Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
JalviewModel	378	26	20	0.8461538684.6%	Show methods
JalviewModel.FeatureSettings	729	6	4	1.0100%	Show methods
JalviewModel.FeatureSettings.Group	815	4	4	1.0100%	Show methods
JalviewModel.FeatureSettings.Setting	902	31	29	0.967741996.8%	Show methods
JalviewModel.JGroup	1311	51	46	0.941176594.1%	Show methods
JalviewModel.JSeq	1969	24	20	0.979166797.9%	Show methods
JalviewModel.JSeq.Pdbids	2274	3	2	1.0100%	Show methods
JalviewModel.JSeq.Pdbids.StructureState	2338	28	25	0.821428682.1%	Show methods
JalviewModel.JSeq.RnaViewer	2683	19	18	0.00%	Show methods
JalviewModel.JSeq.RnaViewer.SecondaryStructure	2948	8	8	0.00%	Show methods
JalviewModel.PcaViewer	3137	46	44	1.0100%	Show methods
JalviewModel.PcaViewer.Axis	3742	6	6	1.0100%	Show methods
JalviewModel.PcaViewer.SeqPointMax	3845	6	6	1.0100%	Show methods
JalviewModel.PcaViewer.SeqPointMin	3948	6	6	1.0100%	Show methods
JalviewModel.PcaViewer.SequencePoint	4052	8	8	1.0100%	Show methods
JalviewModel.Tree	4201	36	35	1.0100%	Show methods
JalviewModel.UserColours	4680	4	4	0.00%	Show methods
JalviewModel.Viewport	4828	128	113	0.9062590.6%	Show methods
JalviewModel.Viewport.CalcIdParam	6218	8	7	0.00%	Show methods
JalviewModel.Viewport.HiddenColumns	6320	4	4	1.0100%	Show methods

Class JalviewModel

Class JalviewModel	Line # 378	Total Statements 26	Complexity 20	TOTAL Coverage 0.8461538684.6%
getCreationDate() : XMLGregorianCalendar   getCreationDate() : XMLGregorianCalendar	409409	1.01	1.01	0.0 0.00%
setCreationDate(XMLGregorianCalendar) : void   setCreationDate(XMLGregorianCalendar) : void	421421	1.01	1.01	1.0 1.0100%
getVersion() : String   getVersion() : String	433433	1.01	1.01	1.0 1.0100%
setVersion(String) : void   setVersion(String) : void	445445	1.01	1.01	1.0 1.0100%
getVamsasModel() : VAMSAS   getVamsasModel() : VAMSAS	457457	1.01	1.01	1.0 1.0100%
setVamsasModel(VAMSAS) : void   setVamsasModel(VAMSAS) : void	469469	1.01	1.01	1.0 1.0100%
getJSeq() : List<JalviewModel.JSeq>   getJSeq() : List<JalviewModel.JSeq>	495495	3.03	2.02	1.0 1.0100%
getJGroup() : List<JalviewModel.JGroup>   getJGroup() : List<JalviewModel.JGroup>	524524	3.03	2.02	1.0 1.0100%
getViewport() : List<JalviewModel.Viewport>   getViewport() : List<JalviewModel.Viewport>	553553	3.03	2.02	1.0 1.0100%
getUserColours() : List<JalviewModel.UserColours>   getUserColours() : List<JalviewModel.UserColours>	582582	3.03	2.02	0.0 0.00%
getTree() : List<JalviewModel.Tree>   getTree() : List<JalviewModel.Tree>	611611	3.03	2.02	1.0 1.0100%
getPcaViewer() : List<JalviewModel.PcaViewer>   getPcaViewer() : List<JalviewModel.PcaViewer>	640640	3.03	2.02	1.0 1.0100%
getFeatureSettings() : JalviewModel.FeatureSettings   getFeatureSettings() : JalviewModel.FeatureSettings	655655	1.01	1.01	1.0 1.0100%
setFeatureSettings(JalviewModel.FeatureSettings) : void   setFeatureSettings(JalviewModel.FeatureSettings) : void	667667	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.FeatureSettings

Class JalviewModel.FeatureSettings	Line # 729	Total Statements 6	Complexity 4	TOTAL Coverage 1.0100%
getSetting() : List<JalviewModel.FeatureSettings.Setting>   getSetting() : List<JalviewModel.FeatureSettings.Setting>	758758	3.03	2.02	1.0 1.0100%
getGroup() : List<JalviewModel.FeatureSettings.Group>   getGroup() : List<JalviewModel.FeatureSettings.Group>	787787	3.03	2.02	1.0 1.0100%

 

Class JalviewModel.FeatureSettings.Group

Class JalviewModel.FeatureSettings.Group	Line # 815	Total Statements 4	Complexity 4	TOTAL Coverage 1.0100%
getName() : String   getName() : String	830830	1.01	1.01	1.0 1.0100%
setName(String) : void   setName(String) : void	842842	1.01	1.01	1.0 1.0100%
isDisplay() : boolean   isDisplay() : boolean	850850	1.01	1.01	1.0 1.0100%
setDisplay(boolean) : void   setDisplay(boolean) : void	858858	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.FeatureSettings.Setting

Class JalviewModel.FeatureSettings.Setting	Line # 902	Total Statements 31	Complexity 29	TOTAL Coverage 0.967741996.8%
getAttributeName() : List<String>   getAttributeName() : List<String>	955955	3.03	2.02	1.0 1.0100%
getMatcherSet() : FeatureMatcherSet   getMatcherSet() : FeatureMatcherSet	970970	1.01	1.01	1.0 1.0100%
setMatcherSet(FeatureMatcherSet) : void   setMatcherSet(FeatureMatcherSet) : void	982982	1.01	1.01	1.0 1.0100%
getType() : String   getType() : String	994994	1.01	1.01	1.0 1.0100%
setType(String) : void   setType(String) : void	10061006	1.01	1.01	1.0 1.0100%
getColour() : int   getColour() : int	10141014	1.01	1.01	1.0 1.0100%
setColour(int) : void   setColour(int) : void	10221022	1.01	1.01	1.0 1.0100%
isDisplay() : boolean   isDisplay() : boolean	10301030	1.01	1.01	1.0 1.0100%
setDisplay(boolean) : void   setDisplay(boolean) : void	10381038	1.01	1.01	1.0 1.0100%
getOrder() : Float   getOrder() : Float	10501050	1.01	1.01	1.0 1.0100%
setOrder(Float) : void   setOrder(Float) : void	10621062	1.01	1.01	1.0 1.0100%
getMincolour() : Integer   getMincolour() : Integer	10741074	1.01	1.01	1.0 1.0100%
setMincolour(Integer) : void   setMincolour(Integer) : void	10861086	1.01	1.01	1.0 1.0100%
getNoValueColour() : NoValueColour   getNoValueColour() : NoValueColour	10981098	3.03	2.02	0.6 0.660%
setNoValueColour(NoValueColour) : void   setNoValueColour(NoValueColour) : void	11141114	1.01	1.01	1.0 1.0100%
getThreshold() : Float   getThreshold() : Float	11261126	1.01	1.01	1.0 1.0100%
setThreshold(Float) : void   setThreshold(Float) : void	11381138	1.01	1.01	1.0 1.0100%
getThreshstate() : Integer   getThreshstate() : Integer	11501150	1.01	1.01	1.0 1.0100%
setThreshstate(Integer) : void   setThreshstate(Integer) : void	11621162	1.01	1.01	1.0 1.0100%
getMax() : Float   getMax() : Float	11741174	1.01	1.01	1.0 1.0100%
setMax(Float) : void   setMax(Float) : void	11861186	1.01	1.01	1.0 1.0100%
getMin() : Float   getMin() : Float	11981198	1.01	1.01	1.0 1.0100%
setMin(Float) : void   setMin(Float) : void	12101210	1.01	1.01	1.0 1.0100%
isColourByLabel() : Boolean   isColourByLabel() : Boolean	12221222	1.01	1.01	1.0 1.0100%
setColourByLabel(Boolean) : void   setColourByLabel(Boolean) : void	12341234	1.01	1.01	1.0 1.0100%
isAutoScale() : Boolean   isAutoScale() : Boolean	12461246	1.01	1.01	1.0 1.0100%
setAutoScale(Boolean) : void   setAutoScale(Boolean) : void	12581258	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.JGroup

Class JalviewModel.JGroup	Line # 1311	Total Statements 51	Complexity 46	TOTAL Coverage 0.941176594.1%
getSeq() : List<String>   getSeq() : List<String>	13781378	3.03	2.02	1.0 1.0100%
getAnnotationColours() : AnnotationColourScheme   getAnnotationColours() : AnnotationColourScheme	13931393	1.01	1.01	1.0 1.0100%
setAnnotationColours(AnnotationColourScheme) : void   setAnnotationColours(AnnotationColourScheme) : void	14051405	1.01	1.01	1.0 1.0100%
getStart() : Integer   getStart() : Integer	14171417	1.01	1.01	1.0 1.0100%
setStart(Integer) : void   setStart(Integer) : void	14291429	1.01	1.01	1.0 1.0100%
getEnd() : Integer   getEnd() : Integer	14411441	1.01	1.01	1.0 1.0100%
setEnd(Integer) : void   setEnd(Integer) : void	14531453	1.01	1.01	1.0 1.0100%
getName() : String   getName() : String	14651465	1.01	1.01	1.0 1.0100%
setName(String) : void   setName(String) : void	14771477	1.01	1.01	1.0 1.0100%
getColour() : String   getColour() : String	14891489	1.01	1.01	1.0 1.0100%
setColour(String) : void   setColour(String) : void	15011501	1.01	1.01	1.0 1.0100%
getConsThreshold() : Integer   getConsThreshold() : Integer	15131513	1.01	1.01	1.0 1.0100%
setConsThreshold(Integer) : void   setConsThreshold(Integer) : void	15251525	1.01	1.01	1.0 1.0100%
getPidThreshold() : Integer   getPidThreshold() : Integer	15371537	1.01	1.01	1.0 1.0100%
setPidThreshold(Integer) : void   setPidThreshold(Integer) : void	15491549	1.01	1.01	1.0 1.0100%
getOutlineColour() : Integer   getOutlineColour() : Integer	15611561	1.01	1.01	1.0 1.0100%
setOutlineColour(Integer) : void   setOutlineColour(Integer) : void	15731573	1.01	1.01	1.0 1.0100%
isDisplayBoxes() : Boolean   isDisplayBoxes() : Boolean	15851585	1.01	1.01	1.0 1.0100%
setDisplayBoxes(Boolean) : void   setDisplayBoxes(Boolean) : void	15971597	1.01	1.01	1.0 1.0100%
isDisplayText() : Boolean   isDisplayText() : Boolean	16091609	1.01	1.01	1.0 1.0100%
setDisplayText(Boolean) : void   setDisplayText(Boolean) : void	16211621	1.01	1.01	1.0 1.0100%
isColourText() : Boolean   isColourText() : Boolean	16331633	1.01	1.01	1.0 1.0100%
setColourText(Boolean) : void   setColourText(Boolean) : void	16451645	1.01	1.01	1.0 1.0100%
getTextCol1() : Integer   getTextCol1() : Integer	16571657	1.01	1.01	1.0 1.0100%
setTextCol1(Integer) : void   setTextCol1(Integer) : void	16691669	1.01	1.01	1.0 1.0100%
getTextCol2() : Integer   getTextCol2() : Integer	16811681	1.01	1.01	1.0 1.0100%
setTextCol2(Integer) : void   setTextCol2(Integer) : void	16931693	1.01	1.01	1.0 1.0100%
getTextColThreshold() : Integer   getTextColThreshold() : Integer	17051705	1.01	1.01	1.0 1.0100%
setTextColThreshold(Integer) : void   setTextColThreshold(Integer) : void	17171717	1.01	1.01	1.0 1.0100%
isShowUnconserved() : Boolean   isShowUnconserved() : Boolean	17291729	1.01	1.01	1.0 1.0100%
setShowUnconserved(Boolean) : void   setShowUnconserved(Boolean) : void	17411741	1.01	1.01	1.0 1.0100%
isIgnoreGapsinConsensus() : boolean   isIgnoreGapsinConsensus() : boolean	17531753	3.03	2.02	0.6 0.660%
setIgnoreGapsinConsensus(Boolean) : void   setIgnoreGapsinConsensus(Boolean) : void	17691769	1.01	1.01	1.0 1.0100%
isShowConsensusHistogram() : boolean   isShowConsensusHistogram() : boolean	17811781	3.03	2.02	0.6 0.660%
setShowConsensusHistogram(Boolean) : void   setShowConsensusHistogram(Boolean) : void	17971797	1.01	1.01	1.0 1.0100%
isShowSequenceLogo() : boolean   isShowSequenceLogo() : boolean	18091809	3.03	2.02	0.6 0.660%
setShowSequenceLogo(Boolean) : void   setShowSequenceLogo(Boolean) : void	18251825	1.01	1.01	1.0 1.0100%
isNormaliseSequenceLogo() : boolean   isNormaliseSequenceLogo() : boolean	18371837	3.03	2.02	1.0 1.0100%
setNormaliseSequenceLogo(Boolean) : void   setNormaliseSequenceLogo(Boolean) : void	18531853	1.01	1.01	1.0 1.0100%
getId() : String   getId() : String	18651865	1.01	1.01	1.0 1.0100%
setId(String) : void   setId(String) : void	18771877	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.JSeq

Class JalviewModel.JSeq	Line # 1969	Total Statements 24	Complexity 20	TOTAL Coverage 0.979166797.9%
getFeatures() : List<Feature>   getFeatures() : List<Feature>	20142014	3.03	2.02	1.0 1.0100%
getPdbids() : List<JalviewModel.JSeq.Pdbids>   getPdbids() : List<JalviewModel.JSeq.Pdbids>	20432043	3.03	2.02	1.0 1.0100%
getHiddenSequences() : List<Integer>   getHiddenSequences() : List<Integer>	20722072	3.03	2.02	1.0 1.0100%
getRnaViewer() : List<JalviewModel.JSeq.RnaViewer>   getRnaViewer() : List<JalviewModel.JSeq.RnaViewer>	21012101	3.03	2.02	0.8 0.880%
getColour() : Integer   getColour() : Integer	21162116	1.01	1.01	1.0 1.0100%
setColour(Integer) : void   setColour(Integer) : void	21282128	1.01	1.01	1.0 1.0100%
getStart() : int   getStart() : int	21362136	1.01	1.01	1.0 1.0100%
setStart(int) : void   setStart(int) : void	21442144	1.01	1.01	1.0 1.0100%
getEnd() : int   getEnd() : int	21522152	1.01	1.01	1.0 1.0100%
setEnd(int) : void   setEnd(int) : void	21602160	1.01	1.01	1.0 1.0100%
getId() : String   getId() : String	21722172	1.01	1.01	1.0 1.0100%
setId(String) : void   setId(String) : void	21842184	1.01	1.01	1.0 1.0100%
isHidden() : Boolean   isHidden() : Boolean	21962196	1.01	1.01	1.0 1.0100%
setHidden(Boolean) : void   setHidden(Boolean) : void	22082208	1.01	1.01	1.0 1.0100%
isViewreference() : Boolean   isViewreference() : Boolean	22202220	1.01	1.01	1.0 1.0100%
setViewreference(Boolean) : void   setViewreference(Boolean) : void	22322232	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.JSeq.Pdbids

Class JalviewModel.JSeq.Pdbids	Line # 2274	Total Statements 3	Complexity 2	TOTAL Coverage 1.0100%
getStructureState() : List<JalviewModel.JSeq.Pdbids.StructureState>   getStructureState() : List<JalviewModel.JSeq.Pdbids.StructureState>	23032303	3.03	2.02	1.0 1.0100%

 

Class JalviewModel.JSeq.Pdbids.StructureState

Class JalviewModel.JSeq.Pdbids.StructureState	Line # 2338	Total Statements 28	Complexity 25	TOTAL Coverage 0.821428682.1%
getValue() : String   getValue() : String	23712371	1.01	1.01	1.0 1.0100%
setValue(String) : void   setValue(String) : void	23832383	1.01	1.01	0.0 0.00%
isVisible() : Boolean   isVisible() : Boolean	23952395	1.01	1.01	0.0 0.00%
setVisible(Boolean) : void   setVisible(Boolean) : void	24072407	1.01	1.01	1.0 1.0100%
getViewId() : String   getViewId() : String	24192419	1.01	1.01	1.0 1.0100%
setViewId(String) : void   setViewId(String) : void	24312431	1.01	1.01	1.0 1.0100%
isAlignwithAlignPanel() : boolean   isAlignwithAlignPanel() : boolean	24432443	3.03	2.02	0.6 0.660%
setAlignwithAlignPanel(Boolean) : void   setAlignwithAlignPanel(Boolean) : void	24592459	1.01	1.01	1.0 1.0100%
isColourwithAlignPanel() : boolean   isColourwithAlignPanel() : boolean	24712471	3.03	2.02	0.6 0.660%
setColourwithAlignPanel(Boolean) : void   setColourwithAlignPanel(Boolean) : void	24872487	1.01	1.01	1.0 1.0100%
isColourByJmol() : boolean   isColourByJmol() : boolean	24992499	3.03	2.02	0.6 0.660%
setColourByJmol(Boolean) : void   setColourByJmol(Boolean) : void	25152515	1.01	1.01	1.0 1.0100%
getType() : String   getType() : String	25272527	1.01	1.01	1.0 1.0100%
setType(String) : void   setType(String) : void	25392539	1.01	1.01	1.0 1.0100%
getWidth() : Integer   getWidth() : Integer	25512551	1.01	1.01	1.0 1.0100%
setWidth(Integer) : void   setWidth(Integer) : void	25632563	1.01	1.01	1.0 1.0100%
getHeight() : Integer   getHeight() : Integer	25752575	1.01	1.01	1.0 1.0100%
setHeight(Integer) : void   setHeight(Integer) : void	25872587	1.01	1.01	1.0 1.0100%
getXpos() : Integer   getXpos() : Integer	25992599	1.01	1.01	1.0 1.0100%
setXpos(Integer) : void   setXpos(Integer) : void	26112611	1.01	1.01	1.0 1.0100%
getYpos() : Integer   getYpos() : Integer	26232623	1.01	1.01	1.0 1.0100%
setYpos(Integer) : void   setYpos(Integer) : void	26352635	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.JSeq.RnaViewer

Class JalviewModel.JSeq.RnaViewer	Line # 2683	Total Statements 19	Complexity 18	TOTAL Coverage 0.00%
getSecondaryStructure() : List<JalviewModel.JSeq.RnaViewer.SecondaryStructure>   getSecondaryStructure() : List<JalviewModel.JSeq.RnaViewer.SecondaryStructure>	27262726	3.03	2.02	0.0 0.00%
getTitle() : String   getTitle() : String	27412741	1.01	1.01	0.0 0.00%
setTitle(String) : void   setTitle(String) : void	27532753	1.01	1.01	0.0 0.00%
getViewId() : String   getViewId() : String	27652765	1.01	1.01	0.0 0.00%
setViewId(String) : void   setViewId(String) : void	27772777	1.01	1.01	0.0 0.00%
getDividerLocation() : Integer   getDividerLocation() : Integer	27892789	1.01	1.01	0.0 0.00%
setDividerLocation(Integer) : void   setDividerLocation(Integer) : void	28012801	1.01	1.01	0.0 0.00%
getSelectedRna() : Integer   getSelectedRna() : Integer	28132813	1.01	1.01	0.0 0.00%
setSelectedRna(Integer) : void   setSelectedRna(Integer) : void	28252825	1.01	1.01	0.0 0.00%
getWidth() : Integer   getWidth() : Integer	28372837	1.01	1.01	0.0 0.00%
setWidth(Integer) : void   setWidth(Integer) : void	28492849	1.01	1.01	0.0 0.00%
getHeight() : Integer   getHeight() : Integer	28612861	1.01	1.01	0.0 0.00%
setHeight(Integer) : void   setHeight(Integer) : void	28732873	1.01	1.01	0.0 0.00%
getXpos() : Integer   getXpos() : Integer	28852885	1.01	1.01	0.0 0.00%
setXpos(Integer) : void   setXpos(Integer) : void	28972897	1.01	1.01	0.0 0.00%
getYpos() : Integer   getYpos() : Integer	29092909	1.01	1.01	0.0 0.00%
setYpos(Integer) : void   setYpos(Integer) : void	29212921	1.01	1.01	0.0 0.00%

 

Class JalviewModel.JSeq.RnaViewer.SecondaryStructure

Class JalviewModel.JSeq.RnaViewer.SecondaryStructure	Line # 2948	Total Statements 8	Complexity 8	TOTAL Coverage 0.00%
getTitle() : String   getTitle() : String	29672967	1.01	1.01	0.0 0.00%
setTitle(String) : void   setTitle(String) : void	29792979	1.01	1.01	0.0 0.00%
getAnnotationId() : String   getAnnotationId() : String	29912991	1.01	1.01	0.0 0.00%
setAnnotationId(String) : void   setAnnotationId(String) : void	30033003	1.01	1.01	0.0 0.00%
isGapped() : Boolean   isGapped() : Boolean	30153015	1.01	1.01	0.0 0.00%
setGapped(Boolean) : void   setGapped(Boolean) : void	30273027	1.01	1.01	0.0 0.00%
getViewerState() : String   getViewerState() : String	30393039	1.01	1.01	0.0 0.00%
setViewerState(String) : void   setViewerState(String) : void	30513051	1.01	1.01	0.0 0.00%

 

Class JalviewModel.PcaViewer

Class JalviewModel.PcaViewer	Line # 3137	Total Statements 46	Complexity 44	TOTAL Coverage 1.0100%
getSequencePoint() : List<JalviewModel.PcaViewer.SequencePoint>   getSequencePoint() : List<JalviewModel.PcaViewer.SequencePoint>	32063206	3.03	2.02	1.0 1.0100%
getAxis() : List<JalviewModel.PcaViewer.Axis>   getAxis() : List<JalviewModel.PcaViewer.Axis>	32353235	3.03	2.02	1.0 1.0100%
getSeqPointMin() : JalviewModel.PcaViewer.SeqPointMin   getSeqPointMin() : JalviewModel.PcaViewer.SeqPointMin	32503250	1.01	1.01	1.0 1.0100%
setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin) : void   setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin) : void	32623262	1.01	1.01	1.0 1.0100%
getSeqPointMax() : JalviewModel.PcaViewer.SeqPointMax   getSeqPointMax() : JalviewModel.PcaViewer.SeqPointMax	32743274	1.01	1.01	1.0 1.0100%
setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax) : void   setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax) : void	32863286	1.01	1.01	1.0 1.0100%
getPcaData() : PcaDataType   getPcaData() : PcaDataType	32983298	1.01	1.01	1.0 1.0100%
setPcaData(PcaDataType) : void   setPcaData(PcaDataType) : void	33103310	1.01	1.01	1.0 1.0100%
getTitle() : String   getTitle() : String	33223322	1.01	1.01	1.0 1.0100%
setTitle(String) : void   setTitle(String) : void	33343334	1.01	1.01	1.0 1.0100%
getScoreModelName() : String   getScoreModelName() : String	33463346	1.01	1.01	1.0 1.0100%
setScoreModelName(String) : void   setScoreModelName(String) : void	33583358	1.01	1.01	1.0 1.0100%
getXDim() : Integer   getXDim() : Integer	33703370	1.01	1.01	1.0 1.0100%
setXDim(Integer) : void   setXDim(Integer) : void	33823382	1.01	1.01	1.0 1.0100%
getYDim() : Integer   getYDim() : Integer	33943394	1.01	1.01	1.0 1.0100%
setYDim(Integer) : void   setYDim(Integer) : void	34063406	1.01	1.01	1.0 1.0100%
getZDim() : Integer   getZDim() : Integer	34183418	1.01	1.01	1.0 1.0100%
setZDim(Integer) : void   setZDim(Integer) : void	34303430	1.01	1.01	1.0 1.0100%
getBgColour() : Integer   getBgColour() : Integer	34423442	1.01	1.01	1.0 1.0100%
setBgColour(Integer) : void   setBgColour(Integer) : void	34543454	1.01	1.01	1.0 1.0100%
getScaleFactor() : Float   getScaleFactor() : Float	34663466	1.01	1.01	1.0 1.0100%
setScaleFactor(Float) : void   setScaleFactor(Float) : void	34783478	1.01	1.01	1.0 1.0100%
isShowLabels() : Boolean   isShowLabels() : Boolean	34903490	1.01	1.01	1.0 1.0100%
setShowLabels(Boolean) : void   setShowLabels(Boolean) : void	35023502	1.01	1.01	1.0 1.0100%
isLinkToAllViews() : Boolean   isLinkToAllViews() : Boolean	35143514	1.01	1.01	1.0 1.0100%
setLinkToAllViews(Boolean) : void   setLinkToAllViews(Boolean) : void	35263526	1.01	1.01	1.0 1.0100%
getWidth() : Integer   getWidth() : Integer	35383538	1.01	1.01	1.0 1.0100%
setWidth(Integer) : void   setWidth(Integer) : void	35503550	1.01	1.01	1.0 1.0100%
getHeight() : Integer   getHeight() : Integer	35623562	1.01	1.01	1.0 1.0100%
setHeight(Integer) : void   setHeight(Integer) : void	35743574	1.01	1.01	1.0 1.0100%
getXpos() : Integer   getXpos() : Integer	35863586	1.01	1.01	1.0 1.0100%
setXpos(Integer) : void   setXpos(Integer) : void	35983598	1.01	1.01	1.0 1.0100%
getYpos() : Integer   getYpos() : Integer	36103610	1.01	1.01	1.0 1.0100%
setYpos(Integer) : void   setYpos(Integer) : void	36223622	1.01	1.01	1.0 1.0100%
isIncludeGaps() : Boolean   isIncludeGaps() : Boolean	36343634	1.01	1.01	1.0 1.0100%
setIncludeGaps(Boolean) : void   setIncludeGaps(Boolean) : void	36463646	1.01	1.01	1.0 1.0100%
isMatchGaps() : Boolean   isMatchGaps() : Boolean	36583658	1.01	1.01	1.0 1.0100%
setMatchGaps(Boolean) : void   setMatchGaps(Boolean) : void	36703670	1.01	1.01	1.0 1.0100%
isIncludeGappedColumns() : Boolean   isIncludeGappedColumns() : Boolean	36823682	1.01	1.01	1.0 1.0100%
setIncludeGappedColumns(Boolean) : void   setIncludeGappedColumns(Boolean) : void	36943694	1.01	1.01	1.0 1.0100%
isDenominateByShortestLength() : Boolean   isDenominateByShortestLength() : Boolean	37063706	1.01	1.01	1.0 1.0100%
setDenominateByShortestLength(Boolean) : void   setDenominateByShortestLength(Boolean) : void	37183718	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.PcaViewer.Axis

