
438		}
439
440		/**
441		* Sets the value of the creationDate property.
442		*
443		* @param value
444		* allowed object is {@link XMLGregorianCalendar }
445		*
446		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
447	73	public void setCreationDate(XMLGregorianCalendar value)...
448		{
449	73	this.creationDate = value;
450		}
451
452		/**
453		* Gets the value of the version property.
454		*
455		* @return possible object is {@link String }
456		*
457		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
458	203	public String getVersion()...
459		{
460	203	return version;
461		}
462
463		/**
464		* Sets the value of the version property.
465		*
466		* @param value
467		* allowed object is {@link String }
468		*
469		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
470	73	public void setVersion(String value)...
471		{
472	73	this.version = value;
473		}
474
475		/**
476		* Gets the value of the vamsasModel property.
477		*
478		* @return possible object is {@link VAMSAS }
479		*
480		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
481	193	public VAMSAS getVamsasModel()...
482		{
483	193	return vamsasModel;
484		}
485
486		/**
487		* Sets the value of the vamsasModel property.
488		*
489		* @param value
490		* allowed object is {@link VAMSAS }
491		*
492		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
493	73	public void setVamsasModel(VAMSAS value)...
494		{
495	73	this.vamsasModel = value;
496		}
497
498		/**
499		* Gets the value of the jSeq property.
500		*
501		* &lt;p&gt; This accessor method returns a reference to the live list, not a
502		* snapshot. Therefore any modification you make to the returned list will be
503		* present inside the JAXB object. This is why there is not a
504		* &lt;CODE&gt;set&lt;/CODE&gt; method for the jSeq property.
505		*
506		* &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
507		* getJSeq().add(newItem); &lt;/pre&gt;
508		*
509		*
510		* &lt;p&gt; Objects of the following type(s) are allowed in the list
511		* {@link JalviewModel.JSeq }
512		*
513		*
514		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
515	1059	public List<JalviewModel.JSeq> getJSeq()...
516		{
517	1059	if (jSeq == null)
518		{
519	73	jSeq = new ArrayList<JalviewModel.JSeq>();
520		}
521	1059	return this.jSeq;
522		}
523
524		/**
525		* Gets the value of the jGroup property.
526		*
527		* &lt;p&gt; This accessor method returns a reference to the live list, not a
528		* snapshot. Therefore any modification you make to the returned list will be
529		* present inside the JAXB object. This is why there is not a
530		* &lt;CODE&gt;set&lt;/CODE&gt; method for the jGroup property.
531		*
532		* &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
533		* getJGroup().add(newItem); &lt;/pre&gt;
534		*
535		*
536		* &lt;p&gt; Objects of the following type(s) are allowed in the list
537		* {@link JalviewModel.JGroup }
538		*
539		*
540		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
541	156	public List<JalviewModel.JGroup> getJGroup()...
542		{
543	156	if (jGroup == null)
544		{
545	90	jGroup = new ArrayList<JalviewModel.JGroup>();
546		}
547	156	return this.jGroup;
548		}
549
550		/**
551		* Gets the value of the viewport property.
552		*
553		* &lt;p&gt; This accessor method returns a reference to the live list, not a
554		* snapshot. Therefore any modification you make to the returned list will be
555		* present inside the JAXB object. This is why there is not a
556		* &lt;CODE&gt;set&lt;/CODE&gt; method for the viewport property.
557		*
558		* &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
559		* getViewport().add(newItem); &lt;/pre&gt;
560		*
561		*
562		* &lt;p&gt; Objects of the following type(s) are allowed in the list
563		* {@link JalviewModel.Viewport }
564		*
565		*
566		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
567	406	public List<JalviewModel.Viewport> getViewport()...
568		{
569	406	if (viewport == null)
570		{
571	71	viewport = new ArrayList<JalviewModel.Viewport>();
572		}
573	406	return this.viewport;
574		}
575
576		/**
577		* Gets the value of the userColours property.
578		*
579		* &lt;p&gt; This accessor method returns a reference to the live list, not a
580		* snapshot. Therefore any modification you make to the returned list will be
581		* present inside the JAXB object. This is why there is not a
582		* &lt;CODE&gt;set&lt;/CODE&gt; method for the userColours property.
583		*
584		* &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
585		* getUserColours().add(newItem); &lt;/pre&gt;
586		*
587		*
588		* &lt;p&gt; Objects of the following type(s) are allowed in the list
589		* {@link JalviewModel.UserColours }
590		*
591		*
592		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
593	0	public List<JalviewModel.UserColours> getUserColours()...
594		{
595	0	if (userColours == null)
596		{
597	0	userColours = new ArrayList<JalviewModel.UserColours>();
598		}
599	0	return this.userColours;
600		}
601
602		/**
603		* Gets the value of the tree property.
604		*
605		* &lt;p&gt; This accessor method returns a reference to the live list, not a
606		* snapshot. Therefore any modification you make to the returned list will be
607		* present inside the JAXB object. This is why there is not a
608		* &lt;CODE&gt;set&lt;/CODE&gt; method for the tree property.
609		*
610		* &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
611		* getTree().add(newItem); &lt;/pre&gt;
612		*
613		*
614		* &lt;p&gt; Objects of the following type(s) are allowed in the list
615		* {@link JalviewModel.Tree }
616		*
617		*
618		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
619	103	public List<JalviewModel.Tree> getTree()...
620		{
621	103	if (tree == null)
622		{
623	67	tree = new ArrayList<JalviewModel.Tree>();
624		}
625	103	return this.tree;
626		}
627
628		/**
629		* Gets the value of the pcaViewer property.
630		*
631		* &lt;p&gt; This accessor method returns a reference to the live list, not a
632		* snapshot. Therefore any modification you make to the returned list will be
633		* present inside the JAXB object. This is why there is not a
634		* &lt;CODE&gt;set&lt;/CODE&gt; method for the pcaViewer property.
635		*
636		* &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
637		* getPcaViewer().add(newItem); &lt;/pre&gt;
638		*
639		*
640		* &lt;p&gt; Objects of the following type(s) are allowed in the list
641		* {@link JalviewModel.PcaViewer }
642		*
643		*
644		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
645	151	public List<JalviewModel.PcaViewer> getPcaViewer()...
646		{
647	151	if (pcaViewer == null)
648		{
649	75	pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
650		}
651	151	return this.pcaViewer;
652		}
653
654		/**
655		* Gets the value of the featureSettings property.
656		*
657		* @return possible object is {@link JalviewModel.FeatureSettings }
658		*
659		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
660	2071	public JalviewModel.FeatureSettings getFeatureSettings()...
661		{
662	2071	return featureSettings;
663		}
664
665		/**
666		* Sets the value of the featureSettings property.
667		*
668		* @param value
669		* allowed object is {@link JalviewModel.FeatureSettings }
670		*
671		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
672	11	public void setFeatureSettings(JalviewModel.FeatureSettings value)...
673		{
674	11	this.featureSettings = value;
675		}
676
677		/**
678		* &lt;p&gt;Java class for anonymous complex type.
679		*
680		* &lt;p&gt;The following schema fragment specifies the expected content
681		* contained within this class.
682		*
683		* &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
684		* &amp;lt;restriction
685		* base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
686		* &amp;lt;sequence&amp;gt; &amp;lt;element name="setting"
687		* maxOccurs="unbounded" minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
688		* &amp;lt;complexContent&amp;gt; &amp;lt;restriction
689		* base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
690		* &amp;lt;sequence&amp;gt; &amp;lt;element name="attributeName"
691		* type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
692		* minOccurs="0"/&amp;gt; &amp;lt;element name="matcherSet"
693		* type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&amp;gt;
694		* &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="type" use="required"
695		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
696		* name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
697		* /&amp;gt; &amp;lt;attribute name="display" use="required"
698		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
699		* &amp;lt;attribute name="order"
700		* type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt; &amp;lt;attribute
701		* name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
702		* &amp;lt;attribute name="noValueColour"
703		* type="{www.jalview.org/colours}NoValueColour" default="Min" /&amp;gt;
704		* &amp;lt;attribute name="threshold"
705		* type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt; &amp;lt;attribute
706		* name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
707		* &amp;lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
708		* /&amp;gt; &amp;lt;attribute name="min"
709		* type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt; &amp;lt;attribute
710		* name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
711		* /&amp;gt; &amp;lt;attribute name="autoScale"
712		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
713		* &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
714		* &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt; &amp;lt;element
715		* name="group" maxOccurs="unbounded" minOccurs="0"&amp;gt;
716		* &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
717		* &amp;lt;restriction
718		* base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
719		* name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
720		* /&amp;gt; &amp;lt;attribute name="display" use="required"
721		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
722		* &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
723		* &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
724		* &amp;lt;/sequence&amp;gt; &amp;lt;/restriction&amp;gt;
725		* &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
726		*
727		*
728		*/
729		@XmlAccessorType(XmlAccessType.FIELD)
730		@XmlType(name = "", propOrder = { "setting", "group" })
		100% Uncovered Elements: 0 (12) Complexity: 4 Complexity Density: 0.67
731		public static class FeatureSettings
732		{
733
734		@XmlElement(namespace = "www.jalview.org")
735		protected List<JalviewModel.FeatureSettings.Setting> setting;
736
737		@XmlElement(namespace = "www.jalview.org")
738		protected List<JalviewModel.FeatureSettings.Group> group;
739
740		/**
741		* Gets the value of the setting property.
742		*
743		* &lt;p&gt; This accessor method returns a reference to the live list, not
744		* a snapshot. Therefore any modification you make to the returned list will
745		* be present inside the JAXB object. This is why there is not a
746		* &lt;CODE&gt;set&lt;/CODE&gt; method for the setting property.
747		*
748		* &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
749		* getSetting().add(newItem); &lt;/pre&gt;
750		*
751		*
752		* &lt;p&gt; Objects of the following type(s) are allowed in the list
753		* {@link JalviewModel.FeatureSettings.Setting }
754		*
755		*
756		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
757	1887	public List<JalviewModel.FeatureSettings.Setting> getSetting()...
758		{
759	1887	if (setting == null)
760		{
761	11	setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
762		}
763	1887	return this.setting;
764		}
765
766		/**
767		* Gets the value of the group property.
768		*
769		* &lt;p&gt; This accessor method returns a reference to the live list, not
770		* a snapshot. Therefore any modification you make to the returned list will
771		* be present inside the JAXB object. This is why there is not a
772		* &lt;CODE&gt;set&lt;/CODE&gt; method for the group property.
773		*
774		* &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
775		* getGroup().add(newItem); &lt;/pre&gt;
776		*
777		*
778		* &lt;p&gt; Objects of the following type(s) are allowed in the list
779		* {@link JalviewModel.FeatureSettings.Group }
780		*
781		*
782		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
783	323	public List<JalviewModel.FeatureSettings.Group> getGroup()...
784		{
785	323	if (group == null)
786		{
787	11	group = new ArrayList<JalviewModel.FeatureSettings.Group>();
788		}
789	323	return this.group;
790		}
791
792		/**
793		* &lt;p&gt;Java class for anonymous complex type.
794		*
795		* &lt;p&gt;The following schema fragment specifies the expected content
796		* contained within this class.
797		*
798		* &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
799		* &amp;lt;restriction
800		* base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
801		* &amp;lt;attribute name="name" use="required"
802		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
803		* &amp;lt;attribute name="display" use="required"
804		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
805		* &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
806		* &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
807		*
808		*
809		*/
810		@XmlAccessorType(XmlAccessType.FIELD)
811		@XmlType(name = "")
		100% Uncovered Elements: 0 (8) Complexity: 4 Complexity Density: 1
812		public static class Group
813		{
814
815		@XmlAttribute(name = "name", required = true)
816		protected String name;
817
818		@XmlAttribute(name = "display", required = true)
819		protected boolean display;
820
821		/**
822		* Gets the value of the name property.
823		*
824		* @return possible object is {@link String }
825		*
826		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
827	127	public String getName()...
828		{
829	127	return name;
830		}
831
832		/**
833		* Sets the value of the name property.
834		*
835		* @param value
836		* allowed object is {@link String }
837		*
838		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
839	33	public void setName(String value)...
840		{
841	33	this.name = value;
842		}
843
844		/**
845		* Gets the value of the display property.
846		*
847		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
848	127	public boolean isDisplay()...
849		{
850	127	return display;
851		}
852
853		/**
854		* Sets the value of the display property.
855		*
856		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
857	33	public void setDisplay(boolean value)...
858		{
859	33	this.display = value;
860		}
861
862		}
863
864		/**
865		* &lt;p&gt;Java class for anonymous complex type.
866		*
867		* &lt;p&gt;The following schema fragment specifies the expected content
868		* contained within this class.
869		*
870		* &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
871		* &amp;lt;restriction
872		* base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
873		* &amp;lt;sequence&amp;gt; &amp;lt;element name="attributeName"
874		* type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
875		* minOccurs="0"/&amp;gt; &amp;lt;element name="matcherSet"
876		* type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&amp;gt;
877		* &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="type" use="required"
878		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
879		* &amp;lt;attribute name="colour" use="required"
880		* type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
881		* name="display" use="required"
882		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
883		* &amp;lt;attribute name="order"
884		* type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
885		* &amp;lt;attribute name="mincolour"
886		* type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
887		* name="noValueColour" type="{www.jalview.org/colours}NoValueColour"
888		* default="Min" /&amp;gt; &amp;lt;attribute name="threshold"
889		* type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
890		* &amp;lt;attribute name="threshstate"
891		* type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
892		* name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
893		* &amp;lt;attribute name="min"
894		* type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
895		* &amp;lt;attribute name="colourByLabel"
896		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
897		* &amp;lt;attribute name="autoScale"
898		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
899		* &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
900		* &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
901		*
902		*
903		*/
904		@XmlAccessorType(XmlAccessType.FIELD)
905		@XmlType(name = "", propOrder = { "attributeName", "matcherSet" })
		96.8% Uncovered Elements: 2 (62) Complexity: 29 Complexity Density: 0.94
906		public static class Setting
907		{
908
909		@XmlElement(namespace = "www.jalview.org")
910		protected List<String> attributeName;
911
912		@XmlElement(namespace = "www.jalview.org")
913		protected FeatureMatcherSet matcherSet;
914
915		@XmlAttribute(name = "type", required = true)
916		protected String type;
917
918		@XmlAttribute(name = "colour", required = true)
919		protected int colour;
920
921		@XmlAttribute(name = "display", required = true)
922		protected boolean display;
923
924		@XmlAttribute(name = "order")
925		protected Float order;
926
927		@XmlAttribute(name = "mincolour")
928		protected Integer mincolour;
929
930		@XmlAttribute(name = "noValueColour")
931		protected NoValueColour noValueColour;
932
933		@XmlAttribute(name = "threshold")
934		protected Float threshold;
935
936		@XmlAttribute(name = "threshstate")
937		protected Integer threshstate;
938
939		@XmlAttribute(name = "max")
940		protected Float max;
941
942		@XmlAttribute(name = "min")
943		protected Float min;
944
945		@XmlAttribute(name = "colourByLabel")
946		protected Boolean colourByLabel;
947
948		@XmlAttribute(name = "autoScale")
949		protected Boolean autoScale;
950
951		/**
952		* Gets the value of the attributeName property.
953		*
954		* &lt;p&gt; This accessor method returns a reference to the live list,
955		* not a snapshot. Therefore any modification you make to the returned
956		* list will be present inside the JAXB object. This is why there is not a
957		* &lt;CODE&gt;set&lt;/CODE&gt; method for the attributeName property.
958		*
959		* &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
960		* getAttributeName().add(newItem); &lt;/pre&gt;
961		*
962		*
963		* &lt;p&gt; Objects of the following type(s) are allowed in the list
964		* {@link String }
965		*
966		*
967		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
968	12	public List<String> getAttributeName()...
969		{
970	12	if (attributeName == null)
971		{
972	5	attributeName = new ArrayList<String>();
973		}
974	12	return this.attributeName;
975		}
976
977		/**
978		* Gets the value of the matcherSet property.
979		*
980		* @return possible object is {@link FeatureMatcherSet }
981		*
982		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
983	812	public FeatureMatcherSet getMatcherSet()...
984		{
985	812	return matcherSet;
986		}
987
988		/**
989		* Sets the value of the matcherSet property.
990		*
991		* @param value
992		* allowed object is {@link FeatureMatcherSet }
993		*
994		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
995	3	public void setMatcherSet(FeatureMatcherSet value)...
996		{
997	3	this.matcherSet = value;
998		}
999
1000		/**
1001		* Gets the value of the type property.
1002		*
1003		* @return possible object is {@link String }
1004		*
1005		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1006	812	public String getType()...
1007		{
1008	812	return type;
1009		}
1010
1011		/**
1012		* Sets the value of the type property.
1013		*
1014		* @param value
1015		* allowed object is {@link String }
1016		*
1017		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1018	191	public void setType(String value)...
1019		{
1020	191	this.type = value;
1021		}
1022
1023		/**
1024		* Gets the value of the colour property.
1025		*
1026		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1027	812	public int getColour()...
1028		{
1029	812	return colour;
1030		}
1031
1032		/**
1033		* Sets the value of the colour property.
1034		*
1035		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1036	191	public void setColour(int value)...
1037		{
1038	191	this.colour = value;
1039		}
1040
1041		/**
1042		* Gets the value of the display property.
1043		*
1044		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1045	812	public boolean isDisplay()...
1046		{
1047	812	return display;
1048		}
1049
1050		/**
1051		* Sets the value of the display property.
1052		*
1053		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1054	191	public void setDisplay(boolean value)...
1055		{
1056	191	this.display = value;
1057		}
1058
1059		/**
1060		* Gets the value of the order property.
1061		*
1062		* @return possible object is {@link Float }
1063		*
1064		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1065	1624	public Float getOrder()...
1066		{
1067	1624	return order;
1068		}
1069
1070		/**
1071		* Sets the value of the order property.
1072		*
1073		* @param value
1074		* allowed object is {@link Float }
1075		*
1076		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1077	191	public void setOrder(Float value)...
1078		{
1079	191	this.order = value;
1080		}
1081
1082		/**
1083		* Gets the value of the mincolour property.
1084		*
1085		* @return possible object is {@link Integer }
1086		*
1087		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1088	817	public Integer getMincolour()...
1089		{
1090	817	return mincolour;
1091		}
1092
1093		/**
1094		* Sets the value of the mincolour property.
1095		*
1096		* @param value
1097		* allowed object is {@link Integer }
1098		*
1099		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1100	4	public void setMincolour(Integer value)...
1101		{
1102	4	this.mincolour = value;
1103		}
1104
1105		/**
1106		* Gets the value of the noValueColour property.
1107		*
1108		* @return possible object is {@link NoValueColour }
1109		*
1110		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
1111	5	public NoValueColour getNoValueColour()...
1112		{
1113	5	if (noValueColour == null)
1114		{
1115	0	return NoValueColour.MIN;
1116		}
1117		else
1118		{
1119	5	return noValueColour;
1120		}
1121		}
1122
1123		/**
1124		* Sets the value of the noValueColour property.
1125		*
1126		* @param value
1127		* allowed object is {@link NoValueColour }
1128		*
1129		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1130	4	public void setNoValueColour(NoValueColour value)...
1131		{
1132	4	this.noValueColour = value;
1133		}
1134
1135		/**
1136		* Gets the value of the threshold property.
1137		*
1138		* @return possible object is {@link Float }
1139		*
1140		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1141	10	public Float getThreshold()...
1142		{
1143	10	return threshold;
1144		}
1145
1146		/**
1147		* Sets the value of the threshold property.
1148		*
1149		* @param value
1150		* allowed object is {@link Float }
1151		*
1152		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1153	4	public void setThreshold(Float value)...
1154		{
1155	4	this.threshold = value;
1156		}
1157
1158		/**
1159		* Gets the value of the threshstate property.
1160		*
1161		* @return possible object is {@link Integer }
1162		*
1163		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1164	5	public Integer getThreshstate()...
1165		{
1166	5	return threshstate;
1167		}
1168
1169		/**
1170		* Sets the value of the threshstate property.
1171		*
1172		* @param value
1173		* allowed object is {@link Integer }
1174		*
1175		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1176	4	public void setThreshstate(Integer value)...
1177		{
1178	4	this.threshstate = value;
1179		}
1180
1181		/**
1182		* Gets the value of the max property.
1183		*
1184		* @return possible object is {@link Float }
1185		*
1186		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1187	10	public Float getMax()...
1188		{
1189	10	return max;
1190		}
1191
1192		/**
1193		* Sets the value of the max property.
1194		*
1195		* @param value
1196		* allowed object is {@link Float }
1197		*
1198		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1199	4	public void setMax(Float value)...
1200		{
1201	4	this.max = value;
1202		}
1203
1204		/**
1205		* Gets the value of the min property.
1206		*
1207		* @return possible object is {@link Float }
1208		*
1209		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1210	5	public Float getMin()...
1211		{
1212	5	return min;
1213		}
1214
1215		/**
1216		* Sets the value of the min property.
