Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
JalviewModel	414	26	20	0.8461538684.6%	Show methods
JalviewModel.FeatureSettings	783	6	4	1.0100%	Show methods
JalviewModel.FeatureSettings.Group	875	4	4	1.0100%	Show methods
JalviewModel.FeatureSettings.Setting	962	31	29	0.967741996.8%	Show methods
JalviewModel.JGroup	1410	69	61	0.891304489.1%	Show methods
JalviewModel.JSeq	2304	24	20	0.979166797.9%	Show methods
JalviewModel.JSeq.Pdbids	2641	3	2	1.0100%	Show methods
JalviewModel.JSeq.Pdbids.StructureState	2708	28	25	0.821428682.1%	Show methods
JalviewModel.JSeq.RnaViewer	3334	19	18	0.00%	Show methods
JalviewModel.JSeq.RnaViewer.SecondaryStructure	3625	8	8	0.00%	Show methods
JalviewModel.PcaViewer	3875	46	44	1.0100%	Show methods
JalviewModel.PcaViewer.Axis	4492	6	6	1.0100%	Show methods
JalviewModel.PcaViewer.SeqPointMax	4595	6	6	1.0100%	Show methods
JalviewModel.PcaViewer.SeqPointMin	4698	6	6	1.0100%	Show methods
JalviewModel.PcaViewer.SequencePoint	4802	8	8	1.0100%	Show methods
JalviewModel.Tree	4976	52	48	0.9038461490.4%	Show methods
JalviewModel.Tree.TreeColorMap	5634	3	2	1.0100%	Show methods
JalviewModel.Tree.TreeColorMap.ColorEntry	5692	4	4	1.0100%	Show methods
JalviewModel.UserColours	5770	4	4	0.00%	Show methods
JalviewModel.Viewport	5934	155	136	0.896774289.7%	Show methods
JalviewModel.Viewport.CalcIdParam	7663	8	7	0.00%	Show methods
JalviewModel.Viewport.HiddenColumns	7785	4	4	1.0100%	Show methods
JalviewModel.Viewport.Overview	7867	18	18	1.0100%	Show methods

Class JalviewModel

Class JalviewModel	Line # 414	Total Statements 26	Complexity 20	TOTAL Coverage 0.8461538684.6%
getCreationDate() : XMLGregorianCalendar   getCreationDate() : XMLGregorianCalendar	445445	1.01	1.01	0.0 0.00%
setCreationDate(XMLGregorianCalendar) : void   setCreationDate(XMLGregorianCalendar) : void	457457	1.01	1.01	1.0 1.0100%
getVersion() : String   getVersion() : String	469469	1.01	1.01	1.0 1.0100%
setVersion(String) : void   setVersion(String) : void	481481	1.01	1.01	1.0 1.0100%
getVamsasModel() : VAMSAS   getVamsasModel() : VAMSAS	493493	1.01	1.01	1.0 1.0100%
setVamsasModel(VAMSAS) : void   setVamsasModel(VAMSAS) : void	505505	1.01	1.01	1.0 1.0100%
getJSeq() : List<JalviewModel.JSeq>   getJSeq() : List<JalviewModel.JSeq>	534534	3.03	2.02	1.0 1.0100%
getJGroup() : List<JalviewModel.JGroup>   getJGroup() : List<JalviewModel.JGroup>	566566	3.03	2.02	1.0 1.0100%
getViewport() : List<JalviewModel.Viewport>   getViewport() : List<JalviewModel.Viewport>	598598	3.03	2.02	1.0 1.0100%
getUserColours() : List<JalviewModel.UserColours>   getUserColours() : List<JalviewModel.UserColours>	630630	3.03	2.02	0.0 0.00%
getTree() : List<JalviewModel.Tree>   getTree() : List<JalviewModel.Tree>	662662	3.03	2.02	1.0 1.0100%
getPcaViewer() : List<JalviewModel.PcaViewer>   getPcaViewer() : List<JalviewModel.PcaViewer>	694694	3.03	2.02	1.0 1.0100%
getFeatureSettings() : JalviewModel.FeatureSettings   getFeatureSettings() : JalviewModel.FeatureSettings	709709	1.01	1.01	1.0 1.0100%
setFeatureSettings(JalviewModel.FeatureSettings) : void   setFeatureSettings(JalviewModel.FeatureSettings) : void	721721	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.FeatureSettings

Class JalviewModel.FeatureSettings	Line # 783	Total Statements 6	Complexity 4	TOTAL Coverage 1.0100%
getSetting() : List<JalviewModel.FeatureSettings.Setting>   getSetting() : List<JalviewModel.FeatureSettings.Setting>	815815	3.03	2.02	1.0 1.0100%
getGroup() : List<JalviewModel.FeatureSettings.Group>   getGroup() : List<JalviewModel.FeatureSettings.Group>	847847	3.03	2.02	1.0 1.0100%

 

Class JalviewModel.FeatureSettings.Group

Class JalviewModel.FeatureSettings.Group	Line # 875	Total Statements 4	Complexity 4	TOTAL Coverage 1.0100%
getName() : String   getName() : String	890890	1.01	1.01	1.0 1.0100%
setName(String) : void   setName(String) : void	902902	1.01	1.01	1.0 1.0100%
isDisplay() : boolean   isDisplay() : boolean	910910	1.01	1.01	1.0 1.0100%
setDisplay(boolean) : void   setDisplay(boolean) : void	918918	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.FeatureSettings.Setting

Class JalviewModel.FeatureSettings.Setting	Line # 962	Total Statements 31	Complexity 29	TOTAL Coverage 0.967741996.8%
getAttributeName() : List<String>   getAttributeName() : List<String>	10451045	3.03	2.02	1.0 1.0100%
getMatcherSet() : FeatureMatcherSet   getMatcherSet() : FeatureMatcherSet	10601060	1.01	1.01	1.0 1.0100%
setMatcherSet(FeatureMatcherSet) : void   setMatcherSet(FeatureMatcherSet) : void	10731073	1.01	1.01	1.0 1.0100%
getType() : String   getType() : String	10851085	1.01	1.01	1.0 1.0100%
setType(String) : void   setType(String) : void	10971097	1.01	1.01	1.0 1.0100%
getColour() : int   getColour() : int	11051105	1.01	1.01	1.0 1.0100%
setColour(int) : void   setColour(int) : void	11131113	1.01	1.01	1.0 1.0100%
isDisplay() : boolean   isDisplay() : boolean	11211121	1.01	1.01	1.0 1.0100%
setDisplay(boolean) : void   setDisplay(boolean) : void	11291129	1.01	1.01	1.0 1.0100%
getOrder() : Float   getOrder() : Float	11411141	1.01	1.01	1.0 1.0100%
setOrder(Float) : void   setOrder(Float) : void	11531153	1.01	1.01	1.0 1.0100%
getMincolour() : Integer   getMincolour() : Integer	11681168	1.01	1.01	1.0 1.0100%
setMincolour(Integer) : void   setMincolour(Integer) : void	11811181	1.01	1.01	1.0 1.0100%
getNoValueColour() : NoValueColour   getNoValueColour() : NoValueColour	11931193	3.03	2.02	0.6 0.660%
setNoValueColour(NoValueColour) : void   setNoValueColour(NoValueColour) : void	12091209	1.01	1.01	1.0 1.0100%
getThreshold() : Float   getThreshold() : Float	12221222	1.01	1.01	1.0 1.0100%
setThreshold(Float) : void   setThreshold(Float) : void	12351235	1.01	1.01	1.0 1.0100%
getThreshstate() : Integer   getThreshstate() : Integer	12481248	1.01	1.01	1.0 1.0100%
setThreshstate(Integer) : void   setThreshstate(Integer) : void	12611261	1.01	1.01	1.0 1.0100%
getMax() : Float   getMax() : Float	12731273	1.01	1.01	1.0 1.0100%
setMax(Float) : void   setMax(Float) : void	12851285	1.01	1.01	1.0 1.0100%
getMin() : Float   getMin() : Float	12971297	1.01	1.01	1.0 1.0100%
setMin(Float) : void   setMin(Float) : void	13091309	1.01	1.01	1.0 1.0100%
isColourByLabel() : Boolean   isColourByLabel() : Boolean	13211321	1.01	1.01	1.0 1.0100%
setColourByLabel(Boolean) : void   setColourByLabel(Boolean) : void	13331333	1.01	1.01	1.0 1.0100%
isAutoScale() : Boolean   isAutoScale() : Boolean	13451345	1.01	1.01	1.0 1.0100%
setAutoScale(Boolean) : void   setAutoScale(Boolean) : void	13571357	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.JGroup

Class JalviewModel.JGroup	Line # 1410	Total Statements 69	Complexity 61	TOTAL Coverage 0.891304489.1%
getSeq() : List<String>   getSeq() : List<String>	15171517	3.03	2.02	1.0 1.0100%
getAnnotationColours() : AnnotationColourScheme   getAnnotationColours() : AnnotationColourScheme	15321532	1.01	1.01	1.0 1.0100%
setAnnotationColours(AnnotationColourScheme) : void   setAnnotationColours(AnnotationColourScheme) : void	15441544	1.01	1.01	1.0 1.0100%
getAnnotationFromTree() : List<String>   getAnnotationFromTree() : List<String>	15731573	3.03	2.02	1.0 1.0100%
getSecStrProvider() : List<String>   getSecStrProvider() : List<String>	16051605	3.03	2.02	0.8 0.880%
getStart() : Integer   getStart() : Integer	16201620	1.01	1.01	1.0 1.0100%
setStart(Integer) : void   setStart(Integer) : void	16321632	1.01	1.01	1.0 1.0100%
getEnd() : Integer   getEnd() : Integer	16441644	1.01	1.01	1.0 1.0100%
setEnd(Integer) : void   setEnd(Integer) : void	16561656	1.01	1.01	1.0 1.0100%
getName() : String   getName() : String	16681668	1.01	1.01	1.0 1.0100%
setName(String) : void   setName(String) : void	16801680	1.01	1.01	1.0 1.0100%
getColour() : String   getColour() : String	16921692	1.01	1.01	1.0 1.0100%
setColour(String) : void   setColour(String) : void	17041704	1.01	1.01	1.0 1.0100%
getIdColour() : Integer   getIdColour() : Integer	17161716	1.01	1.01	1.0 1.0100%
setIdColour(Integer) : void   setIdColour(Integer) : void	17281728	1.01	1.01	1.0 1.0100%
getOutlineColour() : Integer   getOutlineColour() : Integer	17401740	1.01	1.01	1.0 1.0100%
setOutlineColour(Integer) : void   setOutlineColour(Integer) : void	17521752	1.01	1.01	1.0 1.0100%
isDisplayBoxes() : Boolean   isDisplayBoxes() : Boolean	17641764	1.01	1.01	1.0 1.0100%
setDisplayBoxes(Boolean) : void   setDisplayBoxes(Boolean) : void	17761776	1.01	1.01	1.0 1.0100%
isDisplayText() : Boolean   isDisplayText() : Boolean	17881788	1.01	1.01	1.0 1.0100%
setDisplayText(Boolean) : void   setDisplayText(Boolean) : void	18001800	1.01	1.01	1.0 1.0100%
isColourText() : Boolean   isColourText() : Boolean	18121812	1.01	1.01	1.0 1.0100%
setColourText(Boolean) : void   setColourText(Boolean) : void	18241824	1.01	1.01	1.0 1.0100%
getTextCol1() : Integer   getTextCol1() : Integer	18361836	1.01	1.01	1.0 1.0100%
setTextCol1(Integer) : void   setTextCol1(Integer) : void	18481848	1.01	1.01	1.0 1.0100%
getTextCol2() : Integer   getTextCol2() : Integer	18601860	1.01	1.01	1.0 1.0100%
setTextCol2(Integer) : void   setTextCol2(Integer) : void	18721872	1.01	1.01	1.0 1.0100%
getTextColThreshold() : Integer   getTextColThreshold() : Integer	18841884	1.01	1.01	1.0 1.0100%
setTextColThreshold(Integer) : void   setTextColThreshold(Integer) : void	18961896	1.01	1.01	1.0 1.0100%
isShowUnconserved() : Boolean   isShowUnconserved() : Boolean	19081908	1.01	1.01	1.0 1.0100%
setShowUnconserved(Boolean) : void   setShowUnconserved(Boolean) : void	19201920	1.01	1.01	1.0 1.0100%
getId() : String   getId() : String	19351935	1.01	1.01	1.0 1.0100%
setId(String) : void   setId(String) : void	19481948	1.01	1.01	1.0 1.0100%
isConservationSelected() : Boolean   isConservationSelected() : Boolean	19601960	1.01	1.01	0.0 0.00%
setConservationSelected(Boolean) : void   setConservationSelected(Boolean) : void	19721972	1.01	1.01	0.0 0.00%
getConsThreshold() : Integer   getConsThreshold() : Integer	19841984	1.01	1.01	1.0 1.0100%
setConsThreshold(Integer) : void   setConsThreshold(Integer) : void	19971997	1.01	1.01	1.0 1.0100%
isPidSelected() : Boolean   isPidSelected() : Boolean	20092009	1.01	1.01	0.0 0.00%
setPidSelected(Boolean) : void   setPidSelected(Boolean) : void	20212021	1.01	1.01	0.0 0.00%
getPidThreshold() : Integer   getPidThreshold() : Integer	20332033	1.01	1.01	1.0 1.0100%
setPidThreshold(Integer) : void   setPidThreshold(Integer) : void	20462046	1.01	1.01	1.0 1.0100%
isSecstrSelected() : boolean   isSecstrSelected() : boolean	20582058	3.03	2.02	1.0 1.0100%
setSecstrSelected(Boolean) : void   setSecstrSelected(Boolean) : void	20752075	1.01	1.01	1.0 1.0100%
getSecstrThreshold() : Integer   getSecstrThreshold() : Integer	20872087	1.01	1.01	1.0 1.0100%
setSecstrThreshold(Integer) : void   setSecstrThreshold(Integer) : void	21002100	1.01	1.01	1.0 1.0100%
isShowConsensusHistogram() : boolean   isShowConsensusHistogram() : boolean	21122112	3.03	2.02	0.6 0.660%
setShowConsensusHistogram(Boolean) : void   setShowConsensusHistogram(Boolean) : void	21282128	1.01	1.01	1.0 1.0100%
isShowSequenceLogo() : boolean   isShowSequenceLogo() : boolean	21402140	3.03	2.02	0.6 0.660%
setShowSequenceLogo(Boolean) : void   setShowSequenceLogo(Boolean) : void	21562156	1.01	1.01	1.0 1.0100%
isNormaliseSequenceLogo() : boolean   isNormaliseSequenceLogo() : boolean	21682168	3.03	2.02	1.0 1.0100%
setNormaliseSequenceLogo(Boolean) : void   setNormaliseSequenceLogo(Boolean) : void	21842184	1.01	1.01	1.0 1.0100%
isIgnoreGapsinConsensus() : boolean   isIgnoreGapsinConsensus() : boolean	21962196	3.03	2.02	0.6 0.660%
setIgnoreGapsinConsensus(Boolean) : void   setIgnoreGapsinConsensus(Boolean) : void	22122212	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.JSeq

Class JalviewModel.JSeq	Line # 2304	Total Statements 24	Complexity 20	TOTAL Coverage 0.979166797.9%
getFeatures() : List<Feature>   getFeatures() : List<Feature>	23632363	3.03	2.02	1.0 1.0100%
getPdbids() : List<JalviewModel.JSeq.Pdbids>   getPdbids() : List<JalviewModel.JSeq.Pdbids>	23952395	3.03	2.02	1.0 1.0100%
getHiddenSequences() : List<Integer>   getHiddenSequences() : List<Integer>	24272427	3.03	2.02	1.0 1.0100%
getRnaViewer() : List<JalviewModel.JSeq.RnaViewer>   getRnaViewer() : List<JalviewModel.JSeq.RnaViewer>	24682468	3.03	2.02	0.8 0.880%
getColour() : Integer   getColour() : Integer	24832483	1.01	1.01	1.0 1.0100%
setColour(Integer) : void   setColour(Integer) : void	24952495	1.01	1.01	1.0 1.0100%
getStart() : int   getStart() : int	25032503	1.01	1.01	1.0 1.0100%
setStart(int) : void   setStart(int) : void	25112511	1.01	1.01	1.0 1.0100%
getEnd() : int   getEnd() : int	25192519	1.01	1.01	1.0 1.0100%
setEnd(int) : void   setEnd(int) : void	25272527	1.01	1.01	1.0 1.0100%
getId() : String   getId() : String	25392539	1.01	1.01	1.0 1.0100%
setId(String) : void   setId(String) : void	25512551	1.01	1.01	1.0 1.0100%
isHidden() : Boolean   isHidden() : Boolean	25632563	1.01	1.01	1.0 1.0100%
setHidden(Boolean) : void   setHidden(Boolean) : void	25752575	1.01	1.01	1.0 1.0100%
isViewreference() : Boolean   isViewreference() : Boolean	25872587	1.01	1.01	1.0 1.0100%
setViewreference(Boolean) : void   setViewreference(Boolean) : void	25992599	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.JSeq.Pdbids

Class JalviewModel.JSeq.Pdbids	Line # 2641	Total Statements 3	Complexity 2	TOTAL Coverage 1.0100%
getStructureState() : List<JalviewModel.JSeq.Pdbids.StructureState>   getStructureState() : List<JalviewModel.JSeq.Pdbids.StructureState>	26732673	3.03	2.02	1.0 1.0100%

 

Class JalviewModel.JSeq.Pdbids.StructureState

Class JalviewModel.JSeq.Pdbids.StructureState	Line # 2708	Total Statements 28	Complexity 25	TOTAL Coverage 0.821428682.1%
getValue() : String   getValue() : String	28892889	1.01	1.01	1.0 1.0100%
setValue(String) : void   setValue(String) : void	29012901	1.01	1.01	0.0 0.00%
isVisible() : Boolean   isVisible() : Boolean	29132913	1.01	1.01	0.0 0.00%
setVisible(Boolean) : void   setVisible(Boolean) : void	29252925	1.01	1.01	1.0 1.0100%
getViewId() : String   getViewId() : String	29892989	1.01	1.01	1.0 1.0100%
setViewId(String) : void   setViewId(String) : void	30023002	1.01	1.01	1.0 1.0100%
isAlignwithAlignPanel() : boolean   isAlignwithAlignPanel() : boolean	30363036	3.03	2.02	0.6 0.660%
setAlignwithAlignPanel(Boolean) : void   setAlignwithAlignPanel(Boolean) : void	30533053	1.01	1.01	1.0 1.0100%
isColourwithAlignPanel() : boolean   isColourwithAlignPanel() : boolean	30893089	3.03	2.02	0.6 0.660%
setColourwithAlignPanel(Boolean) : void   setColourwithAlignPanel(Boolean) : void	31063106	1.01	1.01	1.0 1.0100%
isColourByJmol() : boolean   isColourByJmol() : boolean	31383138	3.03	2.02	0.6 0.660%
setColourByJmol(Boolean) : void   setColourByJmol(Boolean) : void	31553155	1.01	1.01	1.0 1.0100%
getType() : String   getType() : String	31773177	1.01	1.01	1.0 1.0100%
setType(String) : void   setType(String) : void	31903190	1.01	1.01	1.0 1.0100%
getWidth() : Integer   getWidth() : Integer	32023202	1.01	1.01	1.0 1.0100%
setWidth(Integer) : void   setWidth(Integer) : void	32143214	1.01	1.01	1.0 1.0100%
getHeight() : Integer   getHeight() : Integer	32263226	1.01	1.01	1.0 1.0100%
setHeight(Integer) : void   setHeight(Integer) : void	32383238	1.01	1.01	1.0 1.0100%
getXpos() : Integer   getXpos() : Integer	32503250	1.01	1.01	1.0 1.0100%
setXpos(Integer) : void   setXpos(Integer) : void	32623262	1.01	1.01	1.0 1.0100%
getYpos() : Integer   getYpos() : Integer	32743274	1.01	1.01	1.0 1.0100%
setYpos(Integer) : void   setYpos(Integer) : void	32863286	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.JSeq.RnaViewer

Class JalviewModel.JSeq.RnaViewer	Line # 3334	Total Statements 19	Complexity 18	TOTAL Coverage 0.00%
getSecondaryStructure() : List<JalviewModel.JSeq.RnaViewer.SecondaryStructure>   getSecondaryStructure() : List<JalviewModel.JSeq.RnaViewer.SecondaryStructure>	33963396	3.03	2.02	0.0 0.00%
getTitle() : String   getTitle() : String	34113411	1.01	1.01	0.0 0.00%
setTitle(String) : void   setTitle(String) : void	34233423	1.01	1.01	0.0 0.00%
getViewId() : String   getViewId() : String	34363436	1.01	1.01	0.0 0.00%
setViewId(String) : void   setViewId(String) : void	34493449	1.01	1.01	0.0 0.00%
getDividerLocation() : Integer   getDividerLocation() : Integer	34623462	1.01	1.01	0.0 0.00%
setDividerLocation(Integer) : void   setDividerLocation(Integer) : void	34753475	1.01	1.01	0.0 0.00%
getSelectedRna() : Integer   getSelectedRna() : Integer	34893489	1.01	1.01	0.0 0.00%
setSelectedRna(Integer) : void   setSelectedRna(Integer) : void	35023502	1.01	1.01	0.0 0.00%
getWidth() : Integer   getWidth() : Integer	35143514	1.01	1.01	0.0 0.00%
setWidth(Integer) : void   setWidth(Integer) : void	35263526	1.01	1.01	0.0 0.00%
getHeight() : Integer   getHeight() : Integer	35383538	1.01	1.01	0.0 0.00%
setHeight(Integer) : void   setHeight(Integer) : void	35503550	1.01	1.01	0.0 0.00%
getXpos() : Integer   getXpos() : Integer	35623562	1.01	1.01	0.0 0.00%
setXpos(Integer) : void   setXpos(Integer) : void	35743574	1.01	1.01	0.0 0.00%
getYpos() : Integer   getYpos() : Integer	35863586	1.01	1.01	0.0 0.00%
setYpos(Integer) : void   setYpos(Integer) : void	35983598	1.01	1.01	0.0 0.00%

 

Class JalviewModel.JSeq.RnaViewer.SecondaryStructure

Class JalviewModel.JSeq.RnaViewer.SecondaryStructure	Line # 3625	Total Statements 8	Complexity 8	TOTAL Coverage 0.00%
getTitle() : String   getTitle() : String	36793679	1.01	1.01	0.0 0.00%
setTitle(String) : void   setTitle(String) : void	36913691	1.01	1.01	0.0 0.00%
getAnnotationId() : String   getAnnotationId() : String	37133713	1.01	1.01	0.0 0.00%
setAnnotationId(String) : void   setAnnotationId(String) : void	37263726	1.01	1.01	0.0 0.00%
isGapped() : Boolean   isGapped() : Boolean	37443744	1.01	1.01	0.0 0.00%
setGapped(Boolean) : void   setGapped(Boolean) : void	37573757	1.01	1.01	0.0 0.00%
getViewerState() : String   getViewerState() : String	37763776	1.01	1.01	0.0 0.00%
setViewerState(String) : void   setViewerState(String) : void	37893789	1.01	1.01	0.0 0.00%

 

Class JalviewModel.PcaViewer

Class JalviewModel.PcaViewer	Line # 3875	Total Statements 46	Complexity 44	TOTAL Coverage 1.0100%
getSequencePoint() : List<JalviewModel.PcaViewer.SequencePoint>   getSequencePoint() : List<JalviewModel.PcaViewer.SequencePoint>	39513951	3.03	2.02	1.0 1.0100%
getAxis() : List<JalviewModel.PcaViewer.Axis>   getAxis() : List<JalviewModel.PcaViewer.Axis>	39853985	3.03	2.02	1.0 1.0100%
getSeqPointMin() : JalviewModel.PcaViewer.SeqPointMin   getSeqPointMin() : JalviewModel.PcaViewer.SeqPointMin	40004000	1.01	1.01	1.0 1.0100%
setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin) : void   setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin) : void	40124012	1.01	1.01	1.0 1.0100%
getSeqPointMax() : JalviewModel.PcaViewer.SeqPointMax   getSeqPointMax() : JalviewModel.PcaViewer.SeqPointMax	40244024	1.01	1.01	1.0 1.0100%
setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax) : void   setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax) : void	40364036	1.01	1.01	1.0 1.0100%
getPcaData() : PcaDataType   getPcaData() : PcaDataType	40484048	1.01	1.01	1.0 1.0100%
setPcaData(PcaDataType) : void   setPcaData(PcaDataType) : void	40604060	1.01	1.01	1.0 1.0100%
getTitle() : String   getTitle() : String	40724072	1.01	1.01	1.0 1.0100%
setTitle(String) : void   setTitle(String) : void	40844084	1.01	1.01	1.0 1.0100%
getScoreModelName() : String   getScoreModelName() : String	40964096	1.01	1.01	1.0 1.0100%
setScoreModelName(String) : void   setScoreModelName(String) : void	41084108	1.01	1.01	1.0 1.0100%
getXDim() : Integer   getXDim() : Integer	41204120	1.01	1.01	1.0 1.0100%
setXDim(Integer) : void   setXDim(Integer) : void	41324132	1.01	1.01	1.0 1.0100%
getYDim() : Integer   getYDim() : Integer	41444144	1.01	1.01	1.0 1.0100%
setYDim(Integer) : void   setYDim(Integer) : void	41564156	1.01	1.01	1.0 1.0100%
getZDim() : Integer   getZDim() : Integer	41684168	1.01	1.01	1.0 1.0100%
setZDim(Integer) : void   setZDim(Integer) : void	41804180	1.01	1.01	1.0 1.0100%
getBgColour() : Integer   getBgColour() : Integer	41924192	1.01	1.01	1.0 1.0100%
setBgColour(Integer) : void   setBgColour(Integer) : void	42044204	1.01	1.01	1.0 1.0100%
getScaleFactor() : Float   getScaleFactor() : Float	42164216	1.01	1.01	1.0 1.0100%
setScaleFactor(Float) : void   setScaleFactor(Float) : void	42284228	1.01	1.01	1.0 1.0100%
isShowLabels() : Boolean   isShowLabels() : Boolean	42404240	1.01	1.01	1.0 1.0100%
setShowLabels(Boolean) : void   setShowLabels(Boolean) : void	42524252	1.01	1.01	1.0 1.0100%
isLinkToAllViews() : Boolean   isLinkToAllViews() : Boolean	42644264	1.01	1.01	1.0 1.0100%
setLinkToAllViews(Boolean) : void   setLinkToAllViews(Boolean) : void	42764276	1.01	1.01	1.0 1.0100%
isIncludeGaps() : Boolean   isIncludeGaps() : Boolean	42884288	1.01	1.01	1.0 1.0100%
setIncludeGaps(Boolean) : void   setIncludeGaps(Boolean) : void	43004300	1.01	1.01	1.0 1.0100%
isMatchGaps() : Boolean   isMatchGaps() : Boolean	43124312	1.01	1.01	1.0 1.0100%
setMatchGaps(Boolean) : void   setMatchGaps(Boolean) : void	43244324	1.01	1.01	1.0 1.0100%
isIncludeGappedColumns() : Boolean   isIncludeGappedColumns() : Boolean	43364336	1.01	1.01	1.0 1.0100%
setIncludeGappedColumns(Boolean) : void   setIncludeGappedColumns(Boolean) : void	43484348	1.01	1.01	1.0 1.0100%
isDenominateByShortestLength() : Boolean   isDenominateByShortestLength() : Boolean	43604360	1.01	1.01	1.0 1.0100%
setDenominateByShortestLength(Boolean) : void   setDenominateByShortestLength(Boolean) : void	43724372	1.01	1.01	1.0 1.0100%
getWidth() : Integer   getWidth() : Integer	43844384	1.01	1.01	1.0 1.0100%
setWidth(Integer) : void   setWidth(Integer) : void	43964396	1.01	1.01	1.0 1.0100%
getHeight() : Integer   getHeight() : Integer	44084408	1.01	1.01	1.0 1.0100%
setHeight(Integer) : void   setHeight(Integer) : void	44204420	1.01	1.01	1.0 1.0100%
getXpos() : Integer   getXpos() : Integer	44324432	1.01	1.01	1.0 1.0100%
setXpos(Integer) : void   setXpos(Integer) : void	44444444	1.01	1.01	1.0 1.0100%
getYpos() : Integer   getYpos() : Integer	44564456	1.01	1.01	1.0 1.0100%
setYpos(Integer) : void   setYpos(Integer) : void	44684468	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.PcaViewer.Axis

Class JalviewModel.PcaViewer.Axis	Line # 4492	Total Statements 6	Complexity 6	TOTAL Coverage 1.0100%
getXPos() : Float   getXPos() : Float	45094509	1.01	1.01	1.0 1.0100%
setXPos(Float) : void   setXPos(Float) : void	45214521	1.01	1.01	1.0 1.0100%
getYPos() : Float   getYPos() : Float	45334533	1.01	1.01	1.0 1.0100%
setYPos(Float) : void   setYPos(Float) : void	45454545	1.01	1.01	1.0 1.0100%
getZPos() : Float   getZPos() : Float	45574557	1.01	1.01	1.0 1.0100%
setZPos(Float) : void   setZPos(Float) : void	45694569	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.PcaViewer.SeqPointMax

Class JalviewModel.PcaViewer.SeqPointMax	Line # 4595	Total Statements 6	Complexity 6	TOTAL Coverage 1.0100%
getXPos() : Float   getXPos() : Float	46124612	1.01	1.01	1.0 1.0100%
setXPos(Float) : void   setXPos(Float) : void	46244624	1.01	1.01	1.0 1.0100%
getYPos() : Float   getYPos() : Float	46364636	1.01	1.01	1.0 1.0100%
setYPos(Float) : void   setYPos(Float) : void	46484648	1.01	1.01	1.0 1.0100%
getZPos() : Float   getZPos() : Float	46604660	1.01	1.01	1.0 1.0100%
setZPos(Float) : void   setZPos(Float) : void	46724672	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.PcaViewer.SeqPointMin

Class JalviewModel.PcaViewer.SeqPointMin	Line # 4698	Total Statements 6	Complexity 6	TOTAL Coverage 1.0100%
getXPos() : Float   getXPos() : Float	47154715	1.01	1.01	1.0 1.0100%
setXPos(Float) : void   setXPos(Float) : void	47274727	1.01	1.01	1.0 1.0100%
getYPos() : Float   getYPos() : Float	47394739	1.01	1.01	1.0 1.0100%
setYPos(Float) : void   setYPos(Float) : void	47514751	1.01	1.01	1.0 1.0100%
getZPos() : Float   getZPos() : Float	47634763	1.01	1.01	1.0 1.0100%
setZPos(Float) : void   setZPos(Float) : void	47754775	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.PcaViewer.SequencePoint

Class JalviewModel.PcaViewer.SequencePoint	Line # 4802	Total Statements 8	Complexity 8	TOTAL Coverage 1.0100%
getSequenceRef() : String   getSequenceRef() : String	48214821	1.01	1.01	1.0 1.0100%
setSequenceRef(String) : void   setSequenceRef(String) : void	48334833	1.01	1.01	1.0 1.0100%
getXPos() : Float   getXPos() : Float	48454845	1.01	1.01	1.0 1.0100%
setXPos(Float) : void   setXPos(Float) : void	48574857	1.01	1.01	1.0 1.0100%
getYPos() : Float   getYPos() : Float	48694869	1.01	1.01	1.0 1.0100%
setYPos(Float) : void   setYPos(Float) : void	48814881	1.01	1.01	1.0 1.0100%
getZPos() : Float   getZPos() : Float	48934893	1.01	1.01	1.0 1.0100%
setZPos(Float) : void   setZPos(Float) : void	49054905	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.Tree