Class JalviewModel.PcaViewer.Axis	Line # 3742	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	37833783	1.01	1.01	1.0 1.0100%
setYPos(Float) : void   setYPos(Float) : void	37953795	1.01	1.01	1.0 1.0100%
getZPos() : Float   getZPos() : Float	38073807	1.01	1.01	1.0 1.0100%
setZPos(Float) : void   setZPos(Float) : void	38193819	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.PcaViewer.SeqPointMax

Class JalviewModel.PcaViewer.SeqPointMax	Line # 3845	Total Statements 6	Complexity 6	TOTAL Coverage 1.0100%
getXPos() : Float   getXPos() : Float	38623862	1.01	1.01	1.0 1.0100%
setXPos(Float) : void   setXPos(Float) : void	38743874	1.01	1.01	1.0 1.0100%
getYPos() : Float   getYPos() : Float	38863886	1.01	1.01	1.0 1.0100%
setYPos(Float) : void   setYPos(Float) : void	38983898	1.01	1.01	1.0 1.0100%
getZPos() : Float   getZPos() : Float	39103910	1.01	1.01	1.0 1.0100%
setZPos(Float) : void   setZPos(Float) : void	39223922	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.PcaViewer.SeqPointMin

Class JalviewModel.PcaViewer.SeqPointMin	Line # 3948	Total Statements 6	Complexity 6	TOTAL Coverage 1.0100%
getXPos() : Float   getXPos() : Float	39653965	1.01	1.01	1.0 1.0100%
setXPos(Float) : void   setXPos(Float) : void	39773977	1.01	1.01	1.0 1.0100%
getYPos() : Float   getYPos() : Float	39893989	1.01	1.01	1.0 1.0100%
setYPos(Float) : void   setYPos(Float) : void	40014001	1.01	1.01	1.0 1.0100%
getZPos() : Float   getZPos() : Float	40134013	1.01	1.01	1.0 1.0100%
setZPos(Float) : void   setZPos(Float) : void	40254025	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.PcaViewer.SequencePoint

Class JalviewModel.PcaViewer.SequencePoint	Line # 4052	Total Statements 8	Complexity 8	TOTAL Coverage 1.0100%
getSequenceRef() : String   getSequenceRef() : String	40714071	1.01	1.01	1.0 1.0100%
setSequenceRef(String) : void   setSequenceRef(String) : void	40834083	1.01	1.01	1.0 1.0100%
getXPos() : Float   getXPos() : Float	40954095	1.01	1.01	1.0 1.0100%
setXPos(Float) : void   setXPos(Float) : void	41074107	1.01	1.01	1.0 1.0100%
getYPos() : Float   getYPos() : Float	41194119	1.01	1.01	1.0 1.0100%
setYPos(Float) : void   setYPos(Float) : void	41314131	1.01	1.01	1.0 1.0100%
getZPos() : Float   getZPos() : Float	41434143	1.01	1.01	1.0 1.0100%
setZPos(Float) : void   setZPos(Float) : void	41554155	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.Tree

Class JalviewModel.Tree	Line # 4201	Total Statements 36	Complexity 35	TOTAL Coverage 1.0100%
getTitle() : String   getTitle() : String	42494249	1.01	1.01	1.0 1.0100%
setTitle(String) : void   setTitle(String) : void	42614261	1.01	1.01	1.0 1.0100%
getNewick() : String   getNewick() : String	42734273	1.01	1.01	1.0 1.0100%
setNewick(String) : void   setNewick(String) : void	42854285	1.01	1.01	1.0 1.0100%
getFontName() : String   getFontName() : String	42974297	1.01	1.01	1.0 1.0100%
setFontName(String) : void   setFontName(String) : void	43094309	1.01	1.01	1.0 1.0100%
getFontSize() : Integer   getFontSize() : Integer	43214321	1.01	1.01	1.0 1.0100%
setFontSize(Integer) : void   setFontSize(Integer) : void	43334333	1.01	1.01	1.0 1.0100%
getFontStyle() : Integer   getFontStyle() : Integer	43454345	1.01	1.01	1.0 1.0100%
setFontStyle(Integer) : void   setFontStyle(Integer) : void	43574357	1.01	1.01	1.0 1.0100%
getThreshold() : Float   getThreshold() : Float	43694369	1.01	1.01	1.0 1.0100%
setThreshold(Float) : void   setThreshold(Float) : void	43814381	1.01	1.01	1.0 1.0100%
isShowBootstrap() : Boolean   isShowBootstrap() : Boolean	43934393	1.01	1.01	1.0 1.0100%
setShowBootstrap(Boolean) : void   setShowBootstrap(Boolean) : void	44054405	1.01	1.01	1.0 1.0100%
isShowDistances() : Boolean   isShowDistances() : Boolean	44174417	1.01	1.01	1.0 1.0100%
setShowDistances(Boolean) : void   setShowDistances(Boolean) : void	44294429	1.01	1.01	1.0 1.0100%
isMarkUnlinked() : Boolean   isMarkUnlinked() : Boolean	44414441	1.01	1.01	1.0 1.0100%
setMarkUnlinked(Boolean) : void   setMarkUnlinked(Boolean) : void	44534453	1.01	1.01	1.0 1.0100%
isFitToWindow() : Boolean   isFitToWindow() : Boolean	44654465	1.01	1.01	1.0 1.0100%
setFitToWindow(Boolean) : void   setFitToWindow(Boolean) : void	44774477	1.01	1.01	1.0 1.0100%
isCurrentTree() : Boolean   isCurrentTree() : Boolean	44894489	1.01	1.01	1.0 1.0100%
setCurrentTree(Boolean) : void   setCurrentTree(Boolean) : void	45014501	1.01	1.01	1.0 1.0100%
getId() : String   getId() : String	45134513	1.01	1.01	1.0 1.0100%
setId(String) : void   setId(String) : void	45254525	1.01	1.01	1.0 1.0100%
isLinkToAllViews() : boolean   isLinkToAllViews() : boolean	45374537	3.03	2.02	1.0 1.0100%
setLinkToAllViews(Boolean) : void   setLinkToAllViews(Boolean) : void	45534553	1.01	1.01	1.0 1.0100%
getWidth() : Integer   getWidth() : Integer	45654565	1.01	1.01	1.0 1.0100%
setWidth(Integer) : void   setWidth(Integer) : void	45774577	1.01	1.01	1.0 1.0100%
getHeight() : Integer   getHeight() : Integer	45894589	1.01	1.01	1.0 1.0100%
setHeight(Integer) : void   setHeight(Integer) : void	46014601	1.01	1.01	1.0 1.0100%
getXpos() : Integer   getXpos() : Integer	46134613	1.01	1.01	1.0 1.0100%
setXpos(Integer) : void   setXpos(Integer) : void	46254625	1.01	1.01	1.0 1.0100%
getYpos() : Integer   getYpos() : Integer	46374637	1.01	1.01	1.0 1.0100%
setYpos(Integer) : void   setYpos(Integer) : void	46494649	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.UserColours

Class JalviewModel.UserColours	Line # 4680	Total Statements 4	Complexity 4	TOTAL Coverage 0.00%
getUserColourScheme() : JalviewUserColours   getUserColourScheme() : JalviewUserColours	46954695	1.01	1.01	0.0 0.00%
setUserColourScheme(JalviewUserColours) : void   setUserColourScheme(JalviewUserColours) : void	47074707	1.01	1.01	0.0 0.00%
getId() : String   getId() : String	47194719	1.01	1.01	0.0 0.00%
setId(String) : void   setId(String) : void	47314731	1.01	1.01	0.0 0.00%

 

Class JalviewModel.Viewport

Class JalviewModel.Viewport	Line # 4828	Total Statements 128	Complexity 113	TOTAL Coverage 0.9062590.6%
getAnnotationColours() : AnnotationColourScheme   getAnnotationColours() : AnnotationColourScheme	49424942	1.01	1.01	1.0 1.0100%
setAnnotationColours(AnnotationColourScheme) : void   setAnnotationColours(AnnotationColourScheme) : void	49544954	1.01	1.01	1.0 1.0100%
getHiddenColumns() : List<JalviewModel.Viewport.HiddenColumns>   getHiddenColumns() : List<JalviewModel.Viewport.HiddenColumns>	49804980	3.03	2.02	1.0 1.0100%
getCalcIdParam() : List<JalviewModel.Viewport.CalcIdParam>   getCalcIdParam() : List<JalviewModel.Viewport.CalcIdParam>	50095009	3.03	2.02	1.0 1.0100%
isConservationSelected() : Boolean   isConservationSelected() : Boolean	50245024	1.01	1.01	1.0 1.0100%
setConservationSelected(Boolean) : void   setConservationSelected(Boolean) : void	50365036	1.01	1.01	1.0 1.0100%
isPidSelected() : Boolean   isPidSelected() : Boolean	50485048	1.01	1.01	1.0 1.0100%
setPidSelected(Boolean) : void   setPidSelected(Boolean) : void	50605060	1.01	1.01	1.0 1.0100%
getBgColour() : String   getBgColour() : String	50725072	1.01	1.01	1.0 1.0100%
setBgColour(String) : void   setBgColour(String) : void	50845084	1.01	1.01	1.0 1.0100%
getConsThreshold() : Integer   getConsThreshold() : Integer	50965096	1.01	1.01	1.0 1.0100%
setConsThreshold(Integer) : void   setConsThreshold(Integer) : void	51085108	1.01	1.01	1.0 1.0100%
getPidThreshold() : Integer   getPidThreshold() : Integer	51205120	1.01	1.01	1.0 1.0100%
setPidThreshold(Integer) : void   setPidThreshold(Integer) : void	51325132	1.01	1.01	1.0 1.0100%
getTitle() : String   getTitle() : String	51445144	1.01	1.01	1.0 1.0100%
setTitle(String) : void   setTitle(String) : void	51565156	1.01	1.01	1.0 1.0100%
isShowFullId() : Boolean   isShowFullId() : Boolean	51685168	1.01	1.01	1.0 1.0100%
setShowFullId(Boolean) : void   setShowFullId(Boolean) : void	51805180	1.01	1.01	1.0 1.0100%
isRightAlignIds() : Boolean   isRightAlignIds() : Boolean	51925192	1.01	1.01	1.0 1.0100%
setRightAlignIds(Boolean) : void   setRightAlignIds(Boolean) : void	52045204	1.01	1.01	1.0 1.0100%
isShowText() : Boolean   isShowText() : Boolean	52165216	1.01	1.01	1.0 1.0100%
setShowText(Boolean) : void   setShowText(Boolean) : void	52285228	1.01	1.01	1.0 1.0100%
isShowColourText() : Boolean   isShowColourText() : Boolean	52405240	1.01	1.01	1.0 1.0100%
setShowColourText(Boolean) : void   setShowColourText(Boolean) : void	52525252	1.01	1.01	1.0 1.0100%
isShowUnconserved() : boolean   isShowUnconserved() : boolean	52645264	3.03	2.02	0.6 0.660%
setShowUnconserved(Boolean) : void   setShowUnconserved(Boolean) : void	52805280	1.01	1.01	1.0 1.0100%
isShowBoxes() : Boolean   isShowBoxes() : Boolean	52925292	1.01	1.01	1.0 1.0100%
setShowBoxes(Boolean) : void   setShowBoxes(Boolean) : void	53045304	1.01	1.01	1.0 1.0100%
isWrapAlignment() : Boolean   isWrapAlignment() : Boolean	53165316	1.01	1.01	1.0 1.0100%
setWrapAlignment(Boolean) : void   setWrapAlignment(Boolean) : void	53285328	1.01	1.01	1.0 1.0100%
isRenderGaps() : Boolean   isRenderGaps() : Boolean	53405340	1.01	1.01	1.0 1.0100%
setRenderGaps(Boolean) : void   setRenderGaps(Boolean) : void	53525352	1.01	1.01	1.0 1.0100%
isShowSequenceFeatures() : Boolean   isShowSequenceFeatures() : Boolean	53645364	1.01	1.01	1.0 1.0100%
setShowSequenceFeatures(Boolean) : void   setShowSequenceFeatures(Boolean) : void	53765376	1.01	1.01	1.0 1.0100%
isShowNPfeatureTooltip() : Boolean   isShowNPfeatureTooltip() : Boolean	53885388	1.01	1.01	1.0 1.0100%
setShowNPfeatureTooltip(Boolean) : void   setShowNPfeatureTooltip(Boolean) : void	54005400	1.01	1.01	1.0 1.0100%
isShowDbRefTooltip() : Boolean   isShowDbRefTooltip() : Boolean	54125412	1.01	1.01	1.0 1.0100%
setShowDbRefTooltip(Boolean) : void   setShowDbRefTooltip(Boolean) : void	54245424	1.01	1.01	1.0 1.0100%
isFollowHighlight() : boolean   isFollowHighlight() : boolean	54365436	3.03	2.02	0.6 0.660%
setFollowHighlight(Boolean) : void   setFollowHighlight(Boolean) : void	54525452	1.01	1.01	1.0 1.0100%
isFollowSelection() : boolean   isFollowSelection() : boolean	54645464	3.03	2.02	0.6 0.660%
setFollowSelection(Boolean) : void   setFollowSelection(Boolean) : void	54805480	1.01	1.01	1.0 1.0100%
isShowAnnotation() : Boolean   isShowAnnotation() : Boolean	54925492	1.01	1.01	1.0 1.0100%
setShowAnnotation(Boolean) : void   setShowAnnotation(Boolean) : void	55045504	1.01	1.01	1.0 1.0100%
isCentreColumnLabels() : boolean   isCentreColumnLabels() : boolean	55165516	3.03	2.02	0.6 0.660%
setCentreColumnLabels(Boolean) : void   setCentreColumnLabels(Boolean) : void	55325532	1.01	1.01	0.0 0.00%
isShowGroupConservation() : boolean   isShowGroupConservation() : boolean	55445544	3.03	2.02	0.6 0.660%
setShowGroupConservation(Boolean) : void   setShowGroupConservation(Boolean) : void	55605560	1.01	1.01	1.0 1.0100%
isShowGroupConsensus() : boolean   isShowGroupConsensus() : boolean	55725572	3.03	2.02	0.6 0.660%
setShowGroupConsensus(Boolean) : void   setShowGroupConsensus(Boolean) : void	55885588	1.01	1.01	1.0 1.0100%
isShowConsensusHistogram() : boolean   isShowConsensusHistogram() : boolean	56005600	3.03	2.02	0.6 0.660%
setShowConsensusHistogram(Boolean) : void   setShowConsensusHistogram(Boolean) : void	56165616	1.01	1.01	1.0 1.0100%
isShowSequenceLogo() : boolean   isShowSequenceLogo() : boolean	56285628	3.03	2.02	0.6 0.660%
setShowSequenceLogo(Boolean) : void   setShowSequenceLogo(Boolean) : void	56445644	1.01	1.01	1.0 1.0100%
isNormaliseSequenceLogo() : boolean   isNormaliseSequenceLogo() : boolean	56565656	3.03	2.02	1.0 1.0100%
setNormaliseSequenceLogo(Boolean) : void   setNormaliseSequenceLogo(Boolean) : void	56725672	1.01	1.01	1.0 1.0100%
isIgnoreGapsinConsensus() : boolean   isIgnoreGapsinConsensus() : boolean	56845684	3.03	2.02	0.6 0.660%
setIgnoreGapsinConsensus(Boolean) : void   setIgnoreGapsinConsensus(Boolean) : void	57005700	1.01	1.01	1.0 1.0100%
getStartRes() : Integer   getStartRes() : Integer	57125712	1.01	1.01	1.0 1.0100%
setStartRes(Integer) : void   setStartRes(Integer) : void	57245724	1.01	1.01	1.0 1.0100%
getStartSeq() : Integer   getStartSeq() : Integer	57365736	1.01	1.01	0.0 0.00%
setStartSeq(Integer) : void   setStartSeq(Integer) : void	57485748	1.01	1.01	1.0 1.0100%
getFontName() : String   getFontName() : String	57605760	1.01	1.01	1.0 1.0100%
setFontName(String) : void   setFontName(String) : void	57725772	1.01	1.01	1.0 1.0100%
getFontSize() : Integer   getFontSize() : Integer	57845784	1.01	1.01	1.0 1.0100%
setFontSize(Integer) : void   setFontSize(Integer) : void	57965796	1.01	1.01	1.0 1.0100%
getFontStyle() : Integer   getFontStyle() : Integer	58085808	1.01	1.01	1.0 1.0100%
setFontStyle(Integer) : void   setFontStyle(Integer) : void	58205820	1.01	1.01	1.0 1.0100%
isScaleProteinAsCdna() : boolean   isScaleProteinAsCdna() : boolean	58325832	3.03	2.02	1.0 1.0100%
setScaleProteinAsCdna(Boolean) : void   setScaleProteinAsCdna(Boolean) : void	58485848	1.01	1.01	1.0 1.0100%
getViewName() : String   getViewName() : String	58605860	1.01	1.01	1.0 1.0100%
setViewName(String) : void   setViewName(String) : void	58725872	1.01	1.01	1.0 1.0100%
getSequenceSetId() : String   getSequenceSetId() : String	58845884	1.01	1.01	1.0 1.0100%
setSequenceSetId(String) : void   setSequenceSetId(String) : void	58965896	1.01	1.01	1.0 1.0100%
isGatheredViews() : Boolean   isGatheredViews() : Boolean	59085908	1.01	1.01	1.0 1.0100%
setGatheredViews(Boolean) : void   setGatheredViews(Boolean) : void	59205920	1.01	1.01	1.0 1.0100%
getTextCol1() : Integer   getTextCol1() : Integer	59325932	1.01	1.01	1.0 1.0100%
setTextCol1(Integer) : void   setTextCol1(Integer) : void	59445944	1.01	1.01	1.0 1.0100%
getTextCol2() : Integer   getTextCol2() : Integer	59565956	1.01	1.01	1.0 1.0100%
setTextCol2(Integer) : void   setTextCol2(Integer) : void	59685968	1.01	1.01	1.0 1.0100%
getTextColThreshold() : Integer   getTextColThreshold() : Integer	59805980	1.01	1.01	1.0 1.0100%
setTextColThreshold(Integer) : void   setTextColThreshold(Integer) : void	59925992	1.01	1.01	1.0 1.0100%
getId() : String   getId() : String	60046004	1.01	1.01	1.0 1.0100%
setId(String) : void   setId(String) : void	60166016	1.01	1.01	1.0 1.0100%
getComplementId() : String   getComplementId() : String	60286028	1.01	1.01	1.0 1.0100%
setComplementId(String) : void   setComplementId(String) : void	60406040	1.01	1.01	0.0 0.00%
isShowComplementFeatures() : boolean   isShowComplementFeatures() : boolean	60526052	3.03	2.02	1.0 1.0100%
setShowComplementFeatures(Boolean) : void   setShowComplementFeatures(Boolean) : void	60686068	1.01	1.01	1.0 1.0100%
isShowComplementFeaturesOnTop() : boolean   isShowComplementFeaturesOnTop() : boolean	60806080	3.03	2.02	1.0 1.0100%
setShowComplementFeaturesOnTop(Boolean) : void   setShowComplementFeaturesOnTop(Boolean) : void	60966096	1.01	1.01	1.0 1.0100%
getWidth() : Integer   getWidth() : Integer	61086108	1.01	1.01	1.0 1.0100%
setWidth(Integer) : void   setWidth(Integer) : void	61206120	1.01	1.01	1.0 1.0100%
getHeight() : Integer   getHeight() : Integer	61326132	1.01	1.01	1.0 1.0100%
setHeight(Integer) : void   setHeight(Integer) : void	61446144	1.01	1.01	1.0 1.0100%
getXpos() : Integer   getXpos() : Integer	61566156	1.01	1.01	1.0 1.0100%
setXpos(Integer) : void   setXpos(Integer) : void	61686168	1.01	1.01	1.0 1.0100%
getYpos() : Integer   getYpos() : Integer	61806180	1.01	1.01	1.0 1.0100%
setYpos(Integer) : void   setYpos(Integer) : void	61926192	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.Viewport.CalcIdParam

Class JalviewModel.Viewport.CalcIdParam	Line # 6218	Total Statements 8	Complexity 7	TOTAL Coverage 0.00%
getCalcId() : String   getCalcId() : String	62376237	1.01	1.01	0.0 0.00%
setCalcId(String) : void   setCalcId(String) : void	62496249	1.01	1.01	0.0 0.00%
isNeedsUpdate() : boolean   isNeedsUpdate() : boolean	62616261	3.03	2.02	0.0 0.00%
setNeedsUpdate(Boolean) : void   setNeedsUpdate(Boolean) : void	62776277	1.01	1.01	0.0 0.00%
isAutoUpdate() : boolean   isAutoUpdate() : boolean	62856285	1.01	1.01	0.0 0.00%
setAutoUpdate(boolean) : void   setAutoUpdate(boolean) : void	62936293	1.01	1.01	0.0 0.00%

 

Class JalviewModel.Viewport.HiddenColumns

Class JalviewModel.Viewport.HiddenColumns	Line # 6320	Total Statements 4	Complexity 4	TOTAL Coverage 1.0100%
getStart() : Integer   getStart() : Integer	63356335	1.01	1.01	1.0 1.0100%
setStart(Integer) : void   setStart(Integer) : void	63476347	1.01	1.01	1.0 1.0100%
getEnd() : Integer   getEnd() : Integer	63596359	1.01	1.01	1.0 1.0100%
setEnd(Integer) : void   setEnd(Integer) : void	63716371	1.01	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.63606197	jalview.project.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettingsjalview.project.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettings	1PASS
	0.63384956	jalview.project.Jalview2xmlTests.testStoreAndRecoverExpandedviewsjalview.project.Jalview2xmlTests.testStoreAndRecoverExpandedviews	1PASS
	0.4811947	jalview.project.Jalview2xmlTests.testPcaViewAssociationjalview.project.Jalview2xmlTests.testPcaViewAssociation	1PASS
	0.42809734	jalview.project.Jalview2xmlTests.testColourByAnnotScoresjalview.project.Jalview2xmlTests.testColourByAnnotScores	1PASS
	0.42367256	jalview.project.Jalview2xmlTests.testStoreAndRecoverColourThresholdsjalview.project.Jalview2xmlTests.testStoreAndRecoverColourThresholds	1PASS
	0.41261062	jalview.project.Jalview2xmlTests.testSaveLoadFeatureColoursAndFiltersjalview.project.Jalview2xmlTests.testSaveLoadFeatureColoursAndFilters	1PASS
	0.40597346	jalview.gui.AlignFrameTest.testNewView_colourThresholdsjalview.gui.AlignFrameTest.testNewView_colourThresholds	1PASS
	0.375	jalview.project.Jalview2xmlTests.noDuplicatePdbMappingsMadejalview.project.Jalview2xmlTests.noDuplicatePdbMappingsMade	1PASS
	0.375	jalview.project.Jalview2xmlTests.testCopyViewSettingsjalview.project.Jalview2xmlTests.testCopyViewSettings	1PASS
	0.375	jalview.project.Jalview2xmlTests.viewRefPdbAnnotationjalview.project.Jalview2xmlTests.viewRefPdbAnnotation	1PASS
	0.375	jalview.project.Jalview2xmlTests.gatherViewsHerejalview.project.Jalview2xmlTests.gatherViewsHere	1PASS
	0.3738938	jalview.io.AnnotatedPDBFileInputTest.testJalviewProjectRelocationAnnotationjalview.io.AnnotatedPDBFileInputTest.testJalviewProjectRelocationAnnotation	1PASS
	0.3738938	jalview.project.Jalview2xmlTests.testStoreAndRecoverPDBEntryjalview.project.Jalview2xmlTests.testStoreAndRecoverPDBEntry	1PASS
	0.32964602	jalview.project.Jalview2xmlTests.testStoreAndRecoverGroupRepSeqsjalview.project.Jalview2xmlTests.testStoreAndRecoverGroupRepSeqs	1PASS
	0.32300884	jalview.project.Jalview2xmlTests.testRNAStructureRecoveryjalview.project.Jalview2xmlTests.testRNAStructureRecovery	1PASS
	0.32300884	jalview.project.Jalview2xmlTests.testTCoffeeScoresjalview.project.Jalview2xmlTests.testTCoffeeScores	1PASS
	0.32079646	jalview.project.Jalview2xmlTests.testStoreAndRecoverGeneLocusjalview.project.Jalview2xmlTests.testStoreAndRecoverGeneLocus	1PASS
	0.30309734	jalview.gui.AlignFrameTest.testNewView_dsRefPreservedjalview.gui.AlignFrameTest.testNewView_dsRefPreserved	1PASS
	0.30309734	jalview.gui.AlignViewportTest.testDeregisterMapping_onCloseViewjalview.gui.AlignViewportTest.testDeregisterMapping_onCloseView	1PASS
	0.26548672	jalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwicejalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwice	1PASS
	0.21349558	jalview.project.Jalview2xmlTests.testMergeDatasetsforManyViewsjalview.project.Jalview2xmlTests.testMergeDatasetsforManyViews	1PASS
	0.2079646	jalview.project.Jalview2xmlTests.testMergeDatasetsforViewsjalview.project.Jalview2xmlTests.testMergeDatasetsforViews	1PASS

 