1217		*
1218		* @param value
1219		* allowed object is {@link Float }
1220		*
1221		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1222	4	public void setMin(Float value)...
1223		{
1224	4	this.min = value;
1225		}
1226
1227		/**
1228		* Gets the value of the colourByLabel property.
1229		*
1230		* @return possible object is {@link Boolean }
1231		*
1232		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1233	10	public Boolean isColourByLabel()...
1234		{
1235	10	return colourByLabel;
1236		}
1237
1238		/**
1239		* Sets the value of the colourByLabel property.
1240		*
1241		* @param value
1242		* allowed object is {@link Boolean }
1243		*
1244		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1245	4	public void setColourByLabel(Boolean value)...
1246		{
1247	4	this.colourByLabel = value;
1248		}
1249
1250		/**
1251		* Gets the value of the autoScale property.
1252		*
1253		* @return possible object is {@link Boolean }
1254		*
1255		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1256	10	public Boolean isAutoScale()...
1257		{
1258	10	return autoScale;
1259		}
1260
1261		/**
1262		* Sets the value of the autoScale property.
1263		*
1264		* @param value
1265		* allowed object is {@link Boolean }
1266		*
1267		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1268	4	public void setAutoScale(Boolean value)...
1269		{
1270	4	this.autoScale = value;
1271		}
1272
1273		}
1274
1275		}
1276
1277		/**
1278		* &lt;p&gt;Java class for anonymous complex type.
1279		*
1280		* &lt;p&gt;The following schema fragment specifies the expected content
1281		* contained within this class.
1282		*
1283		* &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
1284		* &amp;lt;restriction
1285		* base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
1286		* &amp;lt;sequence&amp;gt; &amp;lt;element name="seq"
1287		* type="{http://www.w3.org/2001/XMLSchema}string"
1288		* maxOccurs="unbounded"/&amp;gt; &amp;lt;element name="annotationColours"
1289		* type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&amp;gt;
1290		* &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="start"
1291		* type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
1292		* name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1293		* &amp;lt;attribute name="name"
1294		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
1295		* name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1296		* &amp;lt;attribute name="consThreshold"
1297		* type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
1298		* name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1299		* &amp;lt;attribute name="outlineColour"
1300		* type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
1301		* name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean"
1302		* /&amp;gt; &amp;lt;attribute name="displayText"
1303		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
1304		* &amp;lt;attribute name="colourText"
1305		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
1306		* &amp;lt;attribute name="textCol1"
1307		* type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
1308		* name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1309		* &amp;lt;attribute name="textColThreshold"
1310		* type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
1311		* name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean"
1312		* /&amp;gt; &amp;lt;attribute name="ignoreGapsinConsensus"
1313		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
1314		* &amp;lt;attribute name="showConsensusHistogram"
1315		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
1316		* &amp;lt;attribute name="showSequenceLogo"
1317		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
1318		* &amp;lt;attribute name="normaliseSequenceLogo"
1319		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
1320		* &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string"
1321		* /&amp;gt; &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
1322		* &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
1323		*
1324		*
1325		*/
1326		@XmlAccessorType(XmlAccessType.FIELD)
1327		@XmlType(name = "", propOrder = { "seq", "annotationColours" })
		94.1% Uncovered Elements: 6 (102) Complexity: 46 Complexity Density: 0.9
1328		public static class JGroup
1329		{
1330
1331		@XmlElement(namespace = "www.jalview.org", required = true)
1332		protected List<String> seq;
1333
1334		@XmlElement(namespace = "www.jalview.org")
1335		protected AnnotationColourScheme annotationColours;
1336
1337		@XmlAttribute(name = "start")
1338		protected Integer start;
1339
1340		@XmlAttribute(name = "end")
1341		protected Integer end;
1342
1343		@XmlAttribute(name = "name")
1344		protected String name;
1345
1346		@XmlAttribute(name = "colour")
1347		protected String colour;
1348
1349		@XmlAttribute(name = "consThreshold")
1350		protected Integer consThreshold;
1351
1352		@XmlAttribute(name = "pidThreshold")
1353		protected Integer pidThreshold;
1354
1355		@XmlAttribute(name = "outlineColour")
1356		protected Integer outlineColour;
1357
1358		@XmlAttribute(name = "displayBoxes")
1359		protected Boolean displayBoxes;
1360
1361		@XmlAttribute(name = "displayText")
1362		protected Boolean displayText;
1363
1364		@XmlAttribute(name = "colourText")
1365		protected Boolean colourText;
1366
1367		@XmlAttribute(name = "textCol1")
1368		protected Integer textCol1;
1369
1370		@XmlAttribute(name = "textCol2")
1371		protected Integer textCol2;
1372
1373		@XmlAttribute(name = "textColThreshold")
1374		protected Integer textColThreshold;
1375
1376		@XmlAttribute(name = "showUnconserved")
1377		protected Boolean showUnconserved;
1378
1379		@XmlAttribute(name = "ignoreGapsinConsensus")
1380		protected Boolean ignoreGapsinConsensus;
1381
1382		@XmlAttribute(name = "showConsensusHistogram")
1383		protected Boolean showConsensusHistogram;
1384
1385		@XmlAttribute(name = "showSequenceLogo")
1386		protected Boolean showSequenceLogo;
1387
1388		@XmlAttribute(name = "normaliseSequenceLogo")
1389		protected Boolean normaliseSequenceLogo;
1390
1391		@XmlAttribute(name = "id")
1392		protected String id;
1393
1394		/**
1395		* Gets the value of the seq property.
1396		*
1397		* &lt;p&gt; This accessor method returns a reference to the live list, not
1398		* a snapshot. Therefore any modification you make to the returned list will
1399		* be present inside the JAXB object. This is why there is not a
1400		* &lt;CODE&gt;set&lt;/CODE&gt; method for the seq property.
1401		*
1402		* &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
1403		* getSeq().add(newItem); &lt;/pre&gt;
1404		*
1405		*
1406		* &lt;p&gt; Objects of the following type(s) are allowed in the list
1407		* {@link String }
1408		*
1409		*
1410		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
1411	929	public List<String> getSeq()...
1412		{
1413	929	if (seq == null)
1414		{
1415	15	seq = new ArrayList<String>();
1416		}
1417	929	return this.seq;
1418		}
1419
1420		/**
1421		* Gets the value of the annotationColours property.
1422		*
1423		* @return possible object is {@link AnnotationColourScheme }
1424		*
1425		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1426	2	public AnnotationColourScheme getAnnotationColours()...
1427		{
1428	2	return annotationColours;
1429		}
1430
1431		/**
1432		* Sets the value of the annotationColours property.
1433		*
1434		* @param value
1435		* allowed object is {@link AnnotationColourScheme }
1436		*
1437		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1438	1	public void setAnnotationColours(AnnotationColourScheme value)...
1439		{
1440	1	this.annotationColours = value;
1441		}
1442
1443		/**
1444		* Gets the value of the start property.
1445		*
1446		* @return possible object is {@link Integer }
1447		*
1448		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1449	47	public Integer getStart()...
1450		{
1451	47	return start;
1452		}
1453
1454		/**
1455		* Sets the value of the start property.
1456		*
1457		* @param value
1458		* allowed object is {@link Integer }
1459		*
1460		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1461	15	public void setStart(Integer value)...
1462		{
1463	15	this.start = value;
1464		}
1465
1466		/**
1467		* Gets the value of the end property.
1468		*
1469		* @return possible object is {@link Integer }
1470		*
1471		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1472	47	public Integer getEnd()...
1473		{
1474	47	return end;
1475		}
1476
1477		/**
1478		* Sets the value of the end property.
1479		*
1480		* @param value
1481		* allowed object is {@link Integer }
1482		*
1483		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1484	15	public void setEnd(Integer value)...
1485		{
1486	15	this.end = value;
1487		}
1488
1489		/**
1490		* Gets the value of the name property.
1491		*
1492		* @return possible object is {@link String }
1493		*
1494		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1495	47	public String getName()...
1496		{
1497	47	return name;
1498		}
1499
1500		/**
1501		* Sets the value of the name property.
1502		*
1503		* @param value
1504		* allowed object is {@link String }
1505		*
1506		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1507	15	public void setName(String value)...
1508		{
1509	15	this.name = value;
1510		}
1511
1512		/**
1513		* Gets the value of the colour property.
1514		*
1515		* @return possible object is {@link String }
1516		*
1517		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1518	115	public String getColour()...
1519		{
1520	115	return colour;
1521		}
1522
1523		/**
1524		* Sets the value of the colour property.
1525		*
1526		* @param value
1527		* allowed object is {@link String }
1528		*
1529		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1530	9	public void setColour(String value)...
1531		{
1532	9	this.colour = value;
1533		}
1534
1535		/**
1536		* Gets the value of the consThreshold property.
1537		*
1538		* @return possible object is {@link Integer }
1539		*
1540		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1541	96	public Integer getConsThreshold()...
1542		{
1543	96	return consThreshold;
1544		}
1545
1546		/**
1547		* Sets the value of the consThreshold property.
1548		*
1549		* @param value
1550		* allowed object is {@link Integer }
1551		*
1552		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1553	2	public void setConsThreshold(Integer value)...
1554		{
1555	2	this.consThreshold = value;
1556		}
1557
1558		/**
1559		* Gets the value of the pidThreshold property.
1560		*
1561		* @return possible object is {@link Integer }
1562		*
1563		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1564	47	public Integer getPidThreshold()...
1565		{
1566	47	return pidThreshold;
1567		}
1568
1569		/**
1570		* Sets the value of the pidThreshold property.
1571		*
1572		* @param value
1573		* allowed object is {@link Integer }
1574		*
1575		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1576	9	public void setPidThreshold(Integer value)...
1577		{
1578	9	this.pidThreshold = value;
1579		}
1580
1581		/**
1582		* Gets the value of the outlineColour property.
1583		*
1584		* @return possible object is {@link Integer }
1585		*
1586		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1587	47	public Integer getOutlineColour()...
1588		{
1589	47	return outlineColour;
1590		}
1591
1592		/**
1593		* Sets the value of the outlineColour property.
1594		*
1595		* @param value
1596		* allowed object is {@link Integer }
1597		*
1598		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1599	15	public void setOutlineColour(Integer value)...
1600		{
1601	15	this.outlineColour = value;
1602		}
1603
1604		/**
1605		* Gets the value of the displayBoxes property.
1606		*
1607		* @return possible object is {@link Boolean }
1608		*
1609		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1610	47	public Boolean isDisplayBoxes()...
1611		{
1612	47	return displayBoxes;
1613		}
1614
1615		/**
1616		* Sets the value of the displayBoxes property.
1617		*
1618		* @param value
1619		* allowed object is {@link Boolean }
1620		*
1621		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1622	15	public void setDisplayBoxes(Boolean value)...
1623		{
1624	15	this.displayBoxes = value;
1625		}
1626
1627		/**
1628		* Gets the value of the displayText property.
1629		*
1630		* @return possible object is {@link Boolean }
1631		*
1632		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1633	47	public Boolean isDisplayText()...
1634		{
1635	47	return displayText;
1636		}
1637
1638		/**
1639		* Sets the value of the displayText property.
1640		*
1641		* @param value
1642		* allowed object is {@link Boolean }
1643		*
1644		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1645	15	public void setDisplayText(Boolean value)...
1646		{
1647	15	this.displayText = value;
1648		}
1649
1650		/**
1651		* Gets the value of the colourText property.
1652		*
1653		* @return possible object is {@link Boolean }
1654		*
1655		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1656	47	public Boolean isColourText()...
1657		{
1658	47	return colourText;
1659		}
1660
1661		/**
1662		* Sets the value of the colourText property.
1663		*
1664		* @param value
1665		* allowed object is {@link Boolean }
1666		*
1667		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1668	15	public void setColourText(Boolean value)...
1669		{
1670	15	this.colourText = value;
1671		}
1672
1673		/**
1674		* Gets the value of the textCol1 property.
1675		*
1676		* @return possible object is {@link Integer }
1677		*
1678		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1679	47	public Integer getTextCol1()...
1680		{
1681	47	return textCol1;
1682		}
1683
1684		/**
1685		* Sets the value of the textCol1 property.
1686		*
1687		* @param value
1688		* allowed object is {@link Integer }
1689		*
1690		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1691	15	public void setTextCol1(Integer value)...
1692		{
1693	15	this.textCol1 = value;
1694		}
1695
1696		/**
1697		* Gets the value of the textCol2 property.
1698		*
1699		* @return possible object is {@link Integer }
1700		*
1701		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1702	47	public Integer getTextCol2()...
1703		{
1704	47	return textCol2;
1705		}
1706
1707		/**
1708		* Sets the value of the textCol2 property.
1709		*
1710		* @param value
1711		* allowed object is {@link Integer }
1712		*
1713		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1714	15	public void setTextCol2(Integer value)...
1715		{
1716	15	this.textCol2 = value;
1717		}
1718
1719		/**
1720		* Gets the value of the textColThreshold property.
1721		*
1722		* @return possible object is {@link Integer }
1723		*
1724		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1725	47	public Integer getTextColThreshold()...
1726		{
1727	47	return textColThreshold;
1728		}
1729
1730		/**
1731		* Sets the value of the textColThreshold property.
1732		*
1733		* @param value
1734		* allowed object is {@link Integer }
1735		*
1736		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1737	15	public void setTextColThreshold(Integer value)...
1738		{
1739	15	this.textColThreshold = value;
1740		}
1741
1742		/**
1743		* Gets the value of the showUnconserved property.
1744		*
1745		* @return possible object is {@link Boolean }
1746		*
1747		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1748	47	public Boolean isShowUnconserved()...
1749		{
1750	47	return showUnconserved;
1751		}
1752
1753		/**
1754		* Sets the value of the showUnconserved property.
1755		*
1756		* @param value
1757		* allowed object is {@link Boolean }
1758		*
1759		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1760	15	public void setShowUnconserved(Boolean value)...
1761		{
1762	15	this.showUnconserved = value;
1763		}
1764
1765		/**
1766		* Gets the value of the ignoreGapsinConsensus property.
1767		*
1768		* @return possible object is {@link Boolean }
1769		*
1770		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
1771	47	public boolean isIgnoreGapsinConsensus()...
1772		{
1773	47	if (ignoreGapsinConsensus == null)
1774		{
1775	0	return true;
1776		}
1777		else
1778		{
1779	47	return ignoreGapsinConsensus;
1780		}
1781		}
1782
1783		/**
1784		* Sets the value of the ignoreGapsinConsensus property.
1785		*
1786		* @param value
1787		* allowed object is {@link Boolean }
1788		*
1789		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1790	15	public void setIgnoreGapsinConsensus(Boolean value)...
1791		{
1792	15	this.ignoreGapsinConsensus = value;
1793		}
1794
1795		/**
1796		* Gets the value of the showConsensusHistogram property.
1797		*
1798		* @return possible object is {@link Boolean }
1799		*
1800		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
1801	47	public boolean isShowConsensusHistogram()...
1802		{
1803	47	if (showConsensusHistogram == null)
1804		{
1805	0	return true;
1806		}
1807		else
1808		{
1809	47	return showConsensusHistogram;
1810		}
1811		}
1812
1813		/**
1814		* Sets the value of the showConsensusHistogram property.
1815		*
1816		* @param value
1817		* allowed object is {@link Boolean }
1818		*
1819		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1820	15	public void setShowConsensusHistogram(Boolean value)...
1821		{
1822	15	this.showConsensusHistogram = value;
1823		}
1824
1825		/**
1826		* Gets the value of the showSequenceLogo property.
1827		*
1828		* @return possible object is {@link Boolean }
1829		*
1830		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
1831	47	public boolean isShowSequenceLogo()...
1832		{
1833	47	if (showSequenceLogo == null)
1834		{
1835	0	return false;
1836		}
1837		else
1838		{
1839	47	return showSequenceLogo;
1840		}
1841		}
1842
1843		/**
1844		* Sets the value of the showSequenceLogo property.
1845		*
1846		* @param value
1847		* allowed object is {@link Boolean }
1848		*
1849		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1850	15	public void setShowSequenceLogo(Boolean value)...
1851		{
1852	15	this.showSequenceLogo = value;
1853		}
1854
1855		/**
1856		* Gets the value of the normaliseSequenceLogo property.
1857		*
1858		* @return possible object is {@link Boolean }
1859		*
1860		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
1861	47	public boolean isNormaliseSequenceLogo()...
1862		{
1863	47	if (normaliseSequenceLogo == null)
1864		{
1865	30	return false;
1866		}
1867		else
1868		{
1869	17	return normaliseSequenceLogo;
1870		}
1871		}
1872
1873		/**
1874		* Sets the value of the normaliseSequenceLogo property.
1875		*
1876		* @param value
1877		* allowed object is {@link Boolean }
1878		*
1879		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1880	15	public void setNormaliseSequenceLogo(Boolean value)...
1881		{
1882	15	this.normaliseSequenceLogo = value;
1883		}
1884
1885		/**
1886		* Gets the value of the id property.
1887		*
1888		* @return possible object is {@link String }
1889		*
1890		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1891	71	public String getId()...
1892		{
1893	71	return id;
1894		}
1895
1896		/**
1897		* Sets the value of the id property.
1898		*
1899		* @param value
1900		* allowed object is {@link String }
1901		*
1902		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1903	6	public void setId(String value)...
1904		{
1905	6	this.id = value;
1906		}
1907
1908		}
1909
1910		/**
1911		* &lt;p&gt;Java class for anonymous complex type.
1912		*
1913		* &lt;p&gt;The following schema fragment specifies the expected content
1914		* contained within this class.
1915		*
1916		* &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
1917		* &amp;lt;restriction
1918		* base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
1919		* &amp;lt;sequence&amp;gt; &amp;lt;element name="features"
1920		* type="{www.jalview.org}feature" maxOccurs="unbounded"
1921		* minOccurs="0"/&amp;gt; &amp;lt;element name="pdbids" maxOccurs="unbounded"
1922		* minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
1923		* &amp;lt;complexContent&amp;gt; &amp;lt;extension
1924		* base="{www.jalview.org}pdbentry"&amp;gt; &amp;lt;sequence&amp;gt;
1925		* &amp;lt;element name="structureState" maxOccurs="unbounded"
1926		* minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
1927		* &amp;lt;simpleContent&amp;gt; &amp;lt;extension
1928		* base="&amp;lt;http://www.w3.org/2001/XMLSchema&amp;gt;string"&amp;gt;
1929		* &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
1930		* &amp;lt;attribute name="visible"
1931		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
1932		* &amp;lt;attribute name="viewId"
1933		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
1934		* name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean"
1935		* default="true" /&amp;gt; &amp;lt;attribute name="colourwithAlignPanel"
1936		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
1937		* &amp;lt;attribute name="colourByJmol"
1938		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
1939		* &amp;lt;attribute name="type"
1940		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1941		* &amp;lt;/extension&amp;gt; &amp;lt;/simpleContent&amp;gt;
1942		* &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
1943		* &amp;lt;/sequence&amp;gt; &amp;lt;/extension&amp;gt;
1944		* &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt;
1945		* &amp;lt;/element&amp;gt; &amp;lt;element name="hiddenSequences"
1946		* type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded"
1947		* minOccurs="0"/&amp;gt; &amp;lt;element name="rnaViewer"
1948		* maxOccurs="unbounded" minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
1949		* &amp;lt;complexContent&amp;gt; &amp;lt;restriction
1950		* base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
1951		* &amp;lt;sequence&amp;gt; &amp;lt;element name="secondaryStructure"
1952		* maxOccurs="unbounded"&amp;gt; &amp;lt;complexType&amp;gt;
1953		* &amp;lt;complexContent&amp;gt; &amp;lt;restriction
1954		* base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
1955		* name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1956		* &amp;lt;attribute name="annotationId" use="required"
1957		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
1958		* name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
1959		* &amp;lt;attribute name="viewerState"
1960		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1961		* &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
1962		* &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
1963		* &amp;lt;/sequence&amp;gt; &amp;lt;attGroup
1964		* ref="{www.jalview.org}swingwindow"/&amp;gt; &amp;lt;attribute name="title"
1965		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
1966		* name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1967		* &amp;lt;attribute name="dividerLocation"
1968		* type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
1969		* name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1970		* &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
1971		* &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
1972		* &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="colour"
1973		* type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
1974		* name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
1975		* /&amp;gt; &amp;lt;attribute name="end" use="required"
1976		* type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
1977		* name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
1978		* /&amp;gt; &amp;lt;attribute name="hidden"
1979		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
1980		* &amp;lt;attribute name="viewreference"
1981		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
1982		* &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
1983		* &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
1984		*
1985		*
1986		*/
1987		@XmlAccessorType(XmlAccessType.FIELD)
1988		@XmlType(
1989		name = "",
1990		propOrder =
1991		{ "features", "pdbids", "hiddenSequences", "rnaViewer" })
		97.9% Uncovered Elements: 1 (48) Complexity: 20 Complexity Density: 0.83
1992		public static class JSeq
1993		{
1994
1995		@XmlElement(namespace = "www.jalview.org")
1996		protected List<Feature> features;
1997
1998		@XmlElement(namespace = "www.jalview.org")
1999		protected List<JalviewModel.JSeq.Pdbids> pdbids;
2000
2001		@XmlElement(namespace = "www.jalview.org", type = Integer.class)
2002		protected List<Integer> hiddenSequences;
2003
2004		@XmlElement(namespace = "www.jalview.org")
2005		protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
2006
2007		@XmlAttribute(name = "colour")
2008		protected Integer colour;
2009
2010		@XmlAttribute(name = "start", required = true)
2011		protected int start;
2012
2013		@XmlAttribute(name = "end", required = true)
2014		protected int end;
2015
2016		@XmlAttribute(name = "id", required = true)
2017		protected String id;
2018
2019		@XmlAttribute(name = "hidden")
2020		protected Boolean hidden;
2021
2022		@XmlAttribute(name = "viewreference")
2023		protected Boolean viewreference;
2024
2025		/**
2026		* Gets the value of the features property.