Class JalviewModel.Tree	Line # 4976	Total Statements 52	Complexity 48	TOTAL Coverage 0.9038461490.4%
getTitle() : String   getTitle() : String	50575057	1.01	1.01	1.0 1.0100%
setTitle(String) : void   setTitle(String) : void	50695069	1.01	1.01	1.0 1.0100%
getNewick() : String   getNewick() : String	50815081	1.01	1.01	1.0 1.0100%
setNewick(String) : void   setNewick(String) : void	50935093	1.01	1.01	1.0 1.0100%
getTreeColorMap() : JalviewModel.Tree.TreeColorMap   getTreeColorMap() : JalviewModel.Tree.TreeColorMap	51055105	1.01	1.01	1.0 1.0100%
setTreeColorMap(JalviewModel.Tree.TreeColorMap) : void   setTreeColorMap(JalviewModel.Tree.TreeColorMap) : void	51175117	1.01	1.01	1.0 1.0100%
getFontName() : String   getFontName() : String	51295129	1.01	1.01	1.0 1.0100%
setFontName(String) : void   setFontName(String) : void	51415141	1.01	1.01	1.0 1.0100%
getFontSize() : Integer   getFontSize() : Integer	51535153	1.01	1.01	1.0 1.0100%
setFontSize(Integer) : void   setFontSize(Integer) : void	51655165	1.01	1.01	1.0 1.0100%
getFontStyle() : Integer   getFontStyle() : Integer	51775177	1.01	1.01	1.0 1.0100%
setFontStyle(Integer) : void   setFontStyle(Integer) : void	51895189	1.01	1.01	1.0 1.0100%
getThreshold() : Float   getThreshold() : Float	52015201	1.01	1.01	1.0 1.0100%
setThreshold(Float) : void   setThreshold(Float) : void	52135213	1.01	1.01	1.0 1.0100%
isShowBootstrap() : Boolean   isShowBootstrap() : Boolean	52255225	1.01	1.01	1.0 1.0100%
setShowBootstrap(Boolean) : void   setShowBootstrap(Boolean) : void	52375237	1.01	1.01	1.0 1.0100%
isShowDistances() : Boolean   isShowDistances() : Boolean	52495249	1.01	1.01	1.0 1.0100%
setShowDistances(Boolean) : void   setShowDistances(Boolean) : void	52615261	1.01	1.01	1.0 1.0100%
isMarkUnlinked() : Boolean   isMarkUnlinked() : Boolean	52735273	1.01	1.01	1.0 1.0100%
setMarkUnlinked(Boolean) : void   setMarkUnlinked(Boolean) : void	52855285	1.01	1.01	1.0 1.0100%
isFitToWindow() : Boolean   isFitToWindow() : Boolean	52975297	1.01	1.01	1.0 1.0100%
setFitToWindow(Boolean) : void   setFitToWindow(Boolean) : void	53095309	1.01	1.01	1.0 1.0100%
isCurrentTree() : Boolean   isCurrentTree() : Boolean	53215321	1.01	1.01	1.0 1.0100%
setCurrentTree(Boolean) : void   setCurrentTree(Boolean) : void	53335333	1.01	1.01	1.0 1.0100%
isColumnWise() : boolean   isColumnWise() : boolean	53455345	3.03	2.02	0.6 0.660%
setColumnWise(Boolean) : void   setColumnWise(Boolean) : void	53625362	1.01	1.01	0.0 0.00%
isAnnotationBased() : boolean   isAnnotationBased() : boolean	53745374	3.03	2.02	1.0 1.0100%
setAnnotationBased(Boolean) : void   setAnnotationBased(Boolean) : void	53915391	1.01	1.01	1.0 1.0100%
getShowAnnotationAs() : String   getShowAnnotationAs() : String	54035403	3.03	2.02	0.6 0.660%
setShowAnnotationAs(String) : void   setShowAnnotationAs(String) : void	54205420	1.01	1.01	1.0 1.0100%
getColumnReference() : String   getColumnReference() : String	54325432	1.01	1.01	0.0 0.00%
setColumnReference(String) : void   setColumnReference(String) : void	54455445	1.01	1.01	0.0 0.00%
getId() : String   getId() : String	54605460	1.01	1.01	1.0 1.0100%
setId(String) : void   setId(String) : void	54735473	1.01	1.01	1.0 1.0100%
isLinkToAllViews() : boolean   isLinkToAllViews() : boolean	54855485	3.03	2.02	1.0 1.0100%
setLinkToAllViews(Boolean) : void   setLinkToAllViews(Boolean) : void	55015501	1.01	1.01	1.0 1.0100%
getWidth() : Integer   getWidth() : Integer	55135513	1.01	1.01	1.0 1.0100%
setWidth(Integer) : void   setWidth(Integer) : void	55255525	1.01	1.01	1.0 1.0100%
getHeight() : Integer   getHeight() : Integer	55375537	1.01	1.01	1.0 1.0100%
setHeight(Integer) : void   setHeight(Integer) : void	55495549	1.01	1.01	1.0 1.0100%
getXpos() : Integer   getXpos() : Integer	55615561	1.01	1.01	1.0 1.0100%
setXpos(Integer) : void   setXpos(Integer) : void	55735573	1.01	1.01	1.0 1.0100%
getYpos() : Integer   getYpos() : Integer	55855585	1.01	1.01	1.0 1.0100%
setYpos(Integer) : void   setYpos(Integer) : void	55975597	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.Tree.TreeColorMap

Class JalviewModel.Tree.TreeColorMap	Line # 5634	Total Statements 3	Complexity 2	TOTAL Coverage 1.0100%
getColorEntry() : List<JalviewModel.Tree.TreeColorMap.ColorEntry>   getColorEntry() : List<JalviewModel.Tree.TreeColorMap.ColorEntry>	56645664	3.03	2.02	1.0 1.0100%

 

Class JalviewModel.Tree.TreeColorMap.ColorEntry

Class JalviewModel.Tree.TreeColorMap.ColorEntry	Line # 5692	Total Statements 4	Complexity 4	TOTAL Coverage 1.0100%
getLabel() : String   getLabel() : String	57075707	1.01	1.01	1.0 1.0100%
setLabel(String) : void   setLabel(String) : void	57195719	1.01	1.01	1.0 1.0100%
getColor() : int   getColor() : int	57275727	1.01	1.01	1.0 1.0100%
setColor(int) : void   setColor(int) : void	57355735	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.UserColours

Class JalviewModel.UserColours	Line # 5770	Total Statements 4	Complexity 4	TOTAL Coverage 0.00%
getUserColourScheme() : JalviewUserColours   getUserColourScheme() : JalviewUserColours	57855785	1.01	1.01	0.0 0.00%
setUserColourScheme(JalviewUserColours) : void   setUserColourScheme(JalviewUserColours) : void	57975797	1.01	1.01	0.0 0.00%
getId() : String   getId() : String	58095809	1.01	1.01	0.0 0.00%
setId(String) : void   setId(String) : void	58215821	1.01	1.01	0.0 0.00%

 

Class JalviewModel.Viewport

Class JalviewModel.Viewport	Line # 5934	Total Statements 155	Complexity 136	TOTAL Coverage 0.896774289.7%
getAnnotationColours() : AnnotationColourScheme   getAnnotationColours() : AnnotationColourScheme	61086108	1.01	1.01	1.0 1.0100%
setAnnotationColours(AnnotationColourScheme) : void   setAnnotationColours(AnnotationColourScheme) : void	61206120	1.01	1.01	1.0 1.0100%
getHiddenColumns() : List<JalviewModel.Viewport.HiddenColumns>   getHiddenColumns() : List<JalviewModel.Viewport.HiddenColumns>	61496149	3.03	2.02	1.0 1.0100%
getCalcIdParam() : List<JalviewModel.Viewport.CalcIdParam>   getCalcIdParam() : List<JalviewModel.Viewport.CalcIdParam>	61816181	3.03	2.02	1.0 1.0100%
getOverview() : JalviewModel.Viewport.Overview   getOverview() : JalviewModel.Viewport.Overview	61966196	1.01	1.01	1.0 1.0100%
setOverview(JalviewModel.Viewport.Overview) : void   setOverview(JalviewModel.Viewport.Overview) : void	62086208	1.01	1.01	1.0 1.0100%
getSecStrProvider() : List<String>   getSecStrProvider() : List<String>	62376237	3.03	2.02	0.0 0.00%
getBgColour() : String   getBgColour() : String	62526252	1.01	1.01	1.0 1.0100%
setBgColour(String) : void   setBgColour(String) : void	62646264	1.01	1.01	1.0 1.0100%
getTitle() : String   getTitle() : String	62766276	1.01	1.01	1.0 1.0100%
setTitle(String) : void   setTitle(String) : void	62886288	1.01	1.01	1.0 1.0100%
isShowFullId() : Boolean   isShowFullId() : Boolean	63006300	1.01	1.01	1.0 1.0100%
setShowFullId(Boolean) : void   setShowFullId(Boolean) : void	63126312	1.01	1.01	1.0 1.0100%
isRightAlignIds() : Boolean   isRightAlignIds() : Boolean	63246324	1.01	1.01	1.0 1.0100%
setRightAlignIds(Boolean) : void   setRightAlignIds(Boolean) : void	63366336	1.01	1.01	1.0 1.0100%
isShowText() : Boolean   isShowText() : Boolean	63486348	1.01	1.01	1.0 1.0100%
setShowText(Boolean) : void   setShowText(Boolean) : void	63606360	1.01	1.01	1.0 1.0100%
isShowColourText() : Boolean   isShowColourText() : Boolean	63726372	1.01	1.01	1.0 1.0100%
setShowColourText(Boolean) : void   setShowColourText(Boolean) : void	63846384	1.01	1.01	1.0 1.0100%
isShowUnconserved() : boolean   isShowUnconserved() : boolean	63966396	3.03	2.02	0.6 0.660%
setShowUnconserved(Boolean) : void   setShowUnconserved(Boolean) : void	64126412	1.01	1.01	1.0 1.0100%
isShowBoxes() : Boolean   isShowBoxes() : Boolean	64246424	1.01	1.01	1.0 1.0100%
setShowBoxes(Boolean) : void   setShowBoxes(Boolean) : void	64366436	1.01	1.01	1.0 1.0100%
isWrapAlignment() : Boolean   isWrapAlignment() : Boolean	64486448	1.01	1.01	1.0 1.0100%
setWrapAlignment(Boolean) : void   setWrapAlignment(Boolean) : void	64606460	1.01	1.01	1.0 1.0100%
isRenderGaps() : Boolean   isRenderGaps() : Boolean	64726472	1.01	1.01	1.0 1.0100%
setRenderGaps(Boolean) : void   setRenderGaps(Boolean) : void	64846484	1.01	1.01	1.0 1.0100%
isShowSequenceFeatures() : Boolean   isShowSequenceFeatures() : Boolean	64966496	1.01	1.01	1.0 1.0100%
setShowSequenceFeatures(Boolean) : void   setShowSequenceFeatures(Boolean) : void	65086508	1.01	1.01	1.0 1.0100%
isShowNPfeatureTooltip() : Boolean   isShowNPfeatureTooltip() : Boolean	65206520	1.01	1.01	1.0 1.0100%
setShowNPfeatureTooltip(Boolean) : void   setShowNPfeatureTooltip(Boolean) : void	65326532	1.01	1.01	1.0 1.0100%
isShowDbRefTooltip() : Boolean   isShowDbRefTooltip() : Boolean	65446544	1.01	1.01	1.0 1.0100%
setShowDbRefTooltip(Boolean) : void   setShowDbRefTooltip(Boolean) : void	65566556	1.01	1.01	1.0 1.0100%
isFollowHighlight() : boolean   isFollowHighlight() : boolean	65686568	3.03	2.02	0.6 0.660%
setFollowHighlight(Boolean) : void   setFollowHighlight(Boolean) : void	65846584	1.01	1.01	1.0 1.0100%
isFollowSelection() : boolean   isFollowSelection() : boolean	65966596	3.03	2.02	0.6 0.660%
setFollowSelection(Boolean) : void   setFollowSelection(Boolean) : void	66126612	1.01	1.01	1.0 1.0100%
isShowAnnotation() : Boolean   isShowAnnotation() : Boolean	66246624	1.01	1.01	1.0 1.0100%
setShowAnnotation(Boolean) : void   setShowAnnotation(Boolean) : void	66366636	1.01	1.01	1.0 1.0100%
isShowStructureProviders() : boolean   isShowStructureProviders() : boolean	66486648	3.03	2.02	1.0 1.0100%
setShowStructureProviders(Boolean) : void   setShowStructureProviders(Boolean) : void	66646664	1.01	1.01	1.0 1.0100%
isCentreColumnLabels() : boolean   isCentreColumnLabels() : boolean	66766676	3.03	2.02	0.6 0.660%
setCentreColumnLabels(Boolean) : void   setCentreColumnLabels(Boolean) : void	66926692	1.01	1.01	0.0 0.00%
isShowGroupConservation() : boolean   isShowGroupConservation() : boolean	67046704	3.03	2.02	0.6 0.660%
setShowGroupConservation(Boolean) : void   setShowGroupConservation(Boolean) : void	67216721	1.01	1.01	1.0 1.0100%
isShowGroupConsensus() : boolean   isShowGroupConsensus() : boolean	67336733	3.03	2.02	0.6 0.660%
setShowGroupConsensus(Boolean) : void   setShowGroupConsensus(Boolean) : void	67506750	1.01	1.01	1.0 1.0100%
isShowGroupSecStrConsensus() : boolean   isShowGroupSecStrConsensus() : boolean	67626762	3.03	2.02	1.0 1.0100%
setShowGroupSecStrConsensus(Boolean) : void   setShowGroupSecStrConsensus(Boolean) : void	67796779	1.01	1.01	1.0 1.0100%
getStartRes() : Integer   getStartRes() : Integer	67916791	1.01	1.01	1.0 1.0100%
setStartRes(Integer) : void   setStartRes(Integer) : void	68036803	1.01	1.01	1.0 1.0100%
getStartSeq() : Integer   getStartSeq() : Integer	68156815	1.01	1.01	0.0 0.00%
setStartSeq(Integer) : void   setStartSeq(Integer) : void	68276827	1.01	1.01	1.0 1.0100%
getCharWidth() : Integer   getCharWidth() : Integer	68396839	1.01	1.01	1.0 1.0100%
setCharWidth(Integer) : void   setCharWidth(Integer) : void	68516851	1.01	1.01	1.0 1.0100%
getCharHeight() : Integer   getCharHeight() : Integer	68636863	1.01	1.01	1.0 1.0100%
setCharHeight(Integer) : void   setCharHeight(Integer) : void	68756875	1.01	1.01	1.0 1.0100%
getFontName() : String   getFontName() : String	68876887	1.01	1.01	1.0 1.0100%
setFontName(String) : void   setFontName(String) : void	68996899	1.01	1.01	1.0 1.0100%
getFontSize() : Integer   getFontSize() : Integer	69116911	1.01	1.01	1.0 1.0100%
setFontSize(Integer) : void   setFontSize(Integer) : void	69236923	1.01	1.01	1.0 1.0100%
getFontStyle() : Integer   getFontStyle() : Integer	69356935	1.01	1.01	1.0 1.0100%
setFontStyle(Integer) : void   setFontStyle(Integer) : void	69476947	1.01	1.01	1.0 1.0100%
getIdWidth() : Integer   getIdWidth() : Integer	69596959	1.01	1.01	1.0 1.0100%
setIdWidth(Integer) : void   setIdWidth(Integer) : void	69716971	1.01	1.01	1.0 1.0100%
isIdWidthManuallyAdjusted() : Boolean   isIdWidthManuallyAdjusted() : Boolean	69836983	1.01	1.01	1.0 1.0100%
setIdWidthManuallyAdjusted(Boolean) : void   setIdWidthManuallyAdjusted(Boolean) : void	69956995	1.01	1.01	1.0 1.0100%
isScaleProteinAsCdna() : boolean   isScaleProteinAsCdna() : boolean	70077007	3.03	2.02	1.0 1.0100%
setScaleProteinAsCdna(Boolean) : void   setScaleProteinAsCdna(Boolean) : void	70237023	1.01	1.01	1.0 1.0100%
getViewName() : String   getViewName() : String	70357035	1.01	1.01	1.0 1.0100%
setViewName(String) : void   setViewName(String) : void	70477047	1.01	1.01	1.0 1.0100%
getSequenceSetId() : String   getSequenceSetId() : String	70597059	1.01	1.01	1.0 1.0100%
setSequenceSetId(String) : void   setSequenceSetId(String) : void	70717071	1.01	1.01	1.0 1.0100%
isGatheredViews() : Boolean   isGatheredViews() : Boolean	70837083	1.01	1.01	1.0 1.0100%
setGatheredViews(Boolean) : void   setGatheredViews(Boolean) : void	70957095	1.01	1.01	1.0 1.0100%
getTextCol1() : Integer   getTextCol1() : Integer	71077107	1.01	1.01	1.0 1.0100%
setTextCol1(Integer) : void   setTextCol1(Integer) : void	71197119	1.01	1.01	1.0 1.0100%
getTextCol2() : Integer   getTextCol2() : Integer	71317131	1.01	1.01	1.0 1.0100%
setTextCol2(Integer) : void   setTextCol2(Integer) : void	71437143	1.01	1.01	1.0 1.0100%
getTextColThreshold() : Integer   getTextColThreshold() : Integer	71557155	1.01	1.01	1.0 1.0100%
setTextColThreshold(Integer) : void   setTextColThreshold(Integer) : void	71677167	1.01	1.01	1.0 1.0100%
getId() : String   getId() : String	71827182	1.01	1.01	1.0 1.0100%
setId(String) : void   setId(String) : void	71957195	1.01	1.01	1.0 1.0100%
getComplementId() : String   getComplementId() : String	72087208	1.01	1.01	1.0 1.0100%
setComplementId(String) : void   setComplementId(String) : void	72217221	1.01	1.01	0.0 0.00%
isShowComplementFeatures() : boolean   isShowComplementFeatures() : boolean	72337233	3.03	2.02	1.0 1.0100%
setShowComplementFeatures(Boolean) : void   setShowComplementFeatures(Boolean) : void	72497249	1.01	1.01	1.0 1.0100%
isShowComplementFeaturesOnTop() : boolean   isShowComplementFeaturesOnTop() : boolean	72617261	3.03	2.02	1.0 1.0100%
setShowComplementFeaturesOnTop(Boolean) : void   setShowComplementFeaturesOnTop(Boolean) : void	72777277	1.01	1.01	1.0 1.0100%
getWidth() : Integer   getWidth() : Integer	72897289	1.01	1.01	1.0 1.0100%
setWidth(Integer) : void   setWidth(Integer) : void	73017301	1.01	1.01	1.0 1.0100%
getHeight() : Integer   getHeight() : Integer	73137313	1.01	1.01	1.0 1.0100%
setHeight(Integer) : void   setHeight(Integer) : void	73257325	1.01	1.01	1.0 1.0100%
getXpos() : Integer   getXpos() : Integer	73377337	1.01	1.01	1.0 1.0100%
setXpos(Integer) : void   setXpos(Integer) : void	73497349	1.01	1.01	1.0 1.0100%
getYpos() : Integer   getYpos() : Integer	73617361	1.01	1.01	1.0 1.0100%
setYpos(Integer) : void   setYpos(Integer) : void	73737373	1.01	1.01	1.0 1.0100%
isConservationSelected() : Boolean   isConservationSelected() : Boolean	73857385	1.01	1.01	1.0 1.0100%
setConservationSelected(Boolean) : void   setConservationSelected(Boolean) : void	73977397	1.01	1.01	1.0 1.0100%
getConsThreshold() : Integer   getConsThreshold() : Integer	74097409	1.01	1.01	1.0 1.0100%
setConsThreshold(Integer) : void   setConsThreshold(Integer) : void	74227422	1.01	1.01	1.0 1.0100%
isPidSelected() : Boolean   isPidSelected() : Boolean	74347434	1.01	1.01	1.0 1.0100%
setPidSelected(Boolean) : void   setPidSelected(Boolean) : void	74467446	1.01	1.01	1.0 1.0100%
getPidThreshold() : Integer   getPidThreshold() : Integer	74587458	1.01	1.01	1.0 1.0100%
setPidThreshold(Integer) : void   setPidThreshold(Integer) : void	74717471	1.01	1.01	1.0 1.0100%
isSecstrSelected() : boolean   isSecstrSelected() : boolean	74837483	3.03	2.02	1.0 1.0100%
setSecstrSelected(Boolean) : void   setSecstrSelected(Boolean) : void	75007500	1.01	1.01	1.0 1.0100%
getSecstrThreshold() : Integer   getSecstrThreshold() : Integer	75127512	1.01	1.01	1.0 1.0100%
setSecstrThreshold(Integer) : void   setSecstrThreshold(Integer) : void	75257525	1.01	1.01	0.0 0.00%
isShowConsensusHistogram() : boolean   isShowConsensusHistogram() : boolean	75377537	3.03	2.02	0.6 0.660%
setShowConsensusHistogram(Boolean) : void   setShowConsensusHistogram(Boolean) : void	75537553	1.01	1.01	1.0 1.0100%
isShowSequenceLogo() : boolean   isShowSequenceLogo() : boolean	75657565	3.03	2.02	0.6 0.660%
setShowSequenceLogo(Boolean) : void   setShowSequenceLogo(Boolean) : void	75817581	1.01	1.01	1.0 1.0100%
isNormaliseSequenceLogo() : boolean   isNormaliseSequenceLogo() : boolean	75937593	3.03	2.02	1.0 1.0100%
setNormaliseSequenceLogo(Boolean) : void   setNormaliseSequenceLogo(Boolean) : void	76097609	1.01	1.01	1.0 1.0100%
isIgnoreGapsinConsensus() : boolean   isIgnoreGapsinConsensus() : boolean	76217621	3.03	2.02	0.6 0.660%
setIgnoreGapsinConsensus(Boolean) : void   setIgnoreGapsinConsensus(Boolean) : void	76377637	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.Viewport.CalcIdParam

Class JalviewModel.Viewport.CalcIdParam	Line # 7663	Total Statements 8	Complexity 7	TOTAL Coverage 0.00%
getCalcId() : String   getCalcId() : String	76987698	1.01	1.01	0.0 0.00%
setCalcId(String) : void   setCalcId(String) : void	77117711	1.01	1.01	0.0 0.00%
isNeedsUpdate() : boolean   isNeedsUpdate() : boolean	77247724	3.03	2.02	0.0 0.00%
setNeedsUpdate(Boolean) : void   setNeedsUpdate(Boolean) : void	77417741	1.01	1.01	0.0 0.00%
isAutoUpdate() : boolean   isAutoUpdate() : boolean	77507750	1.01	1.01	0.0 0.00%
setAutoUpdate(boolean) : void   setAutoUpdate(boolean) : void	77587758	1.01	1.01	0.0 0.00%

 

Class JalviewModel.Viewport.HiddenColumns

Class JalviewModel.Viewport.HiddenColumns	Line # 7785	Total Statements 4	Complexity 4	TOTAL Coverage 1.0100%
getStart() : Integer   getStart() : Integer	78007800	1.01	1.01	1.0 1.0100%
setStart(Integer) : void   setStart(Integer) : void	78127812	1.01	1.01	1.0 1.0100%
getEnd() : Integer   getEnd() : Integer	78247824	1.01	1.01	1.0 1.0100%
setEnd(Integer) : void   setEnd(Integer) : void	78367836	1.01	1.01	1.0 1.0100%

 

Class JalviewModel.Viewport.Overview

Class JalviewModel.Viewport.Overview	Line # 7867	Total Statements 18	Complexity 18	TOTAL Coverage 1.0100%
isShowHidden() : Boolean   isShowHidden() : Boolean	78967896	1.01	1.01	1.0 1.0100%
setShowHidden(Boolean) : void   setShowHidden(Boolean) : void	79087908	1.01	1.01	1.0 1.0100%
getResidueColour() : Integer   getResidueColour() : Integer	79207920	1.01	1.01	1.0 1.0100%
setResidueColour(Integer) : void   setResidueColour(Integer) : void	79327932	1.01	1.01	1.0 1.0100%
getGapColour() : Integer   getGapColour() : Integer	79447944	1.01	1.01	1.0 1.0100%
setGapColour(Integer) : void   setGapColour(Integer) : void	79567956	1.01	1.01	1.0 1.0100%
getHiddenColour() : Integer   getHiddenColour() : Integer	79687968	1.01	1.01	1.0 1.0100%
setHiddenColour(Integer) : void   setHiddenColour(Integer) : void	79807980	1.01	1.01	1.0 1.0100%
getTitle() : String   getTitle() : String	79927992	1.01	1.01	1.0 1.0100%
setTitle(String) : void   setTitle(String) : void	80048004	1.01	1.01	1.0 1.0100%
getWidth() : Integer   getWidth() : Integer	80168016	1.01	1.01	1.0 1.0100%
setWidth(Integer) : void   setWidth(Integer) : void	80288028	1.01	1.01	1.0 1.0100%
getHeight() : Integer   getHeight() : Integer	80408040	1.01	1.01	1.0 1.0100%
setHeight(Integer) : void   setHeight(Integer) : void	80528052	1.01	1.01	1.0 1.0100%
getXpos() : Integer   getXpos() : Integer	80648064	1.01	1.01	1.0 1.0100%
setXpos(Integer) : void   setXpos(Integer) : void	80768076	1.01	1.01	1.0 1.0100%
getYpos() : Integer   getYpos() : Integer	80888088	1.01	1.01	1.0 1.0100%
setYpos(Integer) : void   setYpos(Integer) : void	81008100	1.01	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.62360597	jalview.project.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettingsjalview.project.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettings	1PASS
	0.5864312	jalview.project.Jalview2xmlTests.testStoreAndRecoverExpandedviewsjalview.project.Jalview2xmlTests.testStoreAndRecoverExpandedviews	1PASS
	0.55390334	jalview.project.Jalview2xmlTests.testSaveAndLoadAnnotationsPropertiesjalview.project.Jalview2xmlTests.testSaveAndLoadAnnotationsProperties	1PASS
	0.54460967	jalview.project.Jalview2xmlTests.testSaveAndLoadAnnotationBasedTreejalview.project.Jalview2xmlTests.testSaveAndLoadAnnotationBasedTree	1PASS
	0.51301116	jalview.project.Jalview2xmlTests.testStoreAndRestoreIDwidthAndAnnotationHeightjalview.project.Jalview2xmlTests.testStoreAndRestoreIDwidthAndAnnotationHeight	1PASS
	0.43959108	jalview.project.Jalview2xmlTests.testPcaViewAssociationjalview.project.Jalview2xmlTests.testPcaViewAssociation	1PASS
	0.41356876	jalview.project.Jalview2xmlTests.testColourByAnnotScoresjalview.project.Jalview2xmlTests.testColourByAnnotScores	1PASS
	0.4098513	jalview.project.Jalview2xmlTests.testStoreAndRecoverColourThresholdsjalview.project.Jalview2xmlTests.testStoreAndRecoverColourThresholds	1PASS
	0.39219332	jalview.gui.AlignFrameTest.testNewView_colourThresholdsjalview.gui.AlignFrameTest.testNewView_colourThresholds	1PASS
	0.38568774	jalview.project.Jalview2xmlTests.testStoreAndRecoverPDBEntryjalview.project.Jalview2xmlTests.testStoreAndRecoverPDBEntry	1PASS
	0.38289964	jalview.project.Jalview2xmlTests.testSaveLoadFeatureColoursAndFiltersjalview.project.Jalview2xmlTests.testSaveLoadFeatureColoursAndFilters	1PASS
	0.35037175	jalview.io.AnnotatedPDBFileInputTest.testJalviewProjectRelocationAnnotationjalview.io.AnnotatedPDBFileInputTest.testJalviewProjectRelocationAnnotation	1PASS
	0.34479553	jalview.project.Jalview2xmlTests.viewRefPdbAnnotationjalview.project.Jalview2xmlTests.viewRefPdbAnnotation	1PASS
	0.34479553	jalview.project.Jalview2xmlTests.gatherViewsHerejalview.project.Jalview2xmlTests.gatherViewsHere	1PASS
	0.34479553	jalview.project.Jalview2xmlTests.testCopyViewSettingsjalview.project.Jalview2xmlTests.testCopyViewSettings	1PASS
	0.34479553	jalview.project.Jalview2xmlTests.noDuplicatePdbMappingsMadejalview.project.Jalview2xmlTests.noDuplicatePdbMappingsMade	1PASS
	0.3429368	jalview.project.Jalview2xmlTests.testTCoffeeScoresjalview.project.Jalview2xmlTests.testTCoffeeScores	1PASS
	0.34107807	jalview.project.Jalview2xmlTests.testStoreAndRecoverOverviewjalview.project.Jalview2xmlTests.testStoreAndRecoverOverview	1PASS
	0.31319702	jalview.project.Jalview2xmlTests.testStoreAndRecoverGroupRepSeqsjalview.project.Jalview2xmlTests.testStoreAndRecoverGroupRepSeqs	1PASS
	0.31133828	jalview.project.Jalview2xmlTests.testStoreAndRecoverAnnotationRowElementColoursjalview.project.Jalview2xmlTests.testStoreAndRecoverAnnotationRowElementColours	1PASS
	0.30762082	jalview.project.Jalview2xmlTests.testRNAStructureRecoveryjalview.project.Jalview2xmlTests.testRNAStructureRecovery	1PASS
	0.30669144	jalview.gui.AlignmentPanelTest.testSetOverviewTitle_automaticOverviewjalview.gui.AlignmentPanelTest.testSetOverviewTitle_automaticOverview	1PASS
	0.30576208	jalview.project.Jalview2xmlTests.testPAEsaveRestorejalview.project.Jalview2xmlTests.testPAEsaveRestore	1PASS
	0.30576208	jalview.project.Jalview2xmlTests.testStoreAndRecoverNoOverviewjalview.project.Jalview2xmlTests.testStoreAndRecoverNoOverview	1PASS
	0.30576208	jalview.project.Jalview2xmlTests.testStoreAndRecoverGeneLocusjalview.project.Jalview2xmlTests.testStoreAndRecoverGeneLocus	1PASS
	0.30669144	jalview.gui.AlignmentPanelTest.testSetOverviewTitlejalview.gui.AlignmentPanelTest.testSetOverviewTitle	1PASS
	0.2881041	jalview.gui.AlignFrameTest.testNewView_dsRefPreservedjalview.gui.AlignFrameTest.testNewView_dsRefPreserved	1PASS
	0.2881041	jalview.gui.AlignViewportTest.testDeregisterMapping_onCloseViewjalview.gui.AlignViewportTest.testDeregisterMapping_onCloseView	1PASS
	0.2843866	jalview.project.Jalview2xmlTests.testAutoShowOverviewForLegacyProjectsjalview.project.Jalview2xmlTests.testAutoShowOverviewForLegacyProjects	1PASS
	0.24256505	jalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwicejalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwice	1PASS
	0.19888476	jalview.project.Jalview2xmlTests.testMergeDatasetsforManyViewsjalview.project.Jalview2xmlTests.testMergeDatasetsforManyViews	1PASS
	0.19423792	jalview.project.Jalview2xmlTests.testMergeDatasetsforViewsjalview.project.Jalview2xmlTests.testMergeDatasetsforViews	1PASS
	0.11802974	jalview.gui.QuitHandlerTest.testSavedProjectChangesjalview.gui.QuitHandlerTest.testSavedProjectChanges	1PASS
	0.11802974	jalview.gui.QuitHandlerTest.testWaitForSaveQuitjalview.gui.QuitHandlerTest.testWaitForSaveQuit	1PASS

 