Source view

1		//
2		// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
3		// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
4		// Any modifications to this file will be lost upon recompilation of the source schema.
5		// Generated on: 2019.06.07 at 02:21:15 PM BST
6		//
7
8
9		package jalview.xml.binding.jalview;
10
11		import java.util.ArrayList;
12		import java.util.List;
13		import javax.xml.bind.annotation.XmlAccessType;
14		import javax.xml.bind.annotation.XmlAccessorType;
15		import javax.xml.bind.annotation.XmlAttribute;
16		import javax.xml.bind.annotation.XmlElement;
17		import javax.xml.bind.annotation.XmlID;
18		import javax.xml.bind.annotation.XmlSchemaType;
19		import javax.xml.bind.annotation.XmlType;
20		import javax.xml.bind.annotation.XmlValue;
21		import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
22		import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
23		import javax.xml.datatype.XMLGregorianCalendar;
24
25
26		/**
27		* <p>Java class for JalviewModel complex type.
28		*
29		* <p>The following schema fragment specifies the expected content contained within this class.
30		*
31		* <pre>
32		* &lt;complexType name="JalviewModel">
33		* &lt;complexContent>
34		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
35		* &lt;sequence>
36		* &lt;element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
37		* &lt;element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
38		* &lt;element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
39		* &lt;sequence>
40		* &lt;element name="JSeq" maxOccurs="unbounded" minOccurs="0">
41		* &lt;complexType>
42		* &lt;complexContent>
43		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
44		* &lt;sequence>
45		* &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
46		* &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
47		* &lt;complexType>
48		* &lt;complexContent>
49		* &lt;extension base="{www.jalview.org}pdbentry">
50		* &lt;sequence>
51		* &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
52		* &lt;complexType>
53		* &lt;simpleContent>
54		* &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
55		* &lt;attGroup ref="{www.jalview.org}swingwindow"/>
56		* &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
57		* &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
58		* &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
59		* &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
60		* &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
61		* &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
62		* &lt;/extension>
63		* &lt;/simpleContent>
64		* &lt;/complexType>
65		* &lt;/element>
66		* &lt;/sequence>
67		* &lt;/extension>
68		* &lt;/complexContent>
69		* &lt;/complexType>
70		* &lt;/element>
71		* &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
72		* &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
73		* &lt;complexType>
74		* &lt;complexContent>
75		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
76		* &lt;sequence>
77		* &lt;element name="secondaryStructure" maxOccurs="unbounded">
78		* &lt;complexType>
79		* &lt;complexContent>
80		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
81		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
82		* &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
83		* &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
84		* &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
85		* &lt;/restriction>
86		* &lt;/complexContent>
87		* &lt;/complexType>
88		* &lt;/element>
89		* &lt;/sequence>
90		* &lt;attGroup ref="{www.jalview.org}swingwindow"/>
91		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
92		* &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
93		* &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
94		* &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
95		* &lt;/restriction>
96		* &lt;/complexContent>
97		* &lt;/complexType>
98		* &lt;/element>
99		* &lt;/sequence>
100		* &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
101		* &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
102		* &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
103		* &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
104		* &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
105		* &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
106		* &lt;/restriction>
107		* &lt;/complexContent>
108		* &lt;/complexType>
109		* &lt;/element>
110		* &lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0">
111		* &lt;complexType>
112		* &lt;complexContent>
113		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
114		* &lt;sequence>
115		* &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
116		* &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
117		* &lt;/sequence>
118		* &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
119		* &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
120		* &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
121		* &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
122		* &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
123		* &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
124		* &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
125		* &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
126		* &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
127		* &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
128		* &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
129		* &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
130		* &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
131		* &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
132		* &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
133		* &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
134		* &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
135		* &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
136		* &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
137		* &lt;/restriction>
138		* &lt;/complexContent>
139		* &lt;/complexType>
140		* &lt;/element>
141		* &lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0">
142		* &lt;complexType>
143		* &lt;complexContent>
144		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
145		* &lt;sequence>
146		* &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
147		* &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
148		* &lt;complexType>
149		* &lt;complexContent>
150		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
151		* &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
152		* &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
153		* &lt;/restriction>
154		* &lt;/complexContent>
155		* &lt;/complexType>
156		* &lt;/element>
157		* &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
158		* &lt;complexType>
159		* &lt;complexContent>
160		* &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
161		* &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
162		* &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
163		* &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
164		* &lt;/extension>
165		* &lt;/complexContent>
166		* &lt;/complexType>
167		* &lt;/element>
168		* &lt;/sequence>
169		* &lt;attGroup ref="{www.jalview.org}swingwindow"/>
170		* &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
171		* &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
172		* &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
173		* &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
174		* &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
175		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
176		* &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
177		* &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
178		* &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
179		* &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
180		* &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
181		* &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
182		* &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
183		* &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
184		* &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
185		* &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
186		* &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
187		* &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
188		* &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
189		* &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
190		* &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
191		* &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
192		* &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
193		* &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
194		* &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
195		* &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
196		* &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
197		* &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
198		* &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
199		* &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
200		* &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
201		* &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
202		* &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
203		* &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
204		* &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
205		* &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
206		* &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
207		* &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
208		* &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
209		* &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
210		* &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
211		* &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
212		* &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
213		* &lt;/restriction>
214		* &lt;/complexContent>
215		* &lt;/complexType>
216		* &lt;/element>
217		* &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0">
218		* &lt;complexType>
219		* &lt;complexContent>
220		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
221		* &lt;sequence>
222		* &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
223		* &lt;/sequence>
224		* &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
225		* &lt;/restriction>
226		* &lt;/complexContent>
227		* &lt;/complexType>
228		* &lt;/element>
229		* &lt;element name="tree" maxOccurs="unbounded" minOccurs="0">
230		* &lt;complexType>
231		* &lt;complexContent>
232		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
233		* &lt;sequence minOccurs="0">
234		* &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
235		* &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
236		* &lt;/sequence>
237		* &lt;attGroup ref="{www.jalview.org}swingwindow"/>
238		* &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
239		* &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
240		* &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
241		* &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
242		* &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
243		* &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
244		* &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
245		* &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
246		* &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
247		* &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
248		* &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
249		* &lt;/restriction>
250		* &lt;/complexContent>
251		* &lt;/complexType>
252		* &lt;/element>
253		* &lt;element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
254		* &lt;complexType>
255		* &lt;complexContent>
256		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
257		* &lt;sequence>
258		* &lt;element name="sequencePoint" maxOccurs="unbounded">
259		* &lt;complexType>
260		* &lt;complexContent>
261		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
262		* &lt;attGroup ref="{www.jalview.org}position"/>
263		* &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
264		* &lt;/restriction>
265		* &lt;/complexContent>
266		* &lt;/complexType>
267		* &lt;/element>
268		* &lt;element name="axis" maxOccurs="3" minOccurs="3">
269		* &lt;complexType>
270		* &lt;complexContent>
271		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
272		* &lt;attGroup ref="{www.jalview.org}position"/>
273		* &lt;/restriction>
274		* &lt;/complexContent>
275		* &lt;/complexType>
276		* &lt;/element>
277		* &lt;element name="seqPointMin">
278		* &lt;complexType>
279		* &lt;complexContent>
280		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
281		* &lt;attGroup ref="{www.jalview.org}position"/>
282		* &lt;/restriction>
283		* &lt;/complexContent>
284		* &lt;/complexType>
285		* &lt;/element>
286		* &lt;element name="seqPointMax">
287		* &lt;complexType>
288		* &lt;complexContent>
289		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
290		* &lt;attGroup ref="{www.jalview.org}position"/>
291		* &lt;/restriction>
292		* &lt;/complexContent>
293		* &lt;/complexType>
294		* &lt;/element>
295		* &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/>
296		* &lt;/sequence>
297		* &lt;attGroup ref="{www.jalview.org}swingwindow"/>
298		* &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
299		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
300		* &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
301		* &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
302		* &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
303		* &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
304		* &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
305		* &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
306		* &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
307		* &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
308		* &lt;/restriction>
309		* &lt;/complexContent>
310		* &lt;/complexType>
311		* &lt;/element>
312		* &lt;element name="FeatureSettings" minOccurs="0">
313		* &lt;complexType>
314		* &lt;complexContent>
315		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
316		* &lt;sequence>
317		* &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
318		* &lt;complexType>
319		* &lt;complexContent>
320		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
321		* &lt;sequence>
322		* &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
323		* &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
324		* &lt;/sequence>
325		* &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
326		* &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
327		* &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
328		* &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
329		* &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
330		* &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
331		* &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
332		* &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
333		* &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
334		* &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
335		* &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
336		* &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
337		* &lt;/restriction>
338		* &lt;/complexContent>
339		* &lt;/complexType>
340		* &lt;/element>
341		* &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
342		* &lt;complexType>
343		* &lt;complexContent>
344		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
345		* &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
346		* &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
347		* &lt;/restriction>
348		* &lt;/complexContent>
349		* &lt;/complexType>
350		* &lt;/element>
351		* &lt;/sequence>
352		* &lt;/restriction>
353		* &lt;/complexContent>
354		* &lt;/complexType>
355		* &lt;/element>
356		* &lt;/sequence>
357		* &lt;/sequence>
358		* &lt;/restriction>
359		* &lt;/complexContent>
360		* &lt;/complexType>
361		* </pre>
362		*
363		*
364		*/
365		@XmlAccessorType(XmlAccessType.FIELD)
366		@XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
367		"creationDate",
368		"version",
369		"vamsasModel",
370		"jSeq",
371		"jGroup",
372		"viewport",
373		"userColours",
374		"tree",
375		"pcaViewer",
376		"featureSettings"
377		})
		84.6% Uncovered Elements: 8 (52) Complexity: 20 Complexity Density: 0.77
378		public class JalviewModel {
379
380		@XmlElement(required = true)
381		@XmlSchemaType(name = "dateTime")
382		protected XMLGregorianCalendar creationDate;
383		@XmlElement(required = true)
384		protected String version;
385		@XmlElement(required = true)
386		protected VAMSAS vamsasModel;
387		@XmlElement(name = "JSeq")
388		protected List<JalviewModel.JSeq> jSeq;
389		@XmlElement(name = "JGroup")
390		protected List<JalviewModel.JGroup> jGroup;
391		@XmlElement(name = "Viewport")
392		protected List<JalviewModel.Viewport> viewport;
393		@XmlElement(name = "UserColours")
394		protected List<JalviewModel.UserColours> userColours;
395		protected List<JalviewModel.Tree> tree;
396		@XmlElement(name = "PcaViewer")
397		protected List<JalviewModel.PcaViewer> pcaViewer;
398		@XmlElement(name = "FeatureSettings")
399		protected JalviewModel.FeatureSettings featureSettings;
400
401		/**
402		* Gets the value of the creationDate property.
403		*
404		* @return
405		* possible object is
406		* {@link XMLGregorianCalendar }
407		*
408		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
409	0	public XMLGregorianCalendar getCreationDate() {...
410	0	return creationDate;
411		}
412
413		/**
414		* Sets the value of the creationDate property.
415		*
416		* @param value
417		* allowed object is
418		* {@link XMLGregorianCalendar }
419		*
420		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
421	45	public void setCreationDate(XMLGregorianCalendar value) {...
422	45	this.creationDate = value;
423		}
424
425		/**
426		* Gets the value of the version property.
427		*
428		* @return
429		* possible object is
430		* {@link String }
431		*
432		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
433	70	public String getVersion() {...
434	70	return version;
435		}
436
437		/**
438		* Sets the value of the version property.
439		*
440		* @param value
441		* allowed object is
442		* {@link String }
443		*
444		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
445	45	public void setVersion(String value) {...
446	45	this.version = value;
447		}
448
449		/**
450		* Gets the value of the vamsasModel property.
451		*
452		* @return
453		* possible object is
454		* {@link VAMSAS }
455		*
456		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
457	137	public VAMSAS getVamsasModel() {...
458	137	return vamsasModel;
459		}
460
461		/**
462		* Sets the value of the vamsasModel property.
463		*
464		* @param value
465		* allowed object is
466		* {@link VAMSAS }
467		*
468		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
469	45	public void setVamsasModel(VAMSAS value) {...
470	45	this.vamsasModel = value;
471		}
472
473		/**
474		* Gets the value of the jSeq property.
475		*
476		* <p>
477		* This accessor method returns a reference to the live list,
478		* not a snapshot. Therefore any modification you make to the
479		* returned list will be present inside the JAXB object.
480		* This is why there is not a <CODE>set</CODE> method for the jSeq property.
481		*
482		* <p>
483		* For example, to add a new item, do as follows:
484		* <pre>
485		* getJSeq().add(newItem);
486		* </pre>
487		*
488		*
489		* <p>
490		* Objects of the following type(s) are allowed in the list
491		* {@link JalviewModel.JSeq }
492		*
493		*
494		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
495	755	public List<JalviewModel.JSeq> getJSeq() {...
496	755	if (jSeq == null) {
497	45	jSeq = new ArrayList<JalviewModel.JSeq>();
498		}
499	755	return this.jSeq;
500		}
501
502		/**
503		* Gets the value of the jGroup property.
504		*
505		* <p>
506		* This accessor method returns a reference to the live list,
507		* not a snapshot. Therefore any modification you make to the
508		* returned list will be present inside the JAXB object.
509		* This is why there is not a <CODE>set</CODE> method for the jGroup property.
510		*
511		* <p>
512		* For example, to add a new item, do as follows:
513		* <pre>
514		* getJGroup().add(newItem);
515		* </pre>
516		*
517		*
518		* <p>
519		* Objects of the following type(s) are allowed in the list
520		* {@link JalviewModel.JGroup }
521		*
522		*
523		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
524	126	public List<JalviewModel.JGroup> getJGroup() {...
525	126	if (jGroup == null) {
526	68	jGroup = new ArrayList<JalviewModel.JGroup>();
527		}
528	126	return this.jGroup;
529		}
530
531		/**
532		* Gets the value of the viewport property.
533		*
534		* <p>
535		* This accessor method returns a reference to the live list,
536		* not a snapshot. Therefore any modification you make to the
537		* returned list will be present inside the JAXB object.
538		* This is why there is not a <CODE>set</CODE> method for the viewport property.
539		*
540		* <p>
541		* For example, to add a new item, do as follows:
542		* <pre>
543		* getViewport().add(newItem);
544		* </pre>
545		*
546		*
547		* <p>
548		* Objects of the following type(s) are allowed in the list
549		* {@link JalviewModel.Viewport }
550		*
551		*
552		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
553	311	public List<JalviewModel.Viewport> getViewport() {...
554	311	if (viewport == null) {
555	45	viewport = new ArrayList<JalviewModel.Viewport>();
556		}
557	311	return this.viewport;
558		}
559
560		/**
561		* Gets the value of the userColours property.
562		*
563		* <p>
564		* This accessor method returns a reference to the live list,
565		* not a snapshot. Therefore any modification you make to the
566		* returned list will be present inside the JAXB object.
567		* This is why there is not a <CODE>set</CODE> method for the userColours property.
568		*
569		* <p>
570		* For example, to add a new item, do as follows:
571		* <pre>
572		* getUserColours().add(newItem);
573		* </pre>
574		*
575		*
576		* <p>
577		* Objects of the following type(s) are allowed in the list
578		* {@link JalviewModel.UserColours }
579		*
580		*
581		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
582	0	public List<JalviewModel.UserColours> getUserColours() {...
583	0	if (userColours == null) {
584	0	userColours = new ArrayList<JalviewModel.UserColours>();
585		}
586	0	return this.userColours;
587		}
588
589		/**
590		* Gets the value of the tree property.
591		*
592		* <p>
593		* This accessor method returns a reference to the live list,
594		* not a snapshot. Therefore any modification you make to the
595		* returned list will be present inside the JAXB object.
596		* This is why there is not a <CODE>set</CODE> method for the tree property.
597		*
598		* <p>
599		* For example, to add a new item, do as follows:
600		* <pre>
601		* getTree().add(newItem);
602		* </pre>
603		*
604		*
605		* <p>
606		* Objects of the following type(s) are allowed in the list
607		* {@link JalviewModel.Tree }
608		*
609		*
610		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
611	82	public List<JalviewModel.Tree> getTree() {...
612	82	if (tree == null) {
613	58	tree = new ArrayList<JalviewModel.Tree>();
614		}
615	82	return this.tree;
616		}
617
618		/**
619		* Gets the value of the pcaViewer property.
620		*
621		* <p>
622		* This accessor method returns a reference to the live list,
623		* not a snapshot. Therefore any modification you make to the
624		* returned list will be present inside the JAXB object.
625		* This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
626		*
627		* <p>
628		* For example, to add a new item, do as follows:
629		* <pre>
630		* getPcaViewer().add(newItem);
631		* </pre>
632		*
633		*
634		* <p>
635		* Objects of the following type(s) are allowed in the list
636		* {@link JalviewModel.PcaViewer }
637		*
638		*
639		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
640	65	public List<JalviewModel.PcaViewer> getPcaViewer() {...
641	65	if (pcaViewer == null) {
642	64	pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
643		}
644	65	return this.pcaViewer;
645		}
646
647		/**
648		* Gets the value of the featureSettings property.
649		*
650		* @return
651		* possible object is
652		* {@link JalviewModel.FeatureSettings }
653		*
654		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
655	2100	public JalviewModel.FeatureSettings getFeatureSettings() {...
656	2100	return featureSettings;
657		}
658
659		/**
660		* Sets the value of the featureSettings property.
661		*
662		* @param value
663		* allowed object is
664		* {@link JalviewModel.FeatureSettings }
665		*
666		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
667	11	public void setFeatureSettings(JalviewModel.FeatureSettings value) {...
668	11	this.featureSettings = value;
669		}
670
671
672		/**
673		* <p>Java class for anonymous complex type.
674		*
675		* <p>The following schema fragment specifies the expected content contained within this class.
676		*
677		* <pre>
678		* &lt;complexType>
679		* &lt;complexContent>
680		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
681		* &lt;sequence>
682		* &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
683		* &lt;complexType>
684		* &lt;complexContent>
685		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
686		* &lt;sequence>
687		* &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
688		* &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
689		* &lt;/sequence>
690		* &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
691		* &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
692		* &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
693		* &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
694		* &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
695		* &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
696		* &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
697		* &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
698		* &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
699		* &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
700		* &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
701		* &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
702		* &lt;/restriction>
703		* &lt;/complexContent>
704		* &lt;/complexType>
705		* &lt;/element>
706		* &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
707		* &lt;complexType>
708		* &lt;complexContent>
709		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
710		* &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
711		* &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
712		* &lt;/restriction>
713		* &lt;/complexContent>
714		* &lt;/complexType>
715		* &lt;/element>
716		* &lt;/sequence>
717		* &lt;/restriction>
718		* &lt;/complexContent>
719		* &lt;/complexType>
720		* </pre>
721		*
722		*
723		*/
724		@XmlAccessorType(XmlAccessType.FIELD)
725		@XmlType(name = "", propOrder = {
726		"setting",
727		"group"
728		})
		100% Uncovered Elements: 0 (12) Complexity: 4 Complexity Density: 0.67
729		public static class FeatureSettings {
730
731		@XmlElement(namespace = "www.jalview.org")
732		protected List<JalviewModel.FeatureSettings.Setting> setting;
733		@XmlElement(namespace = "www.jalview.org")
734		protected List<JalviewModel.FeatureSettings.Group> group;
735
736		/**
737		* Gets the value of the setting property.
738		*
739		* <p>
740		* This accessor method returns a reference to the live list,
741		* not a snapshot. Therefore any modification you make to the
742		* returned list will be present inside the JAXB object.
743		* This is why there is not a <CODE>set</CODE> method for the setting property.
744		*
745		* <p>
746		* For example, to add a new item, do as follows:
747		* <pre>
748		* getSetting().add(newItem);
749		* </pre>
750		*
751		*
752		* <p>
753		* Objects of the following type(s) are allowed in the list
754		* {@link JalviewModel.FeatureSettings.Setting }
755		*
756		*
757		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
758	1953	public List<JalviewModel.FeatureSettings.Setting> getSetting() {...
759	1953	if (setting == null) {
760	11	setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
761		}
762	1953	return this.setting;
763		}
764
765		/**
766		* Gets the value of the group property.
767		*
768		* <p>
769		* This accessor method returns a reference to the live list,
770		* not a snapshot. Therefore any modification you make to the
771		* returned list will be present inside the JAXB object.
772		* This is why there is not a <CODE>set</CODE> method for the group property.
773		*
774		* <p>
775		* For example, to add a new item, do as follows:
776		* <pre>
777		* getGroup().add(newItem);
778		* </pre>
779		*
780		*
781		* <p>
782		* Objects of the following type(s) are allowed in the list
783		* {@link JalviewModel.FeatureSettings.Group }
784		*
785		*
786		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
787	323	public List<JalviewModel.FeatureSettings.Group> getGroup() {...
788	323	if (group == null) {
789	11	group = new ArrayList<JalviewModel.FeatureSettings.Group>();
790		}
791	323	return this.group;
792		}
793
794
795		/**
796		* <p>Java class for anonymous complex type.
797		*
798		* <p>The following schema fragment specifies the expected content contained within this class.
799		*
800		* <pre>
801		* &lt;complexType>
802		* &lt;complexContent>
803		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
804		* &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
805		* &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
806		* &lt;/restriction>
807		* &lt;/complexContent>
808		* &lt;/complexType>
809		* </pre>
810		*
811		*
812		*/
813		@XmlAccessorType(XmlAccessType.FIELD)
814		@XmlType(name = "")
		100% Uncovered Elements: 0 (8) Complexity: 4 Complexity Density: 1
815		public static class Group {
816
817		@XmlAttribute(name = "name", required = true)
818		protected String name;
819		@XmlAttribute(name = "display", required = true)
820		protected boolean display;
821
822		/**
823		* Gets the value of the name property.
824		*
825		* @return
826		* possible object is
827		* {@link String }
828		*
829		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
830	127	public String getName() {...
831	127	return name;
832		}
833
834		/**
835		* Sets the value of the name property.
836		*
837		* @param value
838		* allowed object is