2027		*
2028		* &lt;p&gt; This accessor method returns a reference to the live list, not
2029		* a snapshot. Therefore any modification you make to the returned list will
2030		* be present inside the JAXB object. This is why there is not a
2031		* &lt;CODE&gt;set&lt;/CODE&gt; method for the features property.
2032		*
2033		* &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
2034		* getFeatures().add(newItem); &lt;/pre&gt;
2035		*
2036		*
2037		* &lt;p&gt; Objects of the following type(s) are allowed in the list
2038		* {@link Feature }
2039		*
2040		*
2041		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
2042	11962	public List<Feature> getFeatures()...
2043		{
2044	11962	if (features == null)
2045		{
2046	912	features = new ArrayList<Feature>();
2047		}
2048	11962	return this.features;
2049		}
2050
2051		/**
2052		* Gets the value of the pdbids property.
2053		*
2054		* &lt;p&gt; This accessor method returns a reference to the live list, not
2055		* a snapshot. Therefore any modification you make to the returned list will
2056		* be present inside the JAXB object. This is why there is not a
2057		* &lt;CODE&gt;set&lt;/CODE&gt; method for the pdbids property.
2058		*
2059		* &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
2060		* getPdbids().add(newItem); &lt;/pre&gt;
2061		*
2062		*
2063		* &lt;p&gt; Objects of the following type(s) are allowed in the list
2064		* {@link JalviewModel.JSeq.Pdbids }
2065		*
2066		*
2067		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
2068	2178	public List<JalviewModel.JSeq.Pdbids> getPdbids()...
2069		{
2070	2178	if (pdbids == null)
2071		{
2072	1439	pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
2073		}
2074	2178	return this.pdbids;
2075		}
2076
2077		/**
2078		* Gets the value of the hiddenSequences property.
2079		*
2080		* &lt;p&gt; This accessor method returns a reference to the live list, not
2081		* a snapshot. Therefore any modification you make to the returned list will
2082		* be present inside the JAXB object. This is why there is not a
2083		* &lt;CODE&gt;set&lt;/CODE&gt; method for the hiddenSequences property.
2084		*
2085		* &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
2086		* getHiddenSequences().add(newItem); &lt;/pre&gt;
2087		*
2088		*
2089		* &lt;p&gt; Objects of the following type(s) are allowed in the list
2090		* {@link Integer }
2091		*
2092		*
2093		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
2094	676	public List<Integer> getHiddenSequences()...
2095		{
2096	676	if (hiddenSequences == null)
2097		{
2098	670	hiddenSequences = new ArrayList<Integer>();
2099		}
2100	676	return this.hiddenSequences;
2101		}
2102
2103		/**
2104		* Gets the value of the rnaViewer property.
2105		*
2106		* &lt;p&gt; This accessor method returns a reference to the live list, not
2107		* a snapshot. Therefore any modification you make to the returned list will
2108		* be present inside the JAXB object. This is why there is not a
2109		* &lt;CODE&gt;set&lt;/CODE&gt; method for the rnaViewer property.
2110		*
2111		* &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
2112		* getRnaViewer().add(newItem); &lt;/pre&gt;
2113		*
2114		*
2115		* &lt;p&gt; Objects of the following type(s) are allowed in the list
2116		* {@link JalviewModel.JSeq.RnaViewer }
2117		*
2118		*
2119		*/
		80% Uncovered Elements: 1 (5) Complexity: 2 Complexity Density: 0.67
2120	1070	public List<JalviewModel.JSeq.RnaViewer> getRnaViewer()...
2121		{
2122	1070	if (rnaViewer == null)
2123		{
2124	1070	rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2125		}
2126	1070	return this.rnaViewer;
2127		}
2128
2129		/**
2130		* Gets the value of the colour property.
2131		*
2132		* @return possible object is {@link Integer }
2133		*
2134		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2135	1192	public Integer getColour()...
2136		{
2137	1192	return colour;
2138		}
2139
2140		/**
2141		* Sets the value of the colour property.
2142		*
2143		* @param value
2144		* allowed object is {@link Integer }
2145		*
2146		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2147	949	public void setColour(Integer value)...
2148		{
2149	949	this.colour = value;
2150		}
2151
2152		/**
2153		* Gets the value of the start property.
2154		*
2155		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2156	2608	public int getStart()...
2157		{
2158	2608	return start;
2159		}
2160
2161		/**
2162		* Sets the value of the start property.
2163		*
2164		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2165	949	public void setStart(int value)...
2166		{
2167	949	this.start = value;
2168		}
2169
2170		/**
2171		* Gets the value of the end property.
2172		*
2173		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2174	2608	public int getEnd()...
2175		{
2176	2608	return end;
2177		}
2178
2179		/**
2180		* Sets the value of the end property.
2181		*
2182		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2183	949	public void setEnd(int value)...
2184		{
2185	949	this.end = value;
2186		}
2187
2188		/**
2189		* Gets the value of the id property.
2190		*
2191		* @return possible object is {@link String }
2192		*
2193		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2194	1600	public String getId()...
2195		{
2196	1600	return id;
2197		}
2198
2199		/**
2200		* Sets the value of the id property.
2201		*
2202		* @param value
2203		* allowed object is {@link String }
2204		*
2205		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2206	949	public void setId(String value)...
2207		{
2208	949	this.id = value;
2209		}
2210
2211		/**
2212		* Gets the value of the hidden property.
2213		*
2214		* @return possible object is {@link Boolean }
2215		*
2216		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2217	2190	public Boolean isHidden()...
2218		{
2219	2190	return hidden;
2220		}
2221
2222		/**
2223		* Sets the value of the hidden property.
2224		*
2225		* @param value
2226		* allowed object is {@link Boolean }
2227		*
2228		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2229	190	public void setHidden(Boolean value)...
2230		{
2231	190	this.hidden = value;
2232		}
2233
2234		/**
2235		* Gets the value of the viewreference property.
2236		*
2237		* @return possible object is {@link Boolean }
2238		*
2239		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2240	1520	public Boolean isViewreference()...
2241		{
2242	1520	return viewreference;
2243		}
2244
2245		/**
2246		* Sets the value of the viewreference property.
2247		*
2248		* @param value
2249		* allowed object is {@link Boolean }
2250		*
2251		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2252	80	public void setViewreference(Boolean value)...
2253		{
2254	80	this.viewreference = value;
2255		}
2256
2257		/**
2258		* &lt;p&gt;Java class for anonymous complex type.
2259		*
2260		* &lt;p&gt;The following schema fragment specifies the expected content
2261		* contained within this class.
2262		*
2263		* &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
2264		* &amp;lt;extension base="{www.jalview.org}pdbentry"&amp;gt;
2265		* &amp;lt;sequence&amp;gt; &amp;lt;element name="structureState"
2266		* maxOccurs="unbounded" minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
2267		* &amp;lt;simpleContent&amp;gt; &amp;lt;extension
2268		* base="&amp;lt;http://www.w3.org/2001/XMLSchema&amp;gt;string"&amp;gt;
2269		* &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
2270		* &amp;lt;attribute name="visible"
2271		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
2272		* &amp;lt;attribute name="viewId"
2273		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2274		* &amp;lt;attribute name="alignwithAlignPanel"
2275		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
2276		* &amp;lt;attribute name="colourwithAlignPanel"
2277		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
2278		* /&amp;gt; &amp;lt;attribute name="colourByJmol"
2279		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
2280		* &amp;lt;attribute name="type"
2281		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2282		* &amp;lt;/extension&amp;gt; &amp;lt;/simpleContent&amp;gt;
2283		* &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
2284		* &amp;lt;/sequence&amp;gt; &amp;lt;/extension&amp;gt;
2285		* &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
2286		*
2287		*
2288		*/
2289		@XmlAccessorType(XmlAccessType.FIELD)
2290		@XmlType(name = "", propOrder = { "structureState" })
		100% Uncovered Elements: 0 (6) Complexity: 2 Complexity Density: 0.67
2291		public static class Pdbids extends Pdbentry
2292		{
2293
2294		@XmlElement(namespace = "www.jalview.org")
2295		protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2296
2297		/**
2298		* Gets the value of the structureState property.
2299		*
2300		* &lt;p&gt; This accessor method returns a reference to the live list,
2301		* not a snapshot. Therefore any modification you make to the returned
2302		* list will be present inside the JAXB object. This is why there is not a
2303		* &lt;CODE&gt;set&lt;/CODE&gt; method for the structureState property.
2304		*
2305		* &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
2306		* getStructureState().add(newItem); &lt;/pre&gt;
2307		*
2308		*
2309		* &lt;p&gt; Objects of the following type(s) are allowed in the list
2310		* {@link JalviewModel.JSeq.Pdbids.StructureState }
2311		*
2312		*
2313		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
2314	297	public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState()...
2315		{
2316	297	if (structureState == null)
2317		{
2318	137	structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2319		}
2320	297	return this.structureState;
2321		}
2322
2323		/**
2324		* &lt;p&gt;Java class for anonymous complex type.
2325		*
2326		* &lt;p&gt;The following schema fragment specifies the expected content
2327		* contained within this class.
2328		*
2329		* &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;simpleContent&amp;gt;
2330		* &amp;lt;extension
2331		* base="&amp;lt;http://www.w3.org/2001/XMLSchema&amp;gt;string"&amp;gt;
2332		* &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
2333		* &amp;lt;attribute name="visible"
2334		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
2335		* &amp;lt;attribute name="viewId"
2336		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2337		* &amp;lt;attribute name="alignwithAlignPanel"
2338		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="true"
2339		* /&amp;gt; &amp;lt;attribute name="colourwithAlignPanel"
2340		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
2341		* /&amp;gt; &amp;lt;attribute name="colourByJmol"
2342		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="true"
2343		* /&amp;gt; &amp;lt;attribute name="type"
2344		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2345		* &amp;lt;/extension&amp;gt; &amp;lt;/simpleContent&amp;gt;
2346		* &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
2347		*
2348		*
2349		*/
2350		@XmlAccessorType(XmlAccessType.FIELD)
2351		@XmlType(name = "", propOrder = { "value" })
		82.1% Uncovered Elements: 10 (56) Complexity: 25 Complexity Density: 0.89
2352		public static class StructureState
2353		{
2354
2355		@XmlValue
2356		protected String value;
2357
2358		@XmlAttribute(name = "visible")
2359		protected Boolean visible;
2360
2361		@XmlAttribute(name = "viewId")
2362		protected String viewId;
2363
2364		@XmlAttribute(name = "alignwithAlignPanel")
2365		protected Boolean alignwithAlignPanel;
2366
2367		@XmlAttribute(name = "colourwithAlignPanel")
2368		protected Boolean colourwithAlignPanel;
2369
2370		@XmlAttribute(name = "colourByJmol")
2371		protected Boolean colourByJmol;
2372
2373		@XmlAttribute(name = "type")
2374		protected String type;
2375
2376		@XmlAttribute(name = "width")
2377		protected Integer width;
2378
2379		@XmlAttribute(name = "height")
2380		protected Integer height;
2381
2382		@XmlAttribute(name = "xpos")
2383		protected Integer xpos;
2384
2385		@XmlAttribute(name = "ypos")
2386		protected Integer ypos;
2387
2388		/**
2389		* Gets the value of the value property.
2390		*
2391		* @return possible object is {@link String }
2392		*
2393		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2394	110	public String getValue()...
2395		{
2396	110	return value;
2397		}
2398
2399		/**
2400		* Sets the value of the value property.
2401		*
2402		* @param value
2403		* allowed object is {@link String }
2404		*
2405		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2406	0	public void setValue(String value)...
2407		{
2408	0	this.value = value;
2409		}
2410
2411		/**
2412		* Gets the value of the visible property.
2413		*
2414		* @return possible object is {@link Boolean }
2415		*
2416		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2417	0	public Boolean isVisible()...
2418		{
2419	0	return visible;
2420		}
2421
2422		/**
2423		* Sets the value of the visible property.
2424		*
2425		* @param value
2426		* allowed object is {@link Boolean }
2427		*
2428		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2429	20	public void setVisible(Boolean value)...
2430		{
2431	20	this.visible = value;
2432		}
2433
2434		/**
2435		* Gets the value of the viewId property.
2436		*
2437		* @return possible object is {@link String }
2438		*
2439		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2440	200	public String getViewId()...
2441		{
2442	200	return viewId;
2443		}
2444
2445		/**
2446		* Sets the value of the viewId property.
2447		*
2448		* @param value
2449		* allowed object is {@link String }
2450		*
2451		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2452	20	public void setViewId(String value)...
2453		{
2454	20	this.viewId = value;
2455		}
2456
2457		/**
2458		* Gets the value of the alignwithAlignPanel property.
2459		*
2460		* @return possible object is {@link Boolean }
2461		*
2462		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
2463	80	public boolean isAlignwithAlignPanel()...
2464		{
2465	80	if (alignwithAlignPanel == null)
2466		{
2467	0	return true;
2468		}
2469		else
2470		{
2471	80	return alignwithAlignPanel;
2472		}
2473		}
2474
2475		/**
2476		* Sets the value of the alignwithAlignPanel property.
2477		*
2478		* @param value
2479		* allowed object is {@link Boolean }
2480		*
2481		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2482	20	public void setAlignwithAlignPanel(Boolean value)...
2483		{
2484	20	this.alignwithAlignPanel = value;
2485		}
2486
2487		/**
2488		* Gets the value of the colourwithAlignPanel property.
2489		*
2490		* @return possible object is {@link Boolean }
2491		*
2492		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
2493	80	public boolean isColourwithAlignPanel()...
2494		{
2495	80	if (colourwithAlignPanel == null)
2496		{
2497	0	return false;
2498		}
2499		else
2500		{
2501	80	return colourwithAlignPanel;
2502		}
2503		}
2504
2505		/**
2506		* Sets the value of the colourwithAlignPanel property.
2507		*
2508		* @param value
2509		* allowed object is {@link Boolean }
2510		*
2511		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2512	20	public void setColourwithAlignPanel(Boolean value)...
2513		{
2514	20	this.colourwithAlignPanel = value;
2515		}
2516
2517		/**
2518		* Gets the value of the colourByJmol property.
2519		*
2520		* @return possible object is {@link Boolean }
2521		*
2522		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
2523	80	public boolean isColourByJmol()...
2524		{
2525	80	if (colourByJmol == null)
2526		{
2527	0	return true;
2528		}
2529		else
2530		{
2531	80	return colourByJmol;
2532		}
2533		}
2534
2535		/**
2536		* Sets the value of the colourByJmol property.
2537		*
2538		* @param value
2539		* allowed object is {@link Boolean }
2540		*
2541		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2542	20	public void setColourByJmol(Boolean value)...
2543		{
2544	20	this.colourByJmol = value;
2545		}
2546
2547		/**
2548		* Gets the value of the type property.
2549		*
2550		* @return possible object is {@link String }
2551		*
2552		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2553	40	public String getType()...
2554		{
2555	40	return type;
2556		}
2557
2558		/**
2559		* Sets the value of the type property.
2560		*
2561		* @param value
2562		* allowed object is {@link String }
2563		*
2564		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2565	20	public void setType(String value)...
2566		{
2567	20	this.type = value;
2568		}
2569
2570		/**
2571		* Gets the value of the width property.
2572		*
2573		* @return possible object is {@link Integer }
2574		*
2575		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2576	80	public Integer getWidth()...
2577		{
2578	80	return width;
2579		}
2580
2581		/**
2582		* Sets the value of the width property.
2583		*
2584		* @param value
2585		* allowed object is {@link Integer }
2586		*
2587		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2588	20	public void setWidth(Integer value)...
2589		{
2590	20	this.width = value;
2591		}
2592
2593		/**
2594		* Gets the value of the height property.
2595		*
2596		* @return possible object is {@link Integer }
2597		*
2598		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2599	80	public Integer getHeight()...
2600		{
2601	80	return height;
2602		}
2603
2604		/**
2605		* Sets the value of the height property.
2606		*
2607		* @param value
2608		* allowed object is {@link Integer }
2609		*
2610		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2611	20	public void setHeight(Integer value)...
2612		{
2613	20	this.height = value;
2614		}
2615
2616		/**
2617		* Gets the value of the xpos property.
2618		*
2619		* @return possible object is {@link Integer }
2620		*
2621		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2622	80	public Integer getXpos()...
2623		{
2624	80	return xpos;
2625		}
2626
2627		/**
2628		* Sets the value of the xpos property.
2629		*
2630		* @param value
2631		* allowed object is {@link Integer }
2632		*
2633		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2634	20	public void setXpos(Integer value)...
2635		{
2636	20	this.xpos = value;
2637		}
2638
2639		/**
2640		* Gets the value of the ypos property.
2641		*
2642		* @return possible object is {@link Integer }
2643		*
2644		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2645	80	public Integer getYpos()...
2646		{
2647	80	return ypos;
2648		}
2649
2650		/**
2651		* Sets the value of the ypos property.
2652		*
2653		* @param value
2654		* allowed object is {@link Integer }
2655		*
2656		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2657	20	public void setYpos(Integer value)...
2658		{
2659	20	this.ypos = value;
2660		}
2661
2662		}
2663
2664		}
2665
2666		/**
2667		* &lt;p&gt;Java class for anonymous complex type.
2668		*
2669		* &lt;p&gt;The following schema fragment specifies the expected content
2670		* contained within this class.
2671		*
2672		* &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
2673		* &amp;lt;restriction
2674		* base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
2675		* &amp;lt;sequence&amp;gt; &amp;lt;element name="secondaryStructure"
2676		* maxOccurs="unbounded"&amp;gt; &amp;lt;complexType&amp;gt;
2677		* &amp;lt;complexContent&amp;gt; &amp;lt;restriction
2678		* base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
2679		* &amp;lt;attribute name="title"
2680		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2681		* &amp;lt;attribute name="annotationId" use="required"
2682		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2683		* &amp;lt;attribute name="gapped"
2684		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
2685		* &amp;lt;attribute name="viewerState"
2686		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2687		* &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
2688		* &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
2689		* &amp;lt;/sequence&amp;gt; &amp;lt;attGroup
2690		* ref="{www.jalview.org}swingwindow"/&amp;gt; &amp;lt;attribute
2691		* name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2692		* &amp;lt;attribute name="viewId"
2693		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2694		* &amp;lt;attribute name="dividerLocation"
2695		* type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
2696		* name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
2697		* &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
2698		* &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
2699		*
2700		*
2701		*/
2702		@XmlAccessorType(XmlAccessType.FIELD)
2703		@XmlType(name = "", propOrder = { "secondaryStructure" })
		0% Uncovered Elements: 38 (38) Complexity: 18 Complexity Density: 0.95
2704		public static class RnaViewer
2705		{
2706
2707		@XmlElement(namespace = "www.jalview.org", required = true)
2708		protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
2709
2710		@XmlAttribute(name = "title")
2711		protected String title;
2712
2713		@XmlAttribute(name = "viewId")
2714		protected String viewId;
2715
2716		@XmlAttribute(name = "dividerLocation")
2717		protected Integer dividerLocation;
2718
2719		@XmlAttribute(name = "selectedRna")
2720		protected Integer selectedRna;
2721
2722		@XmlAttribute(name = "width")
2723		protected Integer width;
2724
2725		@XmlAttribute(name = "height")
2726		protected Integer height;
2727
2728		@XmlAttribute(name = "xpos")
2729		protected Integer xpos;
2730
2731		@XmlAttribute(name = "ypos")
2732		protected Integer ypos;
2733
2734		/**
2735		* Gets the value of the secondaryStructure property.
2736		*
2737		* &lt;p&gt; This accessor method returns a reference to the live list,
2738		* not a snapshot. Therefore any modification you make to the returned
2739		* list will be present inside the JAXB object. This is why there is not a
2740		* &lt;CODE&gt;set&lt;/CODE&gt; method for the secondaryStructure
2741		* property.