Source view

1		//
2		// This file was generated by the Eclipse Implementation of JAXB, v2.3.9
3		// See https://eclipse-ee4j.github.io/jaxb-ri
4		// Any modifications to this file will be lost upon recompilation of the source schema.
5		// Generated on: 2025.04.17 at 04:05:44 PM BST
6		//
7
8
9		package jalview.xml.binding.jalview;
10
11		import java.util.ArrayList;
12		import java.util.List;
13		import javax.xml.bind.annotation.XmlAccessType;
14		import javax.xml.bind.annotation.XmlAccessorType;
15		import javax.xml.bind.annotation.XmlAttribute;
16		import javax.xml.bind.annotation.XmlElement;
17		import javax.xml.bind.annotation.XmlID;
18		import javax.xml.bind.annotation.XmlSchemaType;
19		import javax.xml.bind.annotation.XmlType;
20		import javax.xml.bind.annotation.XmlValue;
21		import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
22		import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
23		import javax.xml.datatype.XMLGregorianCalendar;
24
25
26		/**
27		* <p>Java class for JalviewModel complex type</p>.
28		*
29		* <p>The following schema fragment specifies the expected content contained within this class.</p>
30		*
31		* <pre>
32		* &lt;complexType name="JalviewModel"&gt;
33		* &lt;complexContent&gt;
34		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
35		* &lt;sequence&gt;
36		* &lt;element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/&gt;
37		* &lt;element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
38		* &lt;element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/&gt;
39		* &lt;sequence&gt;
40		* &lt;element name="JSeq" maxOccurs="unbounded" minOccurs="0"&gt;
41		* &lt;complexType&gt;
42		* &lt;complexContent&gt;
43		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
44		* &lt;sequence&gt;
45		* &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
46		* &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
47		* &lt;complexType&gt;
48		* &lt;complexContent&gt;
49		* &lt;extension base="{www.jalview.org}pdbentry"&gt;
50		* &lt;sequence&gt;
51		* &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
52		* &lt;complexType&gt;
53		* &lt;simpleContent&gt;
54		* &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
55		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
56		* &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
57		* &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
58		* &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
59		* &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
60		* &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
61		* &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
62		* &lt;/extension&gt;
63		* &lt;/simpleContent&gt;
64		* &lt;/complexType&gt;
65		* &lt;/element&gt;
66		* &lt;/sequence&gt;
67		* &lt;/extension&gt;
68		* &lt;/complexContent&gt;
69		* &lt;/complexType&gt;
70		* &lt;/element&gt;
71		* &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&gt;
72		* &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
73		* &lt;complexType&gt;
74		* &lt;complexContent&gt;
75		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
76		* &lt;sequence&gt;
77		* &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
78		* &lt;complexType&gt;
79		* &lt;complexContent&gt;
80		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
81		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
82		* &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
83		* &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
84		* &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
85		* &lt;/restriction&gt;
86		* &lt;/complexContent&gt;
87		* &lt;/complexType&gt;
88		* &lt;/element&gt;
89		* &lt;/sequence&gt;
90		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
91		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
92		* &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
93		* &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
94		* &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
95		* &lt;/restriction&gt;
96		* &lt;/complexContent&gt;
97		* &lt;/complexType&gt;
98		* &lt;/element&gt;
99		* &lt;/sequence&gt;
100		* &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
101		* &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
102		* &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
103		* &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
104		* &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
105		* &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
106		* &lt;/restriction&gt;
107		* &lt;/complexContent&gt;
108		* &lt;/complexType&gt;
109		* &lt;/element&gt;
110		* &lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0"&gt;
111		* &lt;complexType&gt;
112		* &lt;complexContent&gt;
113		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
114		* &lt;sequence&gt;
115		* &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
116		* &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
117		* &lt;element name="annotationFromTree" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
118		* &lt;element name="SecStrProvider" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt;
119		* &lt;/sequence&gt;
120		* &lt;attGroup ref="{www.jalview.org}conservationShading"/&gt;
121		* &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
122		* &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
123		* &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
124		* &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
125		* &lt;attribute name="idColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
126		* &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
127		* &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
128		* &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
129		* &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
130		* &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
131		* &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
132		* &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
133		* &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
134		* &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
135		* &lt;/restriction&gt;
136		* &lt;/complexContent&gt;
137		* &lt;/complexType&gt;
138		* &lt;/element&gt;
139		* &lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0"&gt;
140		* &lt;complexType&gt;
141		* &lt;complexContent&gt;
142		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
143		* &lt;sequence&gt;
144		* &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
145		* &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&gt;
146		* &lt;complexType&gt;
147		* &lt;complexContent&gt;
148		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
149		* &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
150		* &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
151		* &lt;/restriction&gt;
152		* &lt;/complexContent&gt;
153		* &lt;/complexType&gt;
154		* &lt;/element&gt;
155		* &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
156		* &lt;complexType&gt;
157		* &lt;complexContent&gt;
158		* &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
159		* &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
160		* &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
161		* &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
162		* &lt;/extension&gt;
163		* &lt;/complexContent&gt;
164		* &lt;/complexType&gt;
165		* &lt;/element&gt;
166		* &lt;element name="overview" minOccurs="0"&gt;
167		* &lt;complexType&gt;
168		* &lt;complexContent&gt;
169		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
170		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
171		* &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
172		* &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
173		* &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
174		* &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
175		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
176		* &lt;/restriction&gt;
177		* &lt;/complexContent&gt;
178		* &lt;/complexType&gt;
179		* &lt;/element&gt;
180		* &lt;element name="SecStrProvider" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt;
181		* &lt;/sequence&gt;
182		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
183		* &lt;attGroup ref="{www.jalview.org}conservationShading"/&gt;
184		* &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
185		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
186		* &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
187		* &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
188		* &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
189		* &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
190		* &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
191		* &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
192		* &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
193		* &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
194		* &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
195		* &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
196		* &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
197		* &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
198		* &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
199		* &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
200		* &lt;attribute name="showStructureProviders" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
201		* &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
202		* &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
203		* &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
204		* &lt;attribute name="showGroupSecStrConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
205		* &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
206		* &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
207		* &lt;attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
208		* &lt;attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
209		* &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
210		* &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
211		* &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
212		* &lt;attribute name="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
213		* &lt;attribute name="idWidthManuallyAdjusted" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
214		* &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
215		* &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
216		* &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
217		* &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
218		* &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
219		* &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
220		* &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
221		* &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
222		* &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
223		* &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
224		* &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
225		* &lt;/restriction&gt;
226		* &lt;/complexContent&gt;
227		* &lt;/complexType&gt;
228		* &lt;/element&gt;
229		* &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0"&gt;
230		* &lt;complexType&gt;
231		* &lt;complexContent&gt;
232		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
233		* &lt;sequence&gt;
234		* &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&gt;
235		* &lt;/sequence&gt;
236		* &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
237		* &lt;/restriction&gt;
238		* &lt;/complexContent&gt;
239		* &lt;/complexType&gt;
240		* &lt;/element&gt;
241		* &lt;element name="tree" maxOccurs="unbounded" minOccurs="0"&gt;
242		* &lt;complexType&gt;
243		* &lt;complexContent&gt;
244		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
245		* &lt;sequence minOccurs="0"&gt;
246		* &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
247		* &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
248		* &lt;element name="TreeColorMap" minOccurs="0"&gt;
249		* &lt;complexType&gt;
250		* &lt;complexContent&gt;
251		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
252		* &lt;sequence&gt;
253		* &lt;element name="ColorEntry" maxOccurs="unbounded" minOccurs="0"&gt;
254		* &lt;complexType&gt;
255		* &lt;complexContent&gt;
256		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
257		* &lt;attribute name="label" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
258		* &lt;attribute name="color" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
259		* &lt;/restriction&gt;
260		* &lt;/complexContent&gt;
261		* &lt;/complexType&gt;
262		* &lt;/element&gt;
263		* &lt;/sequence&gt;
264		* &lt;/restriction&gt;
265		* &lt;/complexContent&gt;
266		* &lt;/complexType&gt;
267		* &lt;/element&gt;
268		* &lt;/sequence&gt;
269		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
270		* &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
271		* &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
272		* &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
273		* &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
274		* &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
275		* &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
276		* &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
277		* &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
278		* &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
279		* &lt;attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
280		* &lt;attribute name="annotationBased" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
281		* &lt;attribute name="showAnnotationAs" type="{http://www.w3.org/2001/XMLSchema}string" default="None" /&gt;
282		* &lt;attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
283		* &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
284		* &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
285		* &lt;/restriction&gt;
286		* &lt;/complexContent&gt;
287		* &lt;/complexType&gt;
288		* &lt;/element&gt;
289		* &lt;element name="PcaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
290		* &lt;complexType&gt;
291		* &lt;complexContent&gt;
292		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
293		* &lt;sequence&gt;
294		* &lt;element name="sequencePoint" maxOccurs="unbounded"&gt;
295		* &lt;complexType&gt;
296		* &lt;complexContent&gt;
297		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
298		* &lt;attGroup ref="{www.jalview.org}position"/&gt;
299		* &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
300		* &lt;/restriction&gt;
301		* &lt;/complexContent&gt;
302		* &lt;/complexType&gt;
303		* &lt;/element&gt;
304		* &lt;element name="axis" maxOccurs="3" minOccurs="3"&gt;
305		* &lt;complexType&gt;
306		* &lt;complexContent&gt;
307		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
308		* &lt;attGroup ref="{www.jalview.org}position"/&gt;
309		* &lt;/restriction&gt;
310		* &lt;/complexContent&gt;
311		* &lt;/complexType&gt;
312		* &lt;/element&gt;
313		* &lt;element name="seqPointMin"&gt;
314		* &lt;complexType&gt;
315		* &lt;complexContent&gt;
316		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
317		* &lt;attGroup ref="{www.jalview.org}position"/&gt;
318		* &lt;/restriction&gt;
319		* &lt;/complexContent&gt;
320		* &lt;/complexType&gt;
321		* &lt;/element&gt;
322		* &lt;element name="seqPointMax"&gt;
323		* &lt;complexType&gt;
324		* &lt;complexContent&gt;
325		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
326		* &lt;attGroup ref="{www.jalview.org}position"/&gt;
327		* &lt;/restriction&gt;
328		* &lt;/complexContent&gt;
329		* &lt;/complexType&gt;
330		* &lt;/element&gt;
331		* &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&gt;
332		* &lt;/sequence&gt;
333		* &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
334		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
335		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
336		* &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
337		* &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
338		* &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
339		* &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
340		* &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
341		* &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
342		* &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
343		* &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
344		* &lt;/restriction&gt;
345		* &lt;/complexContent&gt;
346		* &lt;/complexType&gt;
347		* &lt;/element&gt;
348		* &lt;element name="FeatureSettings" minOccurs="0"&gt;
349		* &lt;complexType&gt;
350		* &lt;complexContent&gt;
351		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
352		* &lt;sequence&gt;
353		* &lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&gt;
354		* &lt;complexType&gt;
355		* &lt;complexContent&gt;
356		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
357		* &lt;sequence&gt;
358		* &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
359		* &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
360		* &lt;/sequence&gt;
361		* &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
362		* &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
363		* &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
364		* &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
365		* &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
366		* &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
367		* &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
368		* &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
369		* &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
370		* &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
371		* &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
372		* &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
373		* &lt;/restriction&gt;
374		* &lt;/complexContent&gt;
375		* &lt;/complexType&gt;
376		* &lt;/element&gt;
377		* &lt;element name="group" maxOccurs="unbounded" minOccurs="0"&gt;
378		* &lt;complexType&gt;
379		* &lt;complexContent&gt;
380		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
381		* &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
382		* &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
383		* &lt;/restriction&gt;
384		* &lt;/complexContent&gt;
385		* &lt;/complexType&gt;
386		* &lt;/element&gt;
387		* &lt;/sequence&gt;
388		* &lt;/restriction&gt;
389		* &lt;/complexContent&gt;
390		* &lt;/complexType&gt;
391		* &lt;/element&gt;
392		* &lt;/sequence&gt;
393		* &lt;/sequence&gt;
394		* &lt;/restriction&gt;
395		* &lt;/complexContent&gt;
396		* &lt;/complexType&gt;
397		* </pre>
398		*
399		*
400		*/
401		@XmlAccessorType(XmlAccessType.FIELD)
402		@XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
403		"creationDate",
404		"version",
405		"vamsasModel",
406		"jSeq",
407		"jGroup",
408		"viewport",
409		"userColours",
410		"tree",
411		"pcaViewer",
412		"featureSettings"
413		})
		84.6% Uncovered Elements: 8 (52) Complexity: 20 Complexity Density: 0.77
414		public class JalviewModel {
415
416		@XmlElement(required = true)
417		@XmlSchemaType(name = "dateTime")
418		protected XMLGregorianCalendar creationDate;
419		@XmlElement(required = true)
420		protected String version;
421		@XmlElement(required = true)
422		protected VAMSAS vamsasModel;
423		@XmlElement(name = "JSeq")
424		protected List<JalviewModel.JSeq> jSeq;
425		@XmlElement(name = "JGroup")
426		protected List<JalviewModel.JGroup> jGroup;
427		@XmlElement(name = "Viewport")
428		protected List<JalviewModel.Viewport> viewport;
429		@XmlElement(name = "UserColours")
430		protected List<JalviewModel.UserColours> userColours;
431		protected List<JalviewModel.Tree> tree;
432		@XmlElement(name = "PcaViewer")
433		protected List<JalviewModel.PcaViewer> pcaViewer;
434		@XmlElement(name = "FeatureSettings")
435		protected JalviewModel.FeatureSettings featureSettings;
436
437		/**
438		* Gets the value of the creationDate property.
439		*
440		* @return
441		* possible object is
442		* {@link XMLGregorianCalendar }
443		*
444		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
445	0	public XMLGregorianCalendar getCreationDate() {...
446	0	return creationDate;
447		}
448
449		/**
450		* Sets the value of the creationDate property.
451		*
452		* @param value
453		* allowed object is
454		* {@link XMLGregorianCalendar }
455		*
456		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
457	77	public void setCreationDate(XMLGregorianCalendar value) {...
458	77	this.creationDate = value;
459		}
460
461		/**
462		* Gets the value of the version property.
463		*
464		* @return
465		* possible object is
466		* {@link String }
467		*
468		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
469	221	public String getVersion() {...
470	221	return version;
471		}
472
473		/**
474		* Sets the value of the version property.
475		*
476		* @param value
477		* allowed object is
478		* {@link String }
479		*
480		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
481	77	public void setVersion(String value) {...
482	77	this.version = value;
483		}
484
485		/**
486		* Gets the value of the vamsasModel property.
487		*
488		* @return
489		* possible object is
490		* {@link VAMSAS }
491		*
492		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
493	215	public VAMSAS getVamsasModel() {...
494	215	return vamsasModel;
495		}
496
497		/**
498		* Sets the value of the vamsasModel property.
499		*
500		* @param value
501		* allowed object is
502		* {@link VAMSAS }
503		*
504		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
505	77	public void setVamsasModel(VAMSAS value) {...
506	77	this.vamsasModel = value;
507		}
508
509		/**
510		* Gets the value of the jSeq property.
511		*
512		* <p>This accessor method returns a reference to the live list,
513		* not a snapshot. Therefore any modification you make to the
514		* returned list will be present inside the JAXB object.
515		* This is why there is not a <CODE>set</CODE> method for the jSeq property.</p>
516		*
517		* <p>
518		* For example, to add a new item, do as follows:
519		* </p>
520		* <pre>
521		* getJSeq().add(newItem);
522		* </pre>
523		*
524		*
525		* <p>
526		* Objects of the following type(s) are allowed in the list
527		* {@link JalviewModel.JSeq }
528		* </p>
529		*
530		*
531		* @return
532		* The value of the jSeq property.
533		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
534	8489	public List<JalviewModel.JSeq> getJSeq() {...
535	8489	if (jSeq == null) {
536	77	jSeq = new ArrayList<JalviewModel.JSeq>();
537		}
538	8489	return this.jSeq;
539		}
540
541		/**
542		* Gets the value of the jGroup property.
543		*
544		* <p>This accessor method returns a reference to the live list,
545		* not a snapshot. Therefore any modification you make to the
546		* returned list will be present inside the JAXB object.
547		* This is why there is not a <CODE>set</CODE> method for the jGroup property.</p>
548		*
549		* <p>
550		* For example, to add a new item, do as follows:
551		* </p>
552		* <pre>
553		* getJGroup().add(newItem);
554		* </pre>
555		*
556		*
557		* <p>
558		* Objects of the following type(s) are allowed in the list
559		* {@link JalviewModel.JGroup }
560		* </p>
561		*
562		*
563		* @return
564		* The value of the jGroup property.
565		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
566	184	public List<JalviewModel.JGroup> getJGroup() {...
567	184	if (jGroup == null) {
568	107	jGroup = new ArrayList<JalviewModel.JGroup>();
569		}
570	184	return this.jGroup;
571		}
572
573		/**
574		* Gets the value of the viewport property.
575		*
576		* <p>This accessor method returns a reference to the live list,
577		* not a snapshot. Therefore any modification you make to the
578		* returned list will be present inside the JAXB object.
579		* This is why there is not a <CODE>set</CODE> method for the viewport property.</p>
580		*
581		* <p>
582		* For example, to add a new item, do as follows:
583		* </p>
584		* <pre>
585		* getViewport().add(newItem);
586		* </pre>
587		*
588		*
589		* <p>
590		* Objects of the following type(s) are allowed in the list
591		* {@link JalviewModel.Viewport }
592		* </p>
593		*
594		*
595		* @return
596		* The value of the viewport property.
597		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
598	462	public List<JalviewModel.Viewport> getViewport() {...
599	462	if (viewport == null) {
600	82	viewport = new ArrayList<JalviewModel.Viewport>();
601		}
602	462	return this.viewport;
603		}
604
605		/**
606		* Gets the value of the userColours property.
607		*
608		* <p>This accessor method returns a reference to the live list,
609		* not a snapshot. Therefore any modification you make to the
610		* returned list will be present inside the JAXB object.
611		* This is why there is not a <CODE>set</CODE> method for the userColours property.</p>
612		*
613		* <p>
614		* For example, to add a new item, do as follows:
615		* </p>
616		* <pre>
617		* getUserColours().add(newItem);
618		* </pre>
619		*
620		*
621		* <p>
622		* Objects of the following type(s) are allowed in the list
623		* {@link JalviewModel.UserColours }
624		* </p>
625		*
626		*
627		* @return
628		* The value of the userColours property.
629		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
630	0	public List<JalviewModel.UserColours> getUserColours() {...
631	0	if (userColours == null) {
632	0	userColours = new ArrayList<JalviewModel.UserColours>();
633		}
634	0	return this.userColours;
635		}
636
637		/**
638		* Gets the value of the tree property.
639		*
640		* <p>This accessor method returns a reference to the live list,
641		* not a snapshot. Therefore any modification you make to the
642		* returned list will be present inside the JAXB object.
643		* This is why there is not a <CODE>set</CODE> method for the tree property.</p>
644		*
645		* <p>
646		* For example, to add a new item, do as follows:
647		* </p>
648		* <pre>
649		* getTree().add(newItem);
650		* </pre>
651		*
652		*
653		* <p>
654		* Objects of the following type(s) are allowed in the list
655		* {@link JalviewModel.Tree }
656		* </p>
657		*
658		*
659		* @return
660		* The value of the tree property.
661		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
662	108	public List<JalviewModel.Tree> getTree() {...
663	108	if (tree == null) {
664	75	tree = new ArrayList<JalviewModel.Tree>();
665		}
666	108	return this.tree;
667		}
668
669		/**
670		* Gets the value of the pcaViewer property.
671		*
672		* <p>This accessor method returns a reference to the live list,
673		* not a snapshot. Therefore any modification you make to the
674		* returned list will be present inside the JAXB object.
675		* This is why there is not a <CODE>set</CODE> method for the pcaViewer property.</p>
676		*
677		* <p>
678		* For example, to add a new item, do as follows:
679		* </p>
680		* <pre>
681		* getPcaViewer().add(newItem);
682		* </pre>
683		*
684		*
685		* <p>
686		* Objects of the following type(s) are allowed in the list
687		* {@link JalviewModel.PcaViewer }
688		* </p>
689		*
690		*
691		* @return
692		* The value of the pcaViewer property.
693		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
694	169	public List<JalviewModel.PcaViewer> getPcaViewer() {...
695	169	if (pcaViewer == null) {
696	84	pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
697		}
698	169	return this.pcaViewer;
699		}
700
701		/**
702		* Gets the value of the featureSettings property.
703		*
704		* @return
705		* possible object is
706		* {@link JalviewModel.FeatureSettings }
707		*
708		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
709	2335	public JalviewModel.FeatureSettings getFeatureSettings() {...
710	2335	return featureSettings;
711		}
712
713		/**
714		* Sets the value of the featureSettings property.
715		*
716		* @param value
717		* allowed object is
718		* {@link JalviewModel.FeatureSettings }
719		*
720		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
721	13	public void setFeatureSettings(JalviewModel.FeatureSettings value) {...
722	13	this.featureSettings = value;
723		}
724
725
726		/**
727		* <p>Java class for anonymous complex type</p>.
728		*
729		* <p>The following schema fragment specifies the expected content contained within this class.</p>
730		*
731		* <pre>
732		* &lt;complexType&gt;
733		* &lt;complexContent&gt;
734		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
735		* &lt;sequence&gt;
736		* &lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&gt;
737		* &lt;complexType&gt;
738		* &lt;complexContent&gt;
739		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
740		* &lt;sequence&gt;
741		* &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
742		* &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
743		* &lt;/sequence&gt;
744		* &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
745		* &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
746		* &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
747		* &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
748		* &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
749		* &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
750		* &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
751		* &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
752		* &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
753		* &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
754		* &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
755		* &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
756		* &lt;/restriction&gt;
757		* &lt;/complexContent&gt;
758		* &lt;/complexType&gt;
759		* &lt;/element&gt;
760		* &lt;element name="group" maxOccurs="unbounded" minOccurs="0"&gt;
761		* &lt;complexType&gt;
762		* &lt;complexContent&gt;
763		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
764		* &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
765		* &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
766		* &lt;/restriction&gt;
767		* &lt;/complexContent&gt;
768		* &lt;/complexType&gt;
769		* &lt;/element&gt;
770		* &lt;/sequence&gt;
771		* &lt;/restriction&gt;
772		* &lt;/complexContent&gt;
773		* &lt;/complexType&gt;
774		* </pre>
775		*
776		*
777		*/
778		@XmlAccessorType(XmlAccessType.FIELD)
779		@XmlType(name = "", propOrder = {
780		"setting",
781		"group"
782		})
		100% Uncovered Elements: 0 (12) Complexity: 4 Complexity Density: 0.67
783		public static class FeatureSettings {
784
785		@XmlElement(namespace = "www.jalview.org")
786		protected List<JalviewModel.FeatureSettings.Setting> setting;
787		@XmlElement(namespace = "www.jalview.org")
788		protected List<JalviewModel.FeatureSettings.Group> group;
789
790		/**
791		* Gets the value of the setting property.
792		*
793		* <p>This accessor method returns a reference to the live list,
794		* not a snapshot. Therefore any modification you make to the
795		* returned list will be present inside the JAXB object.
796		* This is why there is not a <CODE>set</CODE> method for the setting property.</p>
797		*
798		* <p>
799		* For example, to add a new item, do as follows:
800		* </p>
801		* <pre>
802		* getSetting().add(newItem);
803		* </pre>
804		*
805		*
806		* <p>
807		* Objects of the following type(s) are allowed in the list
808		* {@link JalviewModel.FeatureSettings.Setting }
809		* </p>
810		*
811		*
812		* @return
813		* The value of the setting property.
814		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
815	2040	public List<JalviewModel.FeatureSettings.Setting> getSetting() {...
816	2040	if (setting == null) {
817	13	setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
818		}
819	2040	return this.setting;
820		}
821
822		/**
823		* Gets the value of the group property.
824		*
825		* <p>This accessor method returns a reference to the live list,
826		* not a snapshot. Therefore any modification you make to the
827		* returned list will be present inside the JAXB object.
828		* This is why there is not a <CODE>set</CODE> method for the group property.</p>
829		*
830		* <p>
831		* For example, to add a new item, do as follows:
832		* </p>
833		* <pre>
834		* getGroup().add(newItem);
835		* </pre>
836		*
837		*
838		* <p>
839		* Objects of the following type(s) are allowed in the list
840		* {@link JalviewModel.FeatureSettings.Group }
841		* </p>
842		*
843		*
844		* @return
845		* The value of the group property.
846		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
847	472	public List<JalviewModel.FeatureSettings.Group> getGroup() {...
848	472	if (group == null) {
849	13	group = new ArrayList<JalviewModel.FeatureSettings.Group>();
850		}
851	472	return this.group;
852		}
853
854
855		/**
856		* <p>Java class for anonymous complex type</p>.
857		*
858		* <p>The following schema fragment specifies the expected content contained within this class.</p>
859		*
860		* <pre>
861		* &lt;complexType&gt;
862		* &lt;complexContent&gt;
863		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
864		* &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
865		* &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
866		* &lt;/restriction&gt;
867		* &lt;/complexContent&gt;
868		* &lt;/complexType&gt;
869		* </pre>
870		*
871		*
872		*/
873		@XmlAccessorType(XmlAccessType.FIELD)
874		@XmlType(name = "")
		100% Uncovered Elements: 0 (8) Complexity: 4 Complexity Density: 1
875		public static class Group {
876
877		@XmlAttribute(name = "name", required = true)
878		protected String name;
879		@XmlAttribute(name = "display", required = true)
880		protected boolean display;
881
882		/**
883		* Gets the value of the name property.
884		*
885		* @return
886		* possible object is
887		* {@link String }
888		*
889		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
890	184	public String getName() {...
891	184	return name;
892		}
893
894		/**
895		* Sets the value of the name property.
896		*
897		* @param value
898		* allowed object is
899		* {@link String }
900		*
901		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
902	59	public void setName(String value) {...
903	59	this.name = value;
904		}
905
906		/**
907		* Gets the value of the display property.
908		*
909		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
910	184	public boolean isDisplay() {...
911	184	return display;
912		}
913
914		/**
915		* Sets the value of the display property.
916		*
917		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
918	59	public void setDisplay(boolean value) {...
919	59	this.display = value;
920		}
921
922		}
923
924
925		/**
926		* <p>Java class for anonymous complex type</p>.
927		*
928		* <p>The following schema fragment specifies the expected content contained within this class.</p>
929		*
930		* <pre>
931		* &lt;complexType&gt;
932		* &lt;complexContent&gt;
933		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
934		* &lt;sequence&gt;
935		* &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
936		* &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
937		* &lt;/sequence&gt;
938		* &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
939		* &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
940		* &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
941		* &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
942		* &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
943		* &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
944		* &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
945		* &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
946		* &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
947		* &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
948		* &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
949		* &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
950		* &lt;/restriction&gt;
951		* &lt;/complexContent&gt;
952		* &lt;/complexType&gt;
953		* </pre>
954		*
955		*
956		*/
957		@XmlAccessorType(XmlAccessType.FIELD)
958		@XmlType(name = "", propOrder = {
959		"attributeName",
960		"matcherSet"
961		})
		96.8% Uncovered Elements: 2 (62) Complexity: 29 Complexity Density: 0.94
962		public static class Setting {
963
964		/**
965		* name of feature attribute to colour by, or attribute and sub-attribute
966		*
967		*/
968		@XmlElement(namespace = "www.jalview.org")
969		protected List<String> attributeName;
970		/**
971		* optional filter(s) applied to the feature type
972		*
973		*/
974		@XmlElement(namespace = "www.jalview.org")
975		protected FeatureMatcherSet matcherSet;
976		@XmlAttribute(name = "type", required = true)