839		* {@link String }
840		*
841		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
842	33	public void setName(String value) {...
843	33	this.name = value;
844		}
845
846		/**
847		* Gets the value of the display property.
848		*
849		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
850	127	public boolean isDisplay() {...
851	127	return display;
852		}
853
854		/**
855		* Sets the value of the display property.
856		*
857		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
858	33	public void setDisplay(boolean value) {...
859	33	this.display = value;
860		}
861
862		}
863
864
865		/**
866		* <p>Java class for anonymous complex type.
867		*
868		* <p>The following schema fragment specifies the expected content contained within this class.
869		*
870		* <pre>
871		* &lt;complexType>
872		* &lt;complexContent>
873		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
874		* &lt;sequence>
875		* &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
876		* &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
877		* &lt;/sequence>
878		* &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
879		* &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
880		* &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
881		* &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
882		* &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
883		* &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
884		* &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
885		* &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
886		* &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
887		* &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
888		* &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
889		* &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
890		* &lt;/restriction>
891		* &lt;/complexContent>
892		* &lt;/complexType>
893		* </pre>
894		*
895		*
896		*/
897		@XmlAccessorType(XmlAccessType.FIELD)
898		@XmlType(name = "", propOrder = {
899		"attributeName",
900		"matcherSet"
901		})
		96.8% Uncovered Elements: 2 (62) Complexity: 29 Complexity Density: 0.94
902		public static class Setting {
903
904		@XmlElement(namespace = "www.jalview.org")
905		protected List<String> attributeName;
906		@XmlElement(namespace = "www.jalview.org")
907		protected FeatureMatcherSet matcherSet;
908		@XmlAttribute(name = "type", required = true)
909		protected String type;
910		@XmlAttribute(name = "colour", required = true)
911		protected int colour;
912		@XmlAttribute(name = "display", required = true)
913		protected boolean display;
914		@XmlAttribute(name = "order")
915		protected Float order;
916		@XmlAttribute(name = "mincolour")
917		protected Integer mincolour;
918		@XmlAttribute(name = "noValueColour")
919		protected NoValueColour noValueColour;
920		@XmlAttribute(name = "threshold")
921		protected Float threshold;
922		@XmlAttribute(name = "threshstate")
923		protected Integer threshstate;
924		@XmlAttribute(name = "max")
925		protected Float max;
926		@XmlAttribute(name = "min")
927		protected Float min;
928		@XmlAttribute(name = "colourByLabel")
929		protected Boolean colourByLabel;
930		@XmlAttribute(name = "autoScale")
931		protected Boolean autoScale;
932
933		/**
934		* Gets the value of the attributeName property.
935		*
936		* <p>
937		* This accessor method returns a reference to the live list,
938		* not a snapshot. Therefore any modification you make to the
939		* returned list will be present inside the JAXB object.
940		* This is why there is not a <CODE>set</CODE> method for the attributeName property.
941		*
942		* <p>
943		* For example, to add a new item, do as follows:
944		* <pre>
945		* getAttributeName().add(newItem);
946		* </pre>
947		*
948		*
949		* <p>
950		* Objects of the following type(s) are allowed in the list
951		* {@link String }
952		*
953		*
954		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
955	12	public List<String> getAttributeName() {...
956	12	if (attributeName == null) {
957	5	attributeName = new ArrayList<String>();
958		}
959	12	return this.attributeName;
960		}
961
962		/**
963		* Gets the value of the matcherSet property.
964		*
965		* @return
966		* possible object is
967		* {@link FeatureMatcherSet }
968		*
969		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
970	834	public FeatureMatcherSet getMatcherSet() {...
971	834	return matcherSet;
972		}
973
974		/**
975		* Sets the value of the matcherSet property.
976		*
977		* @param value
978		* allowed object is
979		* {@link FeatureMatcherSet }
980		*
981		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
982	3	public void setMatcherSet(FeatureMatcherSet value) {...
983	3	this.matcherSet = value;
984		}
985
986		/**
987		* Gets the value of the type property.
988		*
989		* @return
990		* possible object is
991		* {@link String }
992		*
993		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
994	834	public String getType() {...
995	834	return type;
996		}
997
998		/**
999		* Sets the value of the type property.
1000		*
1001		* @param value
1002		* allowed object is
1003		* {@link String }
1004		*
1005		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1006	213	public void setType(String value) {...
1007	213	this.type = value;
1008		}
1009
1010		/**
1011		* Gets the value of the colour property.
1012		*
1013		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1014	834	public int getColour() {...
1015	834	return colour;
1016		}
1017
1018		/**
1019		* Sets the value of the colour property.
1020		*
1021		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1022	213	public void setColour(int value) {...
1023	213	this.colour = value;
1024		}
1025
1026		/**
1027		* Gets the value of the display property.
1028		*
1029		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1030	834	public boolean isDisplay() {...
1031	834	return display;
1032		}
1033
1034		/**
1035		* Sets the value of the display property.
1036		*
1037		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1038	213	public void setDisplay(boolean value) {...
1039	213	this.display = value;
1040		}
1041
1042		/**
1043		* Gets the value of the order property.
1044		*
1045		* @return
1046		* possible object is
1047		* {@link Float }
1048		*
1049		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1050	1668	public Float getOrder() {...
1051	1668	return order;
1052		}
1053
1054		/**
1055		* Sets the value of the order property.
1056		*
1057		* @param value
1058		* allowed object is
1059		* {@link Float }
1060		*
1061		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1062	213	public void setOrder(Float value) {...
1063	213	this.order = value;
1064		}
1065
1066		/**
1067		* Gets the value of the mincolour property.
1068		*
1069		* @return
1070		* possible object is
1071		* {@link Integer }
1072		*
1073		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1074	839	public Integer getMincolour() {...
1075	839	return mincolour;
1076		}
1077
1078		/**
1079		* Sets the value of the mincolour property.
1080		*
1081		* @param value
1082		* allowed object is
1083		* {@link Integer }
1084		*
1085		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1086	4	public void setMincolour(Integer value) {...
1087	4	this.mincolour = value;
1088		}
1089
1090		/**
1091		* Gets the value of the noValueColour property.
1092		*
1093		* @return
1094		* possible object is
1095		* {@link NoValueColour }
1096		*
1097		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
1098	5	public NoValueColour getNoValueColour() {...
1099	5	if (noValueColour == null) {
1100	0	return NoValueColour.MIN;
1101		} else {
1102	5	return noValueColour;
1103		}
1104		}
1105
1106		/**
1107		* Sets the value of the noValueColour property.
1108		*
1109		* @param value
1110		* allowed object is
1111		* {@link NoValueColour }
1112		*
1113		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1114	4	public void setNoValueColour(NoValueColour value) {...
1115	4	this.noValueColour = value;
1116		}
1117
1118		/**
1119		* Gets the value of the threshold property.
1120		*
1121		* @return
1122		* possible object is
1123		* {@link Float }
1124		*
1125		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1126	10	public Float getThreshold() {...
1127	10	return threshold;
1128		}
1129
1130		/**
1131		* Sets the value of the threshold property.
1132		*
1133		* @param value
1134		* allowed object is
1135		* {@link Float }
1136		*
1137		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1138	4	public void setThreshold(Float value) {...
1139	4	this.threshold = value;
1140		}
1141
1142		/**
1143		* Gets the value of the threshstate property.
1144		*
1145		* @return
1146		* possible object is
1147		* {@link Integer }
1148		*
1149		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1150	5	public Integer getThreshstate() {...
1151	5	return threshstate;
1152		}
1153
1154		/**
1155		* Sets the value of the threshstate property.
1156		*
1157		* @param value
1158		* allowed object is
1159		* {@link Integer }
1160		*
1161		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1162	4	public void setThreshstate(Integer value) {...
1163	4	this.threshstate = value;
1164		}
1165
1166		/**
1167		* Gets the value of the max property.
1168		*
1169		* @return
1170		* possible object is
1171		* {@link Float }
1172		*
1173		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1174	10	public Float getMax() {...
1175	10	return max;
1176		}
1177
1178		/**
1179		* Sets the value of the max property.
1180		*
1181		* @param value
1182		* allowed object is
1183		* {@link Float }
1184		*
1185		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1186	4	public void setMax(Float value) {...
1187	4	this.max = value;
1188		}
1189
1190		/**
1191		* Gets the value of the min property.
1192		*
1193		* @return
1194		* possible object is
1195		* {@link Float }
1196		*
1197		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1198	5	public Float getMin() {...
1199	5	return min;
1200		}
1201
1202		/**
1203		* Sets the value of the min property.
1204		*
1205		* @param value
1206		* allowed object is
1207		* {@link Float }
1208		*
1209		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1210	4	public void setMin(Float value) {...
1211	4	this.min = value;
1212		}
1213
1214		/**
1215		* Gets the value of the colourByLabel property.
1216		*
1217		* @return
1218		* possible object is
1219		* {@link Boolean }
1220		*
1221		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1222	10	public Boolean isColourByLabel() {...
1223	10	return colourByLabel;
1224		}
1225
1226		/**
1227		* Sets the value of the colourByLabel property.
1228		*
1229		* @param value
1230		* allowed object is
1231		* {@link Boolean }
1232		*
1233		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1234	4	public void setColourByLabel(Boolean value) {...
1235	4	this.colourByLabel = value;
1236		}
1237
1238		/**
1239		* Gets the value of the autoScale property.
1240		*
1241		* @return
1242		* possible object is
1243		* {@link Boolean }
1244		*
1245		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1246	10	public Boolean isAutoScale() {...
1247	10	return autoScale;
1248		}
1249
1250		/**
1251		* Sets the value of the autoScale property.
1252		*
1253		* @param value
1254		* allowed object is
1255		* {@link Boolean }
1256		*
1257		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1258	4	public void setAutoScale(Boolean value) {...
1259	4	this.autoScale = value;
1260		}
1261
1262		}
1263
1264		}
1265
1266
1267		/**
1268		* <p>Java class for anonymous complex type.
1269		*
1270		* <p>The following schema fragment specifies the expected content contained within this class.
1271		*
1272		* <pre>
1273		* &lt;complexType>
1274		* &lt;complexContent>
1275		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1276		* &lt;sequence>
1277		* &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
1278		* &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
1279		* &lt;/sequence>
1280		* &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
1281		* &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
1282		* &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
1283		* &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
1284		* &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1285		* &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1286		* &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
1287		* &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1288		* &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1289		* &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1290		* &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
1291		* &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
1292		* &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1293		* &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1294		* &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1295		* &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1296		* &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1297		* &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1298		* &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
1299		* &lt;/restriction>
1300		* &lt;/complexContent>
1301		* &lt;/complexType>
1302		* </pre>
1303		*
1304		*
1305		*/
1306		@XmlAccessorType(XmlAccessType.FIELD)
1307		@XmlType(name = "", propOrder = {
1308		"seq",
1309		"annotationColours"
1310		})
		94.1% Uncovered Elements: 6 (102) Complexity: 46 Complexity Density: 0.9
1311		public static class JGroup {
1312
1313		@XmlElement(namespace = "www.jalview.org", required = true)
1314		protected List<String> seq;
1315		@XmlElement(namespace = "www.jalview.org")
1316		protected AnnotationColourScheme annotationColours;
1317		@XmlAttribute(name = "start")
1318		protected Integer start;
1319		@XmlAttribute(name = "end")
1320		protected Integer end;
1321		@XmlAttribute(name = "name")
1322		protected String name;
1323		@XmlAttribute(name = "colour")
1324		protected String colour;
1325		@XmlAttribute(name = "consThreshold")
1326		protected Integer consThreshold;
1327		@XmlAttribute(name = "pidThreshold")
1328		protected Integer pidThreshold;
1329		@XmlAttribute(name = "outlineColour")
1330		protected Integer outlineColour;
1331		@XmlAttribute(name = "displayBoxes")
1332		protected Boolean displayBoxes;
1333		@XmlAttribute(name = "displayText")
1334		protected Boolean displayText;
1335		@XmlAttribute(name = "colourText")
1336		protected Boolean colourText;
1337		@XmlAttribute(name = "textCol1")
1338		protected Integer textCol1;
1339		@XmlAttribute(name = "textCol2")
1340		protected Integer textCol2;
1341		@XmlAttribute(name = "textColThreshold")
1342		protected Integer textColThreshold;
1343		@XmlAttribute(name = "showUnconserved")
1344		protected Boolean showUnconserved;
1345		@XmlAttribute(name = "ignoreGapsinConsensus")
1346		protected Boolean ignoreGapsinConsensus;
1347		@XmlAttribute(name = "showConsensusHistogram")
1348		protected Boolean showConsensusHistogram;
1349		@XmlAttribute(name = "showSequenceLogo")
1350		protected Boolean showSequenceLogo;
1351		@XmlAttribute(name = "normaliseSequenceLogo")
1352		protected Boolean normaliseSequenceLogo;
1353		@XmlAttribute(name = "id")
1354		protected String id;
1355
1356		/**
1357		* Gets the value of the seq property.
1358		*
1359		* <p>
1360		* This accessor method returns a reference to the live list,
1361		* not a snapshot. Therefore any modification you make to the
1362		* returned list will be present inside the JAXB object.
1363		* This is why there is not a <CODE>set</CODE> method for the seq property.
1364		*
1365		* <p>
1366		* For example, to add a new item, do as follows:
1367		* <pre>
1368		* getSeq().add(newItem);
1369		* </pre>
1370		*
1371		*
1372		* <p>
1373		* Objects of the following type(s) are allowed in the list
1374		* {@link String }
1375		*
1376		*
1377		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
1378	775	public List<String> getSeq() {...
1379	775	if (seq == null) {
1380	13	seq = new ArrayList<String>();
1381		}
1382	775	return this.seq;
1383		}
1384
1385		/**
1386		* Gets the value of the annotationColours property.
1387		*
1388		* @return
1389		* possible object is
1390		* {@link AnnotationColourScheme }
1391		*
1392		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1393	2	public AnnotationColourScheme getAnnotationColours() {...
1394	2	return annotationColours;
1395		}
1396
1397		/**
1398		* Sets the value of the annotationColours property.
1399		*
1400		* @param value
1401		* allowed object is
1402		* {@link AnnotationColourScheme }
1403		*
1404		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1405	1	public void setAnnotationColours(AnnotationColourScheme value) {...
1406	1	this.annotationColours = value;
1407		}
1408
1409		/**
1410		* Gets the value of the start property.
1411		*
1412		* @return
1413		* possible object is
1414		* {@link Integer }
1415		*
1416		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1417	43	public Integer getStart() {...
1418	43	return start;
1419		}
1420
1421		/**
1422		* Sets the value of the start property.
1423		*
1424		* @param value
1425		* allowed object is
1426		* {@link Integer }
1427		*
1428		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1429	13	public void setStart(Integer value) {...
1430	13	this.start = value;
1431		}
1432
1433		/**
1434		* Gets the value of the end property.
1435		*
1436		* @return
1437		* possible object is
1438		* {@link Integer }
1439		*
1440		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1441	43	public Integer getEnd() {...
1442	43	return end;
1443		}
1444
1445		/**
1446		* Sets the value of the end property.
1447		*
1448		* @param value
1449		* allowed object is
1450		* {@link Integer }
1451		*
1452		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1453	13	public void setEnd(Integer value) {...
1454	13	this.end = value;
1455		}
1456
1457		/**
1458		* Gets the value of the name property.
1459		*
1460		* @return
1461		* possible object is
1462		* {@link String }
1463		*
1464		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1465	43	public String getName() {...
1466	43	return name;
1467		}
1468
1469		/**
1470		* Sets the value of the name property.
1471		*
1472		* @param value
1473		* allowed object is
1474		* {@link String }
1475		*
1476		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1477	13	public void setName(String value) {...
1478	13	this.name = value;
1479		}
1480
1481		/**
1482		* Gets the value of the colour property.
1483		*
1484		* @return
1485		* possible object is
1486		* {@link String }
1487		*
1488		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1489	99	public String getColour() {...
1490	99	return colour;
1491		}
1492
1493		/**
1494		* Sets the value of the colour property.
1495		*
1496		* @param value
1497		* allowed object is
1498		* {@link String }
1499		*
1500		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1501	7	public void setColour(String value) {...
1502	7	this.colour = value;
1503		}
1504
1505		/**
1506		* Gets the value of the consThreshold property.
1507		*
1508		* @return
1509		* possible object is
1510		* {@link Integer }
1511		*
1512		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1513	88	public Integer getConsThreshold() {...
1514	88	return consThreshold;
1515		}
1516
1517		/**
1518		* Sets the value of the consThreshold property.
1519		*
1520		* @param value
1521		* allowed object is
1522		* {@link Integer }
1523		*
1524		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1525	2	public void setConsThreshold(Integer value) {...
1526	2	this.consThreshold = value;
1527		}
1528
1529		/**
1530		* Gets the value of the pidThreshold property.
1531		*
1532		* @return
1533		* possible object is
1534		* {@link Integer }
1535		*
1536		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1537	43	public Integer getPidThreshold() {...
1538	43	return pidThreshold;
1539		}
1540
1541		/**
1542		* Sets the value of the pidThreshold property.
1543		*
1544		* @param value
1545		* allowed object is
1546		* {@link Integer }
1547		*
1548		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1549	7	public void setPidThreshold(Integer value) {...
1550	7	this.pidThreshold = value;
1551		}
1552
1553		/**
1554		* Gets the value of the outlineColour property.
1555		*
1556		* @return
1557		* possible object is
1558		* {@link Integer }
1559		*
1560		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1561	43	public Integer getOutlineColour() {...
1562	43	return outlineColour;
1563		}
1564
1565		/**
1566		* Sets the value of the outlineColour property.
1567		*
1568		* @param value
1569		* allowed object is
1570		* {@link Integer }
1571		*
1572		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1573	13	public void setOutlineColour(Integer value) {...
1574	13	this.outlineColour = value;
1575		}
1576
1577		/**
1578		* Gets the value of the displayBoxes property.
1579		*
1580		* @return
1581		* possible object is
1582		* {@link Boolean }
1583		*
1584		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1585	43	public Boolean isDisplayBoxes() {...
1586	43	return displayBoxes;
1587		}
1588
1589		/**
1590		* Sets the value of the displayBoxes property.
1591		*
1592		* @param value
1593		* allowed object is
1594		* {@link Boolean }
1595		*
1596		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1597	13	public void setDisplayBoxes(Boolean value) {...
1598	13	this.displayBoxes = value;
1599		}
1600
1601		/**
1602		* Gets the value of the displayText property.
1603		*
1604		* @return
1605		* possible object is
1606		* {@link Boolean }
1607		*
1608		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1609	43	public Boolean isDisplayText() {...
1610	43	return displayText;
1611		}
1612
1613		/**
1614		* Sets the value of the displayText property.
1615		*
1616		* @param value
1617		* allowed object is
1618		* {@link Boolean }
1619		*
1620		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1621	13	public void setDisplayText(Boolean value) {...
1622	13	this.displayText = value;
1623		}
1624
1625		/**
1626		* Gets the value of the colourText property.
1627		*
1628		* @return
1629		* possible object is
1630		* {@link Boolean }
1631		*
1632		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1633	43	public Boolean isColourText() {...
1634	43	return colourText;
1635		}
1636
1637		/**
1638		* Sets the value of the colourText property.
1639		*
1640		* @param value
1641		* allowed object is
1642		* {@link Boolean }
1643		*
1644		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1645	13	public void setColourText(Boolean value) {...
1646	13	this.colourText = value;
1647		}
1648
1649		/**
1650		* Gets the value of the textCol1 property.
1651		*
1652		* @return
1653		* possible object is
1654		* {@link Integer }
1655		*
1656		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1657	43	public Integer getTextCol1() {...
1658	43	return textCol1;
1659		}
1660
1661		/**
1662		* Sets the value of the textCol1 property.
1663		*
1664		* @param value
1665		* allowed object is
1666		* {@link Integer }
1667		*
1668		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1669	13	public void setTextCol1(Integer value) {...
1670	13	this.textCol1 = value;
1671		}
1672
1673		/**
1674		* Gets the value of the textCol2 property.
1675		*
1676		* @return
1677		* possible object is
1678		* {@link Integer }
1679		*
1680		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1681	43	public Integer getTextCol2() {...
1682	43	return textCol2;
1683		}
1684
1685		/**
1686		* Sets the value of the textCol2 property.
1687		*
1688		* @param value
1689		* allowed object is
1690		* {@link Integer }
1691		*
1692		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1693	13	public void setTextCol2(Integer value) {...
1694	13	this.textCol2 = value;
1695		}
1696
1697		/**
1698		* Gets the value of the textColThreshold property.
1699		*
1700		* @return
1701		* possible object is
1702		* {@link Integer }
1703		*
1704		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1705	43	public Integer getTextColThreshold() {...
1706	43	return textColThreshold;
1707		}
1708
1709		/**
1710		* Sets the value of the textColThreshold property.
1711		*
1712		* @param value
1713		* allowed object is
1714		* {@link Integer }
1715		*
1716		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1717	13	public void setTextColThreshold(Integer value) {...
1718	13	this.textColThreshold = value;
1719		}
1720
1721		/**
1722		* Gets the value of the showUnconserved property.
1723		*
1724		* @return
1725		* possible object is
1726		* {@link Boolean }
1727		*
1728		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1729	43	public Boolean isShowUnconserved() {...
1730	43	return showUnconserved;
1731		}
1732
1733		/**
1734		* Sets the value of the showUnconserved property.
1735		*
1736		* @param value
1737		* allowed object is
1738		* {@link Boolean }
1739		*
1740		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1741	13	public void setShowUnconserved(Boolean value) {...
1742	13	this.showUnconserved = value;
1743		}
1744
1745		/**
1746		* Gets the value of the ignoreGapsinConsensus property.
1747		*
1748		* @return
1749		* possible object is
1750		* {@link Boolean }
1751		*
1752		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
1753	43	public boolean isIgnoreGapsinConsensus() {...
1754	43	if (ignoreGapsinConsensus == null) {
1755	0	return true;
1756		} else {
1757	43	return ignoreGapsinConsensus;
1758		}
1759		}
1760
1761		/**
1762		* Sets the value of the ignoreGapsinConsensus property.
1763		*
1764		* @param value
1765		* allowed object is
1766		* {@link Boolean }
1767		*
1768		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1769	13	public void setIgnoreGapsinConsensus(Boolean value) {...
1770	13	this.ignoreGapsinConsensus = value;
1771		}
1772
1773		/**
1774		* Gets the value of the showConsensusHistogram property.
1775		*
1776		* @return
1777		* possible object is
1778		* {@link Boolean }
1779		*
1780		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
1781	43	public boolean isShowConsensusHistogram() {...
1782	43	if (showConsensusHistogram == null) {
1783	0	return true;
1784		} else {
1785	43	return showConsensusHistogram;
1786		}
1787		}
1788
1789		/**
1790		* Sets the value of the showConsensusHistogram property.
1791		*
1792		* @param value
1793		* allowed object is
1794		* {@link Boolean }
1795		*
1796		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1797	13	public void setShowConsensusHistogram(Boolean value) {...
1798	13	this.showConsensusHistogram = value;
1799		}
1800
1801		/**
1802		* Gets the value of the showSequenceLogo property.
1803		*
1804		* @return
1805		* possible object is
1806		* {@link Boolean }
1807		*
1808		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
1809	43	public boolean isShowSequenceLogo() {...
1810	43	if (showSequenceLogo == null) {
1811	0	return false;
1812		} else {
1813	43	return showSequenceLogo;
1814		}
1815		}
1816
1817		/**
1818		* Sets the value of the showSequenceLogo property.
1819		*
1820		* @param value
1821		* allowed object is
1822		* {@link Boolean }
1823		*
1824		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1825	13	public void setShowSequenceLogo(Boolean value) {...
1826	13	this.showSequenceLogo = value;
1827		}
1828
1829		/**
1830		* Gets the value of the normaliseSequenceLogo property.
1831		*
1832		* @return
1833		* possible object is
1834		* {@link Boolean }
1835		*
1836		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
1837	43	public boolean isNormaliseSequenceLogo() {...
1838	43	if (normaliseSequenceLogo == null) {
1839	30	return false;
1840		} else {
1841	13	return normaliseSequenceLogo;
1842		}
1843		}
1844
1845		/**
1846		* Sets the value of the normaliseSequenceLogo property.
1847		*
1848		* @param value
1849		* allowed object is
1850		* {@link Boolean }
1851		*
1852		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1853	13	public void setNormaliseSequenceLogo(Boolean value) {...
1854	13	this.normaliseSequenceLogo = value;
1855		}
1856
1857		/**
1858		* Gets the value of the id property.
1859		*
1860		* @return
1861		* possible object is
1862		* {@link String }
1863		*
1864		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1865	67	public String getId() {...
1866	67	return id;
1867		}
1868
1869		/**
1870		* Sets the value of the id property.
1871		*
1872		* @param value
1873		* allowed object is
1874		* {@link String }
1875		*
1876		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1877	6	public void setId(String value) {...
1878	6	this.id = value;
1879		}
1880
1881		}
1882
1883
1884		/**
1885		* <p>Java class for anonymous complex type.
1886		*
1887		* <p>The following schema fragment specifies the expected content contained within this class.
1888		*
1889		* <pre>
1890		* &lt;complexType>
1891		* &lt;complexContent>
1892		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1893		* &lt;sequence>
1894		* &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
1895		* &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
1896		* &lt;complexType>
1897		* &lt;complexContent>
1898		* &lt;extension base="{www.jalview.org}pdbentry">
1899		* &lt;sequence>
1900		* &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
1901		* &lt;complexType>
1902		* &lt;simpleContent>
1903		* &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
1904		* &lt;attGroup ref="{www.jalview.org}swingwindow"/>
1905		* &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1906		* &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1907		* &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1908		* &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1909		* &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1910		* &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
1911		* &lt;/extension>
1912		* &lt;/simpleContent>
1913		* &lt;/complexType>
1914		* &lt;/element>
1915		* &lt;/sequence>
1916		* &lt;/extension>
1917		* &lt;/complexContent>
1918		* &lt;/complexType>
1919		* &lt;/element>
1920		* &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
1921		* &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
1922		* &lt;complexType>
1923		* &lt;complexContent>
1924		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1925		* &lt;sequence>
1926		* &lt;element name="secondaryStructure" maxOccurs="unbounded">
1927		* &lt;complexType>
1928		* &lt;complexContent>
1929		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1930		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1931		* &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1932		* &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1933		* &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