2742		*
2743		* &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
2744		* getSecondaryStructure().add(newItem); &lt;/pre&gt;
2745		*
2746		*
2747		* &lt;p&gt; Objects of the following type(s) are allowed in the list
2748		* {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
2749		*
2750		*
2751		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
2752	0	public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure()...
2753		{
2754	0	if (secondaryStructure == null)
2755		{
2756	0	secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
2757		}
2758	0	return this.secondaryStructure;
2759		}
2760
2761		/**
2762		* Gets the value of the title property.
2763		*
2764		* @return possible object is {@link String }
2765		*
2766		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2767	0	public String getTitle()...
2768		{
2769	0	return title;
2770		}
2771
2772		/**
2773		* Sets the value of the title property.
2774		*
2775		* @param value
2776		* allowed object is {@link String }
2777		*
2778		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2779	0	public void setTitle(String value)...
2780		{
2781	0	this.title = value;
2782		}
2783
2784		/**
2785		* Gets the value of the viewId property.
2786		*
2787		* @return possible object is {@link String }
2788		*
2789		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2790	0	public String getViewId()...
2791		{
2792	0	return viewId;
2793		}
2794
2795		/**
2796		* Sets the value of the viewId property.
2797		*
2798		* @param value
2799		* allowed object is {@link String }
2800		*
2801		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2802	0	public void setViewId(String value)...
2803		{
2804	0	this.viewId = value;
2805		}
2806
2807		/**
2808		* Gets the value of the dividerLocation property.
2809		*
2810		* @return possible object is {@link Integer }
2811		*
2812		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2813	0	public Integer getDividerLocation()...
2814		{
2815	0	return dividerLocation;
2816		}
2817
2818		/**
2819		* Sets the value of the dividerLocation property.
2820		*
2821		* @param value
2822		* allowed object is {@link Integer }
2823		*
2824		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2825	0	public void setDividerLocation(Integer value)...
2826		{
2827	0	this.dividerLocation = value;
2828		}
2829
2830		/**
2831		* Gets the value of the selectedRna property.
2832		*
2833		* @return possible object is {@link Integer }
2834		*
2835		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2836	0	public Integer getSelectedRna()...
2837		{
2838	0	return selectedRna;
2839		}
2840
2841		/**
2842		* Sets the value of the selectedRna property.
2843		*
2844		* @param value
2845		* allowed object is {@link Integer }
2846		*
2847		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2848	0	public void setSelectedRna(Integer value)...
2849		{
2850	0	this.selectedRna = value;
2851		}
2852
2853		/**
2854		* Gets the value of the width property.
2855		*
2856		* @return possible object is {@link Integer }
2857		*
2858		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2859	0	public Integer getWidth()...
2860		{
2861	0	return width;
2862		}
2863
2864		/**
2865		* Sets the value of the width property.
2866		*
2867		* @param value
2868		* allowed object is {@link Integer }
2869		*
2870		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2871	0	public void setWidth(Integer value)...
2872		{
2873	0	this.width = value;
2874		}
2875
2876		/**
2877		* Gets the value of the height property.
2878		*
2879		* @return possible object is {@link Integer }
2880		*
2881		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2882	0	public Integer getHeight()...
2883		{
2884	0	return height;
2885		}
2886
2887		/**
2888		* Sets the value of the height property.
2889		*
2890		* @param value
2891		* allowed object is {@link Integer }
2892		*
2893		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2894	0	public void setHeight(Integer value)...
2895		{
2896	0	this.height = value;
2897		}
2898
2899		/**
2900		* Gets the value of the xpos property.
2901		*
2902		* @return possible object is {@link Integer }
2903		*
2904		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2905	0	public Integer getXpos()...
2906		{
2907	0	return xpos;
2908		}
2909
2910		/**
2911		* Sets the value of the xpos property.
2912		*
2913		* @param value
2914		* allowed object is {@link Integer }
2915		*
2916		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2917	0	public void setXpos(Integer value)...
2918		{
2919	0	this.xpos = value;
2920		}
2921
2922		/**
2923		* Gets the value of the ypos property.
2924		*
2925		* @return possible object is {@link Integer }
2926		*
2927		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2928	0	public Integer getYpos()...
2929		{
2930	0	return ypos;
2931		}
2932
2933		/**
2934		* Sets the value of the ypos property.
2935		*
2936		* @param value
2937		* allowed object is {@link Integer }
2938		*
2939		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2940	0	public void setYpos(Integer value)...
2941		{
2942	0	this.ypos = value;
2943		}
2944
2945		/**
2946		* &lt;p&gt;Java class for anonymous complex type.
2947		*
2948		* &lt;p&gt;The following schema fragment specifies the expected content
2949		* contained within this class.
2950		*
2951		* &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
2952		* &amp;lt;restriction
2953		* base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
2954		* &amp;lt;attribute name="title"
2955		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2956		* &amp;lt;attribute name="annotationId" use="required"
2957		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2958		* &amp;lt;attribute name="gapped"
2959		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
2960		* &amp;lt;attribute name="viewerState"
2961		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2962		* &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
2963		* &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
2964		*
2965		*
2966		*/
2967		@XmlAccessorType(XmlAccessType.FIELD)
2968		@XmlType(name = "")
		0% Uncovered Elements: 16 (16) Complexity: 8 Complexity Density: 1
2969		public static class SecondaryStructure
2970		{
2971
2972		@XmlAttribute(name = "title")
2973		protected String title;
2974
2975		@XmlAttribute(name = "annotationId", required = true)
2976		protected String annotationId;
2977
2978		@XmlAttribute(name = "gapped")
2979		protected Boolean gapped;
2980
2981		@XmlAttribute(name = "viewerState")
2982		protected String viewerState;
2983
2984		/**
2985		* Gets the value of the title property.
2986		*
2987		* @return possible object is {@link String }
2988		*
2989		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2990	0	public String getTitle()...
2991		{
2992	0	return title;
2993		}
2994
2995		/**
2996		* Sets the value of the title property.
2997		*
2998		* @param value
2999		* allowed object is {@link String }
3000		*
3001		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3002	0	public void setTitle(String value)...
3003		{
3004	0	this.title = value;
3005		}
3006
3007		/**
3008		* Gets the value of the annotationId property.
3009		*
3010		* @return possible object is {@link String }
3011		*
3012		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3013	0	public String getAnnotationId()...
3014		{
3015	0	return annotationId;
3016		}
3017
3018		/**
3019		* Sets the value of the annotationId property.
3020		*
3021		* @param value
3022		* allowed object is {@link String }
3023		*
3024		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3025	0	public void setAnnotationId(String value)...
3026		{
3027	0	this.annotationId = value;
3028		}
3029
3030		/**
3031		* Gets the value of the gapped property.
3032		*
3033		* @return possible object is {@link Boolean }
3034		*
3035		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3036	0	public Boolean isGapped()...
3037		{
3038	0	return gapped;
3039		}
3040
3041		/**
3042		* Sets the value of the gapped property.
3043		*
3044		* @param value
3045		* allowed object is {@link Boolean }
3046		*
3047		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3048	0	public void setGapped(Boolean value)...
3049		{
3050	0	this.gapped = value;
3051		}
3052
3053		/**
3054		* Gets the value of the viewerState property.
3055		*
3056		* @return possible object is {@link String }
3057		*
3058		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3059	0	public String getViewerState()...
3060		{
3061	0	return viewerState;
3062		}
3063
3064		/**
3065		* Sets the value of the viewerState property.
3066		*
3067		* @param value
3068		* allowed object is {@link String }
3069		*
3070		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3071	0	public void setViewerState(String value)...
3072		{
3073	0	this.viewerState = value;
3074		}
3075
3076		}
3077
3078		}
3079
3080		}
3081
3082		/**
3083		* &lt;p&gt;Java class for anonymous complex type.
3084		*
3085		* &lt;p&gt;The following schema fragment specifies the expected content
3086		* contained within this class.
3087		*
3088		* &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
3089		* &amp;lt;restriction
3090		* base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
3091		* &amp;lt;sequence&amp;gt; &amp;lt;element name="sequencePoint"
3092		* maxOccurs="unbounded"&amp;gt; &amp;lt;complexType&amp;gt;
3093		* &amp;lt;complexContent&amp;gt; &amp;lt;restriction
3094		* base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
3095		* ref="{www.jalview.org}position"/&amp;gt; &amp;lt;attribute
3096		* name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string"
3097		* /&amp;gt; &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
3098		* &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt; &amp;lt;element
3099		* name="axis" maxOccurs="3" minOccurs="3"&amp;gt; &amp;lt;complexType&amp;gt;
3100		* &amp;lt;complexContent&amp;gt; &amp;lt;restriction
3101		* base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
3102		* ref="{www.jalview.org}position"/&amp;gt; &amp;lt;/restriction&amp;gt;
3103		* &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt;
3104		* &amp;lt;/element&amp;gt; &amp;lt;element name="seqPointMin"&amp;gt;
3105		* &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
3106		* &amp;lt;restriction
3107		* base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
3108		* ref="{www.jalview.org}position"/&amp;gt; &amp;lt;/restriction&amp;gt;
3109		* &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt;
3110		* &amp;lt;/element&amp;gt; &amp;lt;element name="seqPointMax"&amp;gt;
3111		* &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
3112		* &amp;lt;restriction
3113		* base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
3114		* ref="{www.jalview.org}position"/&amp;gt; &amp;lt;/restriction&amp;gt;
3115		* &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt;
3116		* &amp;lt;/element&amp;gt; &amp;lt;element name="pcaData"
3117		* type="{www.jalview.org}PcaDataType"/&amp;gt; &amp;lt;/sequence&amp;gt;
3118		* &amp;lt;attGroup ref="{www.jalview.org}SimilarityParams"/&amp;gt;
3119		* &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
3120		* &amp;lt;attribute name="title"
3121		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
3122		* name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string"
3123		* /&amp;gt; &amp;lt;attribute name="xDim"
3124		* type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
3125		* name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
3126		* &amp;lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int"
3127		* /&amp;gt; &amp;lt;attribute name="bgColour"
3128		* type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
3129		* name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
3130		* &amp;lt;attribute name="showLabels"
3131		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
3132		* &amp;lt;attribute name="linkToAllViews"
3133		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
3134		* &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
3135		* &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
3136		*
3137		*
3138		*/
3139		@XmlAccessorType(XmlAccessType.FIELD)
3140		@XmlType(
3141		name = "",
3142		propOrder =
3143		{ "sequencePoint", "axis", "seqPointMin", "seqPointMax", "pcaData" })
		100% Uncovered Elements: 0 (92) Complexity: 44 Complexity Density: 0.96
3144		public static class PcaViewer
3145		{
3146
3147		@XmlElement(namespace = "www.jalview.org", required = true)
3148		protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
3149
3150		@XmlElement(namespace = "www.jalview.org", required = true)
3151		protected List<JalviewModel.PcaViewer.Axis> axis;
3152
3153		@XmlElement(namespace = "www.jalview.org", required = true)
3154		protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
3155
3156		@XmlElement(namespace = "www.jalview.org", required = true)
3157		protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
3158
3159		@XmlElement(namespace = "www.jalview.org", required = true)
3160		protected PcaDataType pcaData;
3161
3162		@XmlAttribute(name = "title")
3163		protected String title;
3164
3165		@XmlAttribute(name = "scoreModelName")
3166		protected String scoreModelName;
3167
3168		@XmlAttribute(name = "xDim")
3169		protected Integer xDim;
3170
3171		@XmlAttribute(name = "yDim")
3172		protected Integer yDim;
3173
3174		@XmlAttribute(name = "zDim")
3175		protected Integer zDim;
3176
3177		@XmlAttribute(name = "bgColour")
3178		protected Integer bgColour;
3179
3180		@XmlAttribute(name = "scaleFactor")
3181		protected Float scaleFactor;
3182
3183		@XmlAttribute(name = "showLabels")
3184		protected Boolean showLabels;
3185
3186		@XmlAttribute(name = "linkToAllViews")
3187		protected Boolean linkToAllViews;
3188
3189		@XmlAttribute(name = "includeGaps")
3190		protected Boolean includeGaps;
3191
3192		@XmlAttribute(name = "matchGaps")
3193		protected Boolean matchGaps;
3194
3195		@XmlAttribute(name = "includeGappedColumns")
3196		protected Boolean includeGappedColumns;
3197
3198		@XmlAttribute(name = "denominateByShortestLength")
3199		protected Boolean denominateByShortestLength;
3200
3201		@XmlAttribute(name = "width")
3202		protected Integer width;
3203
3204		@XmlAttribute(name = "height")
3205		protected Integer height;
3206
3207		@XmlAttribute(name = "xpos")
3208		protected Integer xpos;
3209
3210		@XmlAttribute(name = "ypos")
3211		protected Integer ypos;
3212
3213		/**
3214		* Gets the value of the sequencePoint property.
3215		*
3216		* &lt;p&gt; This accessor method returns a reference to the live list, not
3217		* a snapshot. Therefore any modification you make to the returned list will
3218		* be present inside the JAXB object. This is why there is not a
3219		* &lt;CODE&gt;set&lt;/CODE&gt; method for the sequencePoint property.
3220		*
3221		* &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
3222		* getSequencePoint().add(newItem); &lt;/pre&gt;
3223		*
3224		*
3225		* &lt;p&gt; Objects of the following type(s) are allowed in the list
3226		* {@link JalviewModel.PcaViewer.SequencePoint }
3227		*
3228		*
3229		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
3230	16	public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint()...
3231		{
3232	16	if (sequencePoint == null)
3233		{
3234	1	sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
3235		}
3236	16	return this.sequencePoint;
3237		}
3238
3239		/**
3240		* Gets the value of the axis property.
3241		*
3242		* &lt;p&gt; This accessor method returns a reference to the live list, not
3243		* a snapshot. Therefore any modification you make to the returned list will
3244		* be present inside the JAXB object. This is why there is not a
3245		* &lt;CODE&gt;set&lt;/CODE&gt; method for the axis property.
3246		*
3247		* &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
3248		* getAxis().add(newItem); &lt;/pre&gt;
3249		*
3250		*
3251		* &lt;p&gt; Objects of the following type(s) are allowed in the list
3252		* {@link JalviewModel.PcaViewer.Axis }
3253		*
3254		*
3255		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
3256	6	public List<JalviewModel.PcaViewer.Axis> getAxis()...
3257		{
3258	6	if (axis == null)
3259		{
3260	1	axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
3261		}
3262	6	return this.axis;
3263		}
3264
3265		/**
3266		* Gets the value of the seqPointMin property.
3267		*
3268		* @return possible object is {@link JalviewModel.PcaViewer.SeqPointMin }
3269		*
3270		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3271	1	public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin()...
3272		{
3273	1	return seqPointMin;
3274		}
3275
3276		/**
3277		* Sets the value of the seqPointMin property.
3278		*
3279		* @param value
3280		* allowed object is {@link JalviewModel.PcaViewer.SeqPointMin }
3281		*
3282		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3283	1	public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value)...
3284		{
3285	1	this.seqPointMin = value;
3286		}
3287
3288		/**
3289		* Gets the value of the seqPointMax property.
3290		*
3291		* @return possible object is {@link JalviewModel.PcaViewer.SeqPointMax }
3292		*
3293		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3294	1	public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax()...
3295		{
3296	1	return seqPointMax;
3297		}
3298
3299		/**
3300		* Sets the value of the seqPointMax property.
3301		*
3302		* @param value
3303		* allowed object is {@link JalviewModel.PcaViewer.SeqPointMax }
3304		*
3305		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3306	1	public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value)...
3307		{
3308	1	this.seqPointMax = value;
3309		}
3310
3311		/**
3312		* Gets the value of the pcaData property.
3313		*
3314		* @return possible object is {@link PcaDataType }
3315		*
3316		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3317	1	public PcaDataType getPcaData()...
3318		{
3319	1	return pcaData;
3320		}
3321
3322		/**
3323		* Sets the value of the pcaData property.
3324		*
3325		* @param value
3326		* allowed object is {@link PcaDataType }
3327		*
3328		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3329	1	public void setPcaData(PcaDataType value)...
3330		{
3331	1	this.pcaData = value;
3332		}
3333
3334		/**
3335		* Gets the value of the title property.
3336		*
3337		* @return possible object is {@link String }
3338		*
3339		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3340	3	public String getTitle()...
3341		{
3342	3	return title;
3343		}
3344
3345		/**
3346		* Sets the value of the title property.
3347		*
3348		* @param value
3349		* allowed object is {@link String }
3350		*
3351		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3352	1	public void setTitle(String value)...
3353		{
3354	1	this.title = value;
3355		}
3356
3357		/**
3358		* Gets the value of the scoreModelName property.
3359		*
3360		* @return possible object is {@link String }
3361		*
3362		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3363	1	public String getScoreModelName()...
3364		{
3365	1	return scoreModelName;
3366		}
3367
3368		/**
3369		* Sets the value of the scoreModelName property.
3370		*
3371		* @param value
3372		* allowed object is {@link String }
3373		*
3374		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3375	1	public void setScoreModelName(String value)...
3376		{
3377	1	this.scoreModelName = value;
3378		}
3379
3380		/**
3381		* Gets the value of the xDim property.
3382		*
3383		* @return possible object is {@link Integer }
3384		*
3385		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3386	1	public Integer getXDim()...
3387		{
3388	1	return xDim;
3389		}
3390
3391		/**
3392		* Sets the value of the xDim property.
3393		*
3394		* @param value
3395		* allowed object is {@link Integer }
3396		*
3397		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3398	1	public void setXDim(Integer value)...
3399		{
3400	1	this.xDim = value;
3401		}
3402
3403		/**
3404		* Gets the value of the yDim property.
3405		*
3406		* @return possible object is {@link Integer }
3407		*
3408		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3409	1	public Integer getYDim()...
3410		{
3411	1	return yDim;
3412		}
3413
3414		/**
3415		* Sets the value of the yDim property.
3416		*
3417		* @param value
3418		* allowed object is {@link Integer }
3419		*
3420		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3421	1	public void setYDim(Integer value)...
3422		{
3423	1	this.yDim = value;
3424		}
3425
3426		/**
3427		* Gets the value of the zDim property.
3428		*
3429		* @return possible object is {@link Integer }
3430		*
3431		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3432	1	public Integer getZDim()...
3433		{
3434	1	return zDim;
3435		}
3436
3437		/**
3438		* Sets the value of the zDim property.
3439		*
3440		* @param value
3441		* allowed object is {@link Integer }
3442		*
3443		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3444	1	public void setZDim(Integer value)...
3445		{
3446	1	this.zDim = value;
3447		}
3448
3449		/**
3450		* Gets the value of the bgColour property.
3451		*
3452		* @return possible object is {@link Integer }
3453		*
3454		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3455	1	public Integer getBgColour()...
3456		{
3457	1	return bgColour;
3458		}
3459
3460		/**
3461		* Sets the value of the bgColour property.
3462		*
3463		* @param value
3464		* allowed object is {@link Integer }
3465		*
3466		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3467	1	public void setBgColour(Integer value)...
3468		{
3469	1	this.bgColour = value;
3470		}
3471
3472		/**
3473		* Gets the value of the scaleFactor property.
3474		*
3475		* @return possible object is {@link Float }
3476		*
3477		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3478	1	public Float getScaleFactor()...
3479		{
3480	1	return scaleFactor;
3481		}
3482
3483		/**
3484		* Sets the value of the scaleFactor property.
3485		*
3486		* @param value
3487		* allowed object is {@link Float }
3488		*
3489		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3490	1	public void setScaleFactor(Float value)...
3491		{
3492	1	this.scaleFactor = value;
3493		}
3494
3495		/**
3496		* Gets the value of the showLabels property.
3497		*
3498		* @return possible object is {@link Boolean }
3499		*
3500		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3501	1	public Boolean isShowLabels()...
3502		{
3503	1	return showLabels;
3504		}
3505
3506		/**
3507		* Sets the value of the showLabels property.
3508		*
3509		* @param value
3510		* allowed object is {@link Boolean }
3511		*
3512		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3513	1	public void setShowLabels(Boolean value)...
3514		{
3515	1	this.showLabels = value;
3516		}
3517
3518		/**
3519		* Gets the value of the linkToAllViews property.
3520		*
3521		* @return possible object is {@link Boolean }
3522		*
3523		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3524	1	public Boolean isLinkToAllViews()...
3525		{
3526	1	return linkToAllViews;
3527		}
3528
3529		/**
3530		* Sets the value of the linkToAllViews property.
3531		*
3532		* @param value
3533		* allowed object is {@link Boolean }
3534		*
3535		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3536	1	public void setLinkToAllViews(Boolean value)...
3537		{
3538	1	this.linkToAllViews = value;
3539		}
3540
3541		/**
3542		* Gets the value of the includeGaps property.
3543		*
3544		* @return possible object is {@link Boolean }
3545		*
3546		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3547	1	public Boolean isIncludeGaps()...