977		protected String type;
978		@XmlAttribute(name = "colour", required = true)
979		protected int colour;
980		@XmlAttribute(name = "display", required = true)
981		protected boolean display;
982		@XmlAttribute(name = "order")
983		protected Float order;
984		/**
985		* Optional minimum colour
986		* for graduated
987		* feature
988		* colour
989		*
990		*/
991		@XmlAttribute(name = "mincolour")
992		protected Integer mincolour;
993		@XmlAttribute(name = "noValueColour")
994		protected NoValueColour noValueColour;
995		/**
996		* threshold value for
997		* graduated feature colour
998		*
999		*/
1000		@XmlAttribute(name = "threshold")
1001		protected Float threshold;
1002		/**
1003		* threshold type for
1004		* graduated feature colour
1005		*
1006		*/
1007		@XmlAttribute(name = "threshstate")
1008		protected Integer threshstate;
1009		@XmlAttribute(name = "max")
1010		protected Float max;
1011		@XmlAttribute(name = "min")
1012		protected Float min;
1013		@XmlAttribute(name = "colourByLabel")
1014		protected Boolean colourByLabel;
1015		@XmlAttribute(name = "autoScale")
1016		protected Boolean autoScale;
1017
1018		/**
1019		* name of feature attribute to colour by, or attribute and sub-attribute
1020		*
1021		* Gets the value of the attributeName property.
1022		*
1023		* <p>This accessor method returns a reference to the live list,
1024		* not a snapshot. Therefore any modification you make to the
1025		* returned list will be present inside the JAXB object.
1026		* This is why there is not a <CODE>set</CODE> method for the attributeName property.</p>
1027		*
1028		* <p>
1029		* For example, to add a new item, do as follows:
1030		* </p>
1031		* <pre>
1032		* getAttributeName().add(newItem);
1033		* </pre>
1034		*
1035		*
1036		* <p>
1037		* Objects of the following type(s) are allowed in the list
1038		* {@link String }
1039		* </p>
1040		*
1041		*
1042		* @return
1043		* The value of the attributeName property.
1044		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
1045	12	public List<String> getAttributeName() {...
1046	12	if (attributeName == null) {
1047	5	attributeName = new ArrayList<String>();
1048		}
1049	12	return this.attributeName;
1050		}
1051
1052		/**
1053		* optional filter(s) applied to the feature type
1054		*
1055		* @return
1056		* possible object is
1057		* {@link FeatureMatcherSet }
1058		*
1059		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1060	869	public FeatureMatcherSet getMatcherSet() {...
1061	869	return matcherSet;
1062		}
1063
1064		/**
1065		* Sets the value of the matcherSet property.
1066		*
1067		* @param value
1068		* allowed object is
1069		* {@link FeatureMatcherSet }
1070		*
1071		* @see #getMatcherSet()
1072		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1073	3	public void setMatcherSet(FeatureMatcherSet value) {...
1074	3	this.matcherSet = value;
1075		}
1076
1077		/**
1078		* Gets the value of the type property.
1079		*
1080		* @return
1081		* possible object is
1082		* {@link String }
1083		*
1084		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1085	869	public String getType() {...
1086	869	return type;
1087		}
1088
1089		/**
1090		* Sets the value of the type property.
1091		*
1092		* @param value
1093		* allowed object is
1094		* {@link String }
1095		*
1096		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1097	212	public void setType(String value) {...
1098	212	this.type = value;
1099		}
1100
1101		/**
1102		* Gets the value of the colour property.
1103		*
1104		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1105	869	public int getColour() {...
1106	869	return colour;
1107		}
1108
1109		/**
1110		* Sets the value of the colour property.
1111		*
1112		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1113	212	public void setColour(int value) {...
1114	212	this.colour = value;
1115		}
1116
1117		/**
1118		* Gets the value of the display property.
1119		*
1120		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1121	869	public boolean isDisplay() {...
1122	869	return display;
1123		}
1124
1125		/**
1126		* Sets the value of the display property.
1127		*
1128		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1129	212	public void setDisplay(boolean value) {...
1130	212	this.display = value;
1131		}
1132
1133		/**
1134		* Gets the value of the order property.
1135		*
1136		* @return
1137		* possible object is
1138		* {@link Float }
1139		*
1140		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1141	1738	public Float getOrder() {...
1142	1738	return order;
1143		}
1144
1145		/**
1146		* Sets the value of the order property.
1147		*
1148		* @param value
1149		* allowed object is
1150		* {@link Float }
1151		*
1152		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1153	212	public void setOrder(Float value) {...
1154	212	this.order = value;
1155		}
1156
1157		/**
1158		* Optional minimum colour
1159		* for graduated
1160		* feature
1161		* colour
1162		*
1163		* @return
1164		* possible object is
1165		* {@link Integer }
1166		*
1167		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1168	874	public Integer getMincolour() {...
1169	874	return mincolour;
1170		}
1171
1172		/**
1173		* Sets the value of the mincolour property.
1174		*
1175		* @param value
1176		* allowed object is
1177		* {@link Integer }
1178		*
1179		* @see #getMincolour()
1180		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1181	4	public void setMincolour(Integer value) {...
1182	4	this.mincolour = value;
1183		}
1184
1185		/**
1186		* Gets the value of the noValueColour property.
1187		*
1188		* @return
1189		* possible object is
1190		* {@link NoValueColour }
1191		*
1192		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
1193	5	public NoValueColour getNoValueColour() {...
1194	5	if (noValueColour == null) {
1195	0	return NoValueColour.MIN;
1196		} else {
1197	5	return noValueColour;
1198		}
1199		}
1200
1201		/**
1202		* Sets the value of the noValueColour property.
1203		*
1204		* @param value
1205		* allowed object is
1206		* {@link NoValueColour }
1207		*
1208		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1209	4	public void setNoValueColour(NoValueColour value) {...
1210	4	this.noValueColour = value;
1211		}
1212
1213		/**
1214		* threshold value for
1215		* graduated feature colour
1216		*
1217		* @return
1218		* possible object is
1219		* {@link Float }
1220		*
1221		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1222	10	public Float getThreshold() {...
1223	10	return threshold;
1224		}
1225
1226		/**
1227		* Sets the value of the threshold property.
1228		*
1229		* @param value
1230		* allowed object is
1231		* {@link Float }
1232		*
1233		* @see #getThreshold()
1234		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1235	4	public void setThreshold(Float value) {...
1236	4	this.threshold = value;
1237		}
1238
1239		/**
1240		* threshold type for
1241		* graduated feature colour
1242		*
1243		* @return
1244		* possible object is
1245		* {@link Integer }
1246		*
1247		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1248	5	public Integer getThreshstate() {...
1249	5	return threshstate;
1250		}
1251
1252		/**
1253		* Sets the value of the threshstate property.
1254		*
1255		* @param value
1256		* allowed object is
1257		* {@link Integer }
1258		*
1259		* @see #getThreshstate()
1260		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1261	4	public void setThreshstate(Integer value) {...
1262	4	this.threshstate = value;
1263		}
1264
1265		/**
1266		* Gets the value of the max property.
1267		*
1268		* @return
1269		* possible object is
1270		* {@link Float }
1271		*
1272		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1273	10	public Float getMax() {...
1274	10	return max;
1275		}
1276
1277		/**
1278		* Sets the value of the max property.
1279		*
1280		* @param value
1281		* allowed object is
1282		* {@link Float }
1283		*
1284		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1285	4	public void setMax(Float value) {...
1286	4	this.max = value;
1287		}
1288
1289		/**
1290		* Gets the value of the min property.
1291		*
1292		* @return
1293		* possible object is
1294		* {@link Float }
1295		*
1296		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1297	5	public Float getMin() {...
1298	5	return min;
1299		}
1300
1301		/**
1302		* Sets the value of the min property.
1303		*
1304		* @param value
1305		* allowed object is
1306		* {@link Float }
1307		*
1308		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1309	4	public void setMin(Float value) {...
1310	4	this.min = value;
1311		}
1312
1313		/**
1314		* Gets the value of the colourByLabel property.
1315		*
1316		* @return
1317		* possible object is
1318		* {@link Boolean }
1319		*
1320		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1321	10	public Boolean isColourByLabel() {...
1322	10	return colourByLabel;
1323		}
1324
1325		/**
1326		* Sets the value of the colourByLabel property.
1327		*
1328		* @param value
1329		* allowed object is
1330		* {@link Boolean }
1331		*
1332		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1333	4	public void setColourByLabel(Boolean value) {...
1334	4	this.colourByLabel = value;
1335		}
1336
1337		/**
1338		* Gets the value of the autoScale property.
1339		*
1340		* @return
1341		* possible object is
1342		* {@link Boolean }
1343		*
1344		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1345	10	public Boolean isAutoScale() {...
1346	10	return autoScale;
1347		}
1348
1349		/**
1350		* Sets the value of the autoScale property.
1351		*
1352		* @param value
1353		* allowed object is
1354		* {@link Boolean }
1355		*
1356		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1357	4	public void setAutoScale(Boolean value) {...
1358	4	this.autoScale = value;
1359		}
1360
1361		}
1362
1363		}
1364
1365
1366		/**
1367		* <p>Java class for anonymous complex type</p>.
1368		*
1369		* <p>The following schema fragment specifies the expected content contained within this class.</p>
1370		*
1371		* <pre>
1372		* &lt;complexType&gt;
1373		* &lt;complexContent&gt;
1374		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
1375		* &lt;sequence&gt;
1376		* &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
1377		* &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
1378		* &lt;element name="annotationFromTree" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
1379		* &lt;element name="SecStrProvider" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt;
1380		* &lt;/sequence&gt;
1381		* &lt;attGroup ref="{www.jalview.org}conservationShading"/&gt;
1382		* &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1383		* &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1384		* &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1385		* &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1386		* &lt;attribute name="idColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1387		* &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1388		* &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1389		* &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1390		* &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1391		* &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1392		* &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1393		* &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1394		* &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1395		* &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1396		* &lt;/restriction&gt;
1397		* &lt;/complexContent&gt;
1398		* &lt;/complexType&gt;
1399		* </pre>
1400		*
1401		*
1402		*/
1403		@XmlAccessorType(XmlAccessType.FIELD)
1404		@XmlType(name = "", propOrder = {
1405		"seq",
1406		"annotationColours",
1407		"annotationFromTree",
1408		"secStrProvider"
1409		})
		89.1% Uncovered Elements: 15 (138) Complexity: 61 Complexity Density: 0.88
1410		public static class JGroup {
1411
1412		@XmlElement(namespace = "www.jalview.org", required = true)
1413		protected List<String> seq;
1414		@XmlElement(namespace = "www.jalview.org")
1415		protected AnnotationColourScheme annotationColours;
1416		@XmlElement(namespace = "www.jalview.org", required = true)
1417		protected List<String> annotationFromTree;
1418		@XmlElement(name = "SecStrProvider", namespace = "www.jalview.org")
1419		protected List<String> secStrProvider;
1420		@XmlAttribute(name = "start")
1421		protected Integer start;
1422		@XmlAttribute(name = "end")
1423		protected Integer end;
1424		@XmlAttribute(name = "name")
1425		protected String name;
1426		@XmlAttribute(name = "colour")
1427		protected String colour;
1428		@XmlAttribute(name = "idColour")
1429		protected Integer idColour;
1430		@XmlAttribute(name = "outlineColour")
1431		protected Integer outlineColour;
1432		@XmlAttribute(name = "displayBoxes")
1433		protected Boolean displayBoxes;
1434		@XmlAttribute(name = "displayText")
1435		protected Boolean displayText;
1436		@XmlAttribute(name = "colourText")
1437		protected Boolean colourText;
1438		@XmlAttribute(name = "textCol1")
1439		protected Integer textCol1;
1440		@XmlAttribute(name = "textCol2")
1441		protected Integer textCol2;
1442		@XmlAttribute(name = "textColThreshold")
1443		protected Integer textColThreshold;
1444		@XmlAttribute(name = "showUnconserved")
1445		protected Boolean showUnconserved;
1446		/**
1447		* Optional sequence group ID (only
1448		* needs to be
1449		* unique for this
1450		* alignment)
1451		*
1452		*/
1453		@XmlAttribute(name = "id")
1454		protected String id;
1455		@XmlAttribute(name = "conservationSelected")
1456		protected Boolean conservationSelected;
1457		/**
1458		* Conservation shading increment
1459		*
1460		*/
1461		@XmlAttribute(name = "consThreshold")
1462		protected Integer consThreshold;
1463		@XmlAttribute(name = "pidSelected")
1464		protected Boolean pidSelected;
1465		/**
1466		* Percent Identity Threshold
1467		*
1468		*/
1469		@XmlAttribute(name = "pidThreshold")
1470		protected Integer pidThreshold;
1471		/**
1472		* Secondary structure consensus shading - since 2.11.4
1473		*
1474		*/
1475		@XmlAttribute(name = "secstrSelected")
1476		protected Boolean secstrSelected;
1477		/**
1478		* Secondary structure consensus increment
1479		*
1480		*/
1481		@XmlAttribute(name = "secstrThreshold")
1482		protected Integer secstrThreshold;
1483		@XmlAttribute(name = "showConsensusHistogram")
1484		protected Boolean showConsensusHistogram;
1485		@XmlAttribute(name = "showSequenceLogo")
1486		protected Boolean showSequenceLogo;
1487		@XmlAttribute(name = "normaliseSequenceLogo")
1488		protected Boolean normaliseSequenceLogo;
1489		@XmlAttribute(name = "ignoreGapsinConsensus")
1490		protected Boolean ignoreGapsinConsensus;
1491
1492		/**
1493		* Gets the value of the seq property.
1494		*
1495		* <p>This accessor method returns a reference to the live list,
1496		* not a snapshot. Therefore any modification you make to the
1497		* returned list will be present inside the JAXB object.
1498		* This is why there is not a <CODE>set</CODE> method for the seq property.</p>
1499		*
1500		* <p>
1501		* For example, to add a new item, do as follows:
1502		* </p>
1503		* <pre>
1504		* getSeq().add(newItem);
1505		* </pre>
1506		*
1507		*
1508		* <p>
1509		* Objects of the following type(s) are allowed in the list
1510		* {@link String }
1511		* </p>
1512		*
1513		*
1514		* @return
1515		* The value of the seq property.
1516		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
1517	1081	public List<String> getSeq() {...
1518	1081	if (seq == null) {
1519	22	seq = new ArrayList<String>();
1520		}
1521	1081	return this.seq;
1522		}
1523
1524		/**
1525		* Gets the value of the annotationColours property.
1526		*
1527		* @return
1528		* possible object is
1529		* {@link AnnotationColourScheme }
1530		*
1531		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1532	2	public AnnotationColourScheme getAnnotationColours() {...
1533	2	return annotationColours;
1534		}
1535
1536		/**
1537		* Sets the value of the annotationColours property.
1538		*
1539		* @param value
1540		* allowed object is
1541		* {@link AnnotationColourScheme }
1542		*
1543		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1544	1	public void setAnnotationColours(AnnotationColourScheme value) {...
1545	1	this.annotationColours = value;
1546		}
1547
1548		/**
1549		* Gets the value of the annotationFromTree property.
1550		*
1551		* <p>This accessor method returns a reference to the live list,
1552		* not a snapshot. Therefore any modification you make to the
1553		* returned list will be present inside the JAXB object.
1554		* This is why there is not a <CODE>set</CODE> method for the annotationFromTree property.</p>
1555		*
1556		* <p>
1557		* For example, to add a new item, do as follows:
1558		* </p>
1559		* <pre>
1560		* getAnnotationFromTree().add(newItem);
1561		* </pre>
1562		*
1563		*
1564		* <p>
1565		* Objects of the following type(s) are allowed in the list
1566		* {@link String }
1567		* </p>
1568		*
1569		*
1570		* @return
1571		* The value of the annotationFromTree property.
1572		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
1573	138	public List<String> getAnnotationFromTree() {...
1574	138	if (annotationFromTree == null) {
1575	55	annotationFromTree = new ArrayList<String>();
1576		}
1577	138	return this.annotationFromTree;
1578		}
1579
1580		/**
1581		* Gets the value of the secStrProvider property.
1582		*
1583		* <p>This accessor method returns a reference to the live list,
1584		* not a snapshot. Therefore any modification you make to the
1585		* returned list will be present inside the JAXB object.
1586		* This is why there is not a <CODE>set</CODE> method for the secStrProvider property.</p>
1587		*
1588		* <p>
1589		* For example, to add a new item, do as follows:
1590		* </p>
1591		* <pre>
1592		* getSecStrProvider().add(newItem);
1593		* </pre>
1594		*
1595		*
1596		* <p>
1597		* Objects of the following type(s) are allowed in the list
1598		* {@link String }
1599		* </p>
1600		*
1601		*
1602		* @return
1603		* The value of the secStrProvider property.
1604		*/
		80% Uncovered Elements: 1 (5) Complexity: 2 Complexity Density: 0.67
1605	59	public List<String> getSecStrProvider() {...
1606	59	if (secStrProvider == null) {
1607	59	secStrProvider = new ArrayList<String>();
1608		}
1609	59	return this.secStrProvider;
1610		}
1611
1612		/**
1613		* Gets the value of the start property.
1614		*
1615		* @return
1616		* possible object is
1617		* {@link Integer }
1618		*
1619		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1620	59	public Integer getStart() {...
1621	59	return start;
1622		}
1623
1624		/**
1625		* Sets the value of the start property.
1626		*
1627		* @param value
1628		* allowed object is
1629		* {@link Integer }
1630		*
1631		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1632	22	public void setStart(Integer value) {...
1633	22	this.start = value;
1634		}
1635
1636		/**
1637		* Gets the value of the end property.
1638		*
1639		* @return
1640		* possible object is
1641		* {@link Integer }
1642		*
1643		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1644	59	public Integer getEnd() {...
1645	59	return end;
1646		}
1647
1648		/**
1649		* Sets the value of the end property.
1650		*
1651		* @param value
1652		* allowed object is
1653		* {@link Integer }
1654		*
1655		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1656	22	public void setEnd(Integer value) {...
1657	22	this.end = value;
1658		}
1659
1660		/**
1661		* Gets the value of the name property.
1662		*
1663		* @return
1664		* possible object is
1665		* {@link String }
1666		*
1667		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1668	59	public String getName() {...
1669	59	return name;
1670		}
1671
1672		/**
1673		* Sets the value of the name property.
1674		*
1675		* @param value
1676		* allowed object is
1677		* {@link String }
1678		*
1679		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1680	22	public void setName(String value) {...
1681	22	this.name = value;
1682		}
1683
1684		/**
1685		* Gets the value of the colour property.
1686		*
1687		* @return
1688		* possible object is
1689		* {@link String }
1690		*
1691		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1692	157	public String getColour() {...
1693	157	return colour;
1694		}
1695
1696		/**
1697		* Sets the value of the colour property.
1698		*
1699		* @param value
1700		* allowed object is
1701		* {@link String }
1702		*
1703		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1704	14	public void setColour(String value) {...
1705	14	this.colour = value;
1706		}
1707
1708		/**
1709		* Gets the value of the idColour property.
1710		*
1711		* @return
1712		* possible object is
1713		* {@link Integer }
1714		*
1715		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1716	59	public Integer getIdColour() {...
1717	59	return idColour;
1718		}
1719
1720		/**
1721		* Sets the value of the idColour property.
1722		*
1723		* @param value
1724		* allowed object is
1725		* {@link Integer }
1726		*
1727		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1728	19	public void setIdColour(Integer value) {...
1729	19	this.idColour = value;
1730		}
1731
1732		/**
1733		* Gets the value of the outlineColour property.
1734		*
1735		* @return
1736		* possible object is
1737		* {@link Integer }
1738		*
1739		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1740	59	public Integer getOutlineColour() {...
1741	59	return outlineColour;
1742		}
1743
1744		/**
1745		* Sets the value of the outlineColour property.
1746		*
1747		* @param value
1748		* allowed object is
1749		* {@link Integer }
1750		*
1751		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1752	22	public void setOutlineColour(Integer value) {...
1753	22	this.outlineColour = value;
1754		}
1755
1756		/**
1757		* Gets the value of the displayBoxes property.
1758		*
1759		* @return
1760		* possible object is
1761		* {@link Boolean }
1762		*
1763		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1764	59	public Boolean isDisplayBoxes() {...
1765	59	return displayBoxes;
1766		}
1767
1768		/**
1769		* Sets the value of the displayBoxes property.
1770		*
1771		* @param value
1772		* allowed object is
1773		* {@link Boolean }
1774		*
1775		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1776	22	public void setDisplayBoxes(Boolean value) {...
1777	22	this.displayBoxes = value;
1778		}
1779
1780		/**
1781		* Gets the value of the displayText property.
1782		*
1783		* @return
1784		* possible object is
1785		* {@link Boolean }
1786		*
1787		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1788	59	public Boolean isDisplayText() {...
1789	59	return displayText;
1790		}
1791
1792		/**
1793		* Sets the value of the displayText property.
1794		*
1795		* @param value
1796		* allowed object is
1797		* {@link Boolean }
1798		*
1799		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1800	22	public void setDisplayText(Boolean value) {...
1801	22	this.displayText = value;
1802		}
1803
1804		/**
1805		* Gets the value of the colourText property.
1806		*
1807		* @return
1808		* possible object is
1809		* {@link Boolean }
1810		*
1811		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1812	59	public Boolean isColourText() {...
1813	59	return colourText;
1814		}
1815
1816		/**
1817		* Sets the value of the colourText property.
1818		*
1819		* @param value
1820		* allowed object is
1821		* {@link Boolean }
1822		*
1823		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1824	22	public void setColourText(Boolean value) {...
1825	22	this.colourText = value;
1826		}
1827
1828		/**
1829		* Gets the value of the textCol1 property.
1830		*
1831		* @return
1832		* possible object is
1833		* {@link Integer }
1834		*
1835		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1836	59	public Integer getTextCol1() {...
1837	59	return textCol1;
1838		}
1839
1840		/**
1841		* Sets the value of the textCol1 property.
1842		*
1843		* @param value
1844		* allowed object is
1845		* {@link Integer }
1846		*
1847		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1848	22	public void setTextCol1(Integer value) {...
1849	22	this.textCol1 = value;
1850		}
1851
1852		/**
1853		* Gets the value of the textCol2 property.
1854		*
1855		* @return
1856		* possible object is
1857		* {@link Integer }
1858		*
1859		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1860	59	public Integer getTextCol2() {...
1861	59	return textCol2;
1862		}
1863
1864		/**
1865		* Sets the value of the textCol2 property.
1866		*
1867		* @param value
1868		* allowed object is
1869		* {@link Integer }
1870		*
1871		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1872	22	public void setTextCol2(Integer value) {...
1873	22	this.textCol2 = value;
1874		}
1875
1876		/**
1877		* Gets the value of the textColThreshold property.
1878		*
1879		* @return
1880		* possible object is
1881		* {@link Integer }
1882		*
1883		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1884	59	public Integer getTextColThreshold() {...
1885	59	return textColThreshold;
1886		}
1887
1888		/**
1889		* Sets the value of the textColThreshold property.
1890		*
1891		* @param value
1892		* allowed object is
1893		* {@link Integer }
1894		*
1895		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1896	22	public void setTextColThreshold(Integer value) {...
1897	22	this.textColThreshold = value;
1898		}
1899
1900		/**
1901		* Gets the value of the showUnconserved property.
1902		*
1903		* @return
1904		* possible object is
1905		* {@link Boolean }
1906		*
1907		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1908	59	public Boolean isShowUnconserved() {...
1909	59	return showUnconserved;
1910		}
1911
1912		/**
1913		* Sets the value of the showUnconserved property.
1914		*
1915		* @param value
1916		* allowed object is
1917		* {@link Boolean }
1918		*
1919		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1920	22	public void setShowUnconserved(Boolean value) {...
1921	22	this.showUnconserved = value;
1922		}
1923
1924		/**
1925		* Optional sequence group ID (only
1926		* needs to be
1927		* unique for this
1928		* alignment)
1929		*
1930		* @return
1931		* possible object is
1932		* {@link String }
1933		*
1934		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1935	83	public String getId() {...
1936	83	return id;
1937		}
1938
1939		/**
1940		* Sets the value of the id property.
1941		*
1942		* @param value
1943		* allowed object is
1944		* {@link String }
1945		*
1946		* @see #getId()
1947		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1948	6	public void setId(String value) {...
1949	6	this.id = value;
1950		}
1951
1952		/**
1953		* Gets the value of the conservationSelected property.
1954		*
1955		* @return
1956		* possible object is
1957		* {@link Boolean }
1958		*
1959		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1960	0	public Boolean isConservationSelected() {...
1961	0	return conservationSelected;
1962		}
1963
1964		/**
1965		* Sets the value of the conservationSelected property.
1966		*
1967		* @param value
1968		* allowed object is
1969		* {@link Boolean }
1970		*
1971		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1972	0	public void setConservationSelected(Boolean value) {...
1973	0	this.conservationSelected = value;
1974		}
1975
1976		/**
1977		* Conservation shading increment
1978		*
1979		* @return
1980		* possible object is
1981		* {@link Integer }
1982		*
1983		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1984	120	public Integer getConsThreshold() {...
1985	120	return consThreshold;
1986		}
1987
1988		/**
1989		* Sets the value of the consThreshold property.
1990		*
1991		* @param value
1992		* allowed object is
1993		* {@link Integer }
1994		*
1995		* @see #getConsThreshold()
1996		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1997	2	public void setConsThreshold(Integer value) {...
1998	2	this.consThreshold = value;
1999		}
2000
2001		/**
2002		* Gets the value of the pidSelected property.
2003		*
2004		* @return
2005		* possible object is
2006		* {@link Boolean }
2007		*
2008		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2009	0	public Boolean isPidSelected() {...
2010	0	return pidSelected;
2011		}
2012
2013		/**
2014		* Sets the value of the pidSelected property.
2015		*
2016		* @param value
2017		* allowed object is
2018		* {@link Boolean }
2019		*
2020		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2021	0	public void setPidSelected(Boolean value) {...
2022	0	this.pidSelected = value;
2023		}
2024
2025		/**
2026		* Percent Identity Threshold
2027		*
2028		* @return
2029		* possible object is
2030		* {@link Integer }
2031		*
2032		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2033	59	public Integer getPidThreshold() {...
2034	59	return pidThreshold;
2035		}
2036
2037		/**
2038		* Sets the value of the pidThreshold property.
2039		*
2040		* @param value
2041		* allowed object is
2042		* {@link Integer }
2043		*
2044		* @see #getPidThreshold()
2045		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2046	14	public void setPidThreshold(Integer value) {...
2047	14	this.pidThreshold = value;
2048		}
2049
2050		/**
2051		* Secondary structure consensus shading - since 2.11.4
2052		*
2053		* @return
2054		* possible object is
2055		* {@link Boolean }
2056		*
2057		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
2058	59	public boolean isSecstrSelected() {...
2059	59	if (secstrSelected == null) {
2060	49	return false;
2061		} else {
2062	10	return secstrSelected;
2063		}
2064		}
2065
2066		/**
2067		* Sets the value of the secstrSelected property.
2068		*
2069		* @param value
2070		* allowed object is
2071		* {@link Boolean }
2072		*
2073		* @see #isSecstrSelected()
2074		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2075	5	public void setSecstrSelected(Boolean value) {...
2076	5	this.secstrSelected = value;
2077		}
2078
2079		/**
2080		* Secondary structure consensus increment
2081		*
2082		* @return
2083		* possible object is
2084		* {@link Integer }
2085		*
2086		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2087	59	public Integer getSecstrThreshold() {...
2088	59	return secstrThreshold;
2089		}
2090
2091		/**
2092		* Sets the value of the secstrThreshold property.
2093		*
2094		* @param value
2095		* allowed object is
2096		* {@link Integer }
2097		*
2098		* @see #getSecstrThreshold()
2099		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2100	5	public void setSecstrThreshold(Integer value) {...
2101	5	this.secstrThreshold = value;
2102		}
2103
2104		/**
2105		* Gets the value of the showConsensusHistogram property.
2106		*
2107		* @return
2108		* possible object is
2109		* {@link Boolean }
2110		*
2111		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
2112	59	public boolean isShowConsensusHistogram() {...
2113	59	if (showConsensusHistogram == null) {
2114	0	return true;
2115		} else {
2116	59	return showConsensusHistogram;
2117		}
2118		}
2119
2120		/**
2121		* Sets the value of the showConsensusHistogram property.
2122		*
2123		* @param value
2124		* allowed object is
2125		* {@link Boolean }
2126		*
2127		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2128	22	public void setShowConsensusHistogram(Boolean value) {...
2129	22	this.showConsensusHistogram = value;
2130		}
2131
2132		/**
2133		* Gets the value of the showSequenceLogo property.
2134		*
2135		* @return
2136		* possible object is
2137		* {@link Boolean }
2138		*
2139		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
2140	59	public boolean isShowSequenceLogo() {...
2141	59	if (showSequenceLogo == null) {
2142	0	return false;
2143		} else {
2144	59	return showSequenceLogo;
2145		}
2146		}
2147
2148		/**
2149		* Sets the value of the showSequenceLogo property.
2150		*
2151		* @param value
2152		* allowed object is
2153		* {@link Boolean }
2154		*
2155		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2156	22	public void setShowSequenceLogo(Boolean value) {...
2157	22	this.showSequenceLogo = value;
2158		}
2159
2160		/**
2161		* Gets the value of the normaliseSequenceLogo property.
2162		*
2163		* @return
2164		* possible object is
2165		* {@link Boolean }
2166		*
2167		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
2168	59	public boolean isNormaliseSequenceLogo() {...
2169	59	if (normaliseSequenceLogo == null) {
2170	30	return false;
2171		} else {
2172	29	return normaliseSequenceLogo;
2173		}
2174		}
2175
2176		/**
2177		* Sets the value of the normaliseSequenceLogo property.
2178		*
2179		* @param value
2180		* allowed object is
2181		* {@link Boolean }
2182		*
2183		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2184	22	public void setNormaliseSequenceLogo(Boolean value) {...
2185	22	this.normaliseSequenceLogo = value;
2186		}
2187
2188		/**
2189		* Gets the value of the ignoreGapsinConsensus property.
2190		*
2191		* @return
2192		* possible object is
2193		* {@link Boolean }
2194		*
2195		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
2196	59	public boolean isIgnoreGapsinConsensus() {...
2197	59	if (ignoreGapsinConsensus == null) {
2198	0	return true;
2199		} else {
2200	59	return ignoreGapsinConsensus;
2201		}
2202		}
2203
2204		/**
2205		* Sets the value of the ignoreGapsinConsensus property.
2206		*
2207		* @param value
2208		* allowed object is
2209		* {@link Boolean }
2210		*
2211		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2212	22	public void setIgnoreGapsinConsensus(Boolean value) {...
2213	22	this.ignoreGapsinConsensus = value;
2214		}
2215
2216		}
2217
2218
2219		/**
2220		* <p>Java class for anonymous complex type</p>.
2221		*
2222		* <p>The following schema fragment specifies the expected content contained within this class.</p>
2223		*
2224		* <pre>
2225		* &lt;complexType&gt;
2226		* &lt;complexContent&gt;
2227		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
2228		* &lt;sequence&gt;
2229		* &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
2230		* &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
2231		* &lt;complexType&gt;
2232		* &lt;complexContent&gt;
2233		* &lt;extension base="{www.jalview.org}pdbentry"&gt;
2234		* &lt;sequence&gt;
2235		* &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
2236		* &lt;complexType&gt;
2237		* &lt;simpleContent&gt;
2238		* &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
2239		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
2240		* &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2241		* &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2242		* &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2243		* &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
2244		* &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2245		* &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2246		* &lt;/extension&gt;
2247		* &lt;/simpleContent&gt;
2248		* &lt;/complexType&gt;
2249		* &lt;/element&gt;
2250		* &lt;/sequence&gt;
2251		* &lt;/extension&gt;
2252		* &lt;/complexContent&gt;
2253		* &lt;/complexType&gt;
2254		* &lt;/element&gt;
2255		* &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&gt;
2256		* &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
2257		* &lt;complexType&gt;
2258		* &lt;complexContent&gt;
2259		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
2260		* &lt;sequence&gt;
2261		* &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
2262		* &lt;complexType&gt;
2263		* &lt;complexContent&gt;
2264		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
2265		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2266		* &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2267		* &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2268		* &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2269		* &lt;/restriction&gt;
2270		* &lt;/complexContent&gt;
2271		* &lt;/complexType&gt;
2272		* &lt;/element&gt;
2273		* &lt;/sequence&gt;
2274		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
2275		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2276		* &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2277		* &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
2278		* &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
2279		* &lt;/restriction&gt;
2280		* &lt;/complexContent&gt;
2281		* &lt;/complexType&gt;
2282		* &lt;/element&gt;
2283		* &lt;/sequence&gt;
2284		* &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
2285		* &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
2286		* &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