1934		* &lt;/restriction>
1935		* &lt;/complexContent>
1936		* &lt;/complexType>
1937		* &lt;/element>
1938		* &lt;/sequence>
1939		* &lt;attGroup ref="{www.jalview.org}swingwindow"/>
1940		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1941		* &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1942		* &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
1943		* &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
1944		* &lt;/restriction>
1945		* &lt;/complexContent>
1946		* &lt;/complexType>
1947		* &lt;/element>
1948		* &lt;/sequence>
1949		* &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
1950		* &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1951		* &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1952		* &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1953		* &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1954		* &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1955		* &lt;/restriction>
1956		* &lt;/complexContent>
1957		* &lt;/complexType>
1958		* </pre>
1959		*
1960		*
1961		*/
1962		@XmlAccessorType(XmlAccessType.FIELD)
1963		@XmlType(name = "", propOrder = {
1964		"features",
1965		"pdbids",
1966		"hiddenSequences",
1967		"rnaViewer"
1968		})
		97.9% Uncovered Elements: 1 (48) Complexity: 20 Complexity Density: 0.83
1969		public static class JSeq {
1970
1971		@XmlElement(namespace = "www.jalview.org")
1972		protected List<Feature> features;
1973		@XmlElement(namespace = "www.jalview.org")
1974		protected List<JalviewModel.JSeq.Pdbids> pdbids;
1975		@XmlElement(namespace = "www.jalview.org", type = Integer.class)
1976		protected List<Integer> hiddenSequences;
1977		@XmlElement(namespace = "www.jalview.org")
1978		protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
1979		@XmlAttribute(name = "colour")
1980		protected Integer colour;
1981		@XmlAttribute(name = "start", required = true)
1982		protected int start;
1983		@XmlAttribute(name = "end", required = true)
1984		protected int end;
1985		@XmlAttribute(name = "id", required = true)
1986		protected String id;
1987		@XmlAttribute(name = "hidden")
1988		protected Boolean hidden;
1989		@XmlAttribute(name = "viewreference")
1990		protected Boolean viewreference;
1991
1992		/**
1993		* Gets the value of the features property.
1994		*
1995		* <p>
1996		* This accessor method returns a reference to the live list,
1997		* not a snapshot. Therefore any modification you make to the
1998		* returned list will be present inside the JAXB object.
1999		* This is why there is not a <CODE>set</CODE> method for the features property.
2000		*
2001		* <p>
2002		* For example, to add a new item, do as follows:
2003		* <pre>
2004		* getFeatures().add(newItem);
2005		* </pre>
2006		*
2007		*
2008		* <p>
2009		* Objects of the following type(s) are allowed in the list
2010		* {@link Feature }
2011		*
2012		*
2013		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
2014	11758	public List<Feature> getFeatures() {...
2015	11758	if (features == null) {
2016	708	features = new ArrayList<Feature>();
2017		}
2018	11758	return this.features;
2019		}
2020
2021		/**
2022		* Gets the value of the pdbids property.
2023		*
2024		* <p>
2025		* This accessor method returns a reference to the live list,
2026		* not a snapshot. Therefore any modification you make to the
2027		* returned list will be present inside the JAXB object.
2028		* This is why there is not a <CODE>set</CODE> method for the pdbids property.
2029		*
2030		* <p>
2031		* For example, to add a new item, do as follows:
2032		* <pre>
2033		* getPdbids().add(newItem);
2034		* </pre>
2035		*
2036		*
2037		* <p>
2038		* Objects of the following type(s) are allowed in the list
2039		* {@link JalviewModel.JSeq.Pdbids }
2040		*
2041		*
2042		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
2043	1879	public List<JalviewModel.JSeq.Pdbids> getPdbids() {...
2044	1879	if (pdbids == null) {
2045	1219	pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
2046		}
2047	1879	return this.pdbids;
2048		}
2049
2050		/**
2051		* Gets the value of the hiddenSequences property.
2052		*
2053		* <p>
2054		* This accessor method returns a reference to the live list,
2055		* not a snapshot. Therefore any modification you make to the
2056		* returned list will be present inside the JAXB object.
2057		* This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
2058		*
2059		* <p>
2060		* For example, to add a new item, do as follows:
2061		* <pre>
2062		* getHiddenSequences().add(newItem);
2063		* </pre>
2064		*
2065		*
2066		* <p>
2067		* Objects of the following type(s) are allowed in the list
2068		* {@link Integer }
2069		*
2070		*
2071		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
2072	676	public List<Integer> getHiddenSequences() {...
2073	676	if (hiddenSequences == null) {
2074	670	hiddenSequences = new ArrayList<Integer>();
2075		}
2076	676	return this.hiddenSequences;
2077		}
2078
2079		/**
2080		* Gets the value of the rnaViewer property.
2081		*
2082		* <p>
2083		* This accessor method returns a reference to the live list,
2084		* not a snapshot. Therefore any modification you make to the
2085		* returned list will be present inside the JAXB object.
2086		* This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
2087		*
2088		* <p>
2089		* For example, to add a new item, do as follows:
2090		* <pre>
2091		* getRnaViewer().add(newItem);
2092		* </pre>
2093		*
2094		*
2095		* <p>
2096		* Objects of the following type(s) are allowed in the list
2097		* {@link JalviewModel.JSeq.RnaViewer }
2098		*
2099		*
2100		*/
		80% Uncovered Elements: 1 (5) Complexity: 2 Complexity Density: 0.67
2101	975	public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {...
2102	975	if (rnaViewer == null) {
2103	975	rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2104		}
2105	975	return this.rnaViewer;
2106		}
2107
2108		/**
2109		* Gets the value of the colour property.
2110		*
2111		* @return
2112		* possible object is
2113		* {@link Integer }
2114		*
2115		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2116	1051	public Integer getColour() {...
2117	1051	return colour;
2118		}
2119
2120		/**
2121		* Sets the value of the colour property.
2122		*
2123		* @param value
2124		* allowed object is
2125		* {@link Integer }
2126		*
2127		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2128	669	public void setColour(Integer value) {...
2129	669	this.colour = value;
2130		}
2131
2132		/**
2133		* Gets the value of the start property.
2134		*
2135		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2136	2247	public int getStart() {...
2137	2247	return start;
2138		}
2139
2140		/**
2141		* Sets the value of the start property.
2142		*
2143		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2144	669	public void setStart(int value) {...
2145	669	this.start = value;
2146		}
2147
2148		/**
2149		* Gets the value of the end property.
2150		*
2151		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2152	2247	public int getEnd() {...
2153	2247	return end;
2154		}
2155
2156		/**
2157		* Sets the value of the end property.
2158		*
2159		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2160	669	public void setEnd(int value) {...
2161	669	this.end = value;
2162		}
2163
2164		/**
2165		* Gets the value of the id property.
2166		*
2167		* @return
2168		* possible object is
2169		* {@link String }
2170		*
2171		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2172	1380	public String getId() {...
2173	1380	return id;
2174		}
2175
2176		/**
2177		* Sets the value of the id property.
2178		*
2179		* @param value
2180		* allowed object is
2181		* {@link String }
2182		*
2183		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2184	669	public void setId(String value) {...
2185	669	this.id = value;
2186		}
2187
2188		/**
2189		* Gets the value of the hidden property.
2190		*
2191		* @return
2192		* possible object is
2193		* {@link Boolean }
2194		*
2195		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2196	1970	public Boolean isHidden() {...
2197	1970	return hidden;
2198		}
2199
2200		/**
2201		* Sets the value of the hidden property.
2202		*
2203		* @param value
2204		* allowed object is
2205		* {@link Boolean }
2206		*
2207		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2208	190	public void setHidden(Boolean value) {...
2209	190	this.hidden = value;
2210		}
2211
2212		/**
2213		* Gets the value of the viewreference property.
2214		*
2215		* @return
2216		* possible object is
2217		* {@link Boolean }
2218		*
2219		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2220	1300	public Boolean isViewreference() {...
2221	1300	return viewreference;
2222		}
2223
2224		/**
2225		* Sets the value of the viewreference property.
2226		*
2227		* @param value
2228		* allowed object is
2229		* {@link Boolean }
2230		*
2231		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2232	80	public void setViewreference(Boolean value) {...
2233	80	this.viewreference = value;
2234		}
2235
2236
2237		/**
2238		* <p>Java class for anonymous complex type.
2239		*
2240		* <p>The following schema fragment specifies the expected content contained within this class.
2241		*
2242		* <pre>
2243		* &lt;complexType>
2244		* &lt;complexContent>
2245		* &lt;extension base="{www.jalview.org}pdbentry">
2246		* &lt;sequence>
2247		* &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
2248		* &lt;complexType>
2249		* &lt;simpleContent>
2250		* &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
2251		* &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2252		* &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2253		* &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2254		* &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2255		* &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2256		* &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2257		* &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2258		* &lt;/extension>
2259		* &lt;/simpleContent>
2260		* &lt;/complexType>
2261		* &lt;/element>
2262		* &lt;/sequence>
2263		* &lt;/extension>
2264		* &lt;/complexContent>
2265		* &lt;/complexType>
2266		* </pre>
2267		*
2268		*
2269		*/
2270		@XmlAccessorType(XmlAccessType.FIELD)
2271		@XmlType(name = "", propOrder = {
2272		"structureState"
2273		})
		100% Uncovered Elements: 0 (6) Complexity: 2 Complexity Density: 0.67
2274		public static class Pdbids
2275		extends Pdbentry
2276		{
2277
2278		@XmlElement(namespace = "www.jalview.org")
2279		protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2280
2281		/**
2282		* Gets the value of the structureState property.
2283		*
2284		* <p>
2285		* This accessor method returns a reference to the live list,
2286		* not a snapshot. Therefore any modification you make to the
2287		* returned list will be present inside the JAXB object.
2288		* This is why there is not a <CODE>set</CODE> method for the structureState property.
2289		*
2290		* <p>
2291		* For example, to add a new item, do as follows:
2292		* <pre>
2293		* getStructureState().add(newItem);
2294		* </pre>
2295		*
2296		*
2297		* <p>
2298		* Objects of the following type(s) are allowed in the list
2299		* {@link JalviewModel.JSeq.Pdbids.StructureState }
2300		*
2301		*
2302		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
2303	297	public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {...
2304	297	if (structureState == null) {
2305	137	structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2306		}
2307	297	return this.structureState;
2308		}
2309
2310
2311		/**
2312		* <p>Java class for anonymous complex type.
2313		*
2314		* <p>The following schema fragment specifies the expected content contained within this class.
2315		*
2316		* <pre>
2317		* &lt;complexType>
2318		* &lt;simpleContent>
2319		* &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
2320		* &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2321		* &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2322		* &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2323		* &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2324		* &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2325		* &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2326		* &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2327		* &lt;/extension>
2328		* &lt;/simpleContent>
2329		* &lt;/complexType>
2330		* </pre>
2331		*
2332		*
2333		*/
2334		@XmlAccessorType(XmlAccessType.FIELD)
2335		@XmlType(name = "", propOrder = {
2336		"value"
2337		})
		82.1% Uncovered Elements: 10 (56) Complexity: 25 Complexity Density: 0.89
2338		public static class StructureState {
2339
2340		@XmlValue
2341		protected String value;
2342		@XmlAttribute(name = "visible")
2343		protected Boolean visible;
2344		@XmlAttribute(name = "viewId")
2345		protected String viewId;
2346		@XmlAttribute(name = "alignwithAlignPanel")
2347		protected Boolean alignwithAlignPanel;
2348		@XmlAttribute(name = "colourwithAlignPanel")
2349		protected Boolean colourwithAlignPanel;
2350		@XmlAttribute(name = "colourByJmol")
2351		protected Boolean colourByJmol;
2352		@XmlAttribute(name = "type")
2353		protected String type;
2354		@XmlAttribute(name = "width")
2355		protected Integer width;
2356		@XmlAttribute(name = "height")
2357		protected Integer height;
2358		@XmlAttribute(name = "xpos")
2359		protected Integer xpos;
2360		@XmlAttribute(name = "ypos")
2361		protected Integer ypos;
2362
2363		/**
2364		* Gets the value of the value property.
2365		*
2366		* @return
2367		* possible object is
2368		* {@link String }
2369		*
2370		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2371	110	public String getValue() {...
2372	110	return value;
2373		}
2374
2375		/**
2376		* Sets the value of the value property.
2377		*
2378		* @param value
2379		* allowed object is
2380		* {@link String }
2381		*
2382		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2383	0	public void setValue(String value) {...
2384	0	this.value = value;
2385		}
2386
2387		/**
2388		* Gets the value of the visible property.
2389		*
2390		* @return
2391		* possible object is
2392		* {@link Boolean }
2393		*
2394		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2395	0	public Boolean isVisible() {...
2396	0	return visible;
2397		}
2398
2399		/**
2400		* Sets the value of the visible property.
2401		*
2402		* @param value
2403		* allowed object is
2404		* {@link Boolean }
2405		*
2406		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2407	20	public void setVisible(Boolean value) {...
2408	20	this.visible = value;
2409		}
2410
2411		/**
2412		* Gets the value of the viewId property.
2413		*
2414		* @return
2415		* possible object is
2416		* {@link String }
2417		*
2418		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2419	200	public String getViewId() {...
2420	200	return viewId;
2421		}
2422
2423		/**
2424		* Sets the value of the viewId property.
2425		*
2426		* @param value
2427		* allowed object is
2428		* {@link String }
2429		*
2430		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2431	20	public void setViewId(String value) {...
2432	20	this.viewId = value;
2433		}
2434
2435		/**
2436		* Gets the value of the alignwithAlignPanel property.
2437		*
2438		* @return
2439		* possible object is
2440		* {@link Boolean }
2441		*
2442		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
2443	80	public boolean isAlignwithAlignPanel() {...
2444	80	if (alignwithAlignPanel == null) {
2445	0	return true;
2446		} else {
2447	80	return alignwithAlignPanel;
2448		}
2449		}
2450
2451		/**
2452		* Sets the value of the alignwithAlignPanel property.
2453		*
2454		* @param value
2455		* allowed object is
2456		* {@link Boolean }
2457		*
2458		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2459	20	public void setAlignwithAlignPanel(Boolean value) {...
2460	20	this.alignwithAlignPanel = value;
2461		}
2462
2463		/**
2464		* Gets the value of the colourwithAlignPanel property.
2465		*
2466		* @return
2467		* possible object is
2468		* {@link Boolean }
2469		*
2470		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
2471	80	public boolean isColourwithAlignPanel() {...
2472	80	if (colourwithAlignPanel == null) {
2473	0	return false;
2474		} else {
2475	80	return colourwithAlignPanel;
2476		}
2477		}
2478
2479		/**
2480		* Sets the value of the colourwithAlignPanel property.
2481		*
2482		* @param value
2483		* allowed object is
2484		* {@link Boolean }
2485		*
2486		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2487	20	public void setColourwithAlignPanel(Boolean value) {...
2488	20	this.colourwithAlignPanel = value;
2489		}
2490
2491		/**
2492		* Gets the value of the colourByJmol property.
2493		*
2494		* @return
2495		* possible object is
2496		* {@link Boolean }
2497		*
2498		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
2499	80	public boolean isColourByJmol() {...
2500	80	if (colourByJmol == null) {
2501	0	return true;
2502		} else {
2503	80	return colourByJmol;
2504		}
2505		}
2506
2507		/**
2508		* Sets the value of the colourByJmol property.
2509		*
2510		* @param value
2511		* allowed object is
2512		* {@link Boolean }
2513		*
2514		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2515	20	public void setColourByJmol(Boolean value) {...
2516	20	this.colourByJmol = value;
2517		}
2518
2519		/**
2520		* Gets the value of the type property.
2521		*
2522		* @return
2523		* possible object is
2524		* {@link String }
2525		*
2526		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2527	40	public String getType() {...
2528	40	return type;
2529		}
2530
2531		/**
2532		* Sets the value of the type property.
2533		*
2534		* @param value
2535		* allowed object is
2536		* {@link String }
2537		*
2538		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2539	20	public void setType(String value) {...
2540	20	this.type = value;
2541		}
2542
2543		/**
2544		* Gets the value of the width property.
2545		*
2546		* @return
2547		* possible object is
2548		* {@link Integer }
2549		*
2550		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2551	80	public Integer getWidth() {...
2552	80	return width;
2553		}
2554
2555		/**
2556		* Sets the value of the width property.
2557		*
2558		* @param value
2559		* allowed object is
2560		* {@link Integer }
2561		*
2562		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2563	20	public void setWidth(Integer value) {...
2564	20	this.width = value;
2565		}
2566
2567		/**
2568		* Gets the value of the height property.
2569		*
2570		* @return
2571		* possible object is
2572		* {@link Integer }
2573		*
2574		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2575	80	public Integer getHeight() {...
2576	80	return height;
2577		}
2578
2579		/**
2580		* Sets the value of the height property.
2581		*
2582		* @param value
2583		* allowed object is
2584		* {@link Integer }
2585		*
2586		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2587	20	public void setHeight(Integer value) {...
2588	20	this.height = value;
2589		}
2590
2591		/**
2592		* Gets the value of the xpos property.
2593		*
2594		* @return
2595		* possible object is
2596		* {@link Integer }
2597		*
2598		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2599	80	public Integer getXpos() {...
2600	80	return xpos;
2601		}
2602
2603		/**
2604		* Sets the value of the xpos property.
2605		*
2606		* @param value
2607		* allowed object is
2608		* {@link Integer }
2609		*
2610		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2611	20	public void setXpos(Integer value) {...
2612	20	this.xpos = value;
2613		}
2614
2615		/**
2616		* Gets the value of the ypos property.
2617		*
2618		* @return
2619		* possible object is
2620		* {@link Integer }
2621		*
2622		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2623	80	public Integer getYpos() {...
2624	80	return ypos;
2625		}
2626
2627		/**
2628		* Sets the value of the ypos property.
2629		*
2630		* @param value
2631		* allowed object is
2632		* {@link Integer }
2633		*
2634		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2635	20	public void setYpos(Integer value) {...
2636	20	this.ypos = value;
2637		}
2638
2639		}
2640
2641		}
2642
2643
2644		/**
2645		* <p>Java class for anonymous complex type.
2646		*
2647		* <p>The following schema fragment specifies the expected content contained within this class.
2648		*
2649		* <pre>
2650		* &lt;complexType>
2651		* &lt;complexContent>
2652		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2653		* &lt;sequence>
2654		* &lt;element name="secondaryStructure" maxOccurs="unbounded">
2655		* &lt;complexType>
2656		* &lt;complexContent>
2657		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2658		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2659		* &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2660		* &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2661		* &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2662		* &lt;/restriction>
2663		* &lt;/complexContent>
2664		* &lt;/complexType>
2665		* &lt;/element>
2666		* &lt;/sequence>
2667		* &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2668		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2669		* &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2670		* &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
2671		* &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
2672		* &lt;/restriction>
2673		* &lt;/complexContent>
2674		* &lt;/complexType>
2675		* </pre>
2676		*
2677		*
2678		*/
2679		@XmlAccessorType(XmlAccessType.FIELD)
2680		@XmlType(name = "", propOrder = {
2681		"secondaryStructure"
2682		})
		0% Uncovered Elements: 38 (38) Complexity: 18 Complexity Density: 0.95
2683		public static class RnaViewer {
2684
2685		@XmlElement(namespace = "www.jalview.org", required = true)
2686		protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
2687		@XmlAttribute(name = "title")
2688		protected String title;
2689		@XmlAttribute(name = "viewId")
2690		protected String viewId;
2691		@XmlAttribute(name = "dividerLocation")
2692		protected Integer dividerLocation;
2693		@XmlAttribute(name = "selectedRna")
2694		protected Integer selectedRna;
2695		@XmlAttribute(name = "width")
2696		protected Integer width;
2697		@XmlAttribute(name = "height")
2698		protected Integer height;
2699		@XmlAttribute(name = "xpos")
2700		protected Integer xpos;
2701		@XmlAttribute(name = "ypos")
2702		protected Integer ypos;
2703
2704		/**
2705		* Gets the value of the secondaryStructure property.
2706		*
2707		* <p>
2708		* This accessor method returns a reference to the live list,
2709		* not a snapshot. Therefore any modification you make to the
2710		* returned list will be present inside the JAXB object.
2711		* This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
2712		*
2713		* <p>
2714		* For example, to add a new item, do as follows:
2715		* <pre>
2716		* getSecondaryStructure().add(newItem);
2717		* </pre>
2718		*
2719		*
2720		* <p>
2721		* Objects of the following type(s) are allowed in the list
2722		* {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
2723		*
2724		*
2725		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
2726	0	public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {...
2727	0	if (secondaryStructure == null) {
2728	0	secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
2729		}
2730	0	return this.secondaryStructure;
2731		}
2732
2733		/**
2734		* Gets the value of the title property.
2735		*
2736		* @return
2737		* possible object is
2738		* {@link String }
2739		*
2740		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2741	0	public String getTitle() {...
2742	0	return title;
2743		}
2744
2745		/**
2746		* Sets the value of the title property.
2747		*
2748		* @param value
2749		* allowed object is
2750		* {@link String }
2751		*
2752		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2753	0	public void setTitle(String value) {...
2754	0	this.title = value;
2755		}
2756
2757		/**
2758		* Gets the value of the viewId property.
2759		*
2760		* @return
2761		* possible object is
2762		* {@link String }
2763		*
2764		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2765	0	public String getViewId() {...
2766	0	return viewId;
2767		}
2768
2769		/**
2770		* Sets the value of the viewId property.
2771		*
2772		* @param value
2773		* allowed object is
2774		* {@link String }
2775		*
2776		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2777	0	public void setViewId(String value) {...
2778	0	this.viewId = value;
2779		}
2780
2781		/**
2782		* Gets the value of the dividerLocation property.
2783		*
2784		* @return
2785		* possible object is
2786		* {@link Integer }
2787		*
2788		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2789	0	public Integer getDividerLocation() {...
2790	0	return dividerLocation;
2791		}
2792
2793		/**
2794		* Sets the value of the dividerLocation property.
2795		*
2796		* @param value
2797		* allowed object is
2798		* {@link Integer }
2799		*
2800		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2801	0	public void setDividerLocation(Integer value) {...
2802	0	this.dividerLocation = value;
2803		}
2804
2805		/**
2806		* Gets the value of the selectedRna property.
2807		*
2808		* @return
2809		* possible object is
2810		* {@link Integer }
2811		*
2812		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2813	0	public Integer getSelectedRna() {...
2814	0	return selectedRna;
2815		}
2816
2817		/**
2818		* Sets the value of the selectedRna property.
2819		*
2820		* @param value
2821		* allowed object is
2822		* {@link Integer }
2823		*
2824		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2825	0	public void setSelectedRna(Integer value) {...
2826	0	this.selectedRna = value;
2827		}
2828
2829		/**
2830		* Gets the value of the width property.
2831		*
2832		* @return
2833		* possible object is
2834		* {@link Integer }
2835		*
2836		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2837	0	public Integer getWidth() {...
2838	0	return width;
2839		}
2840
2841		/**
2842		* Sets the value of the width property.
2843		*
2844		* @param value
2845		* allowed object is
2846		* {@link Integer }
2847		*
2848		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2849	0	public void setWidth(Integer value) {...
2850	0	this.width = value;
2851		}
2852
2853		/**
2854		* Gets the value of the height property.
2855		*
2856		* @return
2857		* possible object is
2858		* {@link Integer }
2859		*
2860		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2861	0	public Integer getHeight() {...
2862	0	return height;
2863		}
2864
2865		/**
2866		* Sets the value of the height property.
2867		*
2868		* @param value
2869		* allowed object is
2870		* {@link Integer }
2871		*
2872		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2873	0	public void setHeight(Integer value) {...
2874	0	this.height = value;
2875		}
2876
2877		/**
2878		* Gets the value of the xpos property.
2879		*
2880		* @return
2881		* possible object is
2882		* {@link Integer }
2883		*
2884		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2885	0	public Integer getXpos() {...
2886	0	return xpos;
2887		}
2888
2889		/**
2890		* Sets the value of the xpos property.
2891		*
2892		* @param value
2893		* allowed object is
2894		* {@link Integer }
2895		*
2896		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2897	0	public void setXpos(Integer value) {...
2898	0	this.xpos = value;
2899		}
2900
2901		/**
2902		* Gets the value of the ypos property.
2903		*
2904		* @return
2905		* possible object is
2906		* {@link Integer }
2907		*
2908		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2909	0	public Integer getYpos() {...
2910	0	return ypos;
2911		}
2912
2913		/**
2914		* Sets the value of the ypos property.
2915		*
2916		* @param value
2917		* allowed object is
2918		* {@link Integer }
2919		*
2920		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2921	0	public void setYpos(Integer value) {...
2922	0	this.ypos = value;
2923		}
2924
2925
2926		/**
2927		* <p>Java class for anonymous complex type.
2928		*
2929		* <p>The following schema fragment specifies the expected content contained within this class.
2930		*
2931		* <pre>
2932		* &lt;complexType>
2933		* &lt;complexContent>
2934		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2935		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2936		* &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2937		* &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2938		* &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2939		* &lt;/restriction>
2940		* &lt;/complexContent>
2941		* &lt;/complexType>
2942		* </pre>
2943		*
2944		*
2945		*/
2946		@XmlAccessorType(XmlAccessType.FIELD)
2947		@XmlType(name = "")
		0% Uncovered Elements: 16 (16) Complexity: 8 Complexity Density: 1
2948		public static class SecondaryStructure {
2949
2950		@XmlAttribute(name = "title")
2951		protected String title;
2952		@XmlAttribute(name = "annotationId", required = true)
2953		protected String annotationId;
2954		@XmlAttribute(name = "gapped")
2955		protected Boolean gapped;
2956		@XmlAttribute(name = "viewerState")
2957		protected String viewerState;
2958
2959		/**
2960		* Gets the value of the title property.
2961		*
2962		* @return
2963		* possible object is
2964		* {@link String }
2965		*
2966		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2967	0	public String getTitle() {...
2968	0	return title;
2969		}
2970
2971		/**
2972		* Sets the value of the title property.
2973		*
2974		* @param value
2975		* allowed object is
2976		* {@link String }
2977		*
2978		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2979	0	public void setTitle(String value) {...
2980	0	this.title = value;
2981		}
2982
2983		/**
2984		* Gets the value of the annotationId property.
2985		*
2986		* @return
2987		* possible object is
2988		* {@link String }
2989		*
2990		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2991	0	public String getAnnotationId() {...
2992	0	return annotationId;
2993		}
2994
2995		/**
2996		* Sets the value of the annotationId property.
2997		*
2998		* @param value
2999		* allowed object is
3000		* {@link String }
3001		*
3002		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3003	0	public void setAnnotationId(String value) {...
3004	0	this.annotationId = value;
3005		}
3006
3007		/**
3008		* Gets the value of the gapped property.
3009		*
3010		* @return
3011		* possible object is
3012		* {@link Boolean }
3013		*