3548		{
3549	1	return includeGaps;
3550		}
3551
3552		/**
3553		* Sets the value of the includeGaps property.
3554		*
3555		* @param value
3556		* allowed object is {@link Boolean }
3557		*
3558		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3559	1	public void setIncludeGaps(Boolean value)...
3560		{
3561	1	this.includeGaps = value;
3562		}
3563
3564		/**
3565		* Gets the value of the matchGaps property.
3566		*
3567		* @return possible object is {@link Boolean }
3568		*
3569		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3570	1	public Boolean isMatchGaps()...
3571		{
3572	1	return matchGaps;
3573		}
3574
3575		/**
3576		* Sets the value of the matchGaps property.
3577		*
3578		* @param value
3579		* allowed object is {@link Boolean }
3580		*
3581		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3582	1	public void setMatchGaps(Boolean value)...
3583		{
3584	1	this.matchGaps = value;
3585		}
3586
3587		/**
3588		* Gets the value of the includeGappedColumns property.
3589		*
3590		* @return possible object is {@link Boolean }
3591		*
3592		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3593	1	public Boolean isIncludeGappedColumns()...
3594		{
3595	1	return includeGappedColumns;
3596		}
3597
3598		/**
3599		* Sets the value of the includeGappedColumns property.
3600		*
3601		* @param value
3602		* allowed object is {@link Boolean }
3603		*
3604		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3605	1	public void setIncludeGappedColumns(Boolean value)...
3606		{
3607	1	this.includeGappedColumns = value;
3608		}
3609
3610		/**
3611		* Gets the value of the denominateByShortestLength property.
3612		*
3613		* @return possible object is {@link Boolean }
3614		*
3615		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3616	1	public Boolean isDenominateByShortestLength()...
3617		{
3618	1	return denominateByShortestLength;
3619		}
3620
3621		/**
3622		* Sets the value of the denominateByShortestLength property.
3623		*
3624		* @param value
3625		* allowed object is {@link Boolean }
3626		*
3627		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3628	1	public void setDenominateByShortestLength(Boolean value)...
3629		{
3630	1	this.denominateByShortestLength = value;
3631		}
3632
3633		/**
3634		* Gets the value of the width property.
3635		*
3636		* @return possible object is {@link Integer }
3637		*
3638		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3639	1	public Integer getWidth()...
3640		{
3641	1	return width;
3642		}
3643
3644		/**
3645		* Sets the value of the width property.
3646		*
3647		* @param value
3648		* allowed object is {@link Integer }
3649		*
3650		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3651	1	public void setWidth(Integer value)...
3652		{
3653	1	this.width = value;
3654		}
3655
3656		/**
3657		* Gets the value of the height property.
3658		*
3659		* @return possible object is {@link Integer }
3660		*
3661		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3662	1	public Integer getHeight()...
3663		{
3664	1	return height;
3665		}
3666
3667		/**
3668		* Sets the value of the height property.
3669		*
3670		* @param value
3671		* allowed object is {@link Integer }
3672		*
3673		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3674	1	public void setHeight(Integer value)...
3675		{
3676	1	this.height = value;
3677		}
3678
3679		/**
3680		* Gets the value of the xpos property.
3681		*
3682		* @return possible object is {@link Integer }
3683		*
3684		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3685	1	public Integer getXpos()...
3686		{
3687	1	return xpos;
3688		}
3689
3690		/**
3691		* Sets the value of the xpos property.
3692		*
3693		* @param value
3694		* allowed object is {@link Integer }
3695		*
3696		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3697	1	public void setXpos(Integer value)...
3698		{
3699	1	this.xpos = value;
3700		}
3701
3702		/**
3703		* Gets the value of the ypos property.
3704		*
3705		* @return possible object is {@link Integer }
3706		*
3707		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3708	1	public Integer getYpos()...
3709		{
3710	1	return ypos;
3711		}
3712
3713		/**
3714		* Sets the value of the ypos property.
3715		*
3716		* @param value
3717		* allowed object is {@link Integer }
3718		*
3719		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3720	1	public void setYpos(Integer value)...
3721		{
3722	1	this.ypos = value;
3723		}
3724
3725		/**
3726		* &lt;p&gt;Java class for anonymous complex type.
3727		*
3728		* &lt;p&gt;The following schema fragment specifies the expected content
3729		* contained within this class.
3730		*
3731		* &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
3732		* &amp;lt;restriction
3733		* base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
3734		* ref="{www.jalview.org}position"/&amp;gt; &amp;lt;/restriction&amp;gt;
3735		* &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
3736		*
3737		*
3738		*/
3739		@XmlAccessorType(XmlAccessType.FIELD)
3740		@XmlType(name = "")
		100% Uncovered Elements: 0 (12) Complexity: 6 Complexity Density: 1
3741		public static class Axis
3742		{
3743
3744		@XmlAttribute(name = "xPos")
3745		protected Float xPos;
3746
3747		@XmlAttribute(name = "yPos")
3748		protected Float yPos;
3749
3750		@XmlAttribute(name = "zPos")
3751		protected Float zPos;
3752
3753		/**
3754		* Gets the value of the xPos property.
3755		*
3756		* @return possible object is {@link Float }
3757		*
3758		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3759	3	public Float getXPos()...
3760		{
3761	3	return xPos;
3762		}
3763
3764		/**
3765		* Sets the value of the xPos property.
3766		*
3767		* @param value
3768		* allowed object is {@link Float }
3769		*
3770		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3771	3	public void setXPos(Float value)...
3772		{
3773	3	this.xPos = value;
3774		}
3775
3776		/**
3777		* Gets the value of the yPos property.
3778		*
3779		* @return possible object is {@link Float }
3780		*
3781		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3782	3	public Float getYPos()...
3783		{
3784	3	return yPos;
3785		}
3786
3787		/**
3788		* Sets the value of the yPos property.
3789		*
3790		* @param value
3791		* allowed object is {@link Float }
3792		*
3793		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3794	3	public void setYPos(Float value)...
3795		{
3796	3	this.yPos = value;
3797		}
3798
3799		/**
3800		* Gets the value of the zPos property.
3801		*
3802		* @return possible object is {@link Float }
3803		*
3804		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3805	3	public Float getZPos()...
3806		{
3807	3	return zPos;
3808		}
3809
3810		/**
3811		* Sets the value of the zPos property.
3812		*
3813		* @param value
3814		* allowed object is {@link Float }
3815		*
3816		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3817	3	public void setZPos(Float value)...
3818		{
3819	3	this.zPos = value;
3820		}
3821
3822		}
3823
3824		/**
3825		* &lt;p&gt;Java class for anonymous complex type.
3826		*
3827		* &lt;p&gt;The following schema fragment specifies the expected content
3828		* contained within this class.
3829		*
3830		* &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
3831		* &amp;lt;restriction
3832		* base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
3833		* ref="{www.jalview.org}position"/&amp;gt; &amp;lt;/restriction&amp;gt;
3834		* &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
3835		*
3836		*
3837		*/
3838		@XmlAccessorType(XmlAccessType.FIELD)
3839		@XmlType(name = "")
		100% Uncovered Elements: 0 (12) Complexity: 6 Complexity Density: 1
3840		public static class SeqPointMax
3841		{
3842
3843		@XmlAttribute(name = "xPos")
3844		protected Float xPos;
3845
3846		@XmlAttribute(name = "yPos")
3847		protected Float yPos;
3848
3849		@XmlAttribute(name = "zPos")
3850		protected Float zPos;
3851
3852		/**
3853		* Gets the value of the xPos property.
3854		*
3855		* @return possible object is {@link Float }
3856		*
3857		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3858	1	public Float getXPos()...
3859		{
3860	1	return xPos;
3861		}
3862
3863		/**
3864		* Sets the value of the xPos property.
3865		*
3866		* @param value
3867		* allowed object is {@link Float }
3868		*
3869		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3870	1	public void setXPos(Float value)...
3871		{
3872	1	this.xPos = value;
3873		}
3874
3875		/**
3876		* Gets the value of the yPos property.
3877		*
3878		* @return possible object is {@link Float }
3879		*
3880		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3881	1	public Float getYPos()...
3882		{
3883	1	return yPos;
3884		}
3885
3886		/**
3887		* Sets the value of the yPos property.
3888		*
3889		* @param value
3890		* allowed object is {@link Float }
3891		*
3892		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3893	1	public void setYPos(Float value)...
3894		{
3895	1	this.yPos = value;
3896		}
3897
3898		/**
3899		* Gets the value of the zPos property.
3900		*
3901		* @return possible object is {@link Float }
3902		*
3903		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3904	1	public Float getZPos()...
3905		{
3906	1	return zPos;
3907		}
3908
3909		/**
3910		* Sets the value of the zPos property.
3911		*
3912		* @param value
3913		* allowed object is {@link Float }
3914		*
3915		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3916	1	public void setZPos(Float value)...
3917		{
3918	1	this.zPos = value;
3919		}
3920
3921		}
3922
3923		/**
3924		* &lt;p&gt;Java class for anonymous complex type.
3925		*
3926		* &lt;p&gt;The following schema fragment specifies the expected content
3927		* contained within this class.
3928		*
3929		* &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
3930		* &amp;lt;restriction
3931		* base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
3932		* ref="{www.jalview.org}position"/&amp;gt; &amp;lt;/restriction&amp;gt;
3933		* &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
3934		*
3935		*
3936		*/
3937		@XmlAccessorType(XmlAccessType.FIELD)
3938		@XmlType(name = "")
		100% Uncovered Elements: 0 (12) Complexity: 6 Complexity Density: 1
3939		public static class SeqPointMin
3940		{
3941
3942		@XmlAttribute(name = "xPos")
3943		protected Float xPos;
3944
3945		@XmlAttribute(name = "yPos")
3946		protected Float yPos;
3947
3948		@XmlAttribute(name = "zPos")
3949		protected Float zPos;
3950
3951		/**
3952		* Gets the value of the xPos property.
3953		*
3954		* @return possible object is {@link Float }
3955		*
3956		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3957	1	public Float getXPos()...
3958		{
3959	1	return xPos;
3960		}
3961
3962		/**
3963		* Sets the value of the xPos property.
3964		*
3965		* @param value
3966		* allowed object is {@link Float }
3967		*
3968		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3969	1	public void setXPos(Float value)...
3970		{
3971	1	this.xPos = value;
3972		}
3973
3974		/**
3975		* Gets the value of the yPos property.
3976		*
3977		* @return possible object is {@link Float }
3978		*
3979		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3980	1	public Float getYPos()...
3981		{
3982	1	return yPos;
3983		}
3984
3985		/**
3986		* Sets the value of the yPos property.
3987		*
3988		* @param value
3989		* allowed object is {@link Float }
3990		*
3991		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3992	1	public void setYPos(Float value)...
3993		{
3994	1	this.yPos = value;
3995		}
3996
3997		/**
3998		* Gets the value of the zPos property.
3999		*
4000		* @return possible object is {@link Float }
4001		*
4002		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4003	1	public Float getZPos()...
4004		{
4005	1	return zPos;
4006		}
4007
4008		/**
4009		* Sets the value of the zPos property.
4010		*
4011		* @param value
4012		* allowed object is {@link Float }
4013		*
4014		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4015	1	public void setZPos(Float value)...
4016		{
4017	1	this.zPos = value;
4018		}
4019
4020		}
4021
4022		/**
4023		* &lt;p&gt;Java class for anonymous complex type.
4024		*
4025		* &lt;p&gt;The following schema fragment specifies the expected content
4026		* contained within this class.
4027		*
4028		* &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
4029		* &amp;lt;restriction
4030		* base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
4031		* ref="{www.jalview.org}position"/&amp;gt; &amp;lt;attribute
4032		* name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string"
4033		* /&amp;gt; &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
4034		* &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
4035		*
4036		*
4037		*/
4038		@XmlAccessorType(XmlAccessType.FIELD)
4039		@XmlType(name = "")
		100% Uncovered Elements: 0 (16) Complexity: 8 Complexity Density: 1
4040		public static class SequencePoint
4041		{
4042
4043		@XmlAttribute(name = "sequenceRef")
4044		protected String sequenceRef;
4045
4046		@XmlAttribute(name = "xPos")
4047		protected Float xPos;
4048
4049		@XmlAttribute(name = "yPos")
4050		protected Float yPos;
4051
4052		@XmlAttribute(name = "zPos")
4053		protected Float zPos;
4054
4055		/**
4056		* Gets the value of the sequenceRef property.
4057		*
4058		* @return possible object is {@link String }
4059		*
4060		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4061	15	public String getSequenceRef()...
4062		{
4063	15	return sequenceRef;
4064		}
4065
4066		/**
4067		* Sets the value of the sequenceRef property.
4068		*
4069		* @param value
4070		* allowed object is {@link String }
4071		*
4072		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4073	15	public void setSequenceRef(String value)...
4074		{
4075	15	this.sequenceRef = value;
4076		}
4077
4078		/**
4079		* Gets the value of the xPos property.
4080		*
4081		* @return possible object is {@link Float }
4082		*
4083		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4084	15	public Float getXPos()...
4085		{
4086	15	return xPos;
4087		}
4088
4089		/**
4090		* Sets the value of the xPos property.
4091		*
4092		* @param value
4093		* allowed object is {@link Float }
4094		*
4095		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4096	15	public void setXPos(Float value)...
4097		{
4098	15	this.xPos = value;
4099		}
4100
4101		/**
4102		* Gets the value of the yPos property.
4103		*
4104		* @return possible object is {@link Float }
4105		*
4106		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4107	15	public Float getYPos()...
4108		{
4109	15	return yPos;
4110		}
4111
4112		/**
4113		* Sets the value of the yPos property.
4114		*
4115		* @param value
4116		* allowed object is {@link Float }
4117		*
4118		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4119	15	public void setYPos(Float value)...
4120		{
4121	15	this.yPos = value;
4122		}
4123
4124		/**
4125		* Gets the value of the zPos property.
4126		*
4127		* @return possible object is {@link Float }
4128		*
4129		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4130	15	public Float getZPos()...
4131		{
4132	15	return zPos;
4133		}
4134
4135		/**
4136		* Sets the value of the zPos property.
4137		*
4138		* @param value
4139		* allowed object is {@link Float }
4140		*
4141		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4142	15	public void setZPos(Float value)...
4143		{
4144	15	this.zPos = value;
4145		}
4146
4147		}
4148
4149		}
4150
4151		/**
4152		* &lt;p&gt;Java class for anonymous complex type.
4153		*
4154		* &lt;p&gt;The following schema fragment specifies the expected content
4155		* contained within this class.
4156		*
4157		* &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
4158		* &amp;lt;restriction
4159		* base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;sequence
4160		* minOccurs="0"&amp;gt; &amp;lt;element name="title"
4161		* type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt; &amp;lt;element
4162		* name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt;
4163		* &amp;lt;/sequence&amp;gt; &amp;lt;attGroup
4164		* ref="{www.jalview.org}swingwindow"/&amp;gt; &amp;lt;attribute
4165		* name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4166		* &amp;lt;attribute name="fontSize"
4167		* type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
4168		* name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4169		* &amp;lt;attribute name="threshold"
4170		* type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt; &amp;lt;attribute
4171		* name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean"
4172		* /&amp;gt; &amp;lt;attribute name="showDistances"
4173		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4174		* &amp;lt;attribute name="markUnlinked"
4175		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4176		* &amp;lt;attribute name="fitToWindow"
4177		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4178		* &amp;lt;attribute name="currentTree"
4179		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4180		* &amp;lt;attribute name="columnWise"
4181		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4182		* &amp;lt;attribute name="columnReference"
4183		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
4184		* name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&amp;gt;
4185		* &amp;lt;attribute name="linkToAllViews"
4186		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4187		* &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
4188		* &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
4189		*
4190		*
4191		*/
4192		@XmlAccessorType(XmlAccessType.FIELD)
4193		@XmlType(name = "", propOrder = { "title", "newick" })
		90.5% Uncovered Elements: 8 (84) Complexity: 40 Complexity Density: 0.95
4194		public static class Tree
4195		{
4196
4197		@XmlElement(namespace = "www.jalview.org")
4198		protected String title;
4199
4200		@XmlElement(namespace = "www.jalview.org")
4201		protected String newick;
4202
4203		@XmlAttribute(name = "fontName")
4204		protected String fontName;
4205
4206		@XmlAttribute(name = "fontSize")
4207		protected Integer fontSize;
4208
4209		@XmlAttribute(name = "fontStyle")
4210		protected Integer fontStyle;
4211
4212		@XmlAttribute(name = "threshold")
4213		protected Float threshold;
4214
4215		@XmlAttribute(name = "showBootstrap")
4216		protected Boolean showBootstrap;
4217
4218		@XmlAttribute(name = "showDistances")
4219		protected Boolean showDistances;
4220
4221		@XmlAttribute(name = "markUnlinked")
4222		protected Boolean markUnlinked;
4223
4224		@XmlAttribute(name = "fitToWindow")
4225		protected Boolean fitToWindow;
4226
4227		@XmlAttribute(name = "currentTree")
4228		protected Boolean currentTree;
4229
4230		@XmlAttribute(name = "columnWise")
4231		protected Boolean columnWise;
4232
4233		@XmlAttribute(name = "columnReference")
4234		protected String columnReference;
4235
4236		@XmlAttribute(name = "id")
4237		@XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4238		@XmlID
4239		@XmlSchemaType(name = "ID")
4240		protected String id;
4241
4242		@XmlAttribute(name = "linkToAllViews")
4243		protected Boolean linkToAllViews;
4244
4245		@XmlAttribute(name = "width")
4246		protected Integer width;
4247
4248		@XmlAttribute(name = "height")
4249		protected Integer height;
4250
4251		@XmlAttribute(name = "xpos")
4252		protected Integer xpos;
4253
4254		@XmlAttribute(name = "ypos")
4255		protected Integer ypos;
4256
4257		/**
4258		* Gets the value of the title property.
4259		*
4260		* @return possible object is {@link String }
4261		*
4262		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4263	12	public String getTitle()...
4264		{
4265	12	return title;
4266		}
4267
4268		/**
4269		* Sets the value of the title property.
4270		*
4271		* @param value
4272		* allowed object is {@link String }
4273		*
4274		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4275	4	public void setTitle(String value)...
4276		{
4277	4	this.title = value;
4278		}
4279
4280		/**
4281		* Gets the value of the newick property.
4282		*
4283		* @return possible object is {@link String }
4284		*
4285		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4286	12	public String getNewick()...
4287		{
4288	12	return newick;
4289		}
4290
4291		/**
4292		* Sets the value of the newick property.
4293		*
4294		* @param value
4295		* allowed object is {@link String }
4296		*
4297		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4298	4	public void setNewick(String value)...
4299		{
4300	4	this.newick = value;
4301		}
4302
4303		/**
4304		* Gets the value of the fontName property.
4305		*
4306		* @return possible object is {@link String }
4307		*
4308		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4309	24	public String getFontName()...
4310		{
4311	24	return fontName;
4312		}
4313
4314		/**
4315		* Sets the value of the fontName property.
4316		*
4317		* @param value
4318		* allowed object is {@link String }
4319		*
4320		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4321	4	public void setFontName(String value)...
4322		{
4323	4	this.fontName = value;
4324		}
4325
4326		/**
4327		* Gets the value of the fontSize property.
4328		*
4329		* @return possible object is {@link Integer }
4330		*
4331		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4332	12	public Integer getFontSize()...
4333		{
4334	12	return fontSize;
4335		}
4336
4337		/**
4338		* Sets the value of the fontSize property.
4339		*
4340		* @param value
4341		* allowed object is {@link Integer }
4342		*
4343		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4344	4	public void setFontSize(Integer value)...
4345		{
4346	4	this.fontSize = value;
4347		}
4348
4349		/**
4350		* Gets the value of the fontStyle property.
4351		*
4352		* @return possible object is {@link Integer }
4353		*
4354		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4355	12	public Integer getFontStyle()...
4356		{
4357	12	return fontStyle;
4358		}
4359
4360		/**
4361		* Sets the value of the fontStyle property.
4362		*
4363		* @param value
4364		* allowed object is {@link Integer }
4365		*
4366		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4367	4	public void setFontStyle(Integer value)...
4368		{
4369	4	this.fontStyle = value;
4370		}
4371
4372		/**
4373		* Gets the value of the threshold property.
4374		*
4375		* @return possible object is {@link Float }
4376		*
4377		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4378	12	public Float getThreshold()...
4379		{
4380	12	return threshold;
4381		}
4382
4383		/**
4384		* Sets the value of the threshold property.
4385		*
4386		* @param value
4387		* allowed object is {@link Float }
4388		*
4389		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4390	4	public void setThreshold(Float value)...
4391		{
4392	4	this.threshold = value;
4393		}
4394
4395		/**
4396		* Gets the value of the showBootstrap property.
4397		*
4398		* @return possible object is {@link Boolean }
4399		*
4400		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4401	12	public Boolean isShowBootstrap()...
4402		{
4403	12	return showBootstrap;
4404		}
4405
4406		/**
4407		* Sets the value of the showBootstrap property.