2287		* &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2288		* &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2289		* &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2290		* &lt;/restriction&gt;
2291		* &lt;/complexContent&gt;
2292		* &lt;/complexType&gt;
2293		* </pre>
2294		*
2295		*
2296		*/
2297		@XmlAccessorType(XmlAccessType.FIELD)
2298		@XmlType(name = "", propOrder = {
2299		"features",
2300		"pdbids",
2301		"hiddenSequences",
2302		"rnaViewer"
2303		})
		97.9% Uncovered Elements: 1 (48) Complexity: 20 Complexity Density: 0.83
2304		public static class JSeq {
2305
2306		@XmlElement(namespace = "www.jalview.org")
2307		protected List<Feature> features;
2308		@XmlElement(namespace = "www.jalview.org")
2309		protected List<JalviewModel.JSeq.Pdbids> pdbids;
2310		@XmlElement(namespace = "www.jalview.org", type = Integer.class)
2311		protected List<Integer> hiddenSequences;
2312		/**
2313		* Reference to a viewer showing
2314		* RNA structure for this sequence.
2315		* Schema supports one viewer
2316		* showing multiple annotations for
2317		* multiple sequences, though
2318		* currently only one annotation
2319		* for one sequence (gapped or
2320		* trimmed) is used
2321		*
2322		*/
2323		@XmlElement(namespace = "www.jalview.org")
2324		protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
2325		@XmlAttribute(name = "colour")
2326		protected Integer colour;
2327		@XmlAttribute(name = "start", required = true)
2328		protected int start;
2329		@XmlAttribute(name = "end", required = true)
2330		protected int end;
2331		@XmlAttribute(name = "id", required = true)
2332		protected String id;
2333		@XmlAttribute(name = "hidden")
2334		protected Boolean hidden;
2335		@XmlAttribute(name = "viewreference")
2336		protected Boolean viewreference;
2337
2338		/**
2339		* Gets the value of the features property.
2340		*
2341		* <p>This accessor method returns a reference to the live list,
2342		* not a snapshot. Therefore any modification you make to the
2343		* returned list will be present inside the JAXB object.
2344		* This is why there is not a <CODE>set</CODE> method for the features property.</p>
2345		*
2346		* <p>
2347		* For example, to add a new item, do as follows:
2348		* </p>
2349		* <pre>
2350		* getFeatures().add(newItem);
2351		* </pre>
2352		*
2353		*
2354		* <p>
2355		* Objects of the following type(s) are allowed in the list
2356		* {@link Feature }
2357		* </p>
2358		*
2359		*
2360		* @return
2361		* The value of the features property.
2362		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
2363	32222	public List<Feature> getFeatures() {...
2364	32222	if (features == null) {
2365	15692	features = new ArrayList<Feature>();
2366		}
2367	32222	return this.features;
2368		}
2369
2370		/**
2371		* Gets the value of the pdbids property.
2372		*
2373		* <p>This accessor method returns a reference to the live list,
2374		* not a snapshot. Therefore any modification you make to the
2375		* returned list will be present inside the JAXB object.
2376		* This is why there is not a <CODE>set</CODE> method for the pdbids property.</p>
2377		*
2378		* <p>
2379		* For example, to add a new item, do as follows:
2380		* </p>
2381		* <pre>
2382		* getPdbids().add(newItem);
2383		* </pre>
2384		*
2385		*
2386		* <p>
2387		* Objects of the following type(s) are allowed in the list
2388		* {@link JalviewModel.JSeq.Pdbids }
2389		* </p>
2390		*
2391		*
2392		* @return
2393		* The value of the pdbids property.
2394		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
2395	17259	public List<JalviewModel.JSeq.Pdbids> getPdbids() {...
2396	17259	if (pdbids == null) {
2397	16237	pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
2398		}
2399	17259	return this.pdbids;
2400		}
2401
2402		/**
2403		* Gets the value of the hiddenSequences property.
2404		*
2405		* <p>This accessor method returns a reference to the live list,
2406		* not a snapshot. Therefore any modification you make to the
2407		* returned list will be present inside the JAXB object.
2408		* This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.</p>
2409		*
2410		* <p>
2411		* For example, to add a new item, do as follows:
2412		* </p>
2413		* <pre>
2414		* getHiddenSequences().add(newItem);
2415		* </pre>
2416		*
2417		*
2418		* <p>
2419		* Objects of the following type(s) are allowed in the list
2420		* {@link Integer }
2421		* </p>
2422		*
2423		*
2424		* @return
2425		* The value of the hiddenSequences property.
2426		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
2427	676	public List<Integer> getHiddenSequences() {...
2428	676	if (hiddenSequences == null) {
2429	670	hiddenSequences = new ArrayList<Integer>();
2430		}
2431	676	return this.hiddenSequences;
2432		}
2433
2434		/**
2435		* Reference to a viewer showing
2436		* RNA structure for this sequence.
2437		* Schema supports one viewer
2438		* showing multiple annotations for
2439		* multiple sequences, though
2440		* currently only one annotation
2441		* for one sequence (gapped or
2442		* trimmed) is used
2443		*
2444		* Gets the value of the rnaViewer property.
2445		*
2446		* <p>This accessor method returns a reference to the live list,
2447		* not a snapshot. Therefore any modification you make to the
2448		* returned list will be present inside the JAXB object.
2449		* This is why there is not a <CODE>set</CODE> method for the rnaViewer property.</p>
2450		*
2451		* <p>
2452		* For example, to add a new item, do as follows:
2453		* </p>
2454		* <pre>
2455		* getRnaViewer().add(newItem);
2456		* </pre>
2457		*
2458		*
2459		* <p>
2460		* Objects of the following type(s) are allowed in the list
2461		* {@link JalviewModel.JSeq.RnaViewer }
2462		* </p>
2463		*
2464		*
2465		* @return
2466		* The value of the rnaViewer property.
2467		*/
		80% Uncovered Elements: 1 (5) Complexity: 2 Complexity Density: 0.67
2468	1135	public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {...
2469	1135	if (rnaViewer == null) {
2470	1135	rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2471		}
2472	1135	return this.rnaViewer;
2473		}
2474
2475		/**
2476		* Gets the value of the colour property.
2477		*
2478		* @return
2479		* possible object is
2480		* {@link Integer }
2481		*
2482		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2483	1257	public Integer getColour() {...
2484	1257	return colour;
2485		}
2486
2487		/**
2488		* Sets the value of the colour property.
2489		*
2490		* @param value
2491		* allowed object is
2492		* {@link Integer }
2493		*
2494		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2495	8361	public void setColour(Integer value) {...
2496	8361	this.colour = value;
2497		}
2498
2499		/**
2500		* Gets the value of the start property.
2501		*
2502		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2503	17507	public int getStart() {...
2504	17507	return start;
2505		}
2506
2507		/**
2508		* Sets the value of the start property.
2509		*
2510		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2511	8361	public void setStart(int value) {...
2512	8361	this.start = value;
2513		}
2514
2515		/**
2516		* Gets the value of the end property.
2517		*
2518		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2519	17507	public int getEnd() {...
2520	17507	return end;
2521		}
2522
2523		/**
2524		* Sets the value of the end property.
2525		*
2526		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2527	8361	public void setEnd(int value) {...
2528	8361	this.end = value;
2529		}
2530
2531		/**
2532		* Gets the value of the id property.
2533		*
2534		* @return
2535		* possible object is
2536		* {@link String }
2537		*
2538		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2539	16434	public String getId() {...
2540	16434	return id;
2541		}
2542
2543		/**
2544		* Sets the value of the id property.
2545		*
2546		* @param value
2547		* allowed object is
2548		* {@link String }
2549		*
2550		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2551	8361	public void setId(String value) {...
2552	8361	this.id = value;
2553		}
2554
2555		/**
2556		* Gets the value of the hidden property.
2557		*
2558		* @return
2559		* possible object is
2560		* {@link Boolean }
2561		*
2562		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2563	17024	public Boolean isHidden() {...
2564	17024	return hidden;
2565		}
2566
2567		/**
2568		* Sets the value of the hidden property.
2569		*
2570		* @param value
2571		* allowed object is
2572		* {@link Boolean }
2573		*
2574		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2575	190	public void setHidden(Boolean value) {...
2576	190	this.hidden = value;
2577		}
2578
2579		/**
2580		* Gets the value of the viewreference property.
2581		*
2582		* @return
2583		* possible object is
2584		* {@link Boolean }
2585		*
2586		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2587	16354	public Boolean isViewreference() {...
2588	16354	return viewreference;
2589		}
2590
2591		/**
2592		* Sets the value of the viewreference property.
2593		*
2594		* @param value
2595		* allowed object is
2596		* {@link Boolean }
2597		*
2598		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2599	80	public void setViewreference(Boolean value) {...
2600	80	this.viewreference = value;
2601		}
2602
2603
2604		/**
2605		* <p>Java class for anonymous complex type</p>.
2606		*
2607		* <p>The following schema fragment specifies the expected content contained within this class.</p>
2608		*
2609		* <pre>
2610		* &lt;complexType&gt;
2611		* &lt;complexContent&gt;
2612		* &lt;extension base="{www.jalview.org}pdbentry"&gt;
2613		* &lt;sequence&gt;
2614		* &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
2615		* &lt;complexType&gt;
2616		* &lt;simpleContent&gt;
2617		* &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
2618		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
2619		* &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2620		* &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2621		* &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2622		* &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
2623		* &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2624		* &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2625		* &lt;/extension&gt;
2626		* &lt;/simpleContent&gt;
2627		* &lt;/complexType&gt;
2628		* &lt;/element&gt;
2629		* &lt;/sequence&gt;
2630		* &lt;/extension&gt;
2631		* &lt;/complexContent&gt;
2632		* &lt;/complexType&gt;
2633		* </pre>
2634		*
2635		*
2636		*/
2637		@XmlAccessorType(XmlAccessType.FIELD)
2638		@XmlType(name = "", propOrder = {
2639		"structureState"
2640		})
		100% Uncovered Elements: 0 (6) Complexity: 2 Complexity Density: 0.67
2641		public static class Pdbids
2642		extends Pdbentry
2643		{
2644
2645		@XmlElement(namespace = "www.jalview.org")
2646		protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2647
2648		/**
2649		* Gets the value of the structureState property.
2650		*
2651		* <p>This accessor method returns a reference to the live list,
2652		* not a snapshot. Therefore any modification you make to the
2653		* returned list will be present inside the JAXB object.
2654		* This is why there is not a <CODE>set</CODE> method for the structureState property.</p>
2655		*
2656		* <p>
2657		* For example, to add a new item, do as follows:
2658		* </p>
2659		* <pre>
2660		* getStructureState().add(newItem);
2661		* </pre>
2662		*
2663		*
2664		* <p>
2665		* Objects of the following type(s) are allowed in the list
2666		* {@link JalviewModel.JSeq.Pdbids.StructureState }
2667		* </p>
2668		*
2669		*
2670		* @return
2671		* The value of the structureState property.
2672		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
2673	371	public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {...
2674	371	if (structureState == null) {
2675	211	structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2676		}
2677	371	return this.structureState;
2678		}
2679
2680
2681		/**
2682		* <p>Java class for anonymous complex type</p>.
2683		*
2684		* <p>The following schema fragment specifies the expected content contained within this class.</p>
2685		*
2686		* <pre>
2687		* &lt;complexType&gt;
2688		* &lt;simpleContent&gt;
2689		* &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
2690		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
2691		* &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2692		* &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2693		* &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2694		* &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
2695		* &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2696		* &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2697		* &lt;/extension&gt;
2698		* &lt;/simpleContent&gt;
2699		* &lt;/complexType&gt;
2700		* </pre>
2701		*
2702		*
2703		*/
2704		@XmlAccessorType(XmlAccessType.FIELD)
2705		@XmlType(name = "", propOrder = {
2706		"value"
2707		})
		82.1% Uncovered Elements: 10 (56) Complexity: 25 Complexity Density: 0.89
2708		public static class StructureState {
2709
2710		@XmlValue
2711		protected String value;
2712		@XmlAttribute(name = "visible")
2713		protected Boolean visible;
2714		/**
2715		* additional
2716		* identifier
2717		* which
2718		* properly
2719		* disambiguates
2720		* the
2721		* structure
2722		* view
2723		* from
2724		* any
2725		* other
2726		* view
2727		* with
2728		* the
2729		* same
2730		* attributes.
2731		* This
2732		* is
2733		* not
2734		* an
2735		* ID,
2736		* because
2737		* it
2738		* is
2739		* possible
2740		* to
2741		* have
2742		* many
2743		* references
2744		* to
2745		* the
2746		* same
2747		* physical
2748		* structure
2749		* view
2750		* from
2751		* different
2752		* sequences
2753		* in
2754		* an
2755		* alignment.
2756		* A
2757		* structureState
2758		* element
2759		* citing
2760		* the
2761		* same
2762		* viewId
2763		* will
2764		* appear
2765		* for
2766		* each
2767		* instance.
2768		*
2769		*/
2770		@XmlAttribute(name = "viewId")
2771		protected String viewId;
2772		/**
2773		* Flag
2774		* set
2775		* if
2776		* the
2777		* alignment
2778		* panel
2779		* containing
2780		* this
2781		* JSeq
2782		* should
2783		* be
2784		* included
2785		* in
2786		* those
2787		* used
2788		* to
2789		* perform
2790		* a
2791		* structure
2792		* superposition
2793		* (since
2794		* Jalview
2795		* 2.7).
2796		*
2797		*/
2798		@XmlAttribute(name = "alignwithAlignPanel")
2799		protected Boolean alignwithAlignPanel;
2800		/**
2801		* Flag
2802		* set
2803		* if
2804		* the
2805		* alignment
2806		* panel
2807		* containing
2808		* this
2809		* JSeq
2810		* should
2811		* be
2812		* included
2813		* in
2814		* those
2815		* used
2816		* to
2817		* colour
2818		* its
2819		* associated
2820		* sequences
2821		* in
2822		* this
2823		* structureState(since
2824		* Jalview
2825		* 2.7).
2826		*
2827		*/
2828		@XmlAttribute(name = "colourwithAlignPanel")
2829		protected Boolean colourwithAlignPanel;
2830		/**
2831		* Flag
2832		* set
2833		* if
2834		* the
2835		* structure
2836		* display
2837		* is
2838		* coloured
2839		* by
2840		* the
2841		* Jmol
2842		* state,
2843		* rather
2844		* than
2845		* by
2846		* one
2847		* or
2848		* more
2849		* linked
2850		* alignment
2851		* views.
2852		*
2853		*/
2854		@XmlAttribute(name = "colourByJmol")
2855		protected Boolean colourByJmol;
2856		/**
2857		* An
2858		* identifier
2859		* for
2860		* the
2861		* viewer
2862		* type,
2863		* currently
2864		* either
2865		* JMOL
2866		* or
2867		* CHIMERA
2868		*
2869		*/
2870		@XmlAttribute(name = "type")
2871		protected String type;
2872		@XmlAttribute(name = "width")
2873		protected Integer width;
2874		@XmlAttribute(name = "height")
2875		protected Integer height;
2876		@XmlAttribute(name = "xpos")
2877		protected Integer xpos;
2878		@XmlAttribute(name = "ypos")
2879		protected Integer ypos;
2880
2881		/**
2882		* Gets the value of the value property.
2883		*
2884		* @return
2885		* possible object is
2886		* {@link String }
2887		*
2888		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2889	110	public String getValue() {...
2890	110	return value;
2891		}
2892
2893		/**
2894		* Sets the value of the value property.
2895		*
2896		* @param value
2897		* allowed object is
2898		* {@link String }
2899		*
2900		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2901	0	public void setValue(String value) {...
2902	0	this.value = value;
2903		}
2904
2905		/**
2906		* Gets the value of the visible property.
2907		*
2908		* @return
2909		* possible object is
2910		* {@link Boolean }
2911		*
2912		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2913	0	public Boolean isVisible() {...
2914	0	return visible;
2915		}
2916
2917		/**
2918		* Sets the value of the visible property.
2919		*
2920		* @param value
2921		* allowed object is
2922		* {@link Boolean }
2923		*
2924		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2925	20	public void setVisible(Boolean value) {...
2926	20	this.visible = value;
2927		}
2928
2929		/**
2930		* additional
2931		* identifier
2932		* which
2933		* properly
2934		* disambiguates
2935		* the
2936		* structure
2937		* view
2938		* from
2939		* any
2940		* other
2941		* view
2942		* with
2943		* the
2944		* same
2945		* attributes.
2946		* This
2947		* is
2948		* not
2949		* an
2950		* ID,
2951		* because
2952		* it
2953		* is
2954		* possible
2955		* to
2956		* have
2957		* many
2958		* references
2959		* to
2960		* the
2961		* same
2962		* physical
2963		* structure
2964		* view
2965		* from
2966		* different
2967		* sequences
2968		* in
2969		* an
2970		* alignment.
2971		* A
2972		* structureState
2973		* element
2974		* citing
2975		* the
2976		* same
2977		* viewId
2978		* will
2979		* appear
2980		* for
2981		* each
2982		* instance.
2983		*
2984		* @return
2985		* possible object is
2986		* {@link String }
2987		*
2988		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2989	200	public String getViewId() {...
2990	200	return viewId;
2991		}
2992
2993		/**
2994		* Sets the value of the viewId property.
2995		*
2996		* @param value
2997		* allowed object is
2998		* {@link String }
2999		*
3000		* @see #getViewId()
3001		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3002	20	public void setViewId(String value) {...
3003	20	this.viewId = value;
3004		}
3005
3006		/**
3007		* Flag
3008		* set
3009		* if
3010		* the
3011		* alignment
3012		* panel
3013		* containing
3014		* this
3015		* JSeq
3016		* should
3017		* be
3018		* included
3019		* in
3020		* those
3021		* used
3022		* to
3023		* perform
3024		* a
3025		* structure
3026		* superposition
3027		* (since
3028		* Jalview
3029		* 2.7).
3030		*
3031		* @return
3032		* possible object is
3033		* {@link Boolean }
3034		*
3035		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
3036	80	public boolean isAlignwithAlignPanel() {...
3037	80	if (alignwithAlignPanel == null) {
3038	0	return true;
3039		} else {
3040	80	return alignwithAlignPanel;
3041		}
3042		}
3043
3044		/**
3045		* Sets the value of the alignwithAlignPanel property.
3046		*
3047		* @param value
3048		* allowed object is
3049		* {@link Boolean }
3050		*
3051		* @see #isAlignwithAlignPanel()
3052		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3053	20	public void setAlignwithAlignPanel(Boolean value) {...
3054	20	this.alignwithAlignPanel = value;
3055		}
3056
3057		/**
3058		* Flag
3059		* set
3060		* if
3061		* the
3062		* alignment
3063		* panel
3064		* containing
3065		* this
3066		* JSeq
3067		* should
3068		* be
3069		* included
3070		* in
3071		* those
3072		* used
3073		* to
3074		* colour
3075		* its
3076		* associated
3077		* sequences
3078		* in
3079		* this
3080		* structureState(since
3081		* Jalview
3082		* 2.7).
3083		*
3084		* @return
3085		* possible object is
3086		* {@link Boolean }
3087		*
3088		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
3089	80	public boolean isColourwithAlignPanel() {...
3090	80	if (colourwithAlignPanel == null) {
3091	0	return false;
3092		} else {
3093	80	return colourwithAlignPanel;
3094		}
3095		}
3096
3097		/**
3098		* Sets the value of the colourwithAlignPanel property.
3099		*
3100		* @param value
3101		* allowed object is
3102		* {@link Boolean }
3103		*
3104		* @see #isColourwithAlignPanel()
3105		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3106	20	public void setColourwithAlignPanel(Boolean value) {...
3107	20	this.colourwithAlignPanel = value;
3108		}
3109
3110		/**
3111		* Flag
3112		* set
3113		* if
3114		* the
3115		* structure
3116		* display
3117		* is
3118		* coloured
3119		* by
3120		* the
3121		* Jmol
3122		* state,
3123		* rather
3124		* than
3125		* by
3126		* one
3127		* or
3128		* more
3129		* linked
3130		* alignment
3131		* views.
3132		*
3133		* @return
3134		* possible object is
3135		* {@link Boolean }
3136		*
3137		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
3138	80	public boolean isColourByJmol() {...
3139	80	if (colourByJmol == null) {
3140	0	return true;
3141		} else {
3142	80	return colourByJmol;
3143		}
3144		}
3145
3146		/**
3147		* Sets the value of the colourByJmol property.
3148		*
3149		* @param value
3150		* allowed object is
3151		* {@link Boolean }
3152		*
3153		* @see #isColourByJmol()
3154		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3155	20	public void setColourByJmol(Boolean value) {...
3156	20	this.colourByJmol = value;
3157		}
3158
3159		/**
3160		* An
3161		* identifier
3162		* for
3163		* the
3164		* viewer
3165		* type,
3166		* currently
3167		* either
3168		* JMOL
3169		* or
3170		* CHIMERA
3171		*
3172		* @return
3173		* possible object is
3174		* {@link String }
3175		*
3176		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3177	40	public String getType() {...
3178	40	return type;
3179		}
3180
3181		/**
3182		* Sets the value of the type property.
3183		*
3184		* @param value
3185		* allowed object is
3186		* {@link String }
3187		*
3188		* @see #getType()
3189		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3190	20	public void setType(String value) {...
3191	20	this.type = value;
3192		}
3193
3194		/**
3195		* Gets the value of the width property.
3196		*
3197		* @return
3198		* possible object is
3199		* {@link Integer }
3200		*
3201		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3202	80	public Integer getWidth() {...
3203	80	return width;
3204		}
3205
3206		/**
3207		* Sets the value of the width property.
3208		*
3209		* @param value
3210		* allowed object is
3211		* {@link Integer }
3212		*
3213		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3214	20	public void setWidth(Integer value) {...
3215	20	this.width = value;
3216		}
3217
3218		/**
3219		* Gets the value of the height property.
3220		*
3221		* @return
3222		* possible object is
3223		* {@link Integer }
3224		*
3225		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3226	80	public Integer getHeight() {...
3227	80	return height;
3228		}
3229
3230		/**
3231		* Sets the value of the height property.
3232		*
3233		* @param value
3234		* allowed object is
3235		* {@link Integer }
3236		*
3237		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3238	20	public void setHeight(Integer value) {...
3239	20	this.height = value;
3240		}
3241
3242		/**
3243		* Gets the value of the xpos property.
3244		*
3245		* @return
3246		* possible object is
3247		* {@link Integer }
3248		*
3249		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3250	80	public Integer getXpos() {...
3251	80	return xpos;
3252		}
3253
3254		/**
3255		* Sets the value of the xpos property.
3256		*
3257		* @param value
3258		* allowed object is
3259		* {@link Integer }
3260		*
3261		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3262	20	public void setXpos(Integer value) {...
3263	20	this.xpos = value;
3264		}
3265
3266		/**
3267		* Gets the value of the ypos property.
3268		*
3269		* @return
3270		* possible object is
3271		* {@link Integer }
3272		*
3273		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3274	80	public Integer getYpos() {...
3275	80	return ypos;
3276		}
3277
3278		/**
3279		* Sets the value of the ypos property.
3280		*
3281		* @param value
3282		* allowed object is
3283		* {@link Integer }
3284		*
3285		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
3286	20	public void setYpos(Integer value) {...
3287	20	this.ypos = value;
3288		}
3289
3290		}
3291
3292		}
3293
3294
3295		/**
3296		* <p>Java class for anonymous complex type</p>.
3297		*
3298		* <p>The following schema fragment specifies the expected content contained within this class.</p>
3299		*
3300		* <pre>
3301		* &lt;complexType&gt;
3302		* &lt;complexContent&gt;
3303		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3304		* &lt;sequence&gt;
3305		* &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
3306		* &lt;complexType&gt;
3307		* &lt;complexContent&gt;
3308		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3309		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3310		* &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3311		* &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
3312		* &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3313		* &lt;/restriction&gt;
3314		* &lt;/complexContent&gt;
3315		* &lt;/complexType&gt;
3316		* &lt;/element&gt;
3317		* &lt;/sequence&gt;
3318		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
3319		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3320		* &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3321		* &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3322		* &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3323		* &lt;/restriction&gt;
3324		* &lt;/complexContent&gt;
3325		* &lt;/complexType&gt;
3326		* </pre>
3327		*
3328		*
3329		*/
3330		@XmlAccessorType(XmlAccessType.FIELD)
3331		@XmlType(name = "", propOrder = {
3332		"secondaryStructure"
3333		})
		0% Uncovered Elements: 38 (38) Complexity: 18 Complexity Density: 0.95
3334		public static class RnaViewer {
3335
3336		@XmlElement(namespace = "www.jalview.org", required = true)
3337		protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
3338		@XmlAttribute(name = "title")
3339		protected String title;
3340		/**
3341		* An id unique to the RNA
3342		* viewer panel
3343		*
3344		*/
3345		@XmlAttribute(name = "viewId")
3346		protected String viewId;
3347		/**
3348		* horizontal position of
3349		* split pane divider
3350		*
3351		*/
3352		@XmlAttribute(name = "dividerLocation")
3353		protected Integer dividerLocation;
3354		/**
3355		* Index of the selected
3356		* structure in the viewer
3357		* panel
3358		*
3359		*/
3360		@XmlAttribute(name = "selectedRna")
3361		protected Integer selectedRna;
3362		@XmlAttribute(name = "width")
3363		protected Integer width;
3364		@XmlAttribute(name = "height")
3365		protected Integer height;
3366		@XmlAttribute(name = "xpos")
3367		protected Integer xpos;
3368		@XmlAttribute(name = "ypos")
3369		protected Integer ypos;
3370
3371		/**
3372		* Gets the value of the secondaryStructure property.
3373		*
3374		* <p>This accessor method returns a reference to the live list,
3375		* not a snapshot. Therefore any modification you make to the
3376		* returned list will be present inside the JAXB object.
3377		* This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.</p>
3378		*
3379		* <p>
3380		* For example, to add a new item, do as follows:
3381		* </p>
3382		* <pre>
3383		* getSecondaryStructure().add(newItem);
3384		* </pre>
3385		*
3386		*
3387		* <p>
3388		* Objects of the following type(s) are allowed in the list
3389		* {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
3390		* </p>
3391		*
3392		*
3393		* @return
3394		* The value of the secondaryStructure property.
3395		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
3396	0	public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {...
3397	0	if (secondaryStructure == null) {
3398	0	secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
3399		}
3400	0	return this.secondaryStructure;
3401		}
3402
3403		/**
3404		* Gets the value of the title property.
3405		*
3406		* @return
3407		* possible object is
3408		* {@link String }
3409		*
3410		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3411	0	public String getTitle() {...
3412	0	return title;
3413		}
3414
3415		/**
3416		* Sets the value of the title property.
3417		*
3418		* @param value
3419		* allowed object is
3420		* {@link String }
3421		*
3422		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3423	0	public void setTitle(String value) {...
3424	0	this.title = value;
3425		}
3426
3427		/**
3428		* An id unique to the RNA
3429		* viewer panel
3430		*
3431		* @return
3432		* possible object is
3433		* {@link String }
3434		*
3435		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3436	0	public String getViewId() {...
3437	0	return viewId;
3438		}
3439
3440		/**
3441		* Sets the value of the viewId property.
3442		*
3443		* @param value
3444		* allowed object is
3445		* {@link String }
3446		*
3447		* @see #getViewId()
3448		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3449	0	public void setViewId(String value) {...
3450	0	this.viewId = value;
3451		}
3452
3453		/**
3454		* horizontal position of
3455		* split pane divider
3456		*
3457		* @return
3458		* possible object is
3459		* {@link Integer }
3460		*
3461		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3462	0	public Integer getDividerLocation() {...
3463	0	return dividerLocation;
3464		}
3465
3466		/**
3467		* Sets the value of the dividerLocation property.
3468		*
3469		* @param value
3470		* allowed object is
3471		* {@link Integer }
3472		*
3473		* @see #getDividerLocation()
3474		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3475	0	public void setDividerLocation(Integer value) {...
3476	0	this.dividerLocation = value;
3477		}
3478
3479		/**
3480		* Index of the selected
3481		* structure in the viewer
3482		* panel
3483		*
3484		* @return
3485		* possible object is
3486		* {@link Integer }
3487		*
3488		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3489	0	public Integer getSelectedRna() {...
3490	0	return selectedRna;
3491		}
3492
3493		/**
3494		* Sets the value of the selectedRna property.
3495		*
3496		* @param value
3497		* allowed object is
3498		* {@link Integer }
3499		*
3500		* @see #getSelectedRna()
3501		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3502	0	public void setSelectedRna(Integer value) {...
3503	0	this.selectedRna = value;
3504		}
3505
3506		/**
3507		* Gets the value of the width property.
3508		*
3509		* @return
3510		* possible object is
3511		* {@link Integer }
3512		*
3513		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3514	0	public Integer getWidth() {...
3515	0	return width;
3516		}
3517
3518		/**
3519		* Sets the value of the width property.
3520		*
3521		* @param value
3522		* allowed object is
3523		* {@link Integer }
3524		*
3525		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3526	0	public void setWidth(Integer value) {...
3527	0	this.width = value;
3528		}
3529
3530		/**
3531		* Gets the value of the height property.
3532		*
3533		* @return
3534		* possible object is
3535		* {@link Integer }
3536		*
3537		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3538	0	public Integer getHeight() {...
3539	0	return height;
3540		}
3541
3542		/**
3543		* Sets the value of the height property.
3544		*
3545		* @param value
3546		* allowed object is
3547		* {@link Integer }
3548		*
3549		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3550	0	public void setHeight(Integer value) {...
3551	0	this.height = value;
3552		}
3553
3554		/**
3555		* Gets the value of the xpos property.
3556		*
3557		* @return
3558		* possible object is
3559		* {@link Integer }
3560		*
3561		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3562	0	public Integer getXpos() {...
3563	0	return xpos;
3564		}
3565
3566		/**
3567		* Sets the value of the xpos property.
3568		*
3569		* @param value
3570		* allowed object is
3571		* {@link Integer }
3572		*
3573		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3574	0	public void setXpos(Integer value) {...
3575	0	this.xpos = value;
3576		}
3577
3578		/**
3579		* Gets the value of the ypos property.
3580		*
3581		* @return
3582		* possible object is
3583		* {@link Integer }
3584		*
3585		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3586	0	public Integer getYpos() {...
3587	0	return ypos;
3588		}
3589
3590		/**
3591		* Sets the value of the ypos property.
3592		*
3593		* @param value
3594		* allowed object is
3595		* {@link Integer }
3596		*
3597		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3598	0	public void setYpos(Integer value) {...
3599	0	this.ypos = value;
3600		}
3601
3602
3603		/**
3604		* <p>Java class for anonymous complex type</p>.
3605		*
3606		* <p>The following schema fragment specifies the expected content contained within this class.</p>
3607		*
3608		* <pre>
3609		* &lt;complexType&gt;
3610		* &lt;complexContent&gt;
3611		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3612		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3613		* &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3614		* &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
3615		* &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3616		* &lt;/restriction&gt;
3617		* &lt;/complexContent&gt;
3618		* &lt;/complexType&gt;
3619		* </pre>
3620		*
3621		*
3622		*/
3623		@XmlAccessorType(XmlAccessType.FIELD)
3624		@XmlType(name = "")
		0% Uncovered Elements: 16 (16) Complexity: 8 Complexity Density: 1
3625		public static class SecondaryStructure {
3626
3627		@XmlAttribute(name = "title")
3628		protected String title;
3629		/**
3630		* id attribute
3631		* of
3632		* Annotation
3633		* in
3634		* vamsasModel
3635		* for the
3636		* secondary
3637		* structure
3638		* annotation
3639		* shown in the
3640		* viewer
3641		*
3642		*/
3643		@XmlAttribute(name = "annotationId", required = true)
3644		protected String annotationId;
3645		/**
3646		* if true the
3647		* RNA
3648		* structure is
3649		* shown with
3650		* gaps, if
3651		* false
3652		* without
3653		*
3654		*/
3655		@XmlAttribute(name = "gapped")
3656		protected Boolean gapped;
3657		/**
3658		* name of the
3659		* project jar
3660		* entry that
3661		* holds the
3662		* VARNA viewer
3663		* state for
3664		* the
3665		* structure
3666		*
3667		*/
3668		@XmlAttribute(name = "viewerState")
3669		protected String viewerState;
3670
3671		/**
3672		* Gets the value of the title property.
3673		*
3674		* @return
3675		* possible object is
3676		* {@link String }
3677		*
3678		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3679	0	public String getTitle() {...
3680	0	return title;
3681		}
3682
3683		/**
3684		* Sets the value of the title property.
3685		*
3686		* @param value
3687		* allowed object is
3688		* {@link String }
3689		*
3690		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3691	0	public void setTitle(String value) {...
3692	0	this.title = value;
3693		}
3694
3695		/**
3696		* id attribute
3697		* of
3698		* Annotation
3699		* in
3700		* vamsasModel
3701		* for the
3702		* secondary
3703		* structure
3704		* annotation
3705		* shown in the
3706		* viewer
3707		*
3708		* @return
3709		* possible object is
3710		* {@link String }
3711		*
3712		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3713	0	public String getAnnotationId() {...
3714	0	return annotationId;
3715		}
3716
3717		/**
3718		* Sets the value of the annotationId property.
3719		*
3720		* @param value
3721		* allowed object is
3722		* {@link String }
3723		*
3724		* @see #getAnnotationId()
3725		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3726	0	public void setAnnotationId(String value) {...
3727	0	this.annotationId = value;
3728		}
3729
3730		/**
3731		* if true the
3732		* RNA
3733		* structure is
3734		* shown with
3735		* gaps, if
3736		* false
3737		* without
3738		*
3739		* @return
3740		* possible object is
3741		* {@link Boolean }
3742		*
3743		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3744	0	public Boolean isGapped() {...
3745	0	return gapped;
3746		}
3747
3748		/**
3749		* Sets the value of the gapped property.
3750		*
3751		* @param value
3752		* allowed object is
3753		* {@link Boolean }
3754		*
3755		* @see #isGapped()
3756		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3757	0	public void setGapped(Boolean value) {...
3758	0	this.gapped = value;
3759		}
3760
3761		/**
3762		* name of the