3014		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3015	0	public Boolean isGapped() {...
3016	0	return gapped;
3017		}
3018
3019		/**
3020		* Sets the value of the gapped property.
3021		*
3022		* @param value
3023		* allowed object is
3024		* {@link Boolean }
3025		*
3026		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3027	0	public void setGapped(Boolean value) {...
3028	0	this.gapped = value;
3029		}
3030
3031		/**
3032		* Gets the value of the viewerState property.
3033		*
3034		* @return
3035		* possible object is
3036		* {@link String }
3037		*
3038		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3039	0	public String getViewerState() {...
3040	0	return viewerState;
3041		}
3042
3043		/**
3044		* Sets the value of the viewerState property.
3045		*
3046		* @param value
3047		* allowed object is
3048		* {@link String }
3049		*
3050		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3051	0	public void setViewerState(String value) {...
3052	0	this.viewerState = value;
3053		}
3054
3055		}
3056
3057		}
3058
3059		}
3060
3061
3062		/**
3063		* <p>Java class for anonymous complex type.
3064		*
3065		* <p>The following schema fragment specifies the expected content contained within this class.
3066		*
3067		* <pre>
3068		* &lt;complexType>
3069		* &lt;complexContent>
3070		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3071		* &lt;sequence>
3072		* &lt;element name="sequencePoint" maxOccurs="unbounded">
3073		* &lt;complexType>
3074		* &lt;complexContent>
3075		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3076		* &lt;attGroup ref="{www.jalview.org}position"/>
3077		* &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
3078		* &lt;/restriction>
3079		* &lt;/complexContent>
3080		* &lt;/complexType>
3081		* &lt;/element>
3082		* &lt;element name="axis" maxOccurs="3" minOccurs="3">
3083		* &lt;complexType>
3084		* &lt;complexContent>
3085		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3086		* &lt;attGroup ref="{www.jalview.org}position"/>
3087		* &lt;/restriction>
3088		* &lt;/complexContent>
3089		* &lt;/complexType>
3090		* &lt;/element>
3091		* &lt;element name="seqPointMin">
3092		* &lt;complexType>
3093		* &lt;complexContent>
3094		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3095		* &lt;attGroup ref="{www.jalview.org}position"/>
3096		* &lt;/restriction>
3097		* &lt;/complexContent>
3098		* &lt;/complexType>
3099		* &lt;/element>
3100		* &lt;element name="seqPointMax">
3101		* &lt;complexType>
3102		* &lt;complexContent>
3103		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3104		* &lt;attGroup ref="{www.jalview.org}position"/>
3105		* &lt;/restriction>
3106		* &lt;/complexContent>
3107		* &lt;/complexType>
3108		* &lt;/element>
3109		* &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/>
3110		* &lt;/sequence>
3111		* &lt;attGroup ref="{www.jalview.org}swingwindow"/>
3112		* &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
3113		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
3114		* &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
3115		* &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3116		* &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3117		* &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3118		* &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
3119		* &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
3120		* &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3121		* &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3122		* &lt;/restriction>
3123		* &lt;/complexContent>
3124		* &lt;/complexType>
3125		* </pre>
3126		*
3127		*
3128		*/
3129		@XmlAccessorType(XmlAccessType.FIELD)
3130		@XmlType(name = "", propOrder = {
3131		"sequencePoint",
3132		"axis",
3133		"seqPointMin",
3134		"seqPointMax",
3135		"pcaData"
3136		})
		100% Uncovered Elements: 0 (92) Complexity: 44 Complexity Density: 0.96
3137		public static class PcaViewer {
3138
3139		@XmlElement(namespace = "www.jalview.org", required = true)
3140		protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
3141		@XmlElement(namespace = "www.jalview.org", required = true)
3142		protected List<JalviewModel.PcaViewer.Axis> axis;
3143		@XmlElement(namespace = "www.jalview.org", required = true)
3144		protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
3145		@XmlElement(namespace = "www.jalview.org", required = true)
3146		protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
3147		@XmlElement(namespace = "www.jalview.org", required = true)
3148		protected PcaDataType pcaData;
3149		@XmlAttribute(name = "title")
3150		protected String title;
3151		@XmlAttribute(name = "scoreModelName")
3152		protected String scoreModelName;
3153		@XmlAttribute(name = "xDim")
3154		protected Integer xDim;
3155		@XmlAttribute(name = "yDim")
3156		protected Integer yDim;
3157		@XmlAttribute(name = "zDim")
3158		protected Integer zDim;
3159		@XmlAttribute(name = "bgColour")
3160		protected Integer bgColour;
3161		@XmlAttribute(name = "scaleFactor")
3162		protected Float scaleFactor;
3163		@XmlAttribute(name = "showLabels")
3164		protected Boolean showLabels;
3165		@XmlAttribute(name = "linkToAllViews")
3166		protected Boolean linkToAllViews;
3167		@XmlAttribute(name = "width")
3168		protected Integer width;
3169		@XmlAttribute(name = "height")
3170		protected Integer height;
3171		@XmlAttribute(name = "xpos")
3172		protected Integer xpos;
3173		@XmlAttribute(name = "ypos")
3174		protected Integer ypos;
3175		@XmlAttribute(name = "includeGaps")
3176		protected Boolean includeGaps;
3177		@XmlAttribute(name = "matchGaps")
3178		protected Boolean matchGaps;
3179		@XmlAttribute(name = "includeGappedColumns")
3180		protected Boolean includeGappedColumns;
3181		@XmlAttribute(name = "denominateByShortestLength")
3182		protected Boolean denominateByShortestLength;
3183
3184		/**
3185		* Gets the value of the sequencePoint property.
3186		*
3187		* <p>
3188		* This accessor method returns a reference to the live list,
3189		* not a snapshot. Therefore any modification you make to the
3190		* returned list will be present inside the JAXB object.
3191		* This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
3192		*
3193		* <p>
3194		* For example, to add a new item, do as follows:
3195		* <pre>
3196		* getSequencePoint().add(newItem);
3197		* </pre>
3198		*
3199		*
3200		* <p>
3201		* Objects of the following type(s) are allowed in the list
3202		* {@link JalviewModel.PcaViewer.SequencePoint }
3203		*
3204		*
3205		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
3206	16	public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {...
3207	16	if (sequencePoint == null) {
3208	1	sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
3209		}
3210	16	return this.sequencePoint;
3211		}
3212
3213		/**
3214		* Gets the value of the axis property.
3215		*
3216		* <p>
3217		* This accessor method returns a reference to the live list,
3218		* not a snapshot. Therefore any modification you make to the
3219		* returned list will be present inside the JAXB object.
3220		* This is why there is not a <CODE>set</CODE> method for the axis property.
3221		*
3222		* <p>
3223		* For example, to add a new item, do as follows:
3224		* <pre>
3225		* getAxis().add(newItem);
3226		* </pre>
3227		*
3228		*
3229		* <p>
3230		* Objects of the following type(s) are allowed in the list
3231		* {@link JalviewModel.PcaViewer.Axis }
3232		*
3233		*
3234		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
3235	6	public List<JalviewModel.PcaViewer.Axis> getAxis() {...
3236	6	if (axis == null) {
3237	1	axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
3238		}
3239	6	return this.axis;
3240		}
3241
3242		/**
3243		* Gets the value of the seqPointMin property.
3244		*
3245		* @return
3246		* possible object is
3247		* {@link JalviewModel.PcaViewer.SeqPointMin }
3248		*
3249		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3250	1	public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {...
3251	1	return seqPointMin;
3252		}
3253
3254		/**
3255		* Sets the value of the seqPointMin property.
3256		*
3257		* @param value
3258		* allowed object is
3259		* {@link JalviewModel.PcaViewer.SeqPointMin }
3260		*
3261		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3262	1	public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {...
3263	1	this.seqPointMin = value;
3264		}
3265
3266		/**
3267		* Gets the value of the seqPointMax property.
3268		*
3269		* @return
3270		* possible object is
3271		* {@link JalviewModel.PcaViewer.SeqPointMax }
3272		*
3273		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3274	1	public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {...
3275	1	return seqPointMax;
3276		}
3277
3278		/**
3279		* Sets the value of the seqPointMax property.
3280		*
3281		* @param value
3282		* allowed object is
3283		* {@link JalviewModel.PcaViewer.SeqPointMax }
3284		*
3285		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3286	1	public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {...
3287	1	this.seqPointMax = value;
3288		}
3289
3290		/**
3291		* Gets the value of the pcaData property.
3292		*
3293		* @return
3294		* possible object is
3295		* {@link PcaDataType }
3296		*
3297		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3298	1	public PcaDataType getPcaData() {...
3299	1	return pcaData;
3300		}
3301
3302		/**
3303		* Sets the value of the pcaData property.
3304		*
3305		* @param value
3306		* allowed object is
3307		* {@link PcaDataType }
3308		*
3309		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3310	1	public void setPcaData(PcaDataType value) {...
3311	1	this.pcaData = value;
3312		}
3313
3314		/**
3315		* Gets the value of the title property.
3316		*
3317		* @return
3318		* possible object is
3319		* {@link String }
3320		*
3321		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3322	1	public String getTitle() {...
3323	1	return title;
3324		}
3325
3326		/**
3327		* Sets the value of the title property.
3328		*
3329		* @param value
3330		* allowed object is
3331		* {@link String }
3332		*
3333		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3334	1	public void setTitle(String value) {...
3335	1	this.title = value;
3336		}
3337
3338		/**
3339		* Gets the value of the scoreModelName property.
3340		*
3341		* @return
3342		* possible object is
3343		* {@link String }
3344		*
3345		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3346	1	public String getScoreModelName() {...
3347	1	return scoreModelName;
3348		}
3349
3350		/**
3351		* Sets the value of the scoreModelName property.
3352		*
3353		* @param value
3354		* allowed object is
3355		* {@link String }
3356		*
3357		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3358	1	public void setScoreModelName(String value) {...
3359	1	this.scoreModelName = value;
3360		}
3361
3362		/**
3363		* Gets the value of the xDim property.
3364		*
3365		* @return
3366		* possible object is
3367		* {@link Integer }
3368		*
3369		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3370	1	public Integer getXDim() {...
3371	1	return xDim;
3372		}
3373
3374		/**
3375		* Sets the value of the xDim property.
3376		*
3377		* @param value
3378		* allowed object is
3379		* {@link Integer }
3380		*
3381		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3382	1	public void setXDim(Integer value) {...
3383	1	this.xDim = value;
3384		}
3385
3386		/**
3387		* Gets the value of the yDim property.
3388		*
3389		* @return
3390		* possible object is
3391		* {@link Integer }
3392		*
3393		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3394	1	public Integer getYDim() {...
3395	1	return yDim;
3396		}
3397
3398		/**
3399		* Sets the value of the yDim property.
3400		*
3401		* @param value
3402		* allowed object is
3403		* {@link Integer }
3404		*
3405		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3406	1	public void setYDim(Integer value) {...
3407	1	this.yDim = value;
3408		}
3409
3410		/**
3411		* Gets the value of the zDim property.
3412		*
3413		* @return
3414		* possible object is
3415		* {@link Integer }
3416		*
3417		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3418	1	public Integer getZDim() {...
3419	1	return zDim;
3420		}
3421
3422		/**
3423		* Sets the value of the zDim property.
3424		*
3425		* @param value
3426		* allowed object is
3427		* {@link Integer }
3428		*
3429		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3430	1	public void setZDim(Integer value) {...
3431	1	this.zDim = value;
3432		}
3433
3434		/**
3435		* Gets the value of the bgColour property.
3436		*
3437		* @return
3438		* possible object is
3439		* {@link Integer }
3440		*
3441		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3442	1	public Integer getBgColour() {...
3443	1	return bgColour;
3444		}
3445
3446		/**
3447		* Sets the value of the bgColour property.
3448		*
3449		* @param value
3450		* allowed object is
3451		* {@link Integer }
3452		*
3453		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3454	1	public void setBgColour(Integer value) {...
3455	1	this.bgColour = value;
3456		}
3457
3458		/**
3459		* Gets the value of the scaleFactor property.
3460		*
3461		* @return
3462		* possible object is
3463		* {@link Float }
3464		*
3465		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3466	1	public Float getScaleFactor() {...
3467	1	return scaleFactor;
3468		}
3469
3470		/**
3471		* Sets the value of the scaleFactor property.
3472		*
3473		* @param value
3474		* allowed object is
3475		* {@link Float }
3476		*
3477		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3478	1	public void setScaleFactor(Float value) {...
3479	1	this.scaleFactor = value;
3480		}
3481
3482		/**
3483		* Gets the value of the showLabels property.
3484		*
3485		* @return
3486		* possible object is
3487		* {@link Boolean }
3488		*
3489		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3490	1	public Boolean isShowLabels() {...
3491	1	return showLabels;
3492		}
3493
3494		/**
3495		* Sets the value of the showLabels property.
3496		*
3497		* @param value
3498		* allowed object is
3499		* {@link Boolean }
3500		*
3501		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3502	1	public void setShowLabels(Boolean value) {...
3503	1	this.showLabels = value;
3504		}
3505
3506		/**
3507		* Gets the value of the linkToAllViews property.
3508		*
3509		* @return
3510		* possible object is
3511		* {@link Boolean }
3512		*
3513		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3514	1	public Boolean isLinkToAllViews() {...
3515	1	return linkToAllViews;
3516		}
3517
3518		/**
3519		* Sets the value of the linkToAllViews property.
3520		*
3521		* @param value
3522		* allowed object is
3523		* {@link Boolean }
3524		*
3525		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3526	1	public void setLinkToAllViews(Boolean value) {...
3527	1	this.linkToAllViews = value;
3528		}
3529
3530		/**
3531		* Gets the value of the width property.
3532		*
3533		* @return
3534		* possible object is
3535		* {@link Integer }
3536		*
3537		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3538	1	public Integer getWidth() {...
3539	1	return width;
3540		}
3541
3542		/**
3543		* Sets the value of the width property.
3544		*
3545		* @param value
3546		* allowed object is
3547		* {@link Integer }
3548		*
3549		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3550	1	public void setWidth(Integer value) {...
3551	1	this.width = value;
3552		}
3553
3554		/**
3555		* Gets the value of the height property.
3556		*
3557		* @return
3558		* possible object is
3559		* {@link Integer }
3560		*
3561		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3562	1	public Integer getHeight() {...
3563	1	return height;
3564		}
3565
3566		/**
3567		* Sets the value of the height property.
3568		*
3569		* @param value
3570		* allowed object is
3571		* {@link Integer }
3572		*
3573		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3574	1	public void setHeight(Integer value) {...
3575	1	this.height = value;
3576		}
3577
3578		/**
3579		* Gets the value of the xpos property.
3580		*
3581		* @return
3582		* possible object is
3583		* {@link Integer }
3584		*
3585		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3586	1	public Integer getXpos() {...
3587	1	return xpos;
3588		}
3589
3590		/**
3591		* Sets the value of the xpos property.
3592		*
3593		* @param value
3594		* allowed object is
3595		* {@link Integer }
3596		*
3597		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3598	1	public void setXpos(Integer value) {...
3599	1	this.xpos = value;
3600		}
3601
3602		/**
3603		* Gets the value of the ypos property.
3604		*
3605		* @return
3606		* possible object is
3607		* {@link Integer }
3608		*
3609		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3610	1	public Integer getYpos() {...
3611	1	return ypos;
3612		}
3613
3614		/**
3615		* Sets the value of the ypos property.
3616		*
3617		* @param value
3618		* allowed object is
3619		* {@link Integer }
3620		*
3621		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3622	1	public void setYpos(Integer value) {...
3623	1	this.ypos = value;
3624		}
3625
3626		/**
3627		* Gets the value of the includeGaps property.
3628		*
3629		* @return
3630		* possible object is
3631		* {@link Boolean }
3632		*
3633		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3634	1	public Boolean isIncludeGaps() {...
3635	1	return includeGaps;
3636		}
3637
3638		/**
3639		* Sets the value of the includeGaps property.
3640		*
3641		* @param value
3642		* allowed object is
3643		* {@link Boolean }
3644		*
3645		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3646	1	public void setIncludeGaps(Boolean value) {...
3647	1	this.includeGaps = value;
3648		}
3649
3650		/**
3651		* Gets the value of the matchGaps property.
3652		*
3653		* @return
3654		* possible object is
3655		* {@link Boolean }
3656		*
3657		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3658	1	public Boolean isMatchGaps() {...
3659	1	return matchGaps;
3660		}
3661
3662		/**
3663		* Sets the value of the matchGaps property.
3664		*
3665		* @param value
3666		* allowed object is
3667		* {@link Boolean }
3668		*
3669		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3670	1	public void setMatchGaps(Boolean value) {...
3671	1	this.matchGaps = value;
3672		}
3673
3674		/**
3675		* Gets the value of the includeGappedColumns property.
3676		*
3677		* @return
3678		* possible object is
3679		* {@link Boolean }
3680		*
3681		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3682	1	public Boolean isIncludeGappedColumns() {...
3683	1	return includeGappedColumns;
3684		}
3685
3686		/**
3687		* Sets the value of the includeGappedColumns property.
3688		*
3689		* @param value
3690		* allowed object is
3691		* {@link Boolean }
3692		*
3693		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3694	1	public void setIncludeGappedColumns(Boolean value) {...
3695	1	this.includeGappedColumns = value;
3696		}
3697
3698		/**
3699		* Gets the value of the denominateByShortestLength property.
3700		*
3701		* @return
3702		* possible object is
3703		* {@link Boolean }
3704		*
3705		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3706	1	public Boolean isDenominateByShortestLength() {...
3707	1	return denominateByShortestLength;
3708		}
3709
3710		/**
3711		* Sets the value of the denominateByShortestLength property.
3712		*
3713		* @param value
3714		* allowed object is
3715		* {@link Boolean }
3716		*
3717		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3718	1	public void setDenominateByShortestLength(Boolean value) {...
3719	1	this.denominateByShortestLength = value;
3720		}
3721
3722
3723		/**
3724		* <p>Java class for anonymous complex type.
3725		*
3726		* <p>The following schema fragment specifies the expected content contained within this class.
3727		*
3728		* <pre>
3729		* &lt;complexType>
3730		* &lt;complexContent>
3731		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3732		* &lt;attGroup ref="{www.jalview.org}position"/>
3733		* &lt;/restriction>
3734		* &lt;/complexContent>
3735		* &lt;/complexType>
3736		* </pre>
3737		*
3738		*
3739		*/
3740		@XmlAccessorType(XmlAccessType.FIELD)
3741		@XmlType(name = "")
		100% Uncovered Elements: 0 (12) Complexity: 6 Complexity Density: 1
3742		public static class Axis {
3743
3744		@XmlAttribute(name = "xPos")
3745		protected Float xPos;
3746		@XmlAttribute(name = "yPos")
3747		protected Float yPos;
3748		@XmlAttribute(name = "zPos")
3749		protected Float zPos;
3750
3751		/**
3752		* Gets the value of the xPos property.
3753		*
3754		* @return
3755		* possible object is
3756		* {@link Float }
3757		*
3758		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3759	3	public Float getXPos() {...
3760	3	return xPos;
3761		}
3762
3763		/**
3764		* Sets the value of the xPos property.
3765		*
3766		* @param value
3767		* allowed object is
3768		* {@link Float }
3769		*
3770		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3771	3	public void setXPos(Float value) {...
3772	3	this.xPos = value;
3773		}
3774
3775		/**
3776		* Gets the value of the yPos property.
3777		*
3778		* @return
3779		* possible object is
3780		* {@link Float }
3781		*
3782		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3783	3	public Float getYPos() {...
3784	3	return yPos;
3785		}
3786
3787		/**
3788		* Sets the value of the yPos property.
3789		*
3790		* @param value
3791		* allowed object is
3792		* {@link Float }
3793		*
3794		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3795	3	public void setYPos(Float value) {...
3796	3	this.yPos = value;
3797		}
3798
3799		/**
3800		* Gets the value of the zPos property.
3801		*
3802		* @return
3803		* possible object is
3804		* {@link Float }
3805		*
3806		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3807	3	public Float getZPos() {...
3808	3	return zPos;
3809		}
3810
3811		/**
3812		* Sets the value of the zPos property.
3813		*
3814		* @param value
3815		* allowed object is
3816		* {@link Float }
3817		*
3818		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3819	3	public void setZPos(Float value) {...
3820	3	this.zPos = value;
3821		}
3822
3823		}
3824
3825
3826		/**
3827		* <p>Java class for anonymous complex type.
3828		*
3829		* <p>The following schema fragment specifies the expected content contained within this class.
3830		*
3831		* <pre>
3832		* &lt;complexType>
3833		* &lt;complexContent>
3834		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3835		* &lt;attGroup ref="{www.jalview.org}position"/>
3836		* &lt;/restriction>
3837		* &lt;/complexContent>
3838		* &lt;/complexType>
3839		* </pre>
3840		*
3841		*
3842		*/
3843		@XmlAccessorType(XmlAccessType.FIELD)
3844		@XmlType(name = "")
		100% Uncovered Elements: 0 (12) Complexity: 6 Complexity Density: 1
3845		public static class SeqPointMax {
3846
3847		@XmlAttribute(name = "xPos")
3848		protected Float xPos;
3849		@XmlAttribute(name = "yPos")
3850		protected Float yPos;
3851		@XmlAttribute(name = "zPos")
3852		protected Float zPos;
3853
3854		/**
3855		* Gets the value of the xPos property.
3856		*
3857		* @return
3858		* possible object is
3859		* {@link Float }
3860		*
3861		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3862	1	public Float getXPos() {...
3863	1	return xPos;
3864		}
3865
3866		/**
3867		* Sets the value of the xPos property.
3868		*
3869		* @param value
3870		* allowed object is
3871		* {@link Float }
3872		*
3873		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3874	1	public void setXPos(Float value) {...
3875	1	this.xPos = value;
3876		}
3877
3878		/**
3879		* Gets the value of the yPos property.
3880		*
3881		* @return
3882		* possible object is
3883		* {@link Float }
3884		*
3885		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3886	1	public Float getYPos() {...
3887	1	return yPos;
3888		}
3889
3890		/**
3891		* Sets the value of the yPos property.
3892		*
3893		* @param value
3894		* allowed object is
3895		* {@link Float }
3896		*
3897		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3898	1	public void setYPos(Float value) {...
3899	1	this.yPos = value;
3900		}
3901
3902		/**
3903		* Gets the value of the zPos property.
3904		*
3905		* @return
3906		* possible object is
3907		* {@link Float }
3908		*
3909		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3910	1	public Float getZPos() {...
3911	1	return zPos;
3912		}
3913
3914		/**
3915		* Sets the value of the zPos property.
3916		*
3917		* @param value
3918		* allowed object is
3919		* {@link Float }
3920		*
3921		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3922	1	public void setZPos(Float value) {...
3923	1	this.zPos = value;
3924		}
3925
3926		}
3927
3928
3929		/**
3930		* <p>Java class for anonymous complex type.
3931		*
3932		* <p>The following schema fragment specifies the expected content contained within this class.
3933		*
3934		* <pre>
3935		* &lt;complexType>
3936		* &lt;complexContent>
3937		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3938		* &lt;attGroup ref="{www.jalview.org}position"/>
3939		* &lt;/restriction>
3940		* &lt;/complexContent>
3941		* &lt;/complexType>
3942		* </pre>
3943		*
3944		*
3945		*/
3946		@XmlAccessorType(XmlAccessType.FIELD)
3947		@XmlType(name = "")
		100% Uncovered Elements: 0 (12) Complexity: 6 Complexity Density: 1
3948		public static class SeqPointMin {
3949
3950		@XmlAttribute(name = "xPos")
3951		protected Float xPos;
3952		@XmlAttribute(name = "yPos")
3953		protected Float yPos;
3954		@XmlAttribute(name = "zPos")
3955		protected Float zPos;
3956
3957		/**
3958		* Gets the value of the xPos property.
3959		*
3960		* @return
3961		* possible object is
3962		* {@link Float }
3963		*
3964		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3965	1	public Float getXPos() {...
3966	1	return xPos;
3967		}
3968
3969		/**
3970		* Sets the value of the xPos property.
3971		*
3972		* @param value
3973		* allowed object is
3974		* {@link Float }
3975		*
3976		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3977	1	public void setXPos(Float value) {...
3978	1	this.xPos = value;
3979		}
3980
3981		/**
3982		* Gets the value of the yPos property.
3983		*
3984		* @return
3985		* possible object is
3986		* {@link Float }
3987		*
3988		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3989	1	public Float getYPos() {...
3990	1	return yPos;
3991		}
3992
3993		/**
3994		* Sets the value of the yPos property.
3995		*
3996		* @param value
3997		* allowed object is
3998		* {@link Float }
3999		*
4000		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4001	1	public void setYPos(Float value) {...
4002	1	this.yPos = value;
4003		}
4004
4005		/**
4006		* Gets the value of the zPos property.
4007		*
4008		* @return
4009		* possible object is
4010		* {@link Float }
4011		*
4012		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4013	1	public Float getZPos() {...
4014	1	return zPos;
4015		}
4016
4017		/**
4018		* Sets the value of the zPos property.
4019		*
4020		* @param value
4021		* allowed object is
4022		* {@link Float }
4023		*
4024		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4025	1	public void setZPos(Float value) {...
4026	1	this.zPos = value;
4027		}
4028
4029		}
4030
4031
4032		/**
4033		* <p>Java class for anonymous complex type.
4034		*
4035		* <p>The following schema fragment specifies the expected content contained within this class.
4036		*
4037		* <pre>
4038		* &lt;complexType>
4039		* &lt;complexContent>
4040		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4041		* &lt;attGroup ref="{www.jalview.org}position"/>
4042		* &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
4043		* &lt;/restriction>
4044		* &lt;/complexContent>
4045		* &lt;/complexType>
4046		* </pre>
4047		*
4048		*
4049		*/
4050		@XmlAccessorType(XmlAccessType.FIELD)
4051		@XmlType(name = "")
		100% Uncovered Elements: 0 (16) Complexity: 8 Complexity Density: 1
4052		public static class SequencePoint {
4053
4054		@XmlAttribute(name = "sequenceRef")
4055		protected String sequenceRef;
4056		@XmlAttribute(name = "xPos")
4057		protected Float xPos;
4058		@XmlAttribute(name = "yPos")
4059		protected Float yPos;
4060		@XmlAttribute(name = "zPos")
4061		protected Float zPos;
4062
4063		/**
4064		* Gets the value of the sequenceRef property.
4065		*
4066		* @return
4067		* possible object is
4068		* {@link String }
4069		*
4070		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4071	15	public String getSequenceRef() {...
4072	15	return sequenceRef;
4073		}
4074
4075		/**
4076		* Sets the value of the sequenceRef property.
4077		*
4078		* @param value
4079		* allowed object is
4080		* {@link String }
4081		*
4082		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4083	15	public void setSequenceRef(String value) {...
4084	15	this.sequenceRef = value;
4085		}
4086
4087		/**
4088		* Gets the value of the xPos property.
4089		*
4090		* @return
4091		* possible object is
4092		* {@link Float }
4093		*
4094		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4095	15	public Float getXPos() {...
4096	15	return xPos;
4097		}
4098
4099		/**
4100		* Sets the value of the xPos property.
4101		*
4102		* @param value
4103		* allowed object is
4104		* {@link Float }
4105		*
4106		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4107	15	public void setXPos(Float value) {...
4108	15	this.xPos = value;
4109		}
4110
4111		/**
4112		* Gets the value of the yPos property.
4113		*
4114		* @return
4115		* possible object is
4116		* {@link Float }
4117		*
4118		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4119	15	public Float getYPos() {...
4120	15	return yPos;
4121		}
4122
4123		/**
4124		* Sets the value of the yPos property.
4125		*
4126		* @param value
4127		* allowed object is
4128		* {@link Float }
4129		*
4130		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4131	15	public void setYPos(Float value) {...
4132	15	this.yPos = value;
4133		}
4134
4135		/**
4136		* Gets the value of the zPos property.
4137		*
4138		* @return
4139		* possible object is
4140		* {@link Float }
4141		*
4142		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4143	15	public Float getZPos() {...
4144	15	return zPos;
4145		}
4146
4147		/**
4148		* Sets the value of the zPos property.
4149		*
4150		* @param value
4151		* allowed object is
4152		* {@link Float }
4153		*
4154		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4155	15	public void setZPos(Float value) {...
4156	15	this.zPos = value;
4157		}
4158
4159		}
4160
4161		}
4162
4163
4164		/**
4165		* <p>Java class for anonymous complex type.
4166		*