4408		*
4409		* @param value
4410		* allowed object is {@link Boolean }
4411		*
4412		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4413	4	public void setShowBootstrap(Boolean value)...
4414		{
4415	4	this.showBootstrap = value;
4416		}
4417
4418		/**
4419		* Gets the value of the showDistances property.
4420		*
4421		* @return possible object is {@link Boolean }
4422		*
4423		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4424	12	public Boolean isShowDistances()...
4425		{
4426	12	return showDistances;
4427		}
4428
4429		/**
4430		* Sets the value of the showDistances property.
4431		*
4432		* @param value
4433		* allowed object is {@link Boolean }
4434		*
4435		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4436	4	public void setShowDistances(Boolean value)...
4437		{
4438	4	this.showDistances = value;
4439		}
4440
4441		/**
4442		* Gets the value of the markUnlinked property.
4443		*
4444		* @return possible object is {@link Boolean }
4445		*
4446		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4447	12	public Boolean isMarkUnlinked()...
4448		{
4449	12	return markUnlinked;
4450		}
4451
4452		/**
4453		* Sets the value of the markUnlinked property.
4454		*
4455		* @param value
4456		* allowed object is {@link Boolean }
4457		*
4458		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4459	4	public void setMarkUnlinked(Boolean value)...
4460		{
4461	4	this.markUnlinked = value;
4462		}
4463
4464		/**
4465		* Gets the value of the fitToWindow property.
4466		*
4467		* @return possible object is {@link Boolean }
4468		*
4469		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4470	12	public Boolean isFitToWindow()...
4471		{
4472	12	return fitToWindow;
4473		}
4474
4475		/**
4476		* Sets the value of the fitToWindow property.
4477		*
4478		* @param value
4479		* allowed object is {@link Boolean }
4480		*
4481		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4482	4	public void setFitToWindow(Boolean value)...
4483		{
4484	4	this.fitToWindow = value;
4485		}
4486
4487		/**
4488		* Gets the value of the currentTree property.
4489		*
4490		* @return possible object is {@link Boolean }
4491		*
4492		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4493	12	public Boolean isCurrentTree()...
4494		{
4495	12	return currentTree;
4496		}
4497
4498		/**
4499		* Sets the value of the currentTree property.
4500		*
4501		* @param value
4502		* allowed object is {@link Boolean }
4503		*
4504		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4505	4	public void setCurrentTree(Boolean value)...
4506		{
4507	4	this.currentTree = value;
4508		}
4509
4510		/**
4511		* Gets the value of the columnWise property.
4512		*
4513		* @return possible object is {@link Boolean }
4514		*
4515		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
4516	12	public boolean isColumnWise()...
4517		{
4518	12	if (columnWise == null)
4519		{
4520	12	return false;
4521		}
4522		else
4523		{
4524	0	return columnWise;
4525		}
4526		}
4527
4528		/**
4529		* Sets the value of the columnWise property.
4530		*
4531		* @param value
4532		* allowed object is {@link Boolean }
4533		*
4534		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
4535	0	public void setColumnWise(Boolean value)...
4536		{
4537	0	this.columnWise = value;
4538		}
4539
4540		/**
4541		* Gets the value of the columnReference property.
4542		*
4543		* @return possible object is {@link String }
4544		*
4545		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
4546	0	public String getColumnReference()...
4547		{
4548	0	return columnReference;
4549		}
4550
4551		/**
4552		* Sets the value of the columnReference property.
4553		*
4554		* @param value
4555		* allowed object is {@link String }
4556		*
4557		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
4558	0	public void setColumnReference(String value)...
4559		{
4560	0	this.columnReference = value;
4561		}
4562
4563		/**
4564		* Gets the value of the id property.
4565		*
4566		* @return possible object is {@link String }
4567		*
4568		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4569	24	public String getId()...
4570		{
4571	24	return id;
4572		}
4573
4574		/**
4575		* Sets the value of the id property.
4576		*
4577		* @param value
4578		* allowed object is {@link String }
4579		*
4580		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4581	4	public void setId(String value)...
4582		{
4583	4	this.id = value;
4584		}
4585
4586		/**
4587		* Gets the value of the linkToAllViews property.
4588		*
4589		* @return possible object is {@link Boolean }
4590		*
4591		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
4592	12	public boolean isLinkToAllViews()...
4593		{
4594	12	if (linkToAllViews == null)
4595		{
4596	8	return false;
4597		}
4598		else
4599		{
4600	4	return linkToAllViews;
4601		}
4602		}
4603
4604		/**
4605		* Sets the value of the linkToAllViews property.
4606		*
4607		* @param value
4608		* allowed object is {@link Boolean }
4609		*
4610		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4611	4	public void setLinkToAllViews(Boolean value)...
4612		{
4613	4	this.linkToAllViews = value;
4614		}
4615
4616		/**
4617		* Gets the value of the width property.
4618		*
4619		* @return possible object is {@link Integer }
4620		*
4621		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4622	12	public Integer getWidth()...
4623		{
4624	12	return width;
4625		}
4626
4627		/**
4628		* Sets the value of the width property.
4629		*
4630		* @param value
4631		* allowed object is {@link Integer }
4632		*
4633		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4634	4	public void setWidth(Integer value)...
4635		{
4636	4	this.width = value;
4637		}
4638
4639		/**
4640		* Gets the value of the height property.
4641		*
4642		* @return possible object is {@link Integer }
4643		*
4644		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4645	12	public Integer getHeight()...
4646		{
4647	12	return height;
4648		}
4649
4650		/**
4651		* Sets the value of the height property.
4652		*
4653		* @param value
4654		* allowed object is {@link Integer }
4655		*
4656		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4657	4	public void setHeight(Integer value)...
4658		{
4659	4	this.height = value;
4660		}
4661
4662		/**
4663		* Gets the value of the xpos property.
4664		*
4665		* @return possible object is {@link Integer }
4666		*
4667		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4668	12	public Integer getXpos()...
4669		{
4670	12	return xpos;
4671		}
4672
4673		/**
4674		* Sets the value of the xpos property.
4675		*
4676		* @param value
4677		* allowed object is {@link Integer }
4678		*
4679		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4680	4	public void setXpos(Integer value)...
4681		{
4682	4	this.xpos = value;
4683		}
4684
4685		/**
4686		* Gets the value of the ypos property.
4687		*
4688		* @return possible object is {@link Integer }
4689		*
4690		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4691	12	public Integer getYpos()...
4692		{
4693	12	return ypos;
4694		}
4695
4696		/**
4697		* Sets the value of the ypos property.
4698		*
4699		* @param value
4700		* allowed object is {@link Integer }
4701		*
4702		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4703	4	public void setYpos(Integer value)...
4704		{
4705	4	this.ypos = value;
4706		}
4707
4708		}
4709
4710		/**
4711		* &lt;p&gt;Java class for anonymous complex type.
4712		*
4713		* &lt;p&gt;The following schema fragment specifies the expected content
4714		* contained within this class.
4715		*
4716		* &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
4717		* &amp;lt;restriction
4718		* base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
4719		* &amp;lt;sequence&amp;gt; &amp;lt;element name="UserColourScheme"
4720		* type="{www.jalview.org/colours}JalviewUserColours"/&amp;gt;
4721		* &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="id"
4722		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4723		* &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
4724		* &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
4725		*
4726		*
4727		*/
4728		@XmlAccessorType(XmlAccessType.FIELD)
4729		@XmlType(name = "", propOrder = { "userColourScheme" })
		0% Uncovered Elements: 8 (8) Complexity: 4 Complexity Density: 1
4730		public static class UserColours
4731		{
4732
4733		@XmlElement(
4734		name = "UserColourScheme",
4735		namespace = "www.jalview.org",
4736		required = true)
4737		protected JalviewUserColours userColourScheme;
4738
4739		@XmlAttribute(name = "id")
4740		protected String id;
4741
4742		/**
4743		* Gets the value of the userColourScheme property.
4744		*
4745		* @return possible object is {@link JalviewUserColours }
4746		*
4747		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
4748	0	public JalviewUserColours getUserColourScheme()...
4749		{
4750	0	return userColourScheme;
4751		}
4752
4753		/**
4754		* Sets the value of the userColourScheme property.
4755		*
4756		* @param value
4757		* allowed object is {@link JalviewUserColours }
4758		*
4759		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
4760	0	public void setUserColourScheme(JalviewUserColours value)...
4761		{
4762	0	this.userColourScheme = value;
4763		}
4764
4765		/**
4766		* Gets the value of the id property.
4767		*
4768		* @return possible object is {@link String }
4769		*
4770		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
4771	0	public String getId()...
4772		{
4773	0	return id;
4774		}
4775
4776		/**
4777		* Sets the value of the id property.
4778		*
4779		* @param value
4780		* allowed object is {@link String }
4781		*
4782		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
4783	0	public void setId(String value)...
4784		{
4785	0	this.id = value;
4786		}
4787
4788		}
4789
4790		/**
4791		* &lt;p&gt;Java class for anonymous complex type.
4792		*
4793		* &lt;p&gt;The following schema fragment specifies the expected content
4794		* contained within this class.
4795		*
4796		* &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
4797		* &amp;lt;restriction
4798		* base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
4799		* &amp;lt;sequence&amp;gt; &amp;lt;element name="AnnotationColours"
4800		* type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&amp;gt;
4801		* &amp;lt;element name="hiddenColumns" maxOccurs="unbounded"
4802		* minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
4803		* &amp;lt;complexContent&amp;gt; &amp;lt;restriction
4804		* base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
4805		* name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4806		* &amp;lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int"
4807		* /&amp;gt; &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
4808		* &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt; &amp;lt;element
4809		* name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&amp;gt;
4810		* &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
4811		* &amp;lt;extension
4812		* base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&amp;gt;
4813		* &amp;lt;attribute name="calcId" use="required"
4814		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
4815		* name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean"
4816		* default="false" /&amp;gt; &amp;lt;attribute name="autoUpdate"
4817		* use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4818		* &amp;lt;/extension&amp;gt; &amp;lt;/complexContent&amp;gt;
4819		* &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt; &amp;lt;element
4820		* name="overview" minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
4821		* &amp;lt;complexContent&amp;gt; &amp;lt;restriction
4822		* base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
4823		* ref="{www.jalview.org}swingwindow"/&amp;gt; &amp;lt;attribute
4824		* name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean"
4825		* /&amp;gt; &amp;lt;attribute name="residueColour"
4826		* type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
4827		* name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4828		* &amp;lt;attribute name="hiddenColour"
4829		* type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
4830		* name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4831		* &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
4832		* &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
4833		* &amp;lt;/sequence&amp;gt; &amp;lt;attGroup
4834		* ref="{www.jalview.org}swingwindow"/&amp;gt; &amp;lt;attribute
4835		* name="conservationSelected"
4836		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4837		* &amp;lt;attribute name="pidSelected"
4838		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4839		* &amp;lt;attribute name="bgColour"
4840		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
4841		* name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4842		* &amp;lt;attribute name="pidThreshold"
4843		* type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
4844		* name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4845		* &amp;lt;attribute name="showFullId"
4846		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4847		* &amp;lt;attribute name="rightAlignIds"
4848		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4849		* &amp;lt;attribute name="showText"
4850		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4851		* &amp;lt;attribute name="showColourText"
4852		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4853		* &amp;lt;attribute name="showUnconserved"
4854		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4855		* &amp;lt;attribute name="showBoxes"
4856		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4857		* &amp;lt;attribute name="wrapAlignment"
4858		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4859		* &amp;lt;attribute name="renderGaps"
4860		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4861		* &amp;lt;attribute name="showSequenceFeatures"
4862		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4863		* &amp;lt;attribute name="showNPfeatureTooltip"
4864		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4865		* &amp;lt;attribute name="showDbRefTooltip"
4866		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4867		* &amp;lt;attribute name="followHighlight"
4868		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
4869		* &amp;lt;attribute name="followSelection"
4870		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
4871		* &amp;lt;attribute name="showAnnotation"
4872		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4873		* &amp;lt;attribute name="centreColumnLabels"
4874		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4875		* &amp;lt;attribute name="showGroupConservation"
4876		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4877		* &amp;lt;attribute name="showGroupConsensus"
4878		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4879		* &amp;lt;attribute name="showConsensusHistogram"
4880		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
4881		* &amp;lt;attribute name="showSequenceLogo"
4882		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4883		* &amp;lt;attribute name="normaliseSequenceLogo"
4884		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4885		* &amp;lt;attribute name="ignoreGapsinConsensus"
4886		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
4887		* &amp;lt;attribute name="startRes"
4888		* type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
4889		* name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4890		* &amp;lt;attribute name="charWidth"
4891		* type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
4892		* name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4893		* &amp;lt;attribute name="fontName"
4894		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
4895		* name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4896		* &amp;lt;attribute name="fontStyle"
4897		* type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
4898		* name="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4899		* &amp;lt;attribute name="idWidthManuallyAdjusted"
4900		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4901		* &amp;lt;attribute name="scaleProteinAsCdna"
4902		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
4903		* &amp;lt;attribute name="viewName"
4904		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
4905		* name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string"
4906		* /&amp;gt; &amp;lt;attribute name="gatheredViews"
4907		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4908		* &amp;lt;attribute name="textCol1"
4909		* type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
4910		* name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4911		* &amp;lt;attribute name="textColThreshold"
4912		* type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
4913		* name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&amp;gt;
4914		* &amp;lt;attribute name="complementId"
4915		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
4916		* name="showComplementFeatures"
4917		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4918		* &amp;lt;attribute name="showComplementFeaturesOnTop"
4919		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4920		* &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
4921		* &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
4922		*
4923		*
4924		*/
4925		@XmlAccessorType(XmlAccessType.FIELD)
4926		@XmlType(
4927		name = "",
4928		propOrder =
4929		{ "annotationColours", "hiddenColumns", "calcIdParam", "overview" })
		91.3% Uncovered Elements: 24 (276) Complexity: 123 Complexity Density: 0.89
4930		public static class Viewport
4931		{
4932
4933		@XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
4934		protected AnnotationColourScheme annotationColours;
4935
4936		@XmlElement(namespace = "www.jalview.org")
4937		protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
4938
4939		@XmlElement(namespace = "www.jalview.org")
4940		protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
4941
4942		@XmlElement(namespace = "www.jalview.org")
4943		protected JalviewModel.Viewport.Overview overview;
4944
4945		@XmlAttribute(name = "conservationSelected")
4946		protected Boolean conservationSelected;
4947
4948		@XmlAttribute(name = "pidSelected")
4949		protected Boolean pidSelected;
4950
4951		@XmlAttribute(name = "bgColour")
4952		protected String bgColour;
4953
4954		@XmlAttribute(name = "consThreshold")
4955		protected Integer consThreshold;
4956
4957		@XmlAttribute(name = "pidThreshold")
4958		protected Integer pidThreshold;
4959
4960		@XmlAttribute(name = "title")
4961		protected String title;
4962
4963		@XmlAttribute(name = "showFullId")
4964		protected Boolean showFullId;
4965
4966		@XmlAttribute(name = "rightAlignIds")
4967		protected Boolean rightAlignIds;
4968
4969		@XmlAttribute(name = "showText")
4970		protected Boolean showText;
4971
4972		@XmlAttribute(name = "showColourText")
4973		protected Boolean showColourText;
4974
4975		@XmlAttribute(name = "showUnconserved")
4976		protected Boolean showUnconserved;
4977
4978		@XmlAttribute(name = "showBoxes")
4979		protected Boolean showBoxes;
4980
4981		@XmlAttribute(name = "wrapAlignment")
4982		protected Boolean wrapAlignment;
4983
4984		@XmlAttribute(name = "renderGaps")
4985		protected Boolean renderGaps;
4986
4987		@XmlAttribute(name = "showSequenceFeatures")
4988		protected Boolean showSequenceFeatures;
4989
4990		@XmlAttribute(name = "showNPfeatureTooltip")
4991		protected Boolean showNPfeatureTooltip;
4992
4993		@XmlAttribute(name = "showDbRefTooltip")
4994		protected Boolean showDbRefTooltip;
4995
4996		@XmlAttribute(name = "followHighlight")
4997		protected Boolean followHighlight;
4998
4999		@XmlAttribute(name = "followSelection")
5000		protected Boolean followSelection;
5001
5002		@XmlAttribute(name = "showAnnotation")
5003		protected Boolean showAnnotation;
5004
5005		@XmlAttribute(name = "centreColumnLabels")
5006		protected Boolean centreColumnLabels;
5007
5008		@XmlAttribute(name = "showGroupConservation")
5009		protected Boolean showGroupConservation;
5010
5011		@XmlAttribute(name = "showGroupConsensus")
5012		protected Boolean showGroupConsensus;
5013
5014		@XmlAttribute(name = "showConsensusHistogram")
5015		protected Boolean showConsensusHistogram;
5016
5017		@XmlAttribute(name = "showSequenceLogo")
5018		protected Boolean showSequenceLogo;
5019
5020		@XmlAttribute(name = "normaliseSequenceLogo")
5021		protected Boolean normaliseSequenceLogo;
5022
5023		@XmlAttribute(name = "ignoreGapsinConsensus")
5024		protected Boolean ignoreGapsinConsensus;
5025
5026		@XmlAttribute(name = "startRes")
5027		protected Integer startRes;
5028
5029		@XmlAttribute(name = "startSeq")
5030		protected Integer startSeq;
5031
5032		@XmlAttribute(name = "charWidth")
5033		protected Integer charWidth;
5034
5035		@XmlAttribute(name = "charHeight")
5036		protected Integer charHeight;
5037
5038		@XmlAttribute(name = "fontName")
5039		protected String fontName;
5040
5041		@XmlAttribute(name = "fontSize")
5042		protected Integer fontSize;
5043
5044		@XmlAttribute(name = "fontStyle")
5045		protected Integer fontStyle;
5046
5047		@XmlAttribute(name = "idWidth")
5048		protected Integer idWidth;
5049
5050		@XmlAttribute(name = "idWidthManuallyAdjusted")
5051		protected Boolean idWidthManuallyAdjusted;
5052
5053		@XmlAttribute(name = "scaleProteinAsCdna")
5054		protected Boolean scaleProteinAsCdna;
5055
5056		@XmlAttribute(name = "viewName")
5057		protected String viewName;
5058
5059		@XmlAttribute(name = "sequenceSetId")
5060		protected String sequenceSetId;
5061
5062		@XmlAttribute(name = "gatheredViews")
5063		protected Boolean gatheredViews;
5064
5065		@XmlAttribute(name = "textCol1")
5066		protected Integer textCol1;
5067
5068		@XmlAttribute(name = "textCol2")
5069		protected Integer textCol2;
5070
5071		@XmlAttribute(name = "textColThreshold")
5072		protected Integer textColThreshold;
5073
5074		@XmlAttribute(name = "id")
5075		@XmlJavaTypeAdapter(CollapsedStringAdapter.class)
5076		@XmlID
5077		@XmlSchemaType(name = "ID")
5078		protected String id;
5079
5080		@XmlAttribute(name = "complementId")
5081		protected String complementId;
5082
5083		@XmlAttribute(name = "showComplementFeatures")
5084		protected Boolean showComplementFeatures;
5085
5086		@XmlAttribute(name = "showComplementFeaturesOnTop")
5087		protected Boolean showComplementFeaturesOnTop;
5088
5089		@XmlAttribute(name = "width")
5090		protected Integer width;
5091
5092		@XmlAttribute(name = "height")
5093		protected Integer height;
5094
5095		@XmlAttribute(name = "xpos")
5096		protected Integer xpos;
5097
5098		@XmlAttribute(name = "ypos")
5099		protected Integer ypos;
5100
5101		/**
5102		* Gets the value of the annotationColours property.
5103		*
5104		* @return possible object is {@link AnnotationColourScheme }
5105		*
5106		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5107	2	public AnnotationColourScheme getAnnotationColours()...
5108		{
5109	2	return annotationColours;
5110		}
5111
5112		/**
5113		* Sets the value of the annotationColours property.
5114		*
5115		* @param value
5116		* allowed object is {@link AnnotationColourScheme }
5117		*
5118		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5119	2	public void setAnnotationColours(AnnotationColourScheme value)...
5120		{
5121	2	this.annotationColours = value;
5122		}
5123
5124		/**
5125		* Gets the value of the hiddenColumns property.
5126		*
5127		* &lt;p&gt; This accessor method returns a reference to the live list, not
5128		* a snapshot. Therefore any modification you make to the returned list will
5129		* be present inside the JAXB object. This is why there is not a
5130		* &lt;CODE&gt;set&lt;/CODE&gt; method for the hiddenColumns property.
5131		*
5132		* &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
5133		* getHiddenColumns().add(newItem); &lt;/pre&gt;
5134		*
5135		*
5136		* &lt;p&gt; Objects of the following type(s) are allowed in the list
5137		* {@link JalviewModel.Viewport.HiddenColumns }
5138		*
5139		*
5140		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
5141	221	public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns()...