3763		* project jar
3764		* entry that
3765		* holds the
3766		* VARNA viewer
3767		* state for
3768		* the
3769		* structure
3770		*
3771		* @return
3772		* possible object is
3773		* {@link String }
3774		*
3775		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3776	0	public String getViewerState() {...
3777	0	return viewerState;
3778		}
3779
3780		/**
3781		* Sets the value of the viewerState property.
3782		*
3783		* @param value
3784		* allowed object is
3785		* {@link String }
3786		*
3787		* @see #getViewerState()
3788		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
3789	0	public void setViewerState(String value) {...
3790	0	this.viewerState = value;
3791		}
3792
3793		}
3794
3795		}
3796
3797		}
3798
3799
3800		/**
3801		* <p>Java class for anonymous complex type</p>.
3802		*
3803		* <p>The following schema fragment specifies the expected content contained within this class.</p>
3804		*
3805		* <pre>
3806		* &lt;complexType&gt;
3807		* &lt;complexContent&gt;
3808		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3809		* &lt;sequence&gt;
3810		* &lt;element name="sequencePoint" maxOccurs="unbounded"&gt;
3811		* &lt;complexType&gt;
3812		* &lt;complexContent&gt;
3813		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3814		* &lt;attGroup ref="{www.jalview.org}position"/&gt;
3815		* &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3816		* &lt;/restriction&gt;
3817		* &lt;/complexContent&gt;
3818		* &lt;/complexType&gt;
3819		* &lt;/element&gt;
3820		* &lt;element name="axis" maxOccurs="3" minOccurs="3"&gt;
3821		* &lt;complexType&gt;
3822		* &lt;complexContent&gt;
3823		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3824		* &lt;attGroup ref="{www.jalview.org}position"/&gt;
3825		* &lt;/restriction&gt;
3826		* &lt;/complexContent&gt;
3827		* &lt;/complexType&gt;
3828		* &lt;/element&gt;
3829		* &lt;element name="seqPointMin"&gt;
3830		* &lt;complexType&gt;
3831		* &lt;complexContent&gt;
3832		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3833		* &lt;attGroup ref="{www.jalview.org}position"/&gt;
3834		* &lt;/restriction&gt;
3835		* &lt;/complexContent&gt;
3836		* &lt;/complexType&gt;
3837		* &lt;/element&gt;
3838		* &lt;element name="seqPointMax"&gt;
3839		* &lt;complexType&gt;
3840		* &lt;complexContent&gt;
3841		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3842		* &lt;attGroup ref="{www.jalview.org}position"/&gt;
3843		* &lt;/restriction&gt;
3844		* &lt;/complexContent&gt;
3845		* &lt;/complexType&gt;
3846		* &lt;/element&gt;
3847		* &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&gt;
3848		* &lt;/sequence&gt;
3849		* &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
3850		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
3851		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3852		* &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3853		* &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3854		* &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3855		* &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3856		* &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3857		* &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
3858		* &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
3859		* &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
3860		* &lt;/restriction&gt;
3861		* &lt;/complexContent&gt;
3862		* &lt;/complexType&gt;
3863		* </pre>
3864		*
3865		*
3866		*/
3867		@XmlAccessorType(XmlAccessType.FIELD)
3868		@XmlType(name = "", propOrder = {
3869		"sequencePoint",
3870		"axis",
3871		"seqPointMin",
3872		"seqPointMax",
3873		"pcaData"
3874		})
		100% Uncovered Elements: 0 (92) Complexity: 44 Complexity Density: 0.96
3875		public static class PcaViewer {
3876
3877		@XmlElement(namespace = "www.jalview.org", required = true)
3878		protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
3879		/**
3880		* endpoints of X, Y and Z axes in that order
3881		*
3882		*/
3883		@XmlElement(namespace = "www.jalview.org", required = true)
3884		protected List<JalviewModel.PcaViewer.Axis> axis;
3885		@XmlElement(namespace = "www.jalview.org", required = true)
3886		protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
3887		@XmlElement(namespace = "www.jalview.org", required = true)
3888		protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
3889		@XmlElement(namespace = "www.jalview.org", required = true)
3890		protected PcaDataType pcaData;
3891		@XmlAttribute(name = "title")
3892		protected String title;
3893		@XmlAttribute(name = "scoreModelName")
3894		protected String scoreModelName;
3895		@XmlAttribute(name = "xDim")
3896		protected Integer xDim;
3897		@XmlAttribute(name = "yDim")
3898		protected Integer yDim;
3899		@XmlAttribute(name = "zDim")
3900		protected Integer zDim;
3901		@XmlAttribute(name = "bgColour")
3902		protected Integer bgColour;
3903		@XmlAttribute(name = "scaleFactor")
3904		protected Float scaleFactor;
3905		@XmlAttribute(name = "showLabels")
3906		protected Boolean showLabels;
3907		@XmlAttribute(name = "linkToAllViews")
3908		protected Boolean linkToAllViews;
3909		@XmlAttribute(name = "includeGaps")
3910		protected Boolean includeGaps;
3911		@XmlAttribute(name = "matchGaps")
3912		protected Boolean matchGaps;
3913		@XmlAttribute(name = "includeGappedColumns")
3914		protected Boolean includeGappedColumns;
3915		@XmlAttribute(name = "denominateByShortestLength")
3916		protected Boolean denominateByShortestLength;
3917		@XmlAttribute(name = "width")
3918		protected Integer width;
3919		@XmlAttribute(name = "height")
3920		protected Integer height;
3921		@XmlAttribute(name = "xpos")
3922		protected Integer xpos;
3923		@XmlAttribute(name = "ypos")
3924		protected Integer ypos;
3925
3926		/**
3927		* Gets the value of the sequencePoint property.
3928		*
3929		* <p>This accessor method returns a reference to the live list,
3930		* not a snapshot. Therefore any modification you make to the
3931		* returned list will be present inside the JAXB object.
3932		* This is why there is not a <CODE>set</CODE> method for the sequencePoint property.</p>
3933		*
3934		* <p>
3935		* For example, to add a new item, do as follows:
3936		* </p>
3937		* <pre>
3938		* getSequencePoint().add(newItem);
3939		* </pre>
3940		*
3941		*
3942		* <p>
3943		* Objects of the following type(s) are allowed in the list
3944		* {@link JalviewModel.PcaViewer.SequencePoint }
3945		* </p>
3946		*
3947		*
3948		* @return
3949		* The value of the sequencePoint property.
3950		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
3951	16	public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {...
3952	16	if (sequencePoint == null) {
3953	1	sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
3954		}
3955	16	return this.sequencePoint;
3956		}
3957
3958		/**
3959		* endpoints of X, Y and Z axes in that order
3960		*
3961		* Gets the value of the axis property.
3962		*
3963		* <p>This accessor method returns a reference to the live list,
3964		* not a snapshot. Therefore any modification you make to the
3965		* returned list will be present inside the JAXB object.
3966		* This is why there is not a <CODE>set</CODE> method for the axis property.</p>
3967		*
3968		* <p>
3969		* For example, to add a new item, do as follows:
3970		* </p>
3971		* <pre>
3972		* getAxis().add(newItem);
3973		* </pre>
3974		*
3975		*
3976		* <p>
3977		* Objects of the following type(s) are allowed in the list
3978		* {@link JalviewModel.PcaViewer.Axis }
3979		* </p>
3980		*
3981		*
3982		* @return
3983		* The value of the axis property.
3984		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
3985	6	public List<JalviewModel.PcaViewer.Axis> getAxis() {...
3986	6	if (axis == null) {
3987	1	axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
3988		}
3989	6	return this.axis;
3990		}
3991
3992		/**
3993		* Gets the value of the seqPointMin property.
3994		*
3995		* @return
3996		* possible object is
3997		* {@link JalviewModel.PcaViewer.SeqPointMin }
3998		*
3999		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4000	1	public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {...
4001	1	return seqPointMin;
4002		}
4003
4004		/**
4005		* Sets the value of the seqPointMin property.
4006		*
4007		* @param value
4008		* allowed object is
4009		* {@link JalviewModel.PcaViewer.SeqPointMin }
4010		*
4011		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4012	1	public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {...
4013	1	this.seqPointMin = value;
4014		}
4015
4016		/**
4017		* Gets the value of the seqPointMax property.
4018		*
4019		* @return
4020		* possible object is
4021		* {@link JalviewModel.PcaViewer.SeqPointMax }
4022		*
4023		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4024	1	public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {...
4025	1	return seqPointMax;
4026		}
4027
4028		/**
4029		* Sets the value of the seqPointMax property.
4030		*
4031		* @param value
4032		* allowed object is
4033		* {@link JalviewModel.PcaViewer.SeqPointMax }
4034		*
4035		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4036	1	public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {...
4037	1	this.seqPointMax = value;
4038		}
4039
4040		/**
4041		* Gets the value of the pcaData property.
4042		*
4043		* @return
4044		* possible object is
4045		* {@link PcaDataType }
4046		*
4047		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4048	1	public PcaDataType getPcaData() {...
4049	1	return pcaData;
4050		}
4051
4052		/**
4053		* Sets the value of the pcaData property.
4054		*
4055		* @param value
4056		* allowed object is
4057		* {@link PcaDataType }
4058		*
4059		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4060	1	public void setPcaData(PcaDataType value) {...
4061	1	this.pcaData = value;
4062		}
4063
4064		/**
4065		* Gets the value of the title property.
4066		*
4067		* @return
4068		* possible object is
4069		* {@link String }
4070		*
4071		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4072	3	public String getTitle() {...
4073	3	return title;
4074		}
4075
4076		/**
4077		* Sets the value of the title property.
4078		*
4079		* @param value
4080		* allowed object is
4081		* {@link String }
4082		*
4083		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4084	1	public void setTitle(String value) {...
4085	1	this.title = value;
4086		}
4087
4088		/**
4089		* Gets the value of the scoreModelName property.
4090		*
4091		* @return
4092		* possible object is
4093		* {@link String }
4094		*
4095		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4096	1	public String getScoreModelName() {...
4097	1	return scoreModelName;
4098		}
4099
4100		/**
4101		* Sets the value of the scoreModelName property.
4102		*
4103		* @param value
4104		* allowed object is
4105		* {@link String }
4106		*
4107		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4108	1	public void setScoreModelName(String value) {...
4109	1	this.scoreModelName = value;
4110		}
4111
4112		/**
4113		* Gets the value of the xDim property.
4114		*
4115		* @return
4116		* possible object is
4117		* {@link Integer }
4118		*
4119		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4120	1	public Integer getXDim() {...
4121	1	return xDim;
4122		}
4123
4124		/**
4125		* Sets the value of the xDim property.
4126		*
4127		* @param value
4128		* allowed object is
4129		* {@link Integer }
4130		*
4131		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4132	1	public void setXDim(Integer value) {...
4133	1	this.xDim = value;
4134		}
4135
4136		/**
4137		* Gets the value of the yDim property.
4138		*
4139		* @return
4140		* possible object is
4141		* {@link Integer }
4142		*
4143		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4144	1	public Integer getYDim() {...
4145	1	return yDim;
4146		}
4147
4148		/**
4149		* Sets the value of the yDim property.
4150		*
4151		* @param value
4152		* allowed object is
4153		* {@link Integer }
4154		*
4155		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4156	1	public void setYDim(Integer value) {...
4157	1	this.yDim = value;
4158		}
4159
4160		/**
4161		* Gets the value of the zDim property.
4162		*
4163		* @return
4164		* possible object is
4165		* {@link Integer }
4166		*
4167		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4168	1	public Integer getZDim() {...
4169	1	return zDim;
4170		}
4171
4172		/**
4173		* Sets the value of the zDim property.
4174		*
4175		* @param value
4176		* allowed object is
4177		* {@link Integer }
4178		*
4179		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4180	1	public void setZDim(Integer value) {...
4181	1	this.zDim = value;
4182		}
4183
4184		/**
4185		* Gets the value of the bgColour property.
4186		*
4187		* @return
4188		* possible object is
4189		* {@link Integer }
4190		*
4191		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4192	1	public Integer getBgColour() {...
4193	1	return bgColour;
4194		}
4195
4196		/**
4197		* Sets the value of the bgColour property.
4198		*
4199		* @param value
4200		* allowed object is
4201		* {@link Integer }
4202		*
4203		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4204	1	public void setBgColour(Integer value) {...
4205	1	this.bgColour = value;
4206		}
4207
4208		/**
4209		* Gets the value of the scaleFactor property.
4210		*
4211		* @return
4212		* possible object is
4213		* {@link Float }
4214		*
4215		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4216	1	public Float getScaleFactor() {...
4217	1	return scaleFactor;
4218		}
4219
4220		/**
4221		* Sets the value of the scaleFactor property.
4222		*
4223		* @param value
4224		* allowed object is
4225		* {@link Float }
4226		*
4227		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4228	1	public void setScaleFactor(Float value) {...
4229	1	this.scaleFactor = value;
4230		}
4231
4232		/**
4233		* Gets the value of the showLabels property.
4234		*
4235		* @return
4236		* possible object is
4237		* {@link Boolean }
4238		*
4239		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4240	1	public Boolean isShowLabels() {...
4241	1	return showLabels;
4242		}
4243
4244		/**
4245		* Sets the value of the showLabels property.
4246		*
4247		* @param value
4248		* allowed object is
4249		* {@link Boolean }
4250		*
4251		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4252	1	public void setShowLabels(Boolean value) {...
4253	1	this.showLabels = value;
4254		}
4255
4256		/**
4257		* Gets the value of the linkToAllViews property.
4258		*
4259		* @return
4260		* possible object is
4261		* {@link Boolean }
4262		*
4263		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4264	1	public Boolean isLinkToAllViews() {...
4265	1	return linkToAllViews;
4266		}
4267
4268		/**
4269		* Sets the value of the linkToAllViews property.
4270		*
4271		* @param value
4272		* allowed object is
4273		* {@link Boolean }
4274		*
4275		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4276	1	public void setLinkToAllViews(Boolean value) {...
4277	1	this.linkToAllViews = value;
4278		}
4279
4280		/**
4281		* Gets the value of the includeGaps property.
4282		*
4283		* @return
4284		* possible object is
4285		* {@link Boolean }
4286		*
4287		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4288	1	public Boolean isIncludeGaps() {...
4289	1	return includeGaps;
4290		}
4291
4292		/**
4293		* Sets the value of the includeGaps property.
4294		*
4295		* @param value
4296		* allowed object is
4297		* {@link Boolean }
4298		*
4299		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4300	1	public void setIncludeGaps(Boolean value) {...
4301	1	this.includeGaps = value;
4302		}
4303
4304		/**
4305		* Gets the value of the matchGaps property.
4306		*
4307		* @return
4308		* possible object is
4309		* {@link Boolean }
4310		*
4311		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4312	1	public Boolean isMatchGaps() {...
4313	1	return matchGaps;
4314		}
4315
4316		/**
4317		* Sets the value of the matchGaps property.
4318		*
4319		* @param value
4320		* allowed object is
4321		* {@link Boolean }
4322		*
4323		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4324	1	public void setMatchGaps(Boolean value) {...
4325	1	this.matchGaps = value;
4326		}
4327
4328		/**
4329		* Gets the value of the includeGappedColumns property.
4330		*
4331		* @return
4332		* possible object is
4333		* {@link Boolean }
4334		*
4335		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4336	1	public Boolean isIncludeGappedColumns() {...
4337	1	return includeGappedColumns;
4338		}
4339
4340		/**
4341		* Sets the value of the includeGappedColumns property.
4342		*
4343		* @param value
4344		* allowed object is
4345		* {@link Boolean }
4346		*
4347		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4348	1	public void setIncludeGappedColumns(Boolean value) {...
4349	1	this.includeGappedColumns = value;
4350		}
4351
4352		/**
4353		* Gets the value of the denominateByShortestLength property.
4354		*
4355		* @return
4356		* possible object is
4357		* {@link Boolean }
4358		*
4359		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4360	1	public Boolean isDenominateByShortestLength() {...
4361	1	return denominateByShortestLength;
4362		}
4363
4364		/**
4365		* Sets the value of the denominateByShortestLength property.
4366		*
4367		* @param value
4368		* allowed object is
4369		* {@link Boolean }
4370		*
4371		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4372	1	public void setDenominateByShortestLength(Boolean value) {...
4373	1	this.denominateByShortestLength = value;
4374		}
4375
4376		/**
4377		* Gets the value of the width property.
4378		*
4379		* @return
4380		* possible object is
4381		* {@link Integer }
4382		*
4383		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4384	1	public Integer getWidth() {...
4385	1	return width;
4386		}
4387
4388		/**
4389		* Sets the value of the width property.
4390		*
4391		* @param value
4392		* allowed object is
4393		* {@link Integer }
4394		*
4395		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4396	1	public void setWidth(Integer value) {...
4397	1	this.width = value;
4398		}
4399
4400		/**
4401		* Gets the value of the height property.
4402		*
4403		* @return
4404		* possible object is
4405		* {@link Integer }
4406		*
4407		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4408	1	public Integer getHeight() {...
4409	1	return height;
4410		}
4411
4412		/**
4413		* Sets the value of the height property.
4414		*
4415		* @param value
4416		* allowed object is
4417		* {@link Integer }
4418		*
4419		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4420	1	public void setHeight(Integer value) {...
4421	1	this.height = value;
4422		}
4423
4424		/**
4425		* Gets the value of the xpos property.
4426		*
4427		* @return
4428		* possible object is
4429		* {@link Integer }
4430		*
4431		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4432	1	public Integer getXpos() {...
4433	1	return xpos;
4434		}
4435
4436		/**
4437		* Sets the value of the xpos property.
4438		*
4439		* @param value
4440		* allowed object is
4441		* {@link Integer }
4442		*
4443		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4444	1	public void setXpos(Integer value) {...
4445	1	this.xpos = value;
4446		}
4447
4448		/**
4449		* Gets the value of the ypos property.
4450		*
4451		* @return
4452		* possible object is
4453		* {@link Integer }
4454		*
4455		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4456	1	public Integer getYpos() {...
4457	1	return ypos;
4458		}
4459
4460		/**
4461		* Sets the value of the ypos property.
4462		*
4463		* @param value
4464		* allowed object is
4465		* {@link Integer }
4466		*
4467		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4468	1	public void setYpos(Integer value) {...
4469	1	this.ypos = value;
4470		}
4471
4472
4473		/**
4474		* <p>Java class for anonymous complex type</p>.
4475		*
4476		* <p>The following schema fragment specifies the expected content contained within this class.</p>
4477		*
4478		* <pre>
4479		* &lt;complexType&gt;
4480		* &lt;complexContent&gt;
4481		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4482		* &lt;attGroup ref="{www.jalview.org}position"/&gt;
4483		* &lt;/restriction&gt;
4484		* &lt;/complexContent&gt;
4485		* &lt;/complexType&gt;
4486		* </pre>
4487		*
4488		*
4489		*/
4490		@XmlAccessorType(XmlAccessType.FIELD)
4491		@XmlType(name = "")
		100% Uncovered Elements: 0 (12) Complexity: 6 Complexity Density: 1
4492		public static class Axis {
4493
4494		@XmlAttribute(name = "xPos")
4495		protected Float xPos;
4496		@XmlAttribute(name = "yPos")
4497		protected Float yPos;
4498		@XmlAttribute(name = "zPos")
4499		protected Float zPos;
4500
4501		/**
4502		* Gets the value of the xPos property.
4503		*
4504		* @return
4505		* possible object is
4506		* {@link Float }
4507		*
4508		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4509	3	public Float getXPos() {...
4510	3	return xPos;
4511		}
4512
4513		/**
4514		* Sets the value of the xPos property.
4515		*
4516		* @param value
4517		* allowed object is
4518		* {@link Float }
4519		*
4520		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4521	3	public void setXPos(Float value) {...
4522	3	this.xPos = value;
4523		}
4524
4525		/**
4526		* Gets the value of the yPos property.
4527		*
4528		* @return
4529		* possible object is
4530		* {@link Float }
4531		*
4532		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4533	3	public Float getYPos() {...
4534	3	return yPos;
4535		}
4536
4537		/**
4538		* Sets the value of the yPos property.
4539		*
4540		* @param value
4541		* allowed object is
4542		* {@link Float }
4543		*
4544		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4545	3	public void setYPos(Float value) {...
4546	3	this.yPos = value;
4547		}
4548
4549		/**
4550		* Gets the value of the zPos property.
4551		*
4552		* @return
4553		* possible object is
4554		* {@link Float }
4555		*
4556		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4557	3	public Float getZPos() {...
4558	3	return zPos;
4559		}
4560
4561		/**
4562		* Sets the value of the zPos property.
4563		*
4564		* @param value
4565		* allowed object is
4566		* {@link Float }
4567		*
4568		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4569	3	public void setZPos(Float value) {...
4570	3	this.zPos = value;
4571		}
4572
4573		}
4574
4575
4576		/**
4577		* <p>Java class for anonymous complex type</p>.
4578		*
4579		* <p>The following schema fragment specifies the expected content contained within this class.</p>
4580		*
4581		* <pre>
4582		* &lt;complexType&gt;
4583		* &lt;complexContent&gt;
4584		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4585		* &lt;attGroup ref="{www.jalview.org}position"/&gt;
4586		* &lt;/restriction&gt;
4587		* &lt;/complexContent&gt;
4588		* &lt;/complexType&gt;
4589		* </pre>
4590		*
4591		*
4592		*/
4593		@XmlAccessorType(XmlAccessType.FIELD)
4594		@XmlType(name = "")
		100% Uncovered Elements: 0 (12) Complexity: 6 Complexity Density: 1
4595		public static class SeqPointMax {
4596
4597		@XmlAttribute(name = "xPos")
4598		protected Float xPos;
4599		@XmlAttribute(name = "yPos")
4600		protected Float yPos;
4601		@XmlAttribute(name = "zPos")
4602		protected Float zPos;
4603
4604		/**
4605		* Gets the value of the xPos property.
4606		*
4607		* @return
4608		* possible object is
4609		* {@link Float }
4610		*
4611		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4612	1	public Float getXPos() {...
4613	1	return xPos;
4614		}
4615
4616		/**
4617		* Sets the value of the xPos property.
4618		*
4619		* @param value
4620		* allowed object is
4621		* {@link Float }
4622		*
4623		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4624	1	public void setXPos(Float value) {...
4625	1	this.xPos = value;
4626		}
4627
4628		/**
4629		* Gets the value of the yPos property.
4630		*
4631		* @return
4632		* possible object is
4633		* {@link Float }
4634		*
4635		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4636	1	public Float getYPos() {...
4637	1	return yPos;
4638		}
4639
4640		/**
4641		* Sets the value of the yPos property.
4642		*
4643		* @param value
4644		* allowed object is
4645		* {@link Float }
4646		*
4647		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4648	1	public void setYPos(Float value) {...
4649	1	this.yPos = value;
4650		}
4651
4652		/**
4653		* Gets the value of the zPos property.
4654		*
4655		* @return
4656		* possible object is
4657		* {@link Float }
4658		*
4659		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4660	1	public Float getZPos() {...
4661	1	return zPos;
4662		}
4663
4664		/**
4665		* Sets the value of the zPos property.
4666		*
4667		* @param value
4668		* allowed object is
4669		* {@link Float }
4670		*
4671		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4672	1	public void setZPos(Float value) {...
4673	1	this.zPos = value;
4674		}
4675
4676		}
4677
4678
4679		/**
4680		* <p>Java class for anonymous complex type</p>.
4681		*
4682		* <p>The following schema fragment specifies the expected content contained within this class.</p>
4683		*
4684		* <pre>
4685		* &lt;complexType&gt;
4686		* &lt;complexContent&gt;
4687		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4688		* &lt;attGroup ref="{www.jalview.org}position"/&gt;
4689		* &lt;/restriction&gt;
4690		* &lt;/complexContent&gt;
4691		* &lt;/complexType&gt;
4692		* </pre>
4693		*
4694		*
4695		*/
4696		@XmlAccessorType(XmlAccessType.FIELD)
4697		@XmlType(name = "")
		100% Uncovered Elements: 0 (12) Complexity: 6 Complexity Density: 1
4698		public static class SeqPointMin {
4699
4700		@XmlAttribute(name = "xPos")
4701		protected Float xPos;
4702		@XmlAttribute(name = "yPos")
4703		protected Float yPos;
4704		@XmlAttribute(name = "zPos")
4705		protected Float zPos;
4706
4707		/**
4708		* Gets the value of the xPos property.
4709		*
4710		* @return
4711		* possible object is
4712		* {@link Float }
4713		*
4714		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4715	1	public Float getXPos() {...
4716	1	return xPos;
4717		}
4718
4719		/**
4720		* Sets the value of the xPos property.
4721		*
4722		* @param value
4723		* allowed object is
4724		* {@link Float }
4725		*
4726		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4727	1	public void setXPos(Float value) {...
4728	1	this.xPos = value;
4729		}
4730
4731		/**
4732		* Gets the value of the yPos property.
4733		*
4734		* @return
4735		* possible object is
4736		* {@link Float }
4737		*
4738		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4739	1	public Float getYPos() {...
4740	1	return yPos;
4741		}
4742
4743		/**
4744		* Sets the value of the yPos property.
4745		*
4746		* @param value
4747		* allowed object is
4748		* {@link Float }
4749		*
4750		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4751	1	public void setYPos(Float value) {...
4752	1	this.yPos = value;
4753		}
4754
4755		/**
4756		* Gets the value of the zPos property.
4757		*
4758		* @return
4759		* possible object is
4760		* {@link Float }
4761		*
4762		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4763	1	public Float getZPos() {...
4764	1	return zPos;
4765		}
4766
4767		/**
4768		* Sets the value of the zPos property.
4769		*
4770		* @param value
4771		* allowed object is
4772		* {@link Float }
4773		*
4774		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4775	1	public void setZPos(Float value) {...
4776	1	this.zPos = value;
4777		}
4778
4779		}
4780
4781
4782		/**
4783		* <p>Java class for anonymous complex type</p>.
4784		*
4785		* <p>The following schema fragment specifies the expected content contained within this class.</p>
4786		*
4787		* <pre>
4788		* &lt;complexType&gt;
4789		* &lt;complexContent&gt;
4790		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4791		* &lt;attGroup ref="{www.jalview.org}position"/&gt;
4792		* &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4793		* &lt;/restriction&gt;
4794		* &lt;/complexContent&gt;
4795		* &lt;/complexType&gt;
4796		* </pre>
4797		*
4798		*
4799		*/
4800		@XmlAccessorType(XmlAccessType.FIELD)
4801		@XmlType(name = "")
		100% Uncovered Elements: 0 (16) Complexity: 8 Complexity Density: 1
4802		public static class SequencePoint {
4803
4804		@XmlAttribute(name = "sequenceRef")
4805		protected String sequenceRef;
4806		@XmlAttribute(name = "xPos")
4807		protected Float xPos;
4808		@XmlAttribute(name = "yPos")
4809		protected Float yPos;
4810		@XmlAttribute(name = "zPos")
4811		protected Float zPos;
4812
4813		/**
4814		* Gets the value of the sequenceRef property.
4815		*
4816		* @return
4817		* possible object is
4818		* {@link String }
4819		*
4820		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4821	15	public String getSequenceRef() {...
4822	15	return sequenceRef;
4823		}
4824
4825		/**
4826		* Sets the value of the sequenceRef property.
4827		*
4828		* @param value
4829		* allowed object is
4830		* {@link String }
4831		*
4832		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4833	15	public void setSequenceRef(String value) {...
4834	15	this.sequenceRef = value;
4835		}
4836
4837		/**
4838		* Gets the value of the xPos property.
4839		*
4840		* @return
4841		* possible object is
4842		* {@link Float }
4843		*
4844		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4845	15	public Float getXPos() {...
4846	15	return xPos;
4847		}
4848
4849		/**
4850		* Sets the value of the xPos property.
4851		*
4852		* @param value
4853		* allowed object is
4854		* {@link Float }
4855		*
4856		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4857	15	public void setXPos(Float value) {...
4858	15	this.xPos = value;
4859		}
4860
4861		/**
4862		* Gets the value of the yPos property.
4863		*
4864		* @return
4865		* possible object is
4866		* {@link Float }
4867		*
4868		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4869	15	public Float getYPos() {...
4870	15	return yPos;
4871		}
4872
4873		/**
4874		* Sets the value of the yPos property.
4875		*
4876		* @param value
4877		* allowed object is
4878		* {@link Float }
4879		*
4880		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4881	15	public void setYPos(Float value) {...
4882	15	this.yPos = value;
4883		}
4884
4885		/**
4886		* Gets the value of the zPos property.
4887		*
4888		* @return
4889		* possible object is
4890		* {@link Float }
4891		*
4892		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4893	15	public Float getZPos() {...
4894	15	return zPos;
4895		}
4896
4897		/**
4898		* Sets the value of the zPos property.
4899		*
4900		* @param value
4901		* allowed object is
4902		* {@link Float }
4903		*
4904		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
4905	15	public void setZPos(Float value) {...
4906	15	this.zPos = value;
4907		}
4908
4909		}
4910
4911		}
4912
4913
4914		/**
4915		* <p>Java class for anonymous complex type</p>.
4916		*
4917		* <p>The following schema fragment specifies the expected content contained within this class.</p>
4918		*
4919		* <pre>
4920		* &lt;complexType&gt;
4921		* &lt;complexContent&gt;
4922		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4923		* &lt;sequence minOccurs="0"&gt;
4924		* &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
4925		* &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
4926		* &lt;element name="TreeColorMap" minOccurs="0"&gt;
4927		* &lt;complexType&gt;
4928		* &lt;complexContent&gt;
4929		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4930		* &lt;sequence&gt;
4931		* &lt;element name="ColorEntry" maxOccurs="unbounded" minOccurs="0"&gt;
4932		* &lt;complexType&gt;
4933		* &lt;complexContent&gt;
4934		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4935		* &lt;attribute name="label" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4936		* &lt;attribute name="color" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4937		* &lt;/restriction&gt;
4938		* &lt;/complexContent&gt;
4939		* &lt;/complexType&gt;
4940		* &lt;/element&gt;
4941		* &lt;/sequence&gt;
4942		* &lt;/restriction&gt;
4943		* &lt;/complexContent&gt;
4944		* &lt;/complexType&gt;
4945		* &lt;/element&gt;
4946		* &lt;/sequence&gt;
4947		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
4948		* &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4949		* &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4950		* &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4951		* &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
4952		* &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4953		* &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4954		* &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4955		* &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4956		* &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4957		* &lt;attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4958		* &lt;attribute name="annotationBased" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4959		* &lt;attribute name="showAnnotationAs" type="{http://www.w3.org/2001/XMLSchema}string" default="None" /&gt;
4960		* &lt;attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4961		* &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
4962		* &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4963		* &lt;/restriction&gt;
4964		* &lt;/complexContent&gt;
4965		* &lt;/complexType&gt;
4966		* </pre>
4967		*
4968		*
4969		*/
4970		@XmlAccessorType(XmlAccessType.FIELD)
4971		@XmlType(name = "", propOrder = {
4972		"title",
4973		"newick",
4974		"treeColorMap"
4975		})
		90.4% Uncovered Elements: 10 (104) Complexity: 48 Complexity Density: 0.92
4976		public static class Tree {
4977
4978		@XmlElement(namespace = "www.jalview.org")
4979		protected String title;
4980		@XmlElement(namespace = "www.jalview.org")
4981		protected String newick;
4982		@XmlElement(name = "TreeColorMap", namespace = "www.jalview.org")
4983		protected JalviewModel.Tree.TreeColorMap treeColorMap;
4984		@XmlAttribute(name = "fontName")
4985		protected String fontName;
4986		@XmlAttribute(name = "fontSize")
4987		protected Integer fontSize;
4988		@XmlAttribute(name = "fontStyle")
4989		protected Integer fontStyle;
4990		@XmlAttribute(name = "threshold")
4991		protected Float threshold;
4992		@XmlAttribute(name = "showBootstrap")
4993		protected Boolean showBootstrap;
4994		@XmlAttribute(name = "showDistances")
4995		protected Boolean showDistances;
4996		@XmlAttribute(name = "markUnlinked")
4997		protected Boolean markUnlinked;
4998		@XmlAttribute(name = "fitToWindow")
4999		protected Boolean fitToWindow;
5000		@XmlAttribute(name = "currentTree")
5001		protected Boolean currentTree;
5002		/**
5003		* Set for trees associated with columns of an alignment, sequence or annotation row
5004		*
5005		*/
5006		@XmlAttribute(name = "columnWise")
5007		protected Boolean columnWise;
5008		/**
5009		* Set for trees associated with annotations
5010		*
5011		*/
5012		@XmlAttribute(name = "annotationBased")
5013		protected Boolean annotationBased;
5014		/**
5015		* The view selected for trees, associated with annotations
5016		*
5017		*/
5018		@XmlAttribute(name = "showAnnotationAs")
5019		protected String showAnnotationAs;
5020		/**
5021		* Refers to annotation row the tree is provided by
5022		*
5023		*/
5024		@XmlAttribute(name = "columnReference")
5025		protected String columnReference;
5026		/**
5027		* Tree ID added for binding tree
5028		* visualization
5029		* settings to vamsas
5030		* document trees in jalview 2.4.1
5031		*
5032		*/
5033		@XmlAttribute(name = "id")
5034		@XmlJavaTypeAdapter(CollapsedStringAdapter.class)
5035		@XmlID
5036		@XmlSchemaType(name = "ID")
5037		protected String id;
5038		@XmlAttribute(name = "linkToAllViews")
5039		protected Boolean linkToAllViews;
5040		@XmlAttribute(name = "width")
5041		protected Integer width;
5042		@XmlAttribute(name = "height")
5043		protected Integer height;
5044		@XmlAttribute(name = "xpos")
5045		protected Integer xpos;
5046		@XmlAttribute(name = "ypos")
5047		protected Integer ypos;
5048
5049		/**
5050		* Gets the value of the title property.
5051		*
5052		* @return
5053		* possible object is
5054		* {@link String }
5055		*
5056		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5057	15	public String getTitle() {...
5058	15	return title;
5059		}
5060
5061		/**
5062		* Sets the value of the title property.
5063		*
5064		* @param value
5065		* allowed object is
5066		* {@link String }
5067		*
5068		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5069	6	public void setTitle(String value) {...
5070	6	this.title = value;
5071		}
5072
5073		/**