4167		* <p>The following schema fragment specifies the expected content contained within this class.
4168		*
4169		* <pre>
4170		* &lt;complexType>
4171		* &lt;complexContent>
4172		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4173		* &lt;sequence minOccurs="0">
4174		* &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
4175		* &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
4176		* &lt;/sequence>
4177		* &lt;attGroup ref="{www.jalview.org}swingwindow"/>
4178		* &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4179		* &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4180		* &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4181		* &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
4182		* &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4183		* &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4184		* &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4185		* &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4186		* &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4187		* &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4188		* &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4189		* &lt;/restriction>
4190		* &lt;/complexContent>
4191		* &lt;/complexType>
4192		* </pre>
4193		*
4194		*
4195		*/
4196		@XmlAccessorType(XmlAccessType.FIELD)
4197		@XmlType(name = "", propOrder = {
4198		"title",
4199		"newick"
4200		})
		100% Uncovered Elements: 0 (72) Complexity: 35 Complexity Density: 0.97
4201		public static class Tree {
4202
4203		@XmlElement(namespace = "www.jalview.org")
4204		protected String title;
4205		@XmlElement(namespace = "www.jalview.org")
4206		protected String newick;
4207		@XmlAttribute(name = "fontName")
4208		protected String fontName;
4209		@XmlAttribute(name = "fontSize")
4210		protected Integer fontSize;
4211		@XmlAttribute(name = "fontStyle")
4212		protected Integer fontStyle;
4213		@XmlAttribute(name = "threshold")
4214		protected Float threshold;
4215		@XmlAttribute(name = "showBootstrap")
4216		protected Boolean showBootstrap;
4217		@XmlAttribute(name = "showDistances")
4218		protected Boolean showDistances;
4219		@XmlAttribute(name = "markUnlinked")
4220		protected Boolean markUnlinked;
4221		@XmlAttribute(name = "fitToWindow")
4222		protected Boolean fitToWindow;
4223		@XmlAttribute(name = "currentTree")
4224		protected Boolean currentTree;
4225		@XmlAttribute(name = "id")
4226		@XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4227		@XmlID
4228		@XmlSchemaType(name = "ID")
4229		protected String id;
4230		@XmlAttribute(name = "linkToAllViews")
4231		protected Boolean linkToAllViews;
4232		@XmlAttribute(name = "width")
4233		protected Integer width;
4234		@XmlAttribute(name = "height")
4235		protected Integer height;
4236		@XmlAttribute(name = "xpos")
4237		protected Integer xpos;
4238		@XmlAttribute(name = "ypos")
4239		protected Integer ypos;
4240
4241		/**
4242		* Gets the value of the title property.
4243		*
4244		* @return
4245		* possible object is
4246		* {@link String }
4247		*
4248		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4249	8	public String getTitle() {...
4250	8	return title;
4251		}
4252
4253		/**
4254		* Sets the value of the title property.
4255		*
4256		* @param value
4257		* allowed object is
4258		* {@link String }
4259		*
4260		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4261	2	public void setTitle(String value) {...
4262	2	this.title = value;
4263		}
4264
4265		/**
4266		* Gets the value of the newick property.
4267		*
4268		* @return
4269		* possible object is
4270		* {@link String }
4271		*
4272		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4273	8	public String getNewick() {...
4274	8	return newick;
4275		}
4276
4277		/**
4278		* Sets the value of the newick property.
4279		*
4280		* @param value
4281		* allowed object is
4282		* {@link String }
4283		*
4284		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4285	2	public void setNewick(String value) {...
4286	2	this.newick = value;
4287		}
4288
4289		/**
4290		* Gets the value of the fontName property.
4291		*
4292		* @return
4293		* possible object is
4294		* {@link String }
4295		*
4296		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4297	16	public String getFontName() {...
4298	16	return fontName;
4299		}
4300
4301		/**
4302		* Sets the value of the fontName property.
4303		*
4304		* @param value
4305		* allowed object is
4306		* {@link String }
4307		*
4308		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4309	2	public void setFontName(String value) {...
4310	2	this.fontName = value;
4311		}
4312
4313		/**
4314		* Gets the value of the fontSize property.
4315		*
4316		* @return
4317		* possible object is
4318		* {@link Integer }
4319		*
4320		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4321	8	public Integer getFontSize() {...
4322	8	return fontSize;
4323		}
4324
4325		/**
4326		* Sets the value of the fontSize property.
4327		*
4328		* @param value
4329		* allowed object is
4330		* {@link Integer }
4331		*
4332		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4333	2	public void setFontSize(Integer value) {...
4334	2	this.fontSize = value;
4335		}
4336
4337		/**
4338		* Gets the value of the fontStyle property.
4339		*
4340		* @return
4341		* possible object is
4342		* {@link Integer }
4343		*
4344		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4345	8	public Integer getFontStyle() {...
4346	8	return fontStyle;
4347		}
4348
4349		/**
4350		* Sets the value of the fontStyle property.
4351		*
4352		* @param value
4353		* allowed object is
4354		* {@link Integer }
4355		*
4356		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4357	2	public void setFontStyle(Integer value) {...
4358	2	this.fontStyle = value;
4359		}
4360
4361		/**
4362		* Gets the value of the threshold property.
4363		*
4364		* @return
4365		* possible object is
4366		* {@link Float }
4367		*
4368		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4369	8	public Float getThreshold() {...
4370	8	return threshold;
4371		}
4372
4373		/**
4374		* Sets the value of the threshold property.
4375		*
4376		* @param value
4377		* allowed object is
4378		* {@link Float }
4379		*
4380		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4381	2	public void setThreshold(Float value) {...
4382	2	this.threshold = value;
4383		}
4384
4385		/**
4386		* Gets the value of the showBootstrap property.
4387		*
4388		* @return
4389		* possible object is
4390		* {@link Boolean }
4391		*
4392		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4393	8	public Boolean isShowBootstrap() {...
4394	8	return showBootstrap;
4395		}
4396
4397		/**
4398		* Sets the value of the showBootstrap property.
4399		*
4400		* @param value
4401		* allowed object is
4402		* {@link Boolean }
4403		*
4404		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4405	2	public void setShowBootstrap(Boolean value) {...
4406	2	this.showBootstrap = value;
4407		}
4408
4409		/**
4410		* Gets the value of the showDistances property.
4411		*
4412		* @return
4413		* possible object is
4414		* {@link Boolean }
4415		*
4416		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4417	8	public Boolean isShowDistances() {...
4418	8	return showDistances;
4419		}
4420
4421		/**
4422		* Sets the value of the showDistances property.
4423		*
4424		* @param value
4425		* allowed object is
4426		* {@link Boolean }
4427		*
4428		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4429	2	public void setShowDistances(Boolean value) {...
4430	2	this.showDistances = value;
4431		}
4432
4433		/**
4434		* Gets the value of the markUnlinked property.
4435		*
4436		* @return
4437		* possible object is
4438		* {@link Boolean }
4439		*
4440		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4441	8	public Boolean isMarkUnlinked() {...
4442	8	return markUnlinked;
4443		}
4444
4445		/**
4446		* Sets the value of the markUnlinked property.
4447		*
4448		* @param value
4449		* allowed object is
4450		* {@link Boolean }
4451		*
4452		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4453	2	public void setMarkUnlinked(Boolean value) {...
4454	2	this.markUnlinked = value;
4455		}
4456
4457		/**
4458		* Gets the value of the fitToWindow property.
4459		*
4460		* @return
4461		* possible object is
4462		* {@link Boolean }
4463		*
4464		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4465	8	public Boolean isFitToWindow() {...
4466	8	return fitToWindow;
4467		}
4468
4469		/**
4470		* Sets the value of the fitToWindow property.
4471		*
4472		* @param value
4473		* allowed object is
4474		* {@link Boolean }
4475		*
4476		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4477	2	public void setFitToWindow(Boolean value) {...
4478	2	this.fitToWindow = value;
4479		}
4480
4481		/**
4482		* Gets the value of the currentTree property.
4483		*
4484		* @return
4485		* possible object is
4486		* {@link Boolean }
4487		*
4488		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4489	8	public Boolean isCurrentTree() {...
4490	8	return currentTree;
4491		}
4492
4493		/**
4494		* Sets the value of the currentTree property.
4495		*
4496		* @param value
4497		* allowed object is
4498		* {@link Boolean }
4499		*
4500		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4501	2	public void setCurrentTree(Boolean value) {...
4502	2	this.currentTree = value;
4503		}
4504
4505		/**
4506		* Gets the value of the id property.
4507		*
4508		* @return
4509		* possible object is
4510		* {@link String }
4511		*
4512		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4513	16	public String getId() {...
4514	16	return id;
4515		}
4516
4517		/**
4518		* Sets the value of the id property.
4519		*
4520		* @param value
4521		* allowed object is
4522		* {@link String }
4523		*
4524		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4525	2	public void setId(String value) {...
4526	2	this.id = value;
4527		}
4528
4529		/**
4530		* Gets the value of the linkToAllViews property.
4531		*
4532		* @return
4533		* possible object is
4534		* {@link Boolean }
4535		*
4536		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
4537	8	public boolean isLinkToAllViews() {...
4538	8	if (linkToAllViews == null) {
4539	6	return false;
4540		} else {
4541	2	return linkToAllViews;
4542		}
4543		}
4544
4545		/**
4546		* Sets the value of the linkToAllViews property.
4547		*
4548		* @param value
4549		* allowed object is
4550		* {@link Boolean }
4551		*
4552		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4553	2	public void setLinkToAllViews(Boolean value) {...
4554	2	this.linkToAllViews = value;
4555		}
4556
4557		/**
4558		* Gets the value of the width property.
4559		*
4560		* @return
4561		* possible object is
4562		* {@link Integer }
4563		*
4564		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4565	8	public Integer getWidth() {...
4566	8	return width;
4567		}
4568
4569		/**
4570		* Sets the value of the width property.
4571		*
4572		* @param value
4573		* allowed object is
4574		* {@link Integer }
4575		*
4576		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4577	2	public void setWidth(Integer value) {...
4578	2	this.width = value;
4579		}
4580
4581		/**
4582		* Gets the value of the height property.
4583		*
4584		* @return
4585		* possible object is
4586		* {@link Integer }
4587		*
4588		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4589	8	public Integer getHeight() {...
4590	8	return height;
4591		}
4592
4593		/**
4594		* Sets the value of the height property.
4595		*
4596		* @param value
4597		* allowed object is
4598		* {@link Integer }
4599		*
4600		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4601	2	public void setHeight(Integer value) {...
4602	2	this.height = value;
4603		}
4604
4605		/**
4606		* Gets the value of the xpos property.
4607		*
4608		* @return
4609		* possible object is
4610		* {@link Integer }
4611		*
4612		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4613	8	public Integer getXpos() {...
4614	8	return xpos;
4615		}
4616
4617		/**
4618		* Sets the value of the xpos property.
4619		*
4620		* @param value
4621		* allowed object is
4622		* {@link Integer }
4623		*
4624		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4625	2	public void setXpos(Integer value) {...
4626	2	this.xpos = value;
4627		}
4628
4629		/**
4630		* Gets the value of the ypos property.
4631		*
4632		* @return
4633		* possible object is
4634		* {@link Integer }
4635		*
4636		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4637	8	public Integer getYpos() {...
4638	8	return ypos;
4639		}
4640
4641		/**
4642		* Sets the value of the ypos property.
4643		*
4644		* @param value
4645		* allowed object is
4646		* {@link Integer }
4647		*
4648		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4649	2	public void setYpos(Integer value) {...
4650	2	this.ypos = value;
4651		}
4652
4653		}
4654
4655
4656		/**
4657		* <p>Java class for anonymous complex type.
4658		*
4659		* <p>The following schema fragment specifies the expected content contained within this class.
4660		*
4661		* <pre>
4662		* &lt;complexType>
4663		* &lt;complexContent>
4664		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4665		* &lt;sequence>
4666		* &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
4667		* &lt;/sequence>
4668		* &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
4669		* &lt;/restriction>
4670		* &lt;/complexContent>
4671		* &lt;/complexType>
4672		* </pre>
4673		*
4674		*
4675		*/
4676		@XmlAccessorType(XmlAccessType.FIELD)
4677		@XmlType(name = "", propOrder = {
4678		"userColourScheme"
4679		})
		0% Uncovered Elements: 8 (8) Complexity: 4 Complexity Density: 1
4680		public static class UserColours {
4681
4682		@XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
4683		protected JalviewUserColours userColourScheme;
4684		@XmlAttribute(name = "id")
4685		protected String id;
4686
4687		/**
4688		* Gets the value of the userColourScheme property.
4689		*
4690		* @return
4691		* possible object is
4692		* {@link JalviewUserColours }
4693		*
4694		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
4695	0	public JalviewUserColours getUserColourScheme() {...
4696	0	return userColourScheme;
4697		}
4698
4699		/**
4700		* Sets the value of the userColourScheme property.
4701		*
4702		* @param value
4703		* allowed object is
4704		* {@link JalviewUserColours }
4705		*
4706		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
4707	0	public void setUserColourScheme(JalviewUserColours value) {...
4708	0	this.userColourScheme = value;
4709		}
4710
4711		/**
4712		* Gets the value of the id property.
4713		*
4714		* @return
4715		* possible object is
4716		* {@link String }
4717		*
4718		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
4719	0	public String getId() {...
4720	0	return id;
4721		}
4722
4723		/**
4724		* Sets the value of the id property.
4725		*
4726		* @param value
4727		* allowed object is
4728		* {@link String }
4729		*
4730		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
4731	0	public void setId(String value) {...
4732	0	this.id = value;
4733		}
4734
4735		}
4736
4737
4738		/**
4739		* <p>Java class for anonymous complex type.
4740		*
4741		* <p>The following schema fragment specifies the expected content contained within this class.
4742		*
4743		* <pre>
4744		* &lt;complexType>
4745		* &lt;complexContent>
4746		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4747		* &lt;sequence>
4748		* &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
4749		* &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
4750		* &lt;complexType>
4751		* &lt;complexContent>
4752		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4753		* &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
4754		* &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
4755		* &lt;/restriction>
4756		* &lt;/complexContent>
4757		* &lt;/complexType>
4758		* &lt;/element>
4759		* &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
4760		* &lt;complexType>
4761		* &lt;complexContent>
4762		* &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
4763		* &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
4764		* &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4765		* &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4766		* &lt;/extension>
4767		* &lt;/complexContent>
4768		* &lt;/complexType>
4769		* &lt;/element>
4770		* &lt;/sequence>
4771		* &lt;attGroup ref="{www.jalview.org}swingwindow"/>
4772		* &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4773		* &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4774		* &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
4775		* &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4776		* &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4777		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
4778		* &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4779		* &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4780		* &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4781		* &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4782		* &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4783		* &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4784		* &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4785		* &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4786		* &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4787		* &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4788		* &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4789		* &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4790		* &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4791		* &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4792		* &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4793		* &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4794		* &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4795		* &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4796		* &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4797		* &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4798		* &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4799		* &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
4800		* &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
4801		* &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4802		* &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4803		* &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4804		* &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4805		* &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
4806		* &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
4807		* &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4808		* &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
4809		* &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
4810		* &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4811		* &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4812		* &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
4813		* &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4814		* &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4815		* &lt;/restriction>
4816		* &lt;/complexContent>
4817		* &lt;/complexType>
4818		* </pre>
4819		*
4820		*
4821		*/
4822		@XmlAccessorType(XmlAccessType.FIELD)
4823		@XmlType(name = "", propOrder = {
4824		"annotationColours",
4825		"hiddenColumns",
4826		"calcIdParam"
4827		})
		90.6% Uncovered Elements: 24 (256) Complexity: 113 Complexity Density: 0.88
4828		public static class Viewport {
4829
4830		@XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
4831		protected AnnotationColourScheme annotationColours;
4832		@XmlElement(namespace = "www.jalview.org")
4833		protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
4834		@XmlElement(namespace = "www.jalview.org")
4835		protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
4836		@XmlAttribute(name = "conservationSelected")
4837		protected Boolean conservationSelected;
4838		@XmlAttribute(name = "pidSelected")
4839		protected Boolean pidSelected;
4840		@XmlAttribute(name = "bgColour")
4841		protected String bgColour;
4842		@XmlAttribute(name = "consThreshold")
4843		protected Integer consThreshold;
4844		@XmlAttribute(name = "pidThreshold")
4845		protected Integer pidThreshold;
4846		@XmlAttribute(name = "title")
4847		protected String title;
4848		@XmlAttribute(name = "showFullId")
4849		protected Boolean showFullId;
4850		@XmlAttribute(name = "rightAlignIds")
4851		protected Boolean rightAlignIds;
4852		@XmlAttribute(name = "showText")
4853		protected Boolean showText;
4854		@XmlAttribute(name = "showColourText")
4855		protected Boolean showColourText;
4856		@XmlAttribute(name = "showUnconserved")
4857		protected Boolean showUnconserved;
4858		@XmlAttribute(name = "showBoxes")
4859		protected Boolean showBoxes;
4860		@XmlAttribute(name = "wrapAlignment")
4861		protected Boolean wrapAlignment;
4862		@XmlAttribute(name = "renderGaps")
4863		protected Boolean renderGaps;
4864		@XmlAttribute(name = "showSequenceFeatures")
4865		protected Boolean showSequenceFeatures;
4866		@XmlAttribute(name = "showNPfeatureTooltip")
4867		protected Boolean showNPfeatureTooltip;
4868		@XmlAttribute(name = "showDbRefTooltip")
4869		protected Boolean showDbRefTooltip;
4870		@XmlAttribute(name = "followHighlight")
4871		protected Boolean followHighlight;
4872		@XmlAttribute(name = "followSelection")
4873		protected Boolean followSelection;
4874		@XmlAttribute(name = "showAnnotation")
4875		protected Boolean showAnnotation;
4876		@XmlAttribute(name = "centreColumnLabels")
4877		protected Boolean centreColumnLabels;
4878		@XmlAttribute(name = "showGroupConservation")
4879		protected Boolean showGroupConservation;
4880		@XmlAttribute(name = "showGroupConsensus")
4881		protected Boolean showGroupConsensus;
4882		@XmlAttribute(name = "showConsensusHistogram")
4883		protected Boolean showConsensusHistogram;
4884		@XmlAttribute(name = "showSequenceLogo")
4885		protected Boolean showSequenceLogo;
4886		@XmlAttribute(name = "normaliseSequenceLogo")
4887		protected Boolean normaliseSequenceLogo;
4888		@XmlAttribute(name = "ignoreGapsinConsensus")
4889		protected Boolean ignoreGapsinConsensus;
4890		@XmlAttribute(name = "startRes")
4891		protected Integer startRes;
4892		@XmlAttribute(name = "startSeq")
4893		protected Integer startSeq;
4894		@XmlAttribute(name = "fontName")
4895		protected String fontName;
4896		@XmlAttribute(name = "fontSize")
4897		protected Integer fontSize;
4898		@XmlAttribute(name = "fontStyle")
4899		protected Integer fontStyle;
4900		@XmlAttribute(name = "scaleProteinAsCdna")
4901		protected Boolean scaleProteinAsCdna;
4902		@XmlAttribute(name = "viewName")
4903		protected String viewName;
4904		@XmlAttribute(name = "sequenceSetId")
4905		protected String sequenceSetId;
4906		@XmlAttribute(name = "gatheredViews")
4907		protected Boolean gatheredViews;
4908		@XmlAttribute(name = "textCol1")
4909		protected Integer textCol1;
4910		@XmlAttribute(name = "textCol2")
4911		protected Integer textCol2;
4912		@XmlAttribute(name = "textColThreshold")
4913		protected Integer textColThreshold;
4914		@XmlAttribute(name = "id")
4915		@XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4916		@XmlID
4917		@XmlSchemaType(name = "ID")
4918		protected String id;
4919		@XmlAttribute(name = "complementId")
4920		protected String complementId;
4921		@XmlAttribute(name = "showComplementFeatures")
4922		protected Boolean showComplementFeatures;
4923		@XmlAttribute(name = "showComplementFeaturesOnTop")
4924		protected Boolean showComplementFeaturesOnTop;
4925		@XmlAttribute(name = "width")
4926		protected Integer width;
4927		@XmlAttribute(name = "height")
4928		protected Integer height;
4929		@XmlAttribute(name = "xpos")
4930		protected Integer xpos;
4931		@XmlAttribute(name = "ypos")
4932		protected Integer ypos;
4933
4934		/**
4935		* Gets the value of the annotationColours property.
4936		*
4937		* @return
4938		* possible object is
4939		* {@link AnnotationColourScheme }
4940		*
4941		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4942	1	public AnnotationColourScheme getAnnotationColours() {...
4943	1	return annotationColours;
4944		}
4945
4946		/**
4947		* Sets the value of the annotationColours property.
4948		*
4949		* @param value
4950		* allowed object is
4951		* {@link AnnotationColourScheme }
4952		*
4953		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4954	1	public void setAnnotationColours(AnnotationColourScheme value) {...
4955	1	this.annotationColours = value;
4956		}
4957
4958		/**
4959		* Gets the value of the hiddenColumns property.
4960		*
4961		* <p>
4962		* This accessor method returns a reference to the live list,
4963		* not a snapshot. Therefore any modification you make to the
4964		* returned list will be present inside the JAXB object.
4965		* This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
4966		*
4967		* <p>
4968		* For example, to add a new item, do as follows:
4969		* <pre>
4970		* getHiddenColumns().add(newItem);
4971		* </pre>
4972		*
4973		*
4974		* <p>
4975		* Objects of the following type(s) are allowed in the list
4976		* {@link JalviewModel.Viewport.HiddenColumns }
4977		*
4978		*
4979		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
4980	206	public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {...
4981	206	if (hiddenColumns == null) {
4982	52	hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
4983		}
4984	206	return this.hiddenColumns;
4985		}
4986
4987		/**
4988		* Gets the value of the calcIdParam property.
4989		*
4990		* <p>
4991		* This accessor method returns a reference to the live list,
4992		* not a snapshot. Therefore any modification you make to the
4993		* returned list will be present inside the JAXB object.
4994		* This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
4995		*
4996		* <p>
4997		* For example, to add a new item, do as follows:
4998		* <pre>
4999		* getCalcIdParam().add(newItem);
5000		* </pre>
5001		*
5002		*
5003		* <p>
5004		* Objects of the following type(s) are allowed in the list
5005		* {@link JalviewModel.Viewport.CalcIdParam }
5006		*
5007		*
5008		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
5009	140	public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {...
5010	140	if (calcIdParam == null) {
5011	70	calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
5012		}
5013	140	return this.calcIdParam;
5014		}
5015
5016		/**
5017		* Gets the value of the conservationSelected property.
5018		*
5019		* @return
5020		* possible object is
5021		* {@link Boolean }
5022		*
5023		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5024	140	public Boolean isConservationSelected() {...
5025	140	return conservationSelected;
5026		}
5027
5028		/**
5029		* Sets the value of the conservationSelected property.
5030		*
5031		* @param value
5032		* allowed object is
5033		* {@link Boolean }
5034		*
5035		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5036	29	public void setConservationSelected(Boolean value) {...
5037	29	this.conservationSelected = value;
5038		}
5039
5040		/**
5041		* Gets the value of the pidSelected property.
5042		*
5043		* @return
5044		* possible object is
5045		* {@link Boolean }
5046		*
5047		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5048	70	public Boolean isPidSelected() {...
5049	70	return pidSelected;
5050		}
5051
5052		/**
5053		* Sets the value of the pidSelected property.
5054		*
5055		* @param value
5056		* allowed object is
5057		* {@link Boolean }
5058		*
5059		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5060	29	public void setPidSelected(Boolean value) {...
5061	29	this.pidSelected = value;
5062		}
5063
5064		/**
5065		* Gets the value of the bgColour property.
5066		*
5067		* @return
5068		* possible object is
5069		* {@link String }
5070		*
5071		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5072	279	public String getBgColour() {...
5073	279	return bgColour;
5074		}
5075
5076		/**
5077		* Sets the value of the bgColour property.
5078		*
5079		* @param value
5080		* allowed object is
5081		* {@link String }
5082		*
5083		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5084	29	public void setBgColour(String value) {...
5085	29	this.bgColour = value;
5086		}
5087
5088		/**
5089		* Gets the value of the consThreshold property.
5090		*
5091		* @return
5092		* possible object is
5093		* {@link Integer }
5094		*
5095		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5096	72	public Integer getConsThreshold() {...
5097	72	return consThreshold;
5098		}
5099
5100		/**
5101		* Sets the value of the consThreshold property.
5102		*
5103		* @param value
5104		* allowed object is
5105		* {@link Integer }
5106		*
5107		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5108	2	public void setConsThreshold(Integer value) {...
5109	2	this.consThreshold = value;
5110		}
5111
5112		/**
5113		* Gets the value of the pidThreshold property.
5114		*
5115		* @return
5116		* possible object is
5117		* {@link Integer }
5118		*
5119		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5120	70	public Integer getPidThreshold() {...
5121	70	return pidThreshold;
5122		}
5123
5124		/**
5125		* Sets the value of the pidThreshold property.
5126		*
5127		* @param value
5128		* allowed object is
5129		* {@link Integer }
5130		*
5131		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5132	5	public void setPidThreshold(Integer value) {...
5133	5	this.pidThreshold = value;
5134		}
5135
5136		/**
5137		* Gets the value of the title property.
5138		*
5139		* @return
5140		* possible object is
5141		* {@link String }
5142		*
5143		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5144	140	public String getTitle() {...
5145	140	return title;
5146		}
5147
5148		/**
5149		* Sets the value of the title property.
5150		*
5151		* @param value
5152		* allowed object is
5153		* {@link String }
5154		*
5155		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5156	29	public void setTitle(String value) {...
5157	29	this.title = value;
5158		}
5159
5160		/**
5161		* Gets the value of the showFullId property.
5162		*
5163		* @return
5164		* possible object is
5165		* {@link Boolean }
5166		*
5167		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5168	70	public Boolean isShowFullId() {...
5169	70	return showFullId;
5170		}
5171
5172		/**
5173		* Sets the value of the showFullId property.
5174		*
5175		* @param value
5176		* allowed object is
5177		* {@link Boolean }
5178		*
5179		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5180	29	public void setShowFullId(Boolean value) {...
5181	29	this.showFullId = value;