5142		{
5143	221	if (hiddenColumns == null)
5144		{
5145	67	hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
5146		}
5147	221	return this.hiddenColumns;
5148		}
5149
5150		/**
5151		* Gets the value of the calcIdParam property.
5152		*
5153		* &lt;p&gt; This accessor method returns a reference to the live list, not
5154		* a snapshot. Therefore any modification you make to the returned list will
5155		* be present inside the JAXB object. This is why there is not a
5156		* &lt;CODE&gt;set&lt;/CODE&gt; method for the calcIdParam property.
5157		*
5158		* &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
5159		* getCalcIdParam().add(newItem); &lt;/pre&gt;
5160		*
5161		*
5162		* &lt;p&gt; Objects of the following type(s) are allowed in the list
5163		* {@link JalviewModel.Viewport.CalcIdParam }
5164		*
5165		*
5166		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
5167	170	public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam()...
5168		{
5169	170	if (calcIdParam == null)
5170		{
5171	85	calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
5172		}
5173	170	return this.calcIdParam;
5174		}
5175
5176		/**
5177		* Gets the value of the overview property.
5178		*
5179		* @return possible object is {@link JalviewModel.Viewport.Overview }
5180		*
5181		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5182	75	public JalviewModel.Viewport.Overview getOverview()...
5183		{
5184	75	return overview;
5185		}
5186
5187		/**
5188		* Sets the value of the overview property.
5189		*
5190		* @param value
5191		* allowed object is {@link JalviewModel.Viewport.Overview }
5192		*
5193		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5194	14	public void setOverview(JalviewModel.Viewport.Overview value)...
5195		{
5196	14	this.overview = value;
5197		}
5198
5199		/**
5200		* Gets the value of the conservationSelected property.
5201		*
5202		* @return possible object is {@link Boolean }
5203		*
5204		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5205	170	public Boolean isConservationSelected()...
5206		{
5207	170	return conservationSelected;
5208		}
5209
5210		/**
5211		* Sets the value of the conservationSelected property.
5212		*
5213		* @param value
5214		* allowed object is {@link Boolean }
5215		*
5216		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5217	46	public void setConservationSelected(Boolean value)...
5218		{
5219	46	this.conservationSelected = value;
5220		}
5221
5222		/**
5223		* Gets the value of the pidSelected property.
5224		*
5225		* @return possible object is {@link Boolean }
5226		*
5227		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5228	85	public Boolean isPidSelected()...
5229		{
5230	85	return pidSelected;
5231		}
5232
5233		/**
5234		* Sets the value of the pidSelected property.
5235		*
5236		* @param value
5237		* allowed object is {@link Boolean }
5238		*
5239		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5240	46	public void setPidSelected(Boolean value)...
5241		{
5242	46	this.pidSelected = value;
5243		}
5244
5245		/**
5246		* Gets the value of the bgColour property.
5247		*
5248		* @return possible object is {@link String }
5249		*
5250		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5251	338	public String getBgColour()...
5252		{
5253	338	return bgColour;
5254		}
5255
5256		/**
5257		* Sets the value of the bgColour property.
5258		*
5259		* @param value
5260		* allowed object is {@link String }
5261		*
5262		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5263	46	public void setBgColour(String value)...
5264		{
5265	46	this.bgColour = value;
5266		}
5267
5268		/**
5269		* Gets the value of the consThreshold property.
5270		*
5271		* @return possible object is {@link Integer }
5272		*
5273		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5274	87	public Integer getConsThreshold()...
5275		{
5276	87	return consThreshold;
5277		}
5278
5279		/**
5280		* Sets the value of the consThreshold property.
5281		*
5282		* @param value
5283		* allowed object is {@link Integer }
5284		*
5285		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5286	2	public void setConsThreshold(Integer value)...
5287		{
5288	2	this.consThreshold = value;
5289		}
5290
5291		/**
5292		* Gets the value of the pidThreshold property.
5293		*
5294		* @return possible object is {@link Integer }
5295		*
5296		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5297	85	public Integer getPidThreshold()...
5298		{
5299	85	return pidThreshold;
5300		}
5301
5302		/**
5303		* Sets the value of the pidThreshold property.
5304		*
5305		* @param value
5306		* allowed object is {@link Integer }
5307		*
5308		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5309	8	public void setPidThreshold(Integer value)...
5310		{
5311	8	this.pidThreshold = value;
5312		}
5313
5314		/**
5315		* Gets the value of the title property.
5316		*
5317		* @return possible object is {@link String }
5318		*
5319		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5320	170	public String getTitle()...
5321		{
5322	170	return title;
5323		}
5324
5325		/**
5326		* Sets the value of the title property.
5327		*
5328		* @param value
5329		* allowed object is {@link String }
5330		*
5331		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5332	46	public void setTitle(String value)...
5333		{
5334	46	this.title = value;
5335		}
5336
5337		/**
5338		* Gets the value of the showFullId property.
5339		*
5340		* @return possible object is {@link Boolean }
5341		*
5342		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5343	85	public Boolean isShowFullId()...
5344		{
5345	85	return showFullId;
5346		}
5347
5348		/**
5349		* Sets the value of the showFullId property.
5350		*
5351		* @param value
5352		* allowed object is {@link Boolean }
5353		*
5354		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5355	46	public void setShowFullId(Boolean value)...
5356		{
5357	46	this.showFullId = value;
5358		}
5359
5360		/**
5361		* Gets the value of the rightAlignIds property.
5362		*
5363		* @return possible object is {@link Boolean }
5364		*
5365		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5366	85	public Boolean isRightAlignIds()...
5367		{
5368	85	return rightAlignIds;
5369		}
5370
5371		/**
5372		* Sets the value of the rightAlignIds property.
5373		*
5374		* @param value
5375		* allowed object is {@link Boolean }
5376		*
5377		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5378	46	public void setRightAlignIds(Boolean value)...
5379		{
5380	46	this.rightAlignIds = value;
5381		}
5382
5383		/**
5384		* Gets the value of the showText property.
5385		*
5386		* @return possible object is {@link Boolean }
5387		*
5388		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5389	85	public Boolean isShowText()...
5390		{
5391	85	return showText;
5392		}
5393
5394		/**
5395		* Sets the value of the showText property.
5396		*
5397		* @param value
5398		* allowed object is {@link Boolean }
5399		*
5400		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5401	46	public void setShowText(Boolean value)...
5402		{
5403	46	this.showText = value;
5404		}
5405
5406		/**
5407		* Gets the value of the showColourText property.
5408		*
5409		* @return possible object is {@link Boolean }
5410		*
5411		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5412	85	public Boolean isShowColourText()...
5413		{
5414	85	return showColourText;
5415		}
5416
5417		/**
5418		* Sets the value of the showColourText property.
5419		*
5420		* @param value
5421		* allowed object is {@link Boolean }
5422		*
5423		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5424	46	public void setShowColourText(Boolean value)...
5425		{
5426	46	this.showColourText = value;
5427		}
5428
5429		/**
5430		* Gets the value of the showUnconserved property.
5431		*
5432		* @return possible object is {@link Boolean }
5433		*
5434		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
5435	85	public boolean isShowUnconserved()...
5436		{
5437	85	if (showUnconserved == null)
5438		{
5439	0	return false;
5440		}
5441		else
5442		{
5443	85	return showUnconserved;
5444		}
5445		}
5446
5447		/**
5448		* Sets the value of the showUnconserved property.
5449		*
5450		* @param value
5451		* allowed object is {@link Boolean }
5452		*
5453		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5454	46	public void setShowUnconserved(Boolean value)...
5455		{
5456	46	this.showUnconserved = value;
5457		}
5458
5459		/**
5460		* Gets the value of the showBoxes property.
5461		*
5462		* @return possible object is {@link Boolean }
5463		*
5464		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5465	85	public Boolean isShowBoxes()...
5466		{
5467	85	return showBoxes;
5468		}
5469
5470		/**
5471		* Sets the value of the showBoxes property.
5472		*
5473		* @param value
5474		* allowed object is {@link Boolean }
5475		*
5476		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5477	46	public void setShowBoxes(Boolean value)...
5478		{
5479	46	this.showBoxes = value;
5480		}
5481
5482		/**
5483		* Gets the value of the wrapAlignment property.
5484		*
5485		* @return possible object is {@link Boolean }
5486		*
5487		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5488	85	public Boolean isWrapAlignment()...
5489		{
5490	85	return wrapAlignment;
5491		}
5492
5493		/**
5494		* Sets the value of the wrapAlignment property.
5495		*
5496		* @param value
5497		* allowed object is {@link Boolean }
5498		*
5499		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5500	46	public void setWrapAlignment(Boolean value)...
5501		{
5502	46	this.wrapAlignment = value;
5503		}
5504
5505		/**
5506		* Gets the value of the renderGaps property.
5507		*
5508		* @return possible object is {@link Boolean }
5509		*
5510		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5511	85	public Boolean isRenderGaps()...
5512		{
5513	85	return renderGaps;
5514		}
5515
5516		/**
5517		* Sets the value of the renderGaps property.
5518		*
5519		* @param value
5520		* allowed object is {@link Boolean }
5521		*
5522		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5523	46	public void setRenderGaps(Boolean value)...
5524		{
5525	46	this.renderGaps = value;
5526		}
5527
5528		/**
5529		* Gets the value of the showSequenceFeatures property.
5530		*
5531		* @return possible object is {@link Boolean }
5532		*
5533		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5534	85	public Boolean isShowSequenceFeatures()...
5535		{
5536	85	return showSequenceFeatures;
5537		}
5538
5539		/**
5540		* Sets the value of the showSequenceFeatures property.
5541		*
5542		* @param value
5543		* allowed object is {@link Boolean }
5544		*
5545		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5546	46	public void setShowSequenceFeatures(Boolean value)...
5547		{
5548	46	this.showSequenceFeatures = value;
5549		}
5550
5551		/**
5552		* Gets the value of the showNPfeatureTooltip property.
5553		*
5554		* @return possible object is {@link Boolean }
5555		*
5556		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5557	85	public Boolean isShowNPfeatureTooltip()...
5558		{
5559	85	return showNPfeatureTooltip;
5560		}
5561
5562		/**
5563		* Sets the value of the showNPfeatureTooltip property.
5564		*
5565		* @param value
5566		* allowed object is {@link Boolean }
5567		*
5568		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5569	46	public void setShowNPfeatureTooltip(Boolean value)...
5570		{
5571	46	this.showNPfeatureTooltip = value;
5572		}
5573
5574		/**
5575		* Gets the value of the showDbRefTooltip property.
5576		*
5577		* @return possible object is {@link Boolean }
5578		*
5579		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5580	85	public Boolean isShowDbRefTooltip()...
5581		{
5582	85	return showDbRefTooltip;
5583		}
5584
5585		/**
5586		* Sets the value of the showDbRefTooltip property.
5587		*
5588		* @param value
5589		* allowed object is {@link Boolean }
5590		*
5591		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5592	46	public void setShowDbRefTooltip(Boolean value)...
5593		{
5594	46	this.showDbRefTooltip = value;
5595		}
5596
5597		/**
5598		* Gets the value of the followHighlight property.
5599		*
5600		* @return possible object is {@link Boolean }
5601		*
5602		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
5603	85	public boolean isFollowHighlight()...
5604		{
5605	85	if (followHighlight == null)
5606		{
5607	0	return true;
5608		}
5609		else
5610		{
5611	85	return followHighlight;
5612		}
5613		}
5614
5615		/**
5616		* Sets the value of the followHighlight property.
5617		*
5618		* @param value
5619		* allowed object is {@link Boolean }
5620		*
5621		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5622	46	public void setFollowHighlight(Boolean value)...
5623		{
5624	46	this.followHighlight = value;
5625		}
5626
5627		/**
5628		* Gets the value of the followSelection property.
5629		*
5630		* @return possible object is {@link Boolean }
5631		*
5632		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
5633	85	public boolean isFollowSelection()...
5634		{
5635	85	if (followSelection == null)
5636		{
5637	0	return true;
5638		}
5639		else
5640		{
5641	85	return followSelection;
5642		}
5643		}
5644
5645		/**
5646		* Sets the value of the followSelection property.
5647		*
5648		* @param value
5649		* allowed object is {@link Boolean }
5650		*
5651		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5652	46	public void setFollowSelection(Boolean value)...
5653		{
5654	46	this.followSelection = value;
5655		}
5656
5657		/**
5658		* Gets the value of the showAnnotation property.
5659		*
5660		* @return possible object is {@link Boolean }
5661		*
5662		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5663	170	public Boolean isShowAnnotation()...
5664		{
5665	170	return showAnnotation;
5666		}
5667
5668		/**
5669		* Sets the value of the showAnnotation property.
5670		*
5671		* @param value
5672		* allowed object is {@link Boolean }
5673		*
5674		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5675	46	public void setShowAnnotation(Boolean value)...
5676		{
5677	46	this.showAnnotation = value;
5678		}
5679
5680		/**
5681		* Gets the value of the centreColumnLabels property.
5682		*
5683		* @return possible object is {@link Boolean }
5684		*
5685		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
5686	85	public boolean isCentreColumnLabels()...
5687		{
5688	85	if (centreColumnLabels == null)
5689		{
5690	85	return false;
5691		}
5692		else
5693		{
5694	0	return centreColumnLabels;
5695		}
5696		}
5697
5698		/**
5699		* Sets the value of the centreColumnLabels property.
5700		*
5701		* @param value
5702		* allowed object is {@link Boolean }
5703		*
5704		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
5705	0	public void setCentreColumnLabels(Boolean value)...
5706		{
5707	0	this.centreColumnLabels = value;
5708		}
5709
5710		/**
5711		* Gets the value of the showGroupConservation property.
5712		*
5713		* @return possible object is {@link Boolean }
5714		*
5715		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
5716	85	public boolean isShowGroupConservation()...
5717		{
5718	85	if (showGroupConservation == null)
5719		{
5720	0	return false;
5721		}
5722		else
5723		{
5724	85	return showGroupConservation;
5725		}
5726		}
5727
5728		/**
5729		* Sets the value of the showGroupConservation property.
5730		*
5731		* @param value
5732		* allowed object is {@link Boolean }
5733		*
5734		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5735	46	public void setShowGroupConservation(Boolean value)...
5736		{
5737	46	this.showGroupConservation = value;
5738		}
5739
5740		/**
5741		* Gets the value of the showGroupConsensus property.
5742		*
5743		* @return possible object is {@link Boolean }
5744		*
5745		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
5746	85	public boolean isShowGroupConsensus()...
5747		{
5748	85	if (showGroupConsensus == null)
5749		{
5750	0	return false;
5751		}
5752		else
5753		{
5754	85	return showGroupConsensus;
5755		}
5756		}
5757
5758		/**
5759		* Sets the value of the showGroupConsensus property.
5760		*
5761		* @param value
5762		* allowed object is {@link Boolean }
5763		*
5764		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5765	46	public void setShowGroupConsensus(Boolean value)...
5766		{
5767	46	this.showGroupConsensus = value;
5768		}
5769
5770		/**
5771		* Gets the value of the showConsensusHistogram property.
5772		*
5773		* @return possible object is {@link Boolean }
5774		*
5775		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
5776	85	public boolean isShowConsensusHistogram()...
5777		{
5778	85	if (showConsensusHistogram == null)
5779		{
5780	0	return true;
5781		}
5782		else
5783		{
5784	85	return showConsensusHistogram;
5785		}
5786		}
5787
5788		/**
5789		* Sets the value of the showConsensusHistogram property.
5790		*
5791		* @param value
5792		* allowed object is {@link Boolean }
5793		*
5794		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5795	46	public void setShowConsensusHistogram(Boolean value)...
5796		{
5797	46	this.showConsensusHistogram = value;
5798		}
5799
5800		/**
5801		* Gets the value of the showSequenceLogo property.
5802		*
5803		* @return possible object is {@link Boolean }
5804		*
5805		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
5806	85	public boolean isShowSequenceLogo()...
5807		{
5808	85	if (showSequenceLogo == null)
5809		{
5810	0	return false;
5811		}
5812		else
5813		{
5814	85	return showSequenceLogo;
5815		}
5816		}
5817
5818		/**
5819		* Sets the value of the showSequenceLogo property.
5820		*
5821		* @param value
5822		* allowed object is {@link Boolean }
5823		*
5824		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5825	46	public void setShowSequenceLogo(Boolean value)...
5826		{
5827	46	this.showSequenceLogo = value;
5828		}
5829
5830		/**
5831		* Gets the value of the normaliseSequenceLogo property.
5832		*
5833		* @return possible object is {@link Boolean }
5834		*
5835		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
5836	85	public boolean isNormaliseSequenceLogo()...
5837		{
5838	85	if (normaliseSequenceLogo == null)
5839		{
5840	30	return false;
5841		}
5842		else
5843		{
5844	55	return normaliseSequenceLogo;
5845		}
5846		}
5847
5848		/**
5849		* Sets the value of the normaliseSequenceLogo property.
5850		*
5851		* @param value
5852		* allowed object is {@link Boolean }
5853		*
5854		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5855	46	public void setNormaliseSequenceLogo(Boolean value)...
5856		{
5857	46	this.normaliseSequenceLogo = value;
5858		}
5859
5860		/**
5861		* Gets the value of the ignoreGapsinConsensus property.
5862		*
5863		* @return possible object is {@link Boolean }
5864		*
5865		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
5866	170	public boolean isIgnoreGapsinConsensus()...
5867		{
5868	170	if (ignoreGapsinConsensus == null)
5869		{
5870	0	return true;
5871		}
5872		else
5873		{
5874	170	return ignoreGapsinConsensus;
5875		}
5876		}
5877
5878		/**
5879		* Sets the value of the ignoreGapsinConsensus property.
5880		*
5881		* @param value
5882		* allowed object is {@link Boolean }
5883		*
5884		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5885	46	public void setIgnoreGapsinConsensus(Boolean value)...
5886		{
5887	46	this.ignoreGapsinConsensus = value;
5888		}
5889
5890		/**
5891		* Gets the value of the startRes property.
5892		*
5893		* @return possible object is {@link Integer }
5894		*
5895		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5896	85	public Integer getStartRes()...
5897		{
5898	85	return startRes;
5899		}
5900
5901		/**
5902		* Sets the value of the startRes property.
5903		*
5904		* @param value
5905		* allowed object is {@link Integer }
5906		*
5907		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5908	46	public void setStartRes(Integer value)...
5909		{
5910	46	this.startRes = value;
5911		}
5912
5913		/**
5914		* Gets the value of the startSeq property.
5915		*
5916		* @return possible object is {@link Integer }
5917		*
5918		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
5919	0	public Integer getStartSeq()...
5920		{
5921	0	return startSeq;
5922		}
5923
5924		/**
5925		* Sets the value of the startSeq property.
5926		*
5927		* @param value
5928		* allowed object is {@link Integer }
5929		*
5930		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5931	46	public void setStartSeq(Integer value)...
5932		{
5933	46	this.startSeq = value;
5934		}
5935
5936		/**
5937		* Gets the value of the charWidth property.
5938		*
5939		* @return possible object is {@link Integer }
5940		*
5941		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5942	212	public Integer getCharWidth()...
5943		{
5944	212	return charWidth;
5945		}
5946
5947		/**
5948		* Sets the value of the charWidth property.
5949		*
5950		* @param value
5951		* allowed object is {@link Integer }
5952		*
5953		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5954	46	public void setCharWidth(Integer value)...
5955		{
5956	46	this.charWidth = value;
5957		}
5958
5959		/**
5960		* Gets the value of the charHeight property.
5961		*
5962		* @return possible object is {@link Integer }
5963		*
5964		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5965	42	public Integer getCharHeight()...
5966		{
5967	42	return charHeight;
5968		}
5969
5970		/**
5971		* Sets the value of the charHeight property.
5972		*
5973		* @param value
5974		* allowed object is {@link Integer }
5975		*
5976		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5977	46	public void setCharHeight(Integer value)...
5978		{
5979	46	this.charHeight = value;
5980		}
5981
5982		/**
5983		* Gets the value of the fontName property.
5984		*
5985		* @return possible object is {@link String }
5986		*
5987		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5988	85	public String getFontName()...
5989		{
5990	85	return fontName;
5991		}
5992
5993		/**
5994		* Sets the value of the fontName property.
5995		*
5996		* @param value
5997		* allowed object is {@link String }
5998		*
5999		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6000	46	public void setFontName(String value)...
6001		{
6002	46	this.fontName = value;
6003		}
6004
6005		/**
6006		* Gets the value of the fontSize property.
6007		*
6008		* @return possible object is {@link Integer }
6009		*
6010		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6011	85	public Integer getFontSize()...
6012		{
6013	85	return fontSize;
6014		}
6015
6016		/**
6017		* Sets the value of the fontSize property.
6018		*
6019		* @param value
6020		* allowed object is {@link Integer }
6021		*
6022		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6023	46	public void setFontSize(Integer value)...