5074		* Gets the value of the newick property.
5075		*
5076		* @return
5077		* possible object is
5078		* {@link String }
5079		*
5080		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5081	15	public String getNewick() {...
5082	15	return newick;
5083		}
5084
5085		/**
5086		* Sets the value of the newick property.
5087		*
5088		* @param value
5089		* allowed object is
5090		* {@link String }
5091		*
5092		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5093	6	public void setNewick(String value) {...
5094	6	this.newick = value;
5095		}
5096
5097		/**
5098		* Gets the value of the treeColorMap property.
5099		*
5100		* @return
5101		* possible object is
5102		* {@link JalviewModel.Tree.TreeColorMap }
5103		*
5104		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5105	18	public JalviewModel.Tree.TreeColorMap getTreeColorMap() {...
5106	18	return treeColorMap;
5107		}
5108
5109		/**
5110		* Sets the value of the treeColorMap property.
5111		*
5112		* @param value
5113		* allowed object is
5114		* {@link JalviewModel.Tree.TreeColorMap }
5115		*
5116		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5117	2	public void setTreeColorMap(JalviewModel.Tree.TreeColorMap value) {...
5118	2	this.treeColorMap = value;
5119		}
5120
5121		/**
5122		* Gets the value of the fontName property.
5123		*
5124		* @return
5125		* possible object is
5126		* {@link String }
5127		*
5128		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5129	6	public String getFontName() {...
5130	6	return fontName;
5131		}
5132
5133		/**
5134		* Sets the value of the fontName property.
5135		*
5136		* @param value
5137		* allowed object is
5138		* {@link String }
5139		*
5140		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5141	6	public void setFontName(String value) {...
5142	6	this.fontName = value;
5143		}
5144
5145		/**
5146		* Gets the value of the fontSize property.
5147		*
5148		* @return
5149		* possible object is
5150		* {@link Integer }
5151		*
5152		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5153	3	public Integer getFontSize() {...
5154	3	return fontSize;
5155		}
5156
5157		/**
5158		* Sets the value of the fontSize property.
5159		*
5160		* @param value
5161		* allowed object is
5162		* {@link Integer }
5163		*
5164		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5165	6	public void setFontSize(Integer value) {...
5166	6	this.fontSize = value;
5167		}
5168
5169		/**
5170		* Gets the value of the fontStyle property.
5171		*
5172		* @return
5173		* possible object is
5174		* {@link Integer }
5175		*
5176		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5177	3	public Integer getFontStyle() {...
5178	3	return fontStyle;
5179		}
5180
5181		/**
5182		* Sets the value of the fontStyle property.
5183		*
5184		* @param value
5185		* allowed object is
5186		* {@link Integer }
5187		*
5188		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5189	6	public void setFontStyle(Integer value) {...
5190	6	this.fontStyle = value;
5191		}
5192
5193		/**
5194		* Gets the value of the threshold property.
5195		*
5196		* @return
5197		* possible object is
5198		* {@link Float }
5199		*
5200		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5201	3	public Float getThreshold() {...
5202	3	return threshold;
5203		}
5204
5205		/**
5206		* Sets the value of the threshold property.
5207		*
5208		* @param value
5209		* allowed object is
5210		* {@link Float }
5211		*
5212		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5213	6	public void setThreshold(Float value) {...
5214	6	this.threshold = value;
5215		}
5216
5217		/**
5218		* Gets the value of the showBootstrap property.
5219		*
5220		* @return
5221		* possible object is
5222		* {@link Boolean }
5223		*
5224		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5225	3	public Boolean isShowBootstrap() {...
5226	3	return showBootstrap;
5227		}
5228
5229		/**
5230		* Sets the value of the showBootstrap property.
5231		*
5232		* @param value
5233		* allowed object is
5234		* {@link Boolean }
5235		*
5236		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5237	6	public void setShowBootstrap(Boolean value) {...
5238	6	this.showBootstrap = value;
5239		}
5240
5241		/**
5242		* Gets the value of the showDistances property.
5243		*
5244		* @return
5245		* possible object is
5246		* {@link Boolean }
5247		*
5248		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5249	3	public Boolean isShowDistances() {...
5250	3	return showDistances;
5251		}
5252
5253		/**
5254		* Sets the value of the showDistances property.
5255		*
5256		* @param value
5257		* allowed object is
5258		* {@link Boolean }
5259		*
5260		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5261	6	public void setShowDistances(Boolean value) {...
5262	6	this.showDistances = value;
5263		}
5264
5265		/**
5266		* Gets the value of the markUnlinked property.
5267		*
5268		* @return
5269		* possible object is
5270		* {@link Boolean }
5271		*
5272		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5273	3	public Boolean isMarkUnlinked() {...
5274	3	return markUnlinked;
5275		}
5276
5277		/**
5278		* Sets the value of the markUnlinked property.
5279		*
5280		* @param value
5281		* allowed object is
5282		* {@link Boolean }
5283		*
5284		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5285	6	public void setMarkUnlinked(Boolean value) {...
5286	6	this.markUnlinked = value;
5287		}
5288
5289		/**
5290		* Gets the value of the fitToWindow property.
5291		*
5292		* @return
5293		* possible object is
5294		* {@link Boolean }
5295		*
5296		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5297	3	public Boolean isFitToWindow() {...
5298	3	return fitToWindow;
5299		}
5300
5301		/**
5302		* Sets the value of the fitToWindow property.
5303		*
5304		* @param value
5305		* allowed object is
5306		* {@link Boolean }
5307		*
5308		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5309	6	public void setFitToWindow(Boolean value) {...
5310	6	this.fitToWindow = value;
5311		}
5312
5313		/**
5314		* Gets the value of the currentTree property.
5315		*
5316		* @return
5317		* possible object is
5318		* {@link Boolean }
5319		*
5320		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5321	3	public Boolean isCurrentTree() {...
5322	3	return currentTree;
5323		}
5324
5325		/**
5326		* Sets the value of the currentTree property.
5327		*
5328		* @param value
5329		* allowed object is
5330		* {@link Boolean }
5331		*
5332		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5333	6	public void setCurrentTree(Boolean value) {...
5334	6	this.currentTree = value;
5335		}
5336
5337		/**
5338		* Set for trees associated with columns of an alignment, sequence or annotation row
5339		*
5340		* @return
5341		* possible object is
5342		* {@link Boolean }
5343		*
5344		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
5345	15	public boolean isColumnWise() {...
5346	15	if (columnWise == null) {
5347	15	return false;
5348		} else {
5349	0	return columnWise;
5350		}
5351		}
5352
5353		/**
5354		* Sets the value of the columnWise property.
5355		*
5356		* @param value
5357		* allowed object is
5358		* {@link Boolean }
5359		*
5360		* @see #isColumnWise()
5361		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
5362	0	public void setColumnWise(Boolean value) {...
5363	0	this.columnWise = value;
5364		}
5365
5366		/**
5367		* Set for trees associated with annotations
5368		*
5369		* @return
5370		* possible object is
5371		* {@link Boolean }
5372		*
5373		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
5374	30	public boolean isAnnotationBased() {...
5375	30	if (annotationBased == null) {
5376	24	return false;
5377		} else {
5378	6	return annotationBased;
5379		}
5380		}
5381
5382		/**
5383		* Sets the value of the annotationBased property.
5384		*
5385		* @param value
5386		* allowed object is
5387		* {@link Boolean }
5388		*
5389		* @see #isAnnotationBased()
5390		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5391	2	public void setAnnotationBased(Boolean value) {...
5392	2	this.annotationBased = value;
5393		}
5394
5395		/**
5396		* The view selected for trees, associated with annotations
5397		*
5398		* @return
5399		* possible object is
5400		* {@link String }
5401		*
5402		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
5403	3	public String getShowAnnotationAs() {...
5404	3	if (showAnnotationAs == null) {
5405	0	return "None";
5406		} else {
5407	3	return showAnnotationAs;
5408		}
5409		}
5410
5411		/**
5412		* Sets the value of the showAnnotationAs property.
5413		*
5414		* @param value
5415		* allowed object is
5416		* {@link String }
5417		*
5418		* @see #getShowAnnotationAs()
5419		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5420	2	public void setShowAnnotationAs(String value) {...
5421	2	this.showAnnotationAs = value;
5422		}
5423
5424		/**
5425		* Refers to annotation row the tree is provided by
5426		*
5427		* @return
5428		* possible object is
5429		* {@link String }
5430		*
5431		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
5432	0	public String getColumnReference() {...
5433	0	return columnReference;
5434		}
5435
5436		/**
5437		* Sets the value of the columnReference property.
5438		*
5439		* @param value
5440		* allowed object is
5441		* {@link String }
5442		*
5443		* @see #getColumnReference()
5444		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
5445	0	public void setColumnReference(String value) {...
5446	0	this.columnReference = value;
5447		}
5448
5449		/**
5450		* Tree ID added for binding tree
5451		* visualization
5452		* settings to vamsas
5453		* document trees in jalview 2.4.1
5454		*
5455		* @return
5456		* possible object is
5457		* {@link String }
5458		*
5459		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5460	30	public String getId() {...
5461	30	return id;
5462		}
5463
5464		/**
5465		* Sets the value of the id property.
5466		*
5467		* @param value
5468		* allowed object is
5469		* {@link String }
5470		*
5471		* @see #getId()
5472		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5473	6	public void setId(String value) {...
5474	6	this.id = value;
5475		}
5476
5477		/**
5478		* Gets the value of the linkToAllViews property.
5479		*
5480		* @return
5481		* possible object is
5482		* {@link Boolean }
5483		*
5484		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
5485	15	public boolean isLinkToAllViews() {...
5486	15	if (linkToAllViews == null) {
5487	8	return false;
5488		} else {
5489	7	return linkToAllViews;
5490		}
5491		}
5492
5493		/**
5494		* Sets the value of the linkToAllViews property.
5495		*
5496		* @param value
5497		* allowed object is
5498		* {@link Boolean }
5499		*
5500		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5501	6	public void setLinkToAllViews(Boolean value) {...
5502	6	this.linkToAllViews = value;
5503		}
5504
5505		/**
5506		* Gets the value of the width property.
5507		*
5508		* @return
5509		* possible object is
5510		* {@link Integer }
5511		*
5512		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5513	15	public Integer getWidth() {...
5514	15	return width;
5515		}
5516
5517		/**
5518		* Sets the value of the width property.
5519		*
5520		* @param value
5521		* allowed object is
5522		* {@link Integer }
5523		*
5524		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5525	6	public void setWidth(Integer value) {...
5526	6	this.width = value;
5527		}
5528
5529		/**
5530		* Gets the value of the height property.
5531		*
5532		* @return
5533		* possible object is
5534		* {@link Integer }
5535		*
5536		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5537	15	public Integer getHeight() {...
5538	15	return height;
5539		}
5540
5541		/**
5542		* Sets the value of the height property.
5543		*
5544		* @param value
5545		* allowed object is
5546		* {@link Integer }
5547		*
5548		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5549	6	public void setHeight(Integer value) {...
5550	6	this.height = value;
5551		}
5552
5553		/**
5554		* Gets the value of the xpos property.
5555		*
5556		* @return
5557		* possible object is
5558		* {@link Integer }
5559		*
5560		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5561	15	public Integer getXpos() {...
5562	15	return xpos;
5563		}
5564
5565		/**
5566		* Sets the value of the xpos property.
5567		*
5568		* @param value
5569		* allowed object is
5570		* {@link Integer }
5571		*
5572		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5573	6	public void setXpos(Integer value) {...
5574	6	this.xpos = value;
5575		}
5576
5577		/**
5578		* Gets the value of the ypos property.
5579		*
5580		* @return
5581		* possible object is
5582		* {@link Integer }
5583		*
5584		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5585	15	public Integer getYpos() {...
5586	15	return ypos;
5587		}
5588
5589		/**
5590		* Sets the value of the ypos property.
5591		*
5592		* @param value
5593		* allowed object is
5594		* {@link Integer }
5595		*
5596		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5597	6	public void setYpos(Integer value) {...
5598	6	this.ypos = value;
5599		}
5600
5601
5602		/**
5603		* <p>Java class for anonymous complex type</p>.
5604		*
5605		* <p>The following schema fragment specifies the expected content contained within this class.</p>
5606		*
5607		* <pre>
5608		* &lt;complexType&gt;
5609		* &lt;complexContent&gt;
5610		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
5611		* &lt;sequence&gt;
5612		* &lt;element name="ColorEntry" maxOccurs="unbounded" minOccurs="0"&gt;
5613		* &lt;complexType&gt;
5614		* &lt;complexContent&gt;
5615		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
5616		* &lt;attribute name="label" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
5617		* &lt;attribute name="color" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5618		* &lt;/restriction&gt;
5619		* &lt;/complexContent&gt;
5620		* &lt;/complexType&gt;
5621		* &lt;/element&gt;
5622		* &lt;/sequence&gt;
5623		* &lt;/restriction&gt;
5624		* &lt;/complexContent&gt;
5625		* &lt;/complexType&gt;
5626		* </pre>
5627		*
5628		*
5629		*/
5630		@XmlAccessorType(XmlAccessType.FIELD)
5631		@XmlType(name = "", propOrder = {
5632		"colorEntry"
5633		})
		100% Uncovered Elements: 0 (6) Complexity: 2 Complexity Density: 0.67
5634		public static class TreeColorMap {
5635
5636		@XmlElement(name = "ColorEntry", namespace = "www.jalview.org")
5637		protected List<JalviewModel.Tree.TreeColorMap.ColorEntry> colorEntry;
5638
5639		/**
5640		* Gets the value of the colorEntry property.
5641		*
5642		* <p>This accessor method returns a reference to the live list,
5643		* not a snapshot. Therefore any modification you make to the
5644		* returned list will be present inside the JAXB object.
5645		* This is why there is not a <CODE>set</CODE> method for the colorEntry property.</p>
5646		*
5647		* <p>
5648		* For example, to add a new item, do as follows:
5649		* </p>
5650		* <pre>
5651		* getColorEntry().add(newItem);
5652		* </pre>
5653		*
5654		*
5655		* <p>
5656		* Objects of the following type(s) are allowed in the list
5657		* {@link JalviewModel.Tree.TreeColorMap.ColorEntry }
5658		* </p>
5659		*
5660		*
5661		* @return
5662		* The value of the colorEntry property.
5663		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
5664	10	public List<JalviewModel.Tree.TreeColorMap.ColorEntry> getColorEntry() {...
5665	10	if (colorEntry == null) {
5666	2	colorEntry = new ArrayList<JalviewModel.Tree.TreeColorMap.ColorEntry>();
5667		}
5668	10	return this.colorEntry;
5669		}
5670
5671
5672		/**
5673		* <p>Java class for anonymous complex type</p>.
5674		*
5675		* <p>The following schema fragment specifies the expected content contained within this class.</p>
5676		*
5677		* <pre>
5678		* &lt;complexType&gt;
5679		* &lt;complexContent&gt;
5680		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
5681		* &lt;attribute name="label" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
5682		* &lt;attribute name="color" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5683		* &lt;/restriction&gt;
5684		* &lt;/complexContent&gt;
5685		* &lt;/complexType&gt;
5686		* </pre>
5687		*
5688		*
5689		*/
5690		@XmlAccessorType(XmlAccessType.FIELD)
5691		@XmlType(name = "")
		100% Uncovered Elements: 0 (8) Complexity: 4 Complexity Density: 1
5692		public static class ColorEntry {
5693
5694		@XmlAttribute(name = "label", required = true)
5695		protected String label;
5696		@XmlAttribute(name = "color", required = true)
5697		protected int color;
5698
5699		/**
5700		* Gets the value of the label property.
5701		*
5702		* @return
5703		* possible object is
5704		* {@link String }
5705		*
5706		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5707	12	public String getLabel() {...
5708	12	return label;
5709		}
5710
5711		/**
5712		* Sets the value of the label property.
5713		*
5714		* @param value
5715		* allowed object is
5716		* {@link String }
5717		*
5718		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5719	7	public void setLabel(String value) {...
5720	7	this.label = value;
5721		}
5722
5723		/**
5724		* Gets the value of the color property.
5725		*
5726		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5727	12	public int getColor() {...
5728	12	return color;
5729		}
5730
5731		/**
5732		* Sets the value of the color property.
5733		*
5734		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
5735	7	public void setColor(int value) {...
5736	7	this.color = value;
5737		}
5738
5739		}
5740
5741		}
5742
5743		}
5744
5745
5746		/**
5747		* <p>Java class for anonymous complex type</p>.
5748		*
5749		* <p>The following schema fragment specifies the expected content contained within this class.</p>
5750		*
5751		* <pre>
5752		* &lt;complexType&gt;
5753		* &lt;complexContent&gt;
5754		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
5755		* &lt;sequence&gt;
5756		* &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&gt;
5757		* &lt;/sequence&gt;
5758		* &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
5759		* &lt;/restriction&gt;
5760		* &lt;/complexContent&gt;
5761		* &lt;/complexType&gt;
5762		* </pre>
5763		*
5764		*
5765		*/
5766		@XmlAccessorType(XmlAccessType.FIELD)
5767		@XmlType(name = "", propOrder = {
5768		"userColourScheme"
5769		})
		0% Uncovered Elements: 8 (8) Complexity: 4 Complexity Density: 1
5770		public static class UserColours {
5771
5772		@XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
5773		protected JalviewUserColours userColourScheme;
5774		@XmlAttribute(name = "id")
5775		protected String id;
5776
5777		/**
5778		* Gets the value of the userColourScheme property.
5779		*
5780		* @return
5781		* possible object is
5782		* {@link JalviewUserColours }
5783		*
5784		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
5785	0	public JalviewUserColours getUserColourScheme() {...
5786	0	return userColourScheme;
5787		}
5788
5789		/**
5790		* Sets the value of the userColourScheme property.
5791		*
5792		* @param value
5793		* allowed object is
5794		* {@link JalviewUserColours }
5795		*
5796		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
5797	0	public void setUserColourScheme(JalviewUserColours value) {...
5798	0	this.userColourScheme = value;
5799		}
5800
5801		/**
5802		* Gets the value of the id property.
5803		*
5804		* @return
5805		* possible object is
5806		* {@link String }
5807		*
5808		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
5809	0	public String getId() {...
5810	0	return id;
5811		}
5812
5813		/**
5814		* Sets the value of the id property.
5815		*
5816		* @param value
5817		* allowed object is
5818		* {@link String }
5819		*
5820		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
5821	0	public void setId(String value) {...
5822	0	this.id = value;
5823		}
5824
5825		}
5826
5827
5828		/**
5829		* <p>Java class for anonymous complex type</p>.
5830		*
5831		* <p>The following schema fragment specifies the expected content contained within this class.</p>
5832		*
5833		* <pre>
5834		* &lt;complexType&gt;
5835		* &lt;complexContent&gt;
5836		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
5837		* &lt;sequence&gt;
5838		* &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
5839		* &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&gt;
5840		* &lt;complexType&gt;
5841		* &lt;complexContent&gt;
5842		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
5843		* &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5844		* &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5845		* &lt;/restriction&gt;
5846		* &lt;/complexContent&gt;
5847		* &lt;/complexType&gt;
5848		* &lt;/element&gt;
5849		* &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
5850		* &lt;complexType&gt;
5851		* &lt;complexContent&gt;
5852		* &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
5853		* &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
5854		* &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
5855		* &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5856		* &lt;/extension&gt;
5857		* &lt;/complexContent&gt;
5858		* &lt;/complexType&gt;
5859		* &lt;/element&gt;
5860		* &lt;element name="overview" minOccurs="0"&gt;
5861		* &lt;complexType&gt;
5862		* &lt;complexContent&gt;
5863		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
5864		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
5865		* &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5866		* &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5867		* &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5868		* &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5869		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
5870		* &lt;/restriction&gt;
5871		* &lt;/complexContent&gt;
5872		* &lt;/complexType&gt;
5873		* &lt;/element&gt;
5874		* &lt;element name="SecStrProvider" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt;
5875		* &lt;/sequence&gt;
5876		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
5877		* &lt;attGroup ref="{www.jalview.org}conservationShading"/&gt;
5878		* &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
5879		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
5880		* &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5881		* &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5882		* &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5883		* &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5884		* &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
5885		* &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5886		* &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5887		* &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5888		* &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5889		* &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5890		* &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5891		* &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
5892		* &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
5893		* &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5894		* &lt;attribute name="showStructureProviders" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
5895		* &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
5896		* &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
5897		* &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
5898		* &lt;attribute name="showGroupSecStrConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
5899		* &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5900		* &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5901		* &lt;attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5902		* &lt;attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5903		* &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
5904		* &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5905		* &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5906		* &lt;attribute name="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5907		* &lt;attribute name="idWidthManuallyAdjusted" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5908		* &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
5909		* &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
5910		* &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
5911		* &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
5912		* &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5913		* &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5914		* &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
5915		* &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
5916		* &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
5917		* &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
5918		* &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
5919		* &lt;/restriction&gt;
5920		* &lt;/complexContent&gt;
5921		* &lt;/complexType&gt;
5922		* </pre>
5923		*
5924		*
5925		*/
5926		@XmlAccessorType(XmlAccessType.FIELD)
5927		@XmlType(name = "", propOrder = {
5928		"annotationColours",
5929		"hiddenColumns",
5930		"calcIdParam",
5931		"overview",
5932		"secStrProvider"
5933		})
		89.7% Uncovered Elements: 32 (310) Complexity: 136 Complexity Density: 0.88
5934		public static class Viewport {
5935
5936		@XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
5937		protected AnnotationColourScheme annotationColours;
5938		@XmlElement(namespace = "www.jalview.org")
5939		protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
5940		@XmlElement(namespace = "www.jalview.org")
5941		protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
5942		@XmlElement(namespace = "www.jalview.org")
5943		protected JalviewModel.Viewport.Overview overview;
5944		@XmlElement(name = "SecStrProvider", namespace = "www.jalview.org")
5945		protected List<String> secStrProvider;
5946		@XmlAttribute(name = "bgColour")
5947		protected String bgColour;
5948		@XmlAttribute(name = "title")
5949		protected String title;
5950		@XmlAttribute(name = "showFullId")
5951		protected Boolean showFullId;
5952		@XmlAttribute(name = "rightAlignIds")
5953		protected Boolean rightAlignIds;
5954		@XmlAttribute(name = "showText")
5955		protected Boolean showText;
5956		@XmlAttribute(name = "showColourText")
5957		protected Boolean showColourText;
5958		@XmlAttribute(name = "showUnconserved")
5959		protected Boolean showUnconserved;
5960		@XmlAttribute(name = "showBoxes")
5961		protected Boolean showBoxes;
5962		@XmlAttribute(name = "wrapAlignment")
5963		protected Boolean wrapAlignment;
5964		@XmlAttribute(name = "renderGaps")
5965		protected Boolean renderGaps;
5966		@XmlAttribute(name = "showSequenceFeatures")
5967		protected Boolean showSequenceFeatures;
5968		@XmlAttribute(name = "showNPfeatureTooltip")
5969		protected Boolean showNPfeatureTooltip;
5970		@XmlAttribute(name = "showDbRefTooltip")
5971		protected Boolean showDbRefTooltip;
5972		@XmlAttribute(name = "followHighlight")
5973		protected Boolean followHighlight;
5974		@XmlAttribute(name = "followSelection")
5975		protected Boolean followSelection;
5976		@XmlAttribute(name = "showAnnotation")
5977		protected Boolean showAnnotation;
5978		@XmlAttribute(name = "showStructureProviders")
5979		protected Boolean showStructureProviders;
5980		@XmlAttribute(name = "centreColumnLabels")
5981		protected Boolean centreColumnLabels;
5982		/**
5983		* whether a new group has conservation displayed by default
5984		*
5985		*/
5986		@XmlAttribute(name = "showGroupConservation")
5987		protected Boolean showGroupConservation;
5988		/**
5989		* whether a new group has consensus displayed by default
5990		*
5991		*/
5992		@XmlAttribute(name = "showGroupConsensus")
5993		protected Boolean showGroupConsensus;
5994		/**
5995		* whether a new group has secondary structure consensus displayed by default
5996		*
5997		*/
5998		@XmlAttribute(name = "showGroupSecStrConsensus")
5999		protected Boolean showGroupSecStrConsensus;
6000		@XmlAttribute(name = "startRes")
6001		protected Integer startRes;
6002		@XmlAttribute(name = "startSeq")
6003		protected Integer startSeq;
6004		@XmlAttribute(name = "charWidth")
6005		protected Integer charWidth;
6006		@XmlAttribute(name = "charHeight")
6007		protected Integer charHeight;
6008		@XmlAttribute(name = "fontName")
6009		protected String fontName;
6010		@XmlAttribute(name = "fontSize")
6011		protected Integer fontSize;
6012		@XmlAttribute(name = "fontStyle")
6013		protected Integer fontStyle;
6014		@XmlAttribute(name = "idWidth")
6015		protected Integer idWidth;
6016		@XmlAttribute(name = "idWidthManuallyAdjusted")
6017		protected Boolean idWidthManuallyAdjusted;
6018		@XmlAttribute(name = "scaleProteinAsCdna")
6019		protected Boolean scaleProteinAsCdna;
6020		@XmlAttribute(name = "viewName")
6021		protected String viewName;
6022		@XmlAttribute(name = "sequenceSetId")
6023		protected String sequenceSetId;
6024		@XmlAttribute(name = "gatheredViews")
6025		protected Boolean gatheredViews;
6026		@XmlAttribute(name = "textCol1")
6027		protected Integer textCol1;
6028		@XmlAttribute(name = "textCol2")
6029		protected Integer textCol2;
6030		@XmlAttribute(name = "textColThreshold")
6031		protected Integer textColThreshold;
6032		/**
6033		* unique id used by jalview to
6034		* synchronize
6035		* between stored and
6036		* instantiated views
6037		*
6038		*/
6039		@XmlAttribute(name = "id")
6040		@XmlJavaTypeAdapter(CollapsedStringAdapter.class)
6041		@XmlID
6042		@XmlSchemaType(name = "ID")
6043		protected String id;
6044		/**
6045		* The viewport id of this viewport's
6046		* (cdna/protein) coding complement, if any
6047		*
6048		*/
6049		@XmlAttribute(name = "complementId")
6050		protected String complementId;
6051		@XmlAttribute(name = "showComplementFeatures")
6052		protected Boolean showComplementFeatures;
6053		@XmlAttribute(name = "showComplementFeaturesOnTop")
6054		protected Boolean showComplementFeaturesOnTop;
6055		@XmlAttribute(name = "width")
6056		protected Integer width;
6057		@XmlAttribute(name = "height")
6058		protected Integer height;
6059		@XmlAttribute(name = "xpos")
6060		protected Integer xpos;
6061		@XmlAttribute(name = "ypos")
6062		protected Integer ypos;
6063		@XmlAttribute(name = "conservationSelected")
6064		protected Boolean conservationSelected;
6065		/**
6066		* Conservation shading increment
6067		*
6068		*/
6069		@XmlAttribute(name = "consThreshold")
6070		protected Integer consThreshold;
6071		@XmlAttribute(name = "pidSelected")
6072		protected Boolean pidSelected;
6073		/**
6074		* Percent Identity Threshold
6075		*
6076		*/
6077		@XmlAttribute(name = "pidThreshold")
6078		protected Integer pidThreshold;
6079		/**
6080		* Secondary structure consensus shading - since 2.11.4
6081		*
6082		*/
6083		@XmlAttribute(name = "secstrSelected")
6084		protected Boolean secstrSelected;
6085		/**
6086		* Secondary structure consensus increment
6087		*
6088		*/
6089		@XmlAttribute(name = "secstrThreshold")
6090		protected Integer secstrThreshold;
6091		@XmlAttribute(name = "showConsensusHistogram")
6092		protected Boolean showConsensusHistogram;
6093		@XmlAttribute(name = "showSequenceLogo")
6094		protected Boolean showSequenceLogo;
6095		@XmlAttribute(name = "normaliseSequenceLogo")
6096		protected Boolean normaliseSequenceLogo;
6097		@XmlAttribute(name = "ignoreGapsinConsensus")
6098		protected Boolean ignoreGapsinConsensus;
6099
6100		/**
6101		* Gets the value of the annotationColours property.
6102		*
6103		* @return
6104		* possible object is
6105		* {@link AnnotationColourScheme }
6106		*
6107		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6108	2	public AnnotationColourScheme getAnnotationColours() {...
6109	2	return annotationColours;
6110		}
6111
6112		/**
6113		* Sets the value of the annotationColours property.
6114		*
6115		* @param value
6116		* allowed object is
6117		* {@link AnnotationColourScheme }
6118		*
6119		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6120	2	public void setAnnotationColours(AnnotationColourScheme value) {...
6121	2	this.annotationColours = value;
6122		}
6123
6124		/**
6125		* Gets the value of the hiddenColumns property.
6126		*
6127		* <p>This accessor method returns a reference to the live list,
6128		* not a snapshot. Therefore any modification you make to the
6129		* returned list will be present inside the JAXB object.
6130		* This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.</p>
6131		*
6132		* <p>
6133		* For example, to add a new item, do as follows:
6134		* </p>
6135		* <pre>
6136		* getHiddenColumns().add(newItem);
6137		* </pre>
6138		*
6139		*
6140		* <p>
6141		* Objects of the following type(s) are allowed in the list
6142		* {@link JalviewModel.Viewport.HiddenColumns }
6143		* </p>
6144		*
6145		*
6146		* @return
6147		* The value of the hiddenColumns property.
6148		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
6149	230	public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {...
6150	230	if (hiddenColumns == null) {
6151	76	hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
6152		}
6153	230	return this.hiddenColumns;
6154		}
6155
6156		/**
6157		* Gets the value of the calcIdParam property.
6158		*
6159		* <p>This accessor method returns a reference to the live list,
6160		* not a snapshot. Therefore any modification you make to the
6161		* returned list will be present inside the JAXB object.
6162		* This is why there is not a <CODE>set</CODE> method for the calcIdParam property.</p>
6163		*
6164		* <p>
6165		* For example, to add a new item, do as follows:
6166		* </p>
6167		* <pre>
6168		* getCalcIdParam().add(newItem);
6169		* </pre>
6170		*
6171		*
6172		* <p>
6173		* Objects of the following type(s) are allowed in the list
6174		* {@link JalviewModel.Viewport.CalcIdParam }
6175		* </p>
6176		*
6177		*
6178		* @return
6179		* The value of the calcIdParam property.
6180		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
6181	188	public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {...
6182	188	if (calcIdParam == null) {
6183	94	calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
6184		}
6185	188	return this.calcIdParam;
6186		}
6187
6188		/**
6189		* Gets the value of the overview property.
6190		*
6191		* @return
6192		* possible object is
6193		* {@link JalviewModel.Viewport.Overview }
6194		*
6195		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6196	84	public JalviewModel.Viewport.Overview getOverview() {...
6197	84	return overview;
6198		}
6199
6200		/**
6201		* Sets the value of the overview property.
6202		*
6203		* @param value
6204		* allowed object is
6205		* {@link JalviewModel.Viewport.Overview }
6206		*
6207		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6208	14	public void setOverview(JalviewModel.Viewport.Overview value) {...
6209	14	this.overview = value;
6210		}
6211
6212		/**
6213		* Gets the value of the secStrProvider property.
6214		*
6215		* <p>This accessor method returns a reference to the live list,
6216		* not a snapshot. Therefore any modification you make to the
6217		* returned list will be present inside the JAXB object.
6218		* This is why there is not a <CODE>set</CODE> method for the secStrProvider property.</p>
6219		*
6220		* <p>
6221		* For example, to add a new item, do as follows:
6222		* </p>
6223		* <pre>
6224		* getSecStrProvider().add(newItem);
6225		* </pre>
6226		*
6227		*
6228		* <p>
6229		* Objects of the following type(s) are allowed in the list
6230		* {@link String }
6231		* </p>
6232		*
6233		*
6234		* @return
6235		* The value of the secStrProvider property.
6236		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
6237	0	public List<String> getSecStrProvider() {...
6238	0	if (secStrProvider == null) {
6239	0	secStrProvider = new ArrayList<String>();
6240		}
6241	0	return this.secStrProvider;
6242		}
6243
6244		/**
6245		* Gets the value of the bgColour property.
6246		*
6247		* @return
6248		* possible object is
6249		* {@link String }
6250		*
6251		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6252	374	public String getBgColour() {...
6253	374	return bgColour;
6254		}
6255
6256		/**
6257		* Sets the value of the bgColour property.
6258		*
6259		* @param value
6260		* allowed object is
6261		* {@link String }
6262		*
6263		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6264	48	public void setBgColour(String value) {...
6265	48	this.bgColour = value;
6266		}
6267
6268		/**
6269		* Gets the value of the title property.
6270		*
6271		* @return
6272		* possible object is
6273		* {@link String }
6274		*