5182		}
5183
5184		/**
5185		* Gets the value of the rightAlignIds property.
5186		*
5187		* @return
5188		* possible object is
5189		* {@link Boolean }
5190		*
5191		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5192	70	public Boolean isRightAlignIds() {...
5193	70	return rightAlignIds;
5194		}
5195
5196		/**
5197		* Sets the value of the rightAlignIds property.
5198		*
5199		* @param value
5200		* allowed object is
5201		* {@link Boolean }
5202		*
5203		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5204	29	public void setRightAlignIds(Boolean value) {...
5205	29	this.rightAlignIds = value;
5206		}
5207
5208		/**
5209		* Gets the value of the showText property.
5210		*
5211		* @return
5212		* possible object is
5213		* {@link Boolean }
5214		*
5215		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5216	70	public Boolean isShowText() {...
5217	70	return showText;
5218		}
5219
5220		/**
5221		* Sets the value of the showText property.
5222		*
5223		* @param value
5224		* allowed object is
5225		* {@link Boolean }
5226		*
5227		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5228	29	public void setShowText(Boolean value) {...
5229	29	this.showText = value;
5230		}
5231
5232		/**
5233		* Gets the value of the showColourText property.
5234		*
5235		* @return
5236		* possible object is
5237		* {@link Boolean }
5238		*
5239		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5240	70	public Boolean isShowColourText() {...
5241	70	return showColourText;
5242		}
5243
5244		/**
5245		* Sets the value of the showColourText property.
5246		*
5247		* @param value
5248		* allowed object is
5249		* {@link Boolean }
5250		*
5251		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5252	29	public void setShowColourText(Boolean value) {...
5253	29	this.showColourText = value;
5254		}
5255
5256		/**
5257		* Gets the value of the showUnconserved property.
5258		*
5259		* @return
5260		* possible object is
5261		* {@link Boolean }
5262		*
5263		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
5264	70	public boolean isShowUnconserved() {...
5265	70	if (showUnconserved == null) {
5266	0	return false;
5267		} else {
5268	70	return showUnconserved;
5269		}
5270		}
5271
5272		/**
5273		* Sets the value of the showUnconserved property.
5274		*
5275		* @param value
5276		* allowed object is
5277		* {@link Boolean }
5278		*
5279		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5280	29	public void setShowUnconserved(Boolean value) {...
5281	29	this.showUnconserved = value;
5282		}
5283
5284		/**
5285		* Gets the value of the showBoxes property.
5286		*
5287		* @return
5288		* possible object is
5289		* {@link Boolean }
5290		*
5291		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5292	70	public Boolean isShowBoxes() {...
5293	70	return showBoxes;
5294		}
5295
5296		/**
5297		* Sets the value of the showBoxes property.
5298		*
5299		* @param value
5300		* allowed object is
5301		* {@link Boolean }
5302		*
5303		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5304	29	public void setShowBoxes(Boolean value) {...
5305	29	this.showBoxes = value;
5306		}
5307
5308		/**
5309		* Gets the value of the wrapAlignment property.
5310		*
5311		* @return
5312		* possible object is
5313		* {@link Boolean }
5314		*
5315		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5316	70	public Boolean isWrapAlignment() {...
5317	70	return wrapAlignment;
5318		}
5319
5320		/**
5321		* Sets the value of the wrapAlignment property.
5322		*
5323		* @param value
5324		* allowed object is
5325		* {@link Boolean }
5326		*
5327		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5328	29	public void setWrapAlignment(Boolean value) {...
5329	29	this.wrapAlignment = value;
5330		}
5331
5332		/**
5333		* Gets the value of the renderGaps property.
5334		*
5335		* @return
5336		* possible object is
5337		* {@link Boolean }
5338		*
5339		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5340	70	public Boolean isRenderGaps() {...
5341	70	return renderGaps;
5342		}
5343
5344		/**
5345		* Sets the value of the renderGaps property.
5346		*
5347		* @param value
5348		* allowed object is
5349		* {@link Boolean }
5350		*
5351		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5352	29	public void setRenderGaps(Boolean value) {...
5353	29	this.renderGaps = value;
5354		}
5355
5356		/**
5357		* Gets the value of the showSequenceFeatures property.
5358		*
5359		* @return
5360		* possible object is
5361		* {@link Boolean }
5362		*
5363		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5364	70	public Boolean isShowSequenceFeatures() {...
5365	70	return showSequenceFeatures;
5366		}
5367
5368		/**
5369		* Sets the value of the showSequenceFeatures property.
5370		*
5371		* @param value
5372		* allowed object is
5373		* {@link Boolean }
5374		*
5375		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5376	29	public void setShowSequenceFeatures(Boolean value) {...
5377	29	this.showSequenceFeatures = value;
5378		}
5379
5380		/**
5381		* Gets the value of the showNPfeatureTooltip property.
5382		*
5383		* @return
5384		* possible object is
5385		* {@link Boolean }
5386		*
5387		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5388	70	public Boolean isShowNPfeatureTooltip() {...
5389	70	return showNPfeatureTooltip;
5390		}
5391
5392		/**
5393		* Sets the value of the showNPfeatureTooltip property.
5394		*
5395		* @param value
5396		* allowed object is
5397		* {@link Boolean }
5398		*
5399		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5400	29	public void setShowNPfeatureTooltip(Boolean value) {...
5401	29	this.showNPfeatureTooltip = value;
5402		}
5403
5404		/**
5405		* Gets the value of the showDbRefTooltip property.
5406		*
5407		* @return
5408		* possible object is
5409		* {@link Boolean }
5410		*
5411		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5412	70	public Boolean isShowDbRefTooltip() {...
5413	70	return showDbRefTooltip;
5414		}
5415
5416		/**
5417		* Sets the value of the showDbRefTooltip property.
5418		*
5419		* @param value
5420		* allowed object is
5421		* {@link Boolean }
5422		*
5423		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5424	29	public void setShowDbRefTooltip(Boolean value) {...
5425	29	this.showDbRefTooltip = value;
5426		}
5427
5428		/**
5429		* Gets the value of the followHighlight property.
5430		*
5431		* @return
5432		* possible object is
5433		* {@link Boolean }
5434		*
5435		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
5436	70	public boolean isFollowHighlight() {...
5437	70	if (followHighlight == null) {
5438	0	return true;
5439		} else {
5440	70	return followHighlight;
5441		}
5442		}
5443
5444		/**
5445		* Sets the value of the followHighlight property.
5446		*
5447		* @param value
5448		* allowed object is
5449		* {@link Boolean }
5450		*
5451		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5452	29	public void setFollowHighlight(Boolean value) {...
5453	29	this.followHighlight = value;
5454		}
5455
5456		/**
5457		* Gets the value of the followSelection property.
5458		*
5459		* @return
5460		* possible object is
5461		* {@link Boolean }
5462		*
5463		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
5464	70	public boolean isFollowSelection() {...
5465	70	if (followSelection == null) {
5466	0	return true;
5467		} else {
5468	70	return followSelection;
5469		}
5470		}
5471
5472		/**
5473		* Sets the value of the followSelection property.
5474		*
5475		* @param value
5476		* allowed object is
5477		* {@link Boolean }
5478		*
5479		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5480	29	public void setFollowSelection(Boolean value) {...
5481	29	this.followSelection = value;
5482		}
5483
5484		/**
5485		* Gets the value of the showAnnotation property.
5486		*
5487		* @return
5488		* possible object is
5489		* {@link Boolean }
5490		*
5491		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5492	140	public Boolean isShowAnnotation() {...
5493	140	return showAnnotation;
5494		}
5495
5496		/**
5497		* Sets the value of the showAnnotation property.
5498		*
5499		* @param value
5500		* allowed object is
5501		* {@link Boolean }
5502		*
5503		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5504	29	public void setShowAnnotation(Boolean value) {...
5505	29	this.showAnnotation = value;
5506		}
5507
5508		/**
5509		* Gets the value of the centreColumnLabels property.
5510		*
5511		* @return
5512		* possible object is
5513		* {@link Boolean }
5514		*
5515		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
5516	70	public boolean isCentreColumnLabels() {...
5517	70	if (centreColumnLabels == null) {
5518	70	return false;
5519		} else {
5520	0	return centreColumnLabels;
5521		}
5522		}
5523
5524		/**
5525		* Sets the value of the centreColumnLabels property.
5526		*
5527		* @param value
5528		* allowed object is
5529		* {@link Boolean }
5530		*
5531		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
5532	0	public void setCentreColumnLabels(Boolean value) {...
5533	0	this.centreColumnLabels = value;
5534		}
5535
5536		/**
5537		* Gets the value of the showGroupConservation property.
5538		*
5539		* @return
5540		* possible object is
5541		* {@link Boolean }
5542		*
5543		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
5544	70	public boolean isShowGroupConservation() {...
5545	70	if (showGroupConservation == null) {
5546	0	return false;
5547		} else {
5548	70	return showGroupConservation;
5549		}
5550		}
5551
5552		/**
5553		* Sets the value of the showGroupConservation property.
5554		*
5555		* @param value
5556		* allowed object is
5557		* {@link Boolean }
5558		*
5559		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5560	29	public void setShowGroupConservation(Boolean value) {...
5561	29	this.showGroupConservation = value;
5562		}
5563
5564		/**
5565		* Gets the value of the showGroupConsensus property.
5566		*
5567		* @return
5568		* possible object is
5569		* {@link Boolean }
5570		*
5571		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
5572	70	public boolean isShowGroupConsensus() {...
5573	70	if (showGroupConsensus == null) {
5574	0	return false;
5575		} else {
5576	70	return showGroupConsensus;
5577		}
5578		}
5579
5580		/**
5581		* Sets the value of the showGroupConsensus property.
5582		*
5583		* @param value
5584		* allowed object is
5585		* {@link Boolean }
5586		*
5587		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5588	29	public void setShowGroupConsensus(Boolean value) {...
5589	29	this.showGroupConsensus = value;
5590		}
5591
5592		/**
5593		* Gets the value of the showConsensusHistogram property.
5594		*
5595		* @return
5596		* possible object is
5597		* {@link Boolean }
5598		*
5599		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
5600	70	public boolean isShowConsensusHistogram() {...
5601	70	if (showConsensusHistogram == null) {
5602	0	return true;
5603		} else {
5604	70	return showConsensusHistogram;
5605		}
5606		}
5607
5608		/**
5609		* Sets the value of the showConsensusHistogram property.
5610		*
5611		* @param value
5612		* allowed object is
5613		* {@link Boolean }
5614		*
5615		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5616	29	public void setShowConsensusHistogram(Boolean value) {...
5617	29	this.showConsensusHistogram = value;
5618		}
5619
5620		/**
5621		* Gets the value of the showSequenceLogo property.
5622		*
5623		* @return
5624		* possible object is
5625		* {@link Boolean }
5626		*
5627		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
5628	70	public boolean isShowSequenceLogo() {...
5629	70	if (showSequenceLogo == null) {
5630	0	return false;
5631		} else {
5632	70	return showSequenceLogo;
5633		}
5634		}
5635
5636		/**
5637		* Sets the value of the showSequenceLogo property.
5638		*
5639		* @param value
5640		* allowed object is
5641		* {@link Boolean }
5642		*
5643		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5644	29	public void setShowSequenceLogo(Boolean value) {...
5645	29	this.showSequenceLogo = value;
5646		}
5647
5648		/**
5649		* Gets the value of the normaliseSequenceLogo property.
5650		*
5651		* @return
5652		* possible object is
5653		* {@link Boolean }
5654		*
5655		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
5656	70	public boolean isNormaliseSequenceLogo() {...
5657	70	if (normaliseSequenceLogo == null) {
5658	30	return false;
5659		} else {
5660	40	return normaliseSequenceLogo;
5661		}
5662		}
5663
5664		/**
5665		* Sets the value of the normaliseSequenceLogo property.
5666		*
5667		* @param value
5668		* allowed object is
5669		* {@link Boolean }
5670		*
5671		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5672	29	public void setNormaliseSequenceLogo(Boolean value) {...
5673	29	this.normaliseSequenceLogo = value;
5674		}
5675
5676		/**
5677		* Gets the value of the ignoreGapsinConsensus property.
5678		*
5679		* @return
5680		* possible object is
5681		* {@link Boolean }
5682		*
5683		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
5684	140	public boolean isIgnoreGapsinConsensus() {...
5685	140	if (ignoreGapsinConsensus == null) {
5686	0	return true;
5687		} else {
5688	140	return ignoreGapsinConsensus;
5689		}
5690		}
5691
5692		/**
5693		* Sets the value of the ignoreGapsinConsensus property.
5694		*
5695		* @param value
5696		* allowed object is
5697		* {@link Boolean }
5698		*
5699		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5700	29	public void setIgnoreGapsinConsensus(Boolean value) {...
5701	29	this.ignoreGapsinConsensus = value;
5702		}
5703
5704		/**
5705		* Gets the value of the startRes property.
5706		*
5707		* @return
5708		* possible object is
5709		* {@link Integer }
5710		*
5711		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5712	70	public Integer getStartRes() {...
5713	70	return startRes;
5714		}
5715
5716		/**
5717		* Sets the value of the startRes property.
5718		*
5719		* @param value
5720		* allowed object is
5721		* {@link Integer }
5722		*
5723		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5724	29	public void setStartRes(Integer value) {...
5725	29	this.startRes = value;
5726		}
5727
5728		/**
5729		* Gets the value of the startSeq property.
5730		*
5731		* @return
5732		* possible object is
5733		* {@link Integer }
5734		*
5735		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
5736	0	public Integer getStartSeq() {...
5737	0	return startSeq;
5738		}
5739
5740		/**
5741		* Sets the value of the startSeq property.
5742		*
5743		* @param value
5744		* allowed object is
5745		* {@link Integer }
5746		*
5747		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5748	29	public void setStartSeq(Integer value) {...
5749	29	this.startSeq = value;
5750		}
5751
5752		/**
5753		* Gets the value of the fontName property.
5754		*
5755		* @return
5756		* possible object is
5757		* {@link String }
5758		*
5759		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5760	70	public String getFontName() {...
5761	70	return fontName;
5762		}
5763
5764		/**
5765		* Sets the value of the fontName property.
5766		*
5767		* @param value
5768		* allowed object is
5769		* {@link String }
5770		*
5771		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5772	29	public void setFontName(String value) {...
5773	29	this.fontName = value;
5774		}
5775
5776		/**
5777		* Gets the value of the fontSize property.
5778		*
5779		* @return
5780		* possible object is
5781		* {@link Integer }
5782		*
5783		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5784	70	public Integer getFontSize() {...
5785	70	return fontSize;
5786		}
5787
5788		/**
5789		* Sets the value of the fontSize property.
5790		*
5791		* @param value
5792		* allowed object is
5793		* {@link Integer }
5794		*
5795		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5796	29	public void setFontSize(Integer value) {...
5797	29	this.fontSize = value;
5798		}
5799
5800		/**
5801		* Gets the value of the fontStyle property.
5802		*
5803		* @return
5804		* possible object is
5805		* {@link Integer }
5806		*
5807		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5808	70	public Integer getFontStyle() {...
5809	70	return fontStyle;
5810		}
5811
5812		/**
5813		* Sets the value of the fontStyle property.
5814		*
5815		* @param value
5816		* allowed object is
5817		* {@link Integer }
5818		*
5819		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5820	29	public void setFontStyle(Integer value) {...
5821	29	this.fontStyle = value;
5822		}
5823
5824		/**
5825		* Gets the value of the scaleProteinAsCdna property.
5826		*
5827		* @return
5828		* possible object is
5829		* {@link Boolean }
5830		*
5831		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
5832	70	public boolean isScaleProteinAsCdna() {...
5833	70	if (scaleProteinAsCdna == null) {
5834	30	return true;
5835		} else {
5836	40	return scaleProteinAsCdna;
5837		}
5838		}
5839
5840		/**
5841		* Sets the value of the scaleProteinAsCdna property.
5842		*
5843		* @param value
5844		* allowed object is
5845		* {@link Boolean }
5846		*
5847		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5848	29	public void setScaleProteinAsCdna(Boolean value) {...
5849	29	this.scaleProteinAsCdna = value;
5850		}
5851
5852		/**
5853		* Gets the value of the viewName property.
5854		*
5855		* @return
5856		* possible object is
5857		* {@link String }
5858		*
5859		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5860	125	public String getViewName() {...
5861	125	return viewName;
5862		}
5863
5864		/**
5865		* Sets the value of the viewName property.
5866		*
5867		* @param value
5868		* allowed object is
5869		* {@link String }
5870		*
5871		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5872	29	public void setViewName(String value) {...
5873	29	this.viewName = value;
5874		}
5875
5876		/**
5877		* Gets the value of the sequenceSetId property.
5878		*
5879		* @return
5880		* possible object is
5881		* {@link String }
5882		*
5883		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5884	140	public String getSequenceSetId() {...
5885	140	return sequenceSetId;
5886		}
5887
5888		/**
5889		* Sets the value of the sequenceSetId property.
5890		*
5891		* @param value
5892		* allowed object is
5893		* {@link String }
5894		*
5895		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5896	29	public void setSequenceSetId(String value) {...
5897	29	this.sequenceSetId = value;
5898		}
5899
5900		/**
5901		* Gets the value of the gatheredViews property.
5902		*
5903		* @return
5904		* possible object is
5905		* {@link Boolean }
5906		*
5907		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5908	70	public Boolean isGatheredViews() {...
5909	70	return gatheredViews;
5910		}
5911
5912		/**
5913		* Sets the value of the gatheredViews property.
5914		*
5915		* @param value
5916		* allowed object is
5917		* {@link Boolean }
5918		*
5919		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5920	29	public void setGatheredViews(Boolean value) {...
5921	29	this.gatheredViews = value;
5922		}
5923
5924		/**
5925		* Gets the value of the textCol1 property.
5926		*
5927		* @return
5928		* possible object is
5929		* {@link Integer }
5930		*
5931		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5932	70	public Integer getTextCol1() {...
5933	70	return textCol1;
5934		}
5935
5936		/**
5937		* Sets the value of the textCol1 property.
5938		*
5939		* @param value
5940		* allowed object is
5941		* {@link Integer }
5942		*
5943		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5944	29	public void setTextCol1(Integer value) {...
5945	29	this.textCol1 = value;
5946		}
5947
5948		/**
5949		* Gets the value of the textCol2 property.
5950		*
5951		* @return
5952		* possible object is
5953		* {@link Integer }
5954		*
5955		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5956	70	public Integer getTextCol2() {...
5957	70	return textCol2;
5958		}
5959
5960		/**
5961		* Sets the value of the textCol2 property.
5962		*
5963		* @param value
5964		* allowed object is
5965		* {@link Integer }
5966		*
5967		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5968	29	public void setTextCol2(Integer value) {...
5969	29	this.textCol2 = value;
5970		}
5971
5972		/**
5973		* Gets the value of the textColThreshold property.
5974		*
5975		* @return
5976		* possible object is
5977		* {@link Integer }
5978		*
5979		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5980	70	public Integer getTextColThreshold() {...
5981	70	return textColThreshold;
5982		}
5983
5984		/**
5985		* Sets the value of the textColThreshold property.
5986		*
5987		* @param value
5988		* allowed object is
5989		* {@link Integer }
5990		*
5991		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5992	29	public void setTextColThreshold(Integer value) {...
5993	29	this.textColThreshold = value;
5994		}
5995
5996		/**
5997		* Gets the value of the id property.
5998		*
5999		* @return
6000		* possible object is
6001		* {@link String }
6002		*
6003		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6004	134	public String getId() {...
6005	134	return id;
6006		}
6007
6008		/**
6009		* Sets the value of the id property.
6010		*
6011		* @param value
6012		* allowed object is
6013		* {@link String }
6014		*
6015		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6016	35	public void setId(String value) {...
6017	35	this.id = value;
6018		}
6019
6020		/**
6021		* Gets the value of the complementId property.
6022		*
6023		* @return
6024		* possible object is
6025		* {@link String }
6026		*
6027		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6028	70	public String getComplementId() {...
6029	70	return complementId;
6030		}
6031
6032		/**
6033		* Sets the value of the complementId property.
6034		*
6035		* @param value
6036		* allowed object is
6037		* {@link String }
6038		*
6039		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
6040	0	public void setComplementId(String value) {...
6041	0	this.complementId = value;
6042		}
6043
6044		/**
6045		* Gets the value of the showComplementFeatures property.
6046		*
6047		* @return
6048		* possible object is
6049		* {@link Boolean }
6050		*
6051		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
6052	70	public boolean isShowComplementFeatures() {...
6053	70	if (showComplementFeatures == null) {
6054	41	return false;
6055		} else {
6056	29	return showComplementFeatures;
6057		}
6058		}
6059
6060		/**
6061		* Sets the value of the showComplementFeatures property.
6062		*
6063		* @param value
6064		* allowed object is
6065		* {@link Boolean }
6066		*
6067		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6068	29	public void setShowComplementFeatures(Boolean value) {...
6069	29	this.showComplementFeatures = value;
6070		}
6071
6072		/**
6073		* Gets the value of the showComplementFeaturesOnTop property.
6074		*
6075		* @return
6076		* possible object is
6077		* {@link Boolean }
6078		*
6079		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
6080	70	public boolean isShowComplementFeaturesOnTop() {...
6081	70	if (showComplementFeaturesOnTop == null) {
6082	41	return false;
6083		} else {
6084	29	return showComplementFeaturesOnTop;
6085		}
6086		}
6087
6088		/**
6089		* Sets the value of the showComplementFeaturesOnTop property.
6090		*
6091		* @param value
6092		* allowed object is
6093		* {@link Boolean }
6094		*
6095		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6096	29	public void setShowComplementFeaturesOnTop(Boolean value) {...
6097	29	this.showComplementFeaturesOnTop = value;
6098		}
6099
6100		/**
6101		* Gets the value of the width property.
6102		*
6103		* @return
6104		* possible object is
6105		* {@link Integer }
6106		*
6107		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6108	210	public Integer getWidth() {...
6109	210	return width;
6110		}
6111
6112		/**
6113		* Sets the value of the width property.
6114		*
6115		* @param value
6116		* allowed object is
6117		* {@link Integer }
6118		*
6119		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6120	29	public void setWidth(Integer value) {...
6121	29	this.width = value;
6122		}
6123
6124		/**
6125		* Gets the value of the height property.
6126		*
6127		* @return
6128		* possible object is
6129		* {@link Integer }
6130		*
6131		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6132	210	public Integer getHeight() {...
6133	210	return height;
6134		}
6135
6136		/**
6137		* Sets the value of the height property.
6138		*
6139		* @param value
6140		* allowed object is
6141		* {@link Integer }
6142		*
6143		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6144	29	public void setHeight(Integer value) {...
6145	29	this.height = value;
6146		}
6147
6148		/**
6149		* Gets the value of the xpos property.
6150		*
6151		* @return
6152		* possible object is
6153		* {@link Integer }
6154		*
6155		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6156	70	public Integer getXpos() {...
6157	70	return xpos;
6158		}
6159
6160		/**
6161		* Sets the value of the xpos property.
6162		*
6163		* @param value
6164		* allowed object is
6165		* {@link Integer }
6166		*
6167		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6168	29	public void setXpos(Integer value) {...
6169	29	this.xpos = value;
6170		}
6171
6172		/**
6173		* Gets the value of the ypos property.
6174		*
6175		* @return
6176		* possible object is
6177		* {@link Integer }
6178		*
6179		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6180	70	public Integer getYpos() {...
6181	70	return ypos;
6182		}
6183
6184		/**
6185		* Sets the value of the ypos property.
6186		*
6187		* @param value
6188		* allowed object is
6189		* {@link Integer }
6190		*
6191		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6192	29	public void setYpos(Integer value) {...
6193	29	this.ypos = value;
6194		}
6195
6196
6197		/**
6198		* <p>Java class for anonymous complex type.
6199		*
6200		* <p>The following schema fragment specifies the expected content contained within this class.
6201		*
6202		* <pre>
6203		* &lt;complexType>
6204		* &lt;complexContent>
6205		* &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
6206		* &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
6207		* &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
6208		* &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
6209		* &lt;/extension>
6210		* &lt;/complexContent>
6211		* &lt;/complexType>
6212		* </pre>
6213		*
6214		*
6215		*/
6216		@XmlAccessorType(XmlAccessType.FIELD)
6217		@XmlType(name = "")
		0% Uncovered Elements: 16 (16) Complexity: 7 Complexity Density: 0.88
6218		public static class CalcIdParam
6219		extends WebServiceParameterSet
6220		{
6221
6222		@XmlAttribute(name = "calcId", required = true)
6223		protected String calcId;
6224		@XmlAttribute(name = "needsUpdate")
6225		protected Boolean needsUpdate;
6226		@XmlAttribute(name = "autoUpdate", required = true)
6227		protected boolean autoUpdate;
6228
6229		/**
6230		* Gets the value of the calcId property.
6231		*
6232		* @return
6233		* possible object is
6234		* {@link String }
6235		*
6236		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
6237	0	public String getCalcId() {...
6238	0	return calcId;
6239		}
6240
6241		/**
6242		* Sets the value of the calcId property.
6243		*
6244		* @param value
6245		* allowed object is
6246		* {@link String }
6247		*
6248		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
6249	0	public void setCalcId(String value) {...
6250	0	this.calcId = value;
6251		}
6252
6253		/**
6254		* Gets the value of the needsUpdate property.
6255		*
6256		* @return
6257		* possible object is
6258		* {@link Boolean }
6259		*
6260		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
6261	0	public boolean isNeedsUpdate() {...
6262	0	if (needsUpdate == null) {
6263	0	return false;
6264		} else {
6265	0	return needsUpdate;
6266		}
6267		}
6268
6269		/**
6270		* Sets the value of the needsUpdate property.
6271		*
6272		* @param value
6273		* allowed object is
6274		* {@link Boolean }
6275		*
6276		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
6277	0	public void setNeedsUpdate(Boolean value) {...
6278	0	this.needsUpdate = value;
6279		}
6280
6281		/**
6282		* Gets the value of the autoUpdate property.
6283		*
6284		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
6285	0	public boolean isAutoUpdate() {...
6286	0	return autoUpdate;
6287		}
6288
6289		/**
6290		* Sets the value of the autoUpdate property.
6291		*
6292		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
6293	0	public void setAutoUpdate(boolean value) {...
6294	0	this.autoUpdate = value;
6295		}
6296
6297		}
6298
6299
6300		/**
6301		* <p>Java class for anonymous complex type.
6302		*
6303		* <p>The following schema fragment specifies the expected content contained within this class.
6304		*
6305		* <pre>
6306		* &lt;complexType>
6307		* &lt;complexContent>
6308		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
6309		* &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
6310		* &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
6311		* &lt;/restriction>
6312		* &lt;/complexContent>
6313		* &lt;/complexType>
6314		* </pre>
6315		*
6316		*
6317		*/
6318		@XmlAccessorType(XmlAccessType.FIELD)
6319		@XmlType(name = "")
		100% Uncovered Elements: 0 (8) Complexity: 4 Complexity Density: 1
6320		public static class HiddenColumns {
6321
6322		@XmlAttribute(name = "start")
6323		protected Integer start;
6324		@XmlAttribute(name = "end")
6325		protected Integer end;
6326
6327		/**
6328		* Gets the value of the start property.
6329		*
6330		* @return
6331		* possible object is
6332		* {@link Integer }
6333		*
6334		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6335	54	public Integer getStart() {...
6336	54	return start;
6337		}
6338
6339		/**
6340		* Sets the value of the start property.
6341		*
6342		* @param value
6343		* allowed object is
6344		* {@link Integer }
6345		*
6346		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6347	6	public void setStart(Integer value) {...
6348	6	this.start = value;
6349		}
6350
6351		/**
6352		* Gets the value of the end property.
6353		*
6354		* @return
6355		* possible object is
6356		* {@link Integer }
6357		*
6358		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6359	54	public Integer getEnd() {...
6360	54	return end;
6361		}
6362
6363		/**
6364		* Sets the value of the end property.
6365		*
6366		* @param value
6367		* allowed object is
6368		* {@link Integer }
6369		*
6370		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6371	6	public void setEnd(Integer value) {...
6372	6	this.end = value;
6373		}
6374
6375		}
6376
6377		}
6378
6379		}