6024		{
6025	46	this.fontSize = value;
6026		}
6027
6028		/**
6029		* Gets the value of the fontStyle property.
6030		*
6031		* @return possible object is {@link Integer }
6032		*
6033		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6034	85	public Integer getFontStyle()...
6035		{
6036	85	return fontStyle;
6037		}
6038
6039		/**
6040		* Sets the value of the fontStyle property.
6041		*
6042		* @param value
6043		* allowed object is {@link Integer }
6044		*
6045		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6046	46	public void setFontStyle(Integer value)...
6047		{
6048	46	this.fontStyle = value;
6049		}
6050
6051		/**
6052		* Gets the value of the idWidth property.
6053		*
6054		* @return possible object is {@link Integer }
6055		*
6056		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6057	127	public Integer getIdWidth()...
6058		{
6059	127	return idWidth;
6060		}
6061
6062		/**
6063		* Sets the value of the idWidth property.
6064		*
6065		* @param value
6066		* allowed object is {@link Integer }
6067		*
6068		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6069	46	public void setIdWidth(Integer value)...
6070		{
6071	46	this.idWidth = value;
6072		}
6073
6074		/**
6075		* Gets the value of the idWidthManuallyAdjusted property.
6076		*
6077		* @return possible object is {@link Boolean }
6078		*
6079		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6080	42	public Boolean isIdWidthManuallyAdjusted()...
6081		{
6082	42	return idWidthManuallyAdjusted;
6083		}
6084
6085		/**
6086		* Sets the value of the idWidthManuallyAdjusted property.
6087		*
6088		* @param value
6089		* allowed object is {@link Boolean }
6090		*
6091		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6092	46	public void setIdWidthManuallyAdjusted(Boolean value)...
6093		{
6094	46	this.idWidthManuallyAdjusted = value;
6095		}
6096
6097		/**
6098		* Gets the value of the scaleProteinAsCdna property.
6099		*
6100		* @return possible object is {@link Boolean }
6101		*
6102		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
6103	85	public boolean isScaleProteinAsCdna()...
6104		{
6105	85	if (scaleProteinAsCdna == null)
6106		{
6107	30	return true;
6108		}
6109		else
6110		{
6111	55	return scaleProteinAsCdna;
6112		}
6113		}
6114
6115		/**
6116		* Sets the value of the scaleProteinAsCdna property.
6117		*
6118		* @param value
6119		* allowed object is {@link Boolean }
6120		*
6121		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6122	46	public void setScaleProteinAsCdna(Boolean value)...
6123		{
6124	46	this.scaleProteinAsCdna = value;
6125		}
6126
6127		/**
6128		* Gets the value of the viewName property.
6129		*
6130		* @return possible object is {@link String }
6131		*
6132		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6133	144	public String getViewName()...
6134		{
6135	144	return viewName;
6136		}
6137
6138		/**
6139		* Sets the value of the viewName property.
6140		*
6141		* @param value
6142		* allowed object is {@link String }
6143		*
6144		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6145	46	public void setViewName(String value)...
6146		{
6147	46	this.viewName = value;
6148		}
6149
6150		/**
6151		* Gets the value of the sequenceSetId property.
6152		*
6153		* @return possible object is {@link String }
6154		*
6155		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6156	170	public String getSequenceSetId()...
6157		{
6158	170	return sequenceSetId;
6159		}
6160
6161		/**
6162		* Sets the value of the sequenceSetId property.
6163		*
6164		* @param value
6165		* allowed object is {@link String }
6166		*
6167		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6168	46	public void setSequenceSetId(String value)...
6169		{
6170	46	this.sequenceSetId = value;
6171		}
6172
6173		/**
6174		* Gets the value of the gatheredViews property.
6175		*
6176		* @return possible object is {@link Boolean }
6177		*
6178		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6179	85	public Boolean isGatheredViews()...
6180		{
6181	85	return gatheredViews;
6182		}
6183
6184		/**
6185		* Sets the value of the gatheredViews property.
6186		*
6187		* @param value
6188		* allowed object is {@link Boolean }
6189		*
6190		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6191	46	public void setGatheredViews(Boolean value)...
6192		{
6193	46	this.gatheredViews = value;
6194		}
6195
6196		/**
6197		* Gets the value of the textCol1 property.
6198		*
6199		* @return possible object is {@link Integer }
6200		*
6201		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6202	85	public Integer getTextCol1()...
6203		{
6204	85	return textCol1;
6205		}
6206
6207		/**
6208		* Sets the value of the textCol1 property.
6209		*
6210		* @param value
6211		* allowed object is {@link Integer }
6212		*
6213		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6214	46	public void setTextCol1(Integer value)...
6215		{
6216	46	this.textCol1 = value;
6217		}
6218
6219		/**
6220		* Gets the value of the textCol2 property.
6221		*
6222		* @return possible object is {@link Integer }
6223		*
6224		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6225	85	public Integer getTextCol2()...
6226		{
6227	85	return textCol2;
6228		}
6229
6230		/**
6231		* Sets the value of the textCol2 property.
6232		*
6233		* @param value
6234		* allowed object is {@link Integer }
6235		*
6236		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6237	46	public void setTextCol2(Integer value)...
6238		{
6239	46	this.textCol2 = value;
6240		}
6241
6242		/**
6243		* Gets the value of the textColThreshold property.
6244		*
6245		* @return possible object is {@link Integer }
6246		*
6247		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6248	85	public Integer getTextColThreshold()...
6249		{
6250	85	return textColThreshold;
6251		}
6252
6253		/**
6254		* Sets the value of the textColThreshold property.
6255		*
6256		* @param value
6257		* allowed object is {@link Integer }
6258		*
6259		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6260	46	public void setTextColThreshold(Integer value)...
6261		{
6262	46	this.textColThreshold = value;
6263		}
6264
6265		/**
6266		* Gets the value of the id property.
6267		*
6268		* @return possible object is {@link String }
6269		*
6270		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6271	160	public String getId()...
6272		{
6273	160	return id;
6274		}
6275
6276		/**
6277		* Sets the value of the id property.
6278		*
6279		* @param value
6280		* allowed object is {@link String }
6281		*
6282		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6283	56	public void setId(String value)...
6284		{
6285	56	this.id = value;
6286		}
6287
6288		/**
6289		* Gets the value of the complementId property.
6290		*
6291		* @return possible object is {@link String }
6292		*
6293		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6294	85	public String getComplementId()...
6295		{
6296	85	return complementId;
6297		}
6298
6299		/**
6300		* Sets the value of the complementId property.
6301		*
6302		* @param value
6303		* allowed object is {@link String }
6304		*
6305		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
6306	0	public void setComplementId(String value)...
6307		{
6308	0	this.complementId = value;
6309		}
6310
6311		/**
6312		* Gets the value of the showComplementFeatures property.
6313		*
6314		* @return possible object is {@link Boolean }
6315		*
6316		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
6317	85	public boolean isShowComplementFeatures()...
6318		{
6319	85	if (showComplementFeatures == null)
6320		{
6321	43	return false;
6322		}
6323		else
6324		{
6325	42	return showComplementFeatures;
6326		}
6327		}
6328
6329		/**
6330		* Sets the value of the showComplementFeatures property.
6331		*
6332		* @param value
6333		* allowed object is {@link Boolean }
6334		*
6335		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6336	46	public void setShowComplementFeatures(Boolean value)...
6337		{
6338	46	this.showComplementFeatures = value;
6339		}
6340
6341		/**
6342		* Gets the value of the showComplementFeaturesOnTop property.
6343		*
6344		* @return possible object is {@link Boolean }
6345		*
6346		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
6347	85	public boolean isShowComplementFeaturesOnTop()...
6348		{
6349	85	if (showComplementFeaturesOnTop == null)
6350		{
6351	43	return false;
6352		}
6353		else
6354		{
6355	42	return showComplementFeaturesOnTop;
6356		}
6357		}
6358
6359		/**
6360		* Sets the value of the showComplementFeaturesOnTop property.
6361		*
6362		* @param value
6363		* allowed object is {@link Boolean }
6364		*
6365		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6366	46	public void setShowComplementFeaturesOnTop(Boolean value)...
6367		{
6368	46	this.showComplementFeaturesOnTop = value;
6369		}
6370
6371		/**
6372		* Gets the value of the width property.
6373		*
6374		* @return possible object is {@link Integer }
6375		*
6376		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6377	255	public Integer getWidth()...
6378		{
6379	255	return width;
6380		}
6381
6382		/**
6383		* Sets the value of the width property.
6384		*
6385		* @param value
6386		* allowed object is {@link Integer }
6387		*
6388		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6389	46	public void setWidth(Integer value)...
6390		{
6391	46	this.width = value;
6392		}
6393
6394		/**
6395		* Gets the value of the height property.
6396		*
6397		* @return possible object is {@link Integer }
6398		*
6399		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6400	255	public Integer getHeight()...
6401		{
6402	255	return height;
6403		}
6404
6405		/**
6406		* Sets the value of the height property.
6407		*
6408		* @param value
6409		* allowed object is {@link Integer }
6410		*
6411		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6412	46	public void setHeight(Integer value)...
6413		{
6414	46	this.height = value;
6415		}
6416
6417		/**
6418		* Gets the value of the xpos property.
6419		*
6420		* @return possible object is {@link Integer }
6421		*
6422		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6423	85	public Integer getXpos()...
6424		{
6425	85	return xpos;
6426		}
6427
6428		/**
6429		* Sets the value of the xpos property.
6430		*
6431		* @param value
6432		* allowed object is {@link Integer }
6433		*
6434		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6435	46	public void setXpos(Integer value)...
6436		{
6437	46	this.xpos = value;
6438		}
6439
6440		/**
6441		* Gets the value of the ypos property.
6442		*
6443		* @return possible object is {@link Integer }
6444		*
6445		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6446	85	public Integer getYpos()...
6447		{
6448	85	return ypos;
6449		}
6450
6451		/**
6452		* Sets the value of the ypos property.
6453		*
6454		* @param value
6455		* allowed object is {@link Integer }
6456		*
6457		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6458	46	public void setYpos(Integer value)...
6459		{
6460	46	this.ypos = value;
6461		}
6462
6463		/**
6464		* &lt;p&gt;Java class for anonymous complex type.
6465		*
6466		* &lt;p&gt;The following schema fragment specifies the expected content
6467		* contained within this class.
6468		*
6469		* &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
6470		* &amp;lt;extension
6471		* base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&amp;gt;
6472		* &amp;lt;attribute name="calcId" use="required"
6473		* type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
6474		* &amp;lt;attribute name="needsUpdate"
6475		* type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
6476		* /&amp;gt; &amp;lt;attribute name="autoUpdate" use="required"
6477		* type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
6478		* &amp;lt;/extension&amp;gt; &amp;lt;/complexContent&amp;gt;
6479		* &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
6480		*
6481		*
6482		*/
6483		@XmlAccessorType(XmlAccessType.FIELD)
6484		@XmlType(name = "")
		0% Uncovered Elements: 16 (16) Complexity: 7 Complexity Density: 0.88
6485		public static class CalcIdParam extends WebServiceParameterSet
6486		{
6487
6488		@XmlAttribute(name = "calcId", required = true)
6489		protected String calcId;
6490
6491		@XmlAttribute(name = "needsUpdate")
6492		protected Boolean needsUpdate;
6493
6494		@XmlAttribute(name = "autoUpdate", required = true)
6495		protected boolean autoUpdate;
6496
6497		/**
6498		* Gets the value of the calcId property.
6499		*
6500		* @return possible object is {@link String }
6501		*
6502		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
6503	0	public String getCalcId()...
6504		{
6505	0	return calcId;
6506		}
6507
6508		/**
6509		* Sets the value of the calcId property.
6510		*
6511		* @param value
6512		* allowed object is {@link String }
6513		*
6514		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
6515	0	public void setCalcId(String value)...
6516		{
6517	0	this.calcId = value;
6518		}
6519
6520		/**
6521		* Gets the value of the needsUpdate property.
6522		*
6523		* @return possible object is {@link Boolean }
6524		*
6525		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
6526	0	public boolean isNeedsUpdate()...
6527		{
6528	0	if (needsUpdate == null)
6529		{
6530	0	return false;
6531		}
6532		else
6533		{
6534	0	return needsUpdate;
6535		}
6536		}
6537
6538		/**
6539		* Sets the value of the needsUpdate property.
6540		*
6541		* @param value
6542		* allowed object is {@link Boolean }
6543		*
6544		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
6545	0	public void setNeedsUpdate(Boolean value)...
6546		{
6547	0	this.needsUpdate = value;
6548		}
6549
6550		/**
6551		* Gets the value of the autoUpdate property.
6552		*
6553		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
6554	0	public boolean isAutoUpdate()...
6555		{
6556	0	return autoUpdate;
6557		}
6558
6559		/**
6560		* Sets the value of the autoUpdate property.
6561		*
6562		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
6563	0	public void setAutoUpdate(boolean value)...
6564		{
6565	0	this.autoUpdate = value;
6566		}
6567
6568		}
6569
6570		/**
6571		* &lt;p&gt;Java class for anonymous complex type.
6572		*
6573		* &lt;p&gt;The following schema fragment specifies the expected content
6574		* contained within this class.
6575		*
6576		* &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
6577		* &amp;lt;restriction
6578		* base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
6579		* &amp;lt;attribute name="start"
6580		* type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
6581		* name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
6582		* &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
6583		* &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
6584		*
6585		*
6586		*/
6587		@XmlAccessorType(XmlAccessType.FIELD)
6588		@XmlType(name = "")
		100% Uncovered Elements: 0 (8) Complexity: 4 Complexity Density: 1
6589		public static class HiddenColumns
6590		{
6591
6592		@XmlAttribute(name = "start")
6593		protected Integer start;
6594
6595		@XmlAttribute(name = "end")
6596		protected Integer end;
6597
6598		/**
6599		* Gets the value of the start property.
6600		*
6601		* @return possible object is {@link Integer }
6602		*
6603		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6604	54	public Integer getStart()...
6605		{
6606	54	return start;
6607		}
6608
6609		/**
6610		* Sets the value of the start property.
6611		*
6612		* @param value
6613		* allowed object is {@link Integer }
6614		*
6615		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6616	6	public void setStart(Integer value)...
6617		{
6618	6	this.start = value;
6619		}
6620
6621		/**
6622		* Gets the value of the end property.
6623		*
6624		* @return possible object is {@link Integer }
6625		*
6626		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6627	54	public Integer getEnd()...
6628		{
6629	54	return end;
6630		}
6631
6632		/**
6633		* Sets the value of the end property.
6634		*
6635		* @param value
6636		* allowed object is {@link Integer }
6637		*
6638		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6639	6	public void setEnd(Integer value)...
6640		{
6641	6	this.end = value;
6642		}
6643
6644		}
6645
6646		/**
6647		* &lt;p&gt;Java class for anonymous complex type.
6648		*
6649		* &lt;p&gt;The following schema fragment specifies the expected content
6650		* contained within this class.
6651		*
6652		* &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
6653		* &amp;lt;restriction
6654		* base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
6655		* ref="{www.jalview.org}swingwindow"/&amp;gt; &amp;lt;attribute
6656		* name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean"
6657		* /&amp;gt; &amp;lt;attribute name="residueColour"
6658		* type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
6659		* name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
6660		* &amp;lt;attribute name="hiddenColour"
6661		* type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
6662		* name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
6663		* &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
6664		* &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
6665		*
6666		*
6667		*/
6668		@XmlAccessorType(XmlAccessType.FIELD)
6669		@XmlType(name = "")
		100% Uncovered Elements: 0 (36) Complexity: 18 Complexity Density: 1
6670		public static class Overview
6671		{
6672
6673		@XmlAttribute(name = "showHidden")
6674		protected Boolean showHidden;
6675
6676		@XmlAttribute(name = "residueColour")
6677		protected Integer residueColour;
6678
6679		@XmlAttribute(name = "gapColour")
6680		protected Integer gapColour;
6681
6682		@XmlAttribute(name = "hiddenColour")
6683		protected Integer hiddenColour;
6684
6685		@XmlAttribute(name = "title")
6686		protected String title;
6687
6688		@XmlAttribute(name = "width")
6689		protected Integer width;
6690
6691		@XmlAttribute(name = "height")
6692		protected Integer height;
6693
6694		@XmlAttribute(name = "xpos")
6695		protected Integer xpos;
6696
6697		@XmlAttribute(name = "ypos")
6698		protected Integer ypos;
6699
6700		/**
6701		* Gets the value of the showHidden property.
6702		*
6703		* @return possible object is {@link Boolean }
6704		*
6705		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6706	11	public Boolean isShowHidden()...
6707		{
6708	11	return showHidden;
6709		}
6710
6711		/**
6712		* Sets the value of the showHidden property.
6713		*
6714		* @param value
6715		* allowed object is {@link Boolean }
6716		*
6717		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6718	14	public void setShowHidden(Boolean value)...
6719		{
6720	14	this.showHidden = value;
6721		}
6722
6723		/**
6724		* Gets the value of the residueColour property.
6725		*
6726		* @return possible object is {@link Integer }
6727		*
6728		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6729	11	public Integer getResidueColour()...
6730		{
6731	11	return residueColour;
6732		}
6733
6734		/**
6735		* Sets the value of the residueColour property.
6736		*
6737		* @param value
6738		* allowed object is {@link Integer }
6739		*
6740		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6741	14	public void setResidueColour(Integer value)...
6742		{
6743	14	this.residueColour = value;
6744		}
6745
6746		/**
6747		* Gets the value of the gapColour property.
6748		*
6749		* @return possible object is {@link Integer }
6750		*
6751		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6752	11	public Integer getGapColour()...
6753		{
6754	11	return gapColour;
6755		}
6756
6757		/**
6758		* Sets the value of the gapColour property.
6759		*
6760		* @param value
6761		* allowed object is {@link Integer }
6762		*
6763		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6764	14	public void setGapColour(Integer value)...
6765		{
6766	14	this.gapColour = value;
6767		}
6768
6769		/**
6770		* Gets the value of the hiddenColour property.
6771		*
6772		* @return possible object is {@link Integer }
6773		*
6774		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6775	11	public Integer getHiddenColour()...
6776		{
6777	11	return hiddenColour;
6778		}
6779
6780		/**
6781		* Sets the value of the hiddenColour property.
6782		*
6783		* @param value
6784		* allowed object is {@link Integer }
6785		*
6786		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6787	14	public void setHiddenColour(Integer value)...
6788		{
6789	14	this.hiddenColour = value;
6790		}
6791
6792		/**
6793		* Gets the value of the title property.
6794		*
6795		* @return possible object is {@link String }
6796		*
6797		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6798	11	public String getTitle()...
6799		{
6800	11	return title;
6801		}
6802
6803		/**
6804		* Sets the value of the title property.
6805		*
6806		* @param value
6807		* allowed object is {@link String }
6808		*
6809		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6810	14	public void setTitle(String value)...
6811		{
6812	14	this.title = value;
6813		}
6814
6815		/**
6816		* Gets the value of the width property.
6817		*
6818		* @return possible object is {@link Integer }
6819		*
6820		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6821	11	public Integer getWidth()...
6822		{
6823	11	return width;
6824		}
6825
6826		/**
6827		* Sets the value of the width property.
6828		*
6829		* @param value
6830		* allowed object is {@link Integer }
6831		*
6832		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6833	14	public void setWidth(Integer value)...
6834		{
6835	14	this.width = value;
6836		}
6837
6838		/**
6839		* Gets the value of the height property.
6840		*
6841		* @return possible object is {@link Integer }
6842		*
6843		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6844	11	public Integer getHeight()...
6845		{
6846	11	return height;
6847		}
6848
6849		/**
6850		* Sets the value of the height property.
6851		*
6852		* @param value
6853		* allowed object is {@link Integer }
6854		*
6855		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6856	14	public void setHeight(Integer value)...
6857		{
6858	14	this.height = value;
6859		}
6860
6861		/**
6862		* Gets the value of the xpos property.
6863		*
6864		* @return possible object is {@link Integer }
6865		*
6866		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6867	11	public Integer getXpos()...
6868		{
6869	11	return xpos;
6870		}
6871
6872		/**
6873		* Sets the value of the xpos property.
6874		*
6875		* @param value
6876		* allowed object is {@link Integer }
6877		*
6878		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6879	14	public void setXpos(Integer value)...
6880		{
6881	14	this.xpos = value;
6882		}
6883
6884		/**
6885		* Gets the value of the ypos property.
6886		*
6887		* @return possible object is {@link Integer }
6888		*
6889		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6890	11	public Integer getYpos()...
6891		{
6892	11	return ypos;
6893		}
6894
6895		/**
6896		* Sets the value of the ypos property.
6897		*
6898		* @param value
6899		* allowed object is {@link Integer }
6900		*
6901		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6902	14	public void setYpos(Integer value)...
6903		{
6904	14	this.ypos = value;
6905		}
6906
6907		}
6908
6909		}
6910
6911		}