6275		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6276	188	public String getTitle() {...
6277	188	return title;
6278		}
6279
6280		/**
6281		* Sets the value of the title property.
6282		*
6283		* @param value
6284		* allowed object is
6285		* {@link String }
6286		*
6287		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6288	48	public void setTitle(String value) {...
6289	48	this.title = value;
6290		}
6291
6292		/**
6293		* Gets the value of the showFullId property.
6294		*
6295		* @return
6296		* possible object is
6297		* {@link Boolean }
6298		*
6299		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6300	94	public Boolean isShowFullId() {...
6301	94	return showFullId;
6302		}
6303
6304		/**
6305		* Sets the value of the showFullId property.
6306		*
6307		* @param value
6308		* allowed object is
6309		* {@link Boolean }
6310		*
6311		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6312	48	public void setShowFullId(Boolean value) {...
6313	48	this.showFullId = value;
6314		}
6315
6316		/**
6317		* Gets the value of the rightAlignIds property.
6318		*
6319		* @return
6320		* possible object is
6321		* {@link Boolean }
6322		*
6323		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6324	94	public Boolean isRightAlignIds() {...
6325	94	return rightAlignIds;
6326		}
6327
6328		/**
6329		* Sets the value of the rightAlignIds property.
6330		*
6331		* @param value
6332		* allowed object is
6333		* {@link Boolean }
6334		*
6335		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6336	48	public void setRightAlignIds(Boolean value) {...
6337	48	this.rightAlignIds = value;
6338		}
6339
6340		/**
6341		* Gets the value of the showText property.
6342		*
6343		* @return
6344		* possible object is
6345		* {@link Boolean }
6346		*
6347		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6348	94	public Boolean isShowText() {...
6349	94	return showText;
6350		}
6351
6352		/**
6353		* Sets the value of the showText property.
6354		*
6355		* @param value
6356		* allowed object is
6357		* {@link Boolean }
6358		*
6359		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6360	48	public void setShowText(Boolean value) {...
6361	48	this.showText = value;
6362		}
6363
6364		/**
6365		* Gets the value of the showColourText property.
6366		*
6367		* @return
6368		* possible object is
6369		* {@link Boolean }
6370		*
6371		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6372	94	public Boolean isShowColourText() {...
6373	94	return showColourText;
6374		}
6375
6376		/**
6377		* Sets the value of the showColourText property.
6378		*
6379		* @param value
6380		* allowed object is
6381		* {@link Boolean }
6382		*
6383		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6384	48	public void setShowColourText(Boolean value) {...
6385	48	this.showColourText = value;
6386		}
6387
6388		/**
6389		* Gets the value of the showUnconserved property.
6390		*
6391		* @return
6392		* possible object is
6393		* {@link Boolean }
6394		*
6395		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
6396	94	public boolean isShowUnconserved() {...
6397	94	if (showUnconserved == null) {
6398	0	return false;
6399		} else {
6400	94	return showUnconserved;
6401		}
6402		}
6403
6404		/**
6405		* Sets the value of the showUnconserved property.
6406		*
6407		* @param value
6408		* allowed object is
6409		* {@link Boolean }
6410		*
6411		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6412	48	public void setShowUnconserved(Boolean value) {...
6413	48	this.showUnconserved = value;
6414		}
6415
6416		/**
6417		* Gets the value of the showBoxes property.
6418		*
6419		* @return
6420		* possible object is
6421		* {@link Boolean }
6422		*
6423		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6424	94	public Boolean isShowBoxes() {...
6425	94	return showBoxes;
6426		}
6427
6428		/**
6429		* Sets the value of the showBoxes property.
6430		*
6431		* @param value
6432		* allowed object is
6433		* {@link Boolean }
6434		*
6435		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6436	48	public void setShowBoxes(Boolean value) {...
6437	48	this.showBoxes = value;
6438		}
6439
6440		/**
6441		* Gets the value of the wrapAlignment property.
6442		*
6443		* @return
6444		* possible object is
6445		* {@link Boolean }
6446		*
6447		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6448	94	public Boolean isWrapAlignment() {...
6449	94	return wrapAlignment;
6450		}
6451
6452		/**
6453		* Sets the value of the wrapAlignment property.
6454		*
6455		* @param value
6456		* allowed object is
6457		* {@link Boolean }
6458		*
6459		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6460	48	public void setWrapAlignment(Boolean value) {...
6461	48	this.wrapAlignment = value;
6462		}
6463
6464		/**
6465		* Gets the value of the renderGaps property.
6466		*
6467		* @return
6468		* possible object is
6469		* {@link Boolean }
6470		*
6471		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6472	94	public Boolean isRenderGaps() {...
6473	94	return renderGaps;
6474		}
6475
6476		/**
6477		* Sets the value of the renderGaps property.
6478		*
6479		* @param value
6480		* allowed object is
6481		* {@link Boolean }
6482		*
6483		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6484	48	public void setRenderGaps(Boolean value) {...
6485	48	this.renderGaps = value;
6486		}
6487
6488		/**
6489		* Gets the value of the showSequenceFeatures property.
6490		*
6491		* @return
6492		* possible object is
6493		* {@link Boolean }
6494		*
6495		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6496	94	public Boolean isShowSequenceFeatures() {...
6497	94	return showSequenceFeatures;
6498		}
6499
6500		/**
6501		* Sets the value of the showSequenceFeatures property.
6502		*
6503		* @param value
6504		* allowed object is
6505		* {@link Boolean }
6506		*
6507		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6508	48	public void setShowSequenceFeatures(Boolean value) {...
6509	48	this.showSequenceFeatures = value;
6510		}
6511
6512		/**
6513		* Gets the value of the showNPfeatureTooltip property.
6514		*
6515		* @return
6516		* possible object is
6517		* {@link Boolean }
6518		*
6519		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6520	94	public Boolean isShowNPfeatureTooltip() {...
6521	94	return showNPfeatureTooltip;
6522		}
6523
6524		/**
6525		* Sets the value of the showNPfeatureTooltip property.
6526		*
6527		* @param value
6528		* allowed object is
6529		* {@link Boolean }
6530		*
6531		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6532	48	public void setShowNPfeatureTooltip(Boolean value) {...
6533	48	this.showNPfeatureTooltip = value;
6534		}
6535
6536		/**
6537		* Gets the value of the showDbRefTooltip property.
6538		*
6539		* @return
6540		* possible object is
6541		* {@link Boolean }
6542		*
6543		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6544	94	public Boolean isShowDbRefTooltip() {...
6545	94	return showDbRefTooltip;
6546		}
6547
6548		/**
6549		* Sets the value of the showDbRefTooltip property.
6550		*
6551		* @param value
6552		* allowed object is
6553		* {@link Boolean }
6554		*
6555		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6556	48	public void setShowDbRefTooltip(Boolean value) {...
6557	48	this.showDbRefTooltip = value;
6558		}
6559
6560		/**
6561		* Gets the value of the followHighlight property.
6562		*
6563		* @return
6564		* possible object is
6565		* {@link Boolean }
6566		*
6567		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
6568	94	public boolean isFollowHighlight() {...
6569	94	if (followHighlight == null) {
6570	0	return true;
6571		} else {
6572	94	return followHighlight;
6573		}
6574		}
6575
6576		/**
6577		* Sets the value of the followHighlight property.
6578		*
6579		* @param value
6580		* allowed object is
6581		* {@link Boolean }
6582		*
6583		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6584	48	public void setFollowHighlight(Boolean value) {...
6585	48	this.followHighlight = value;
6586		}
6587
6588		/**
6589		* Gets the value of the followSelection property.
6590		*
6591		* @return
6592		* possible object is
6593		* {@link Boolean }
6594		*
6595		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
6596	94	public boolean isFollowSelection() {...
6597	94	if (followSelection == null) {
6598	0	return true;
6599		} else {
6600	94	return followSelection;
6601		}
6602		}
6603
6604		/**
6605		* Sets the value of the followSelection property.
6606		*
6607		* @param value
6608		* allowed object is
6609		* {@link Boolean }
6610		*
6611		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6612	48	public void setFollowSelection(Boolean value) {...
6613	48	this.followSelection = value;
6614		}
6615
6616		/**
6617		* Gets the value of the showAnnotation property.
6618		*
6619		* @return
6620		* possible object is
6621		* {@link Boolean }
6622		*
6623		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6624	188	public Boolean isShowAnnotation() {...
6625	188	return showAnnotation;
6626		}
6627
6628		/**
6629		* Sets the value of the showAnnotation property.
6630		*
6631		* @param value
6632		* allowed object is
6633		* {@link Boolean }
6634		*
6635		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6636	48	public void setShowAnnotation(Boolean value) {...
6637	48	this.showAnnotation = value;
6638		}
6639
6640		/**
6641		* Gets the value of the showStructureProviders property.
6642		*
6643		* @return
6644		* possible object is
6645		* {@link Boolean }
6646		*
6647		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
6648	94	public boolean isShowStructureProviders() {...
6649	94	if (showStructureProviders == null) {
6650	43	return false;
6651		} else {
6652	51	return showStructureProviders;
6653		}
6654		}
6655
6656		/**
6657		* Sets the value of the showStructureProviders property.
6658		*
6659		* @param value
6660		* allowed object is
6661		* {@link Boolean }
6662		*
6663		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6664	48	public void setShowStructureProviders(Boolean value) {...
6665	48	this.showStructureProviders = value;
6666		}
6667
6668		/**
6669		* Gets the value of the centreColumnLabels property.
6670		*
6671		* @return
6672		* possible object is
6673		* {@link Boolean }
6674		*
6675		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
6676	94	public boolean isCentreColumnLabels() {...
6677	94	if (centreColumnLabels == null) {
6678	94	return false;
6679		} else {
6680	0	return centreColumnLabels;
6681		}
6682		}
6683
6684		/**
6685		* Sets the value of the centreColumnLabels property.
6686		*
6687		* @param value
6688		* allowed object is
6689		* {@link Boolean }
6690		*
6691		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
6692	0	public void setCentreColumnLabels(Boolean value) {...
6693	0	this.centreColumnLabels = value;
6694		}
6695
6696		/**
6697		* whether a new group has conservation displayed by default
6698		*
6699		* @return
6700		* possible object is
6701		* {@link Boolean }
6702		*
6703		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
6704	94	public boolean isShowGroupConservation() {...
6705	94	if (showGroupConservation == null) {
6706	0	return false;
6707		} else {
6708	94	return showGroupConservation;
6709		}
6710		}
6711
6712		/**
6713		* Sets the value of the showGroupConservation property.
6714		*
6715		* @param value
6716		* allowed object is
6717		* {@link Boolean }
6718		*
6719		* @see #isShowGroupConservation()
6720		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6721	48	public void setShowGroupConservation(Boolean value) {...
6722	48	this.showGroupConservation = value;
6723		}
6724
6725		/**
6726		* whether a new group has consensus displayed by default
6727		*
6728		* @return
6729		* possible object is
6730		* {@link Boolean }
6731		*
6732		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
6733	94	public boolean isShowGroupConsensus() {...
6734	94	if (showGroupConsensus == null) {
6735	0	return false;
6736		} else {
6737	94	return showGroupConsensus;
6738		}
6739		}
6740
6741		/**
6742		* Sets the value of the showGroupConsensus property.
6743		*
6744		* @param value
6745		* allowed object is
6746		* {@link Boolean }
6747		*
6748		* @see #isShowGroupConsensus()
6749		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6750	48	public void setShowGroupConsensus(Boolean value) {...
6751	48	this.showGroupConsensus = value;
6752		}
6753
6754		/**
6755		* whether a new group has secondary structure consensus displayed by default
6756		*
6757		* @return
6758		* possible object is
6759		* {@link Boolean }
6760		*
6761		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
6762	94	public boolean isShowGroupSecStrConsensus() {...
6763	94	if (showGroupSecStrConsensus == null) {
6764	43	return false;
6765		} else {
6766	51	return showGroupSecStrConsensus;
6767		}
6768		}
6769
6770		/**
6771		* Sets the value of the showGroupSecStrConsensus property.
6772		*
6773		* @param value
6774		* allowed object is
6775		* {@link Boolean }
6776		*
6777		* @see #isShowGroupSecStrConsensus()
6778		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6779	48	public void setShowGroupSecStrConsensus(Boolean value) {...
6780	48	this.showGroupSecStrConsensus = value;
6781		}
6782
6783		/**
6784		* Gets the value of the startRes property.
6785		*
6786		* @return
6787		* possible object is
6788		* {@link Integer }
6789		*
6790		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6791	94	public Integer getStartRes() {...
6792	94	return startRes;
6793		}
6794
6795		/**
6796		* Sets the value of the startRes property.
6797		*
6798		* @param value
6799		* allowed object is
6800		* {@link Integer }
6801		*
6802		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6803	48	public void setStartRes(Integer value) {...
6804	48	this.startRes = value;
6805		}
6806
6807		/**
6808		* Gets the value of the startSeq property.
6809		*
6810		* @return
6811		* possible object is
6812		* {@link Integer }
6813		*
6814		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
6815	0	public Integer getStartSeq() {...
6816	0	return startSeq;
6817		}
6818
6819		/**
6820		* Sets the value of the startSeq property.
6821		*
6822		* @param value
6823		* allowed object is
6824		* {@link Integer }
6825		*
6826		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6827	48	public void setStartSeq(Integer value) {...
6828	48	this.startSeq = value;
6829		}
6830
6831		/**
6832		* Gets the value of the charWidth property.
6833		*
6834		* @return
6835		* possible object is
6836		* {@link Integer }
6837		*
6838		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6839	239	public Integer getCharWidth() {...
6840	239	return charWidth;
6841		}
6842
6843		/**
6844		* Sets the value of the charWidth property.
6845		*
6846		* @param value
6847		* allowed object is
6848		* {@link Integer }
6849		*
6850		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6851	48	public void setCharWidth(Integer value) {...
6852	48	this.charWidth = value;
6853		}
6854
6855		/**
6856		* Gets the value of the charHeight property.
6857		*
6858		* @return
6859		* possible object is
6860		* {@link Integer }
6861		*
6862		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6863	51	public Integer getCharHeight() {...
6864	51	return charHeight;
6865		}
6866
6867		/**
6868		* Sets the value of the charHeight property.
6869		*
6870		* @param value
6871		* allowed object is
6872		* {@link Integer }
6873		*
6874		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6875	48	public void setCharHeight(Integer value) {...
6876	48	this.charHeight = value;
6877		}
6878
6879		/**
6880		* Gets the value of the fontName property.
6881		*
6882		* @return
6883		* possible object is
6884		* {@link String }
6885		*
6886		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6887	94	public String getFontName() {...
6888	94	return fontName;
6889		}
6890
6891		/**
6892		* Sets the value of the fontName property.
6893		*
6894		* @param value
6895		* allowed object is
6896		* {@link String }
6897		*
6898		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6899	48	public void setFontName(String value) {...
6900	48	this.fontName = value;
6901		}
6902
6903		/**
6904		* Gets the value of the fontSize property.
6905		*
6906		* @return
6907		* possible object is
6908		* {@link Integer }
6909		*
6910		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6911	94	public Integer getFontSize() {...
6912	94	return fontSize;
6913		}
6914
6915		/**
6916		* Sets the value of the fontSize property.
6917		*
6918		* @param value
6919		* allowed object is
6920		* {@link Integer }
6921		*
6922		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6923	48	public void setFontSize(Integer value) {...
6924	48	this.fontSize = value;
6925		}
6926
6927		/**
6928		* Gets the value of the fontStyle property.
6929		*
6930		* @return
6931		* possible object is
6932		* {@link Integer }
6933		*
6934		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6935	94	public Integer getFontStyle() {...
6936	94	return fontStyle;
6937		}
6938
6939		/**
6940		* Sets the value of the fontStyle property.
6941		*
6942		* @param value
6943		* allowed object is
6944		* {@link Integer }
6945		*
6946		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6947	48	public void setFontStyle(Integer value) {...
6948	48	this.fontStyle = value;
6949		}
6950
6951		/**
6952		* Gets the value of the idWidth property.
6953		*
6954		* @return
6955		* possible object is
6956		* {@link Integer }
6957		*
6958		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6959	145	public Integer getIdWidth() {...
6960	145	return idWidth;
6961		}
6962
6963		/**
6964		* Sets the value of the idWidth property.
6965		*
6966		* @param value
6967		* allowed object is
6968		* {@link Integer }
6969		*
6970		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6971	48	public void setIdWidth(Integer value) {...
6972	48	this.idWidth = value;
6973		}
6974
6975		/**
6976		* Gets the value of the idWidthManuallyAdjusted property.
6977		*
6978		* @return
6979		* possible object is
6980		* {@link Boolean }
6981		*
6982		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6983	51	public Boolean isIdWidthManuallyAdjusted() {...
6984	51	return idWidthManuallyAdjusted;
6985		}
6986
6987		/**
6988		* Sets the value of the idWidthManuallyAdjusted property.
6989		*
6990		* @param value
6991		* allowed object is
6992		* {@link Boolean }
6993		*
6994		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
6995	48	public void setIdWidthManuallyAdjusted(Boolean value) {...
6996	48	this.idWidthManuallyAdjusted = value;
6997		}
6998
6999		/**
7000		* Gets the value of the scaleProteinAsCdna property.
7001		*
7002		* @return
7003		* possible object is
7004		* {@link Boolean }
7005		*
7006		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
7007	94	public boolean isScaleProteinAsCdna() {...
7008	94	if (scaleProteinAsCdna == null) {
7009	30	return true;
7010		} else {
7011	64	return scaleProteinAsCdna;
7012		}
7013		}
7014
7015		/**
7016		* Sets the value of the scaleProteinAsCdna property.
7017		*
7018		* @param value
7019		* allowed object is
7020		* {@link Boolean }
7021		*
7022		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7023	48	public void setScaleProteinAsCdna(Boolean value) {...
7024	48	this.scaleProteinAsCdna = value;
7025		}
7026
7027		/**
7028		* Gets the value of the viewName property.
7029		*
7030		* @return
7031		* possible object is
7032		* {@link String }
7033		*
7034		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7035	153	public String getViewName() {...
7036	153	return viewName;
7037		}
7038
7039		/**
7040		* Sets the value of the viewName property.
7041		*
7042		* @param value
7043		* allowed object is
7044		* {@link String }
7045		*
7046		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7047	48	public void setViewName(String value) {...
7048	48	this.viewName = value;
7049		}
7050
7051		/**
7052		* Gets the value of the sequenceSetId property.
7053		*
7054		* @return
7055		* possible object is
7056		* {@link String }
7057		*
7058		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7059	188	public String getSequenceSetId() {...
7060	188	return sequenceSetId;
7061		}
7062
7063		/**
7064		* Sets the value of the sequenceSetId property.
7065		*
7066		* @param value
7067		* allowed object is
7068		* {@link String }
7069		*
7070		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7071	48	public void setSequenceSetId(String value) {...
7072	48	this.sequenceSetId = value;
7073		}
7074
7075		/**
7076		* Gets the value of the gatheredViews property.
7077		*
7078		* @return
7079		* possible object is
7080		* {@link Boolean }
7081		*
7082		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7083	94	public Boolean isGatheredViews() {...
7084	94	return gatheredViews;
7085		}
7086
7087		/**
7088		* Sets the value of the gatheredViews property.
7089		*
7090		* @param value
7091		* allowed object is
7092		* {@link Boolean }
7093		*
7094		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7095	48	public void setGatheredViews(Boolean value) {...
7096	48	this.gatheredViews = value;
7097		}
7098
7099		/**
7100		* Gets the value of the textCol1 property.
7101		*
7102		* @return
7103		* possible object is
7104		* {@link Integer }
7105		*
7106		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7107	94	public Integer getTextCol1() {...
7108	94	return textCol1;
7109		}
7110
7111		/**
7112		* Sets the value of the textCol1 property.
7113		*
7114		* @param value
7115		* allowed object is
7116		* {@link Integer }
7117		*
7118		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7119	48	public void setTextCol1(Integer value) {...
7120	48	this.textCol1 = value;
7121		}
7122
7123		/**
7124		* Gets the value of the textCol2 property.
7125		*
7126		* @return
7127		* possible object is
7128		* {@link Integer }
7129		*
7130		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7131	94	public Integer getTextCol2() {...
7132	94	return textCol2;
7133		}
7134
7135		/**
7136		* Sets the value of the textCol2 property.
7137		*
7138		* @param value
7139		* allowed object is
7140		* {@link Integer }
7141		*
7142		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7143	48	public void setTextCol2(Integer value) {...
7144	48	this.textCol2 = value;
7145		}
7146
7147		/**
7148		* Gets the value of the textColThreshold property.
7149		*
7150		* @return
7151		* possible object is
7152		* {@link Integer }
7153		*
7154		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7155	94	public Integer getTextColThreshold() {...
7156	94	return textColThreshold;
7157		}
7158
7159		/**
7160		* Sets the value of the textColThreshold property.
7161		*
7162		* @param value
7163		* allowed object is
7164		* {@link Integer }
7165		*
7166		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7167	48	public void setTextColThreshold(Integer value) {...
7168	48	this.textColThreshold = value;
7169		}
7170
7171		/**
7172		* unique id used by jalview to
7173		* synchronize
7174		* between stored and
7175		* instantiated views
7176		*
7177		* @return
7178		* possible object is
7179		* {@link String }
7180		*
7181		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7182	178	public String getId() {...
7183	178	return id;
7184		}
7185
7186		/**
7187		* Sets the value of the id property.
7188		*
7189		* @param value
7190		* allowed object is
7191		* {@link String }
7192		*
7193		* @see #getId()
7194		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7195	58	public void setId(String value) {...
7196	58	this.id = value;
7197		}
7198
7199		/**
7200		* The viewport id of this viewport's
7201		* (cdna/protein) coding complement, if any
7202		*
7203		* @return
7204		* possible object is
7205		* {@link String }
7206		*
7207		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7208	94	public String getComplementId() {...
7209	94	return complementId;
7210		}
7211
7212		/**
7213		* Sets the value of the complementId property.
7214		*
7215		* @param value
7216		* allowed object is
7217		* {@link String }
7218		*
7219		* @see #getComplementId()
7220		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
7221	0	public void setComplementId(String value) {...
7222	0	this.complementId = value;
7223		}
7224
7225		/**
7226		* Gets the value of the showComplementFeatures property.
7227		*
7228		* @return
7229		* possible object is
7230		* {@link Boolean }
7231		*
7232		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
7233	94	public boolean isShowComplementFeatures() {...
7234	94	if (showComplementFeatures == null) {
7235	43	return false;
7236		} else {
7237	51	return showComplementFeatures;
7238		}
7239		}
7240
7241		/**
7242		* Sets the value of the showComplementFeatures property.
7243		*
7244		* @param value
7245		* allowed object is
7246		* {@link Boolean }
7247		*
7248		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7249	48	public void setShowComplementFeatures(Boolean value) {...
7250	48	this.showComplementFeatures = value;
7251		}
7252
7253		/**
7254		* Gets the value of the showComplementFeaturesOnTop property.
7255		*
7256		* @return
7257		* possible object is
7258		* {@link Boolean }
7259		*
7260		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
7261	94	public boolean isShowComplementFeaturesOnTop() {...
7262	94	if (showComplementFeaturesOnTop == null) {
7263	43	return false;
7264		} else {
7265	51	return showComplementFeaturesOnTop;
7266		}
7267		}
7268
7269		/**
7270		* Sets the value of the showComplementFeaturesOnTop property.
7271		*
7272		* @param value
7273		* allowed object is
7274		* {@link Boolean }
7275		*
7276		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7277	48	public void setShowComplementFeaturesOnTop(Boolean value) {...
7278	48	this.showComplementFeaturesOnTop = value;
7279		}
7280
7281		/**
7282		* Gets the value of the width property.
7283		*
7284		* @return
7285		* possible object is
7286		* {@link Integer }
7287		*
7288		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7289	282	public Integer getWidth() {...
7290	282	return width;
7291		}
7292
7293		/**
7294		* Sets the value of the width property.
7295		*
7296		* @param value
7297		* allowed object is
7298		* {@link Integer }
7299		*
7300		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7301	48	public void setWidth(Integer value) {...
7302	48	this.width = value;
7303		}
7304
7305		/**
7306		* Gets the value of the height property.
7307		*
7308		* @return
7309		* possible object is
7310		* {@link Integer }
7311		*
7312		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7313	282	public Integer getHeight() {...
7314	282	return height;
7315		}
7316
7317		/**
7318		* Sets the value of the height property.
7319		*
7320		* @param value
7321		* allowed object is
7322		* {@link Integer }
7323		*
7324		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7325	48	public void setHeight(Integer value) {...
7326	48	this.height = value;
7327		}
7328
7329		/**
7330		* Gets the value of the xpos property.
7331		*
7332		* @return
7333		* possible object is
7334		* {@link Integer }
7335		*
7336		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7337	94	public Integer getXpos() {...
7338	94	return xpos;
7339		}
7340
7341		/**
7342		* Sets the value of the xpos property.
7343		*
7344		* @param value
7345		* allowed object is
7346		* {@link Integer }
7347		*
7348		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7349	48	public void setXpos(Integer value) {...
7350	48	this.xpos = value;
7351		}
7352
7353		/**
7354		* Gets the value of the ypos property.
7355		*
7356		* @return
7357		* possible object is
7358		* {@link Integer }
7359		*
7360		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7361	94	public Integer getYpos() {...
7362	94	return ypos;
7363		}
7364
7365		/**
7366		* Sets the value of the ypos property.
7367		*
7368		* @param value
7369		* allowed object is
7370		* {@link Integer }
7371		*
7372		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7373	48	public void setYpos(Integer value) {...
7374	48	this.ypos = value;
7375		}
7376
7377		/**
7378		* Gets the value of the conservationSelected property.
7379		*
7380		* @return
7381		* possible object is
7382		* {@link Boolean }
7383		*
7384		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7385	188	public Boolean isConservationSelected() {...
7386	188	return conservationSelected;
7387		}
7388
7389		/**
7390		* Sets the value of the conservationSelected property.
7391		*
7392		* @param value
7393		* allowed object is
7394		* {@link Boolean }
7395		*
7396		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7397	48	public void setConservationSelected(Boolean value) {...
7398	48	this.conservationSelected = value;
7399		}
7400
7401		/**
7402		* Conservation shading increment
7403		*
7404		* @return
7405		* possible object is
7406		* {@link Integer }
7407		*
7408		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7409	96	public Integer getConsThreshold() {...
7410	96	return consThreshold;
7411		}
7412
7413		/**
7414		* Sets the value of the consThreshold property.
7415		*
7416		* @param value
7417		* allowed object is
7418		* {@link Integer }
7419		*
7420		* @see #getConsThreshold()
7421		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7422	2	public void setConsThreshold(Integer value) {...
7423	2	this.consThreshold = value;
7424		}
7425
7426		/**
7427		* Gets the value of the pidSelected property.
7428		*
7429		* @return
7430		* possible object is
7431		* {@link Boolean }
7432		*
7433		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7434	94	public Boolean isPidSelected() {...
7435	94	return pidSelected;
7436		}
7437
7438		/**
7439		* Sets the value of the pidSelected property.
7440		*
7441		* @param value
7442		* allowed object is
7443		* {@link Boolean }
7444		*
7445		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7446	48	public void setPidSelected(Boolean value) {...
7447	48	this.pidSelected = value;
7448		}
7449
7450		/**
7451		* Percent Identity Threshold
7452		*
7453		* @return
7454		* possible object is
7455		* {@link Integer }
7456		*
7457		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7458	94	public Integer getPidThreshold() {...
7459	94	return pidThreshold;
7460		}
7461
7462		/**
7463		* Sets the value of the pidThreshold property.
7464		*
7465		* @param value
7466		* allowed object is
7467		* {@link Integer }
7468		*
7469		* @see #getPidThreshold()
7470		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7471	9	public void setPidThreshold(Integer value) {...
7472	9	this.pidThreshold = value;
7473		}
7474
7475		/**
7476		* Secondary structure consensus shading - since 2.11.4
7477		*
7478		* @return
7479		* possible object is
7480		* {@link Boolean }
7481		*
7482		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
7483	188	public boolean isSecstrSelected() {...
7484	188	if (secstrSelected == null) {
7485	86	return false;
7486		} else {
7487	102	return secstrSelected;
7488		}
7489		}
7490
7491		/**
7492		* Sets the value of the secstrSelected property.
7493		*
7494		* @param value
7495		* allowed object is
7496		* {@link Boolean }
7497		*
7498		* @see #isSecstrSelected()
7499		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7500	48	public void setSecstrSelected(Boolean value) {...
7501	48	this.secstrSelected = value;
7502		}
7503
7504		/**
7505		* Secondary structure consensus increment
7506		*
7507		* @return
7508		* possible object is
7509		* {@link Integer }
7510		*
7511		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7512	96	public Integer getSecstrThreshold() {...
7513	96	return secstrThreshold;
7514		}
7515
7516		/**
7517		* Sets the value of the secstrThreshold property.
7518		*
7519		* @param value
7520		* allowed object is
7521		* {@link Integer }
7522		*
7523		* @see #getSecstrThreshold()
7524		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
7525	0	public void setSecstrThreshold(Integer value) {...
7526	0	this.secstrThreshold = value;
7527		}
7528
7529		/**
7530		* Gets the value of the showConsensusHistogram property.
7531		*
7532		* @return
7533		* possible object is
7534		* {@link Boolean }
7535		*
7536		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
7537	94	public boolean isShowConsensusHistogram() {...
7538	94	if (showConsensusHistogram == null) {
7539	0	return true;
7540		} else {
7541	94	return showConsensusHistogram;
7542		}
7543		}
7544
7545		/**
7546		* Sets the value of the showConsensusHistogram property.
7547		*
7548		* @param value
7549		* allowed object is
7550		* {@link Boolean }
7551		*
7552		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7553	48	public void setShowConsensusHistogram(Boolean value) {...
7554	48	this.showConsensusHistogram = value;
7555		}
7556
7557		/**
7558		* Gets the value of the showSequenceLogo property.
7559		*
7560		* @return
7561		* possible object is
7562		* {@link Boolean }
7563		*
7564		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
7565	94	public boolean isShowSequenceLogo() {...
7566	94	if (showSequenceLogo == null) {
7567	0	return false;
7568		} else {
7569	94	return showSequenceLogo;
7570		}
7571		}
7572
7573		/**
7574		* Sets the value of the showSequenceLogo property.
7575		*
7576		* @param value
7577		* allowed object is
7578		* {@link Boolean }
7579		*
7580		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7581	48	public void setShowSequenceLogo(Boolean value) {...
7582	48	this.showSequenceLogo = value;
7583		}
7584
7585		/**
7586		* Gets the value of the normaliseSequenceLogo property.
7587		*
7588		* @return
7589		* possible object is
7590		* {@link Boolean }
7591		*
7592		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
7593	94	public boolean isNormaliseSequenceLogo() {...
7594	94	if (normaliseSequenceLogo == null) {
7595	30	return false;
7596		} else {
7597	64	return normaliseSequenceLogo;
7598		}
7599		}
7600
7601		/**
7602		* Sets the value of the normaliseSequenceLogo property.
7603		*
7604		* @param value
7605		* allowed object is
7606		* {@link Boolean }
7607		*
7608		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7609	48	public void setNormaliseSequenceLogo(Boolean value) {...
7610	48	this.normaliseSequenceLogo = value;
7611		}
7612
7613		/**
7614		* Gets the value of the ignoreGapsinConsensus property.
7615		*
7616		* @return
7617		* possible object is
7618		* {@link Boolean }
7619		*
7620		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
7621	188	public boolean isIgnoreGapsinConsensus() {...
7622	188	if (ignoreGapsinConsensus == null) {
7623	0	return true;
7624		} else {
7625	188	return ignoreGapsinConsensus;
7626		}
7627		}
7628
7629		/**
7630		* Sets the value of the ignoreGapsinConsensus property.
7631		*
7632		* @param value
7633		* allowed object is
7634		* {@link Boolean }
7635		*
7636		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7637	48	public void setIgnoreGapsinConsensus(Boolean value) {...
7638	48	this.ignoreGapsinConsensus = value;
7639		}
7640
7641
7642		/**
7643		* <p>Java class for anonymous complex type</p>.
7644		*
7645		* <p>The following schema fragment specifies the expected content contained within this class.</p>
7646		*
7647		* <pre>
7648		* &lt;complexType&gt;
7649		* &lt;complexContent&gt;
7650		* &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
7651		* &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
7652		* &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
7653		* &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
7654		* &lt;/extension&gt;
7655		* &lt;/complexContent&gt;
7656		* &lt;/complexType&gt;
7657		* </pre>
7658		*
7659		*
7660		*/
7661		@XmlAccessorType(XmlAccessType.FIELD)
7662		@XmlType(name = "")
		0% Uncovered Elements: 16 (16) Complexity: 7 Complexity Density: 0.88
7663		public static class CalcIdParam
7664		extends WebServiceParameterSet
7665		{
7666
7667		/**
7668		* handle for the calculation which uses
7669		* this parameter set
7670		*
7671		*/
7672		@XmlAttribute(name = "calcId", required = true)
7673		protected String calcId;
7674		/**
7675		* should the calculation be performed
7676		* immediately after loading in order to refresh results
7677		*
7678		*/
7679		@XmlAttribute(name = "needsUpdate")
7680		protected Boolean needsUpdate;
7681		/**
7682		* should the calculation be automatically
7683		* performed on edits
7684		*
7685		*/
7686		@XmlAttribute(name = "autoUpdate", required = true)
7687		protected boolean autoUpdate;
7688
7689		/**
7690		* handle for the calculation which uses
7691		* this parameter set
7692		*
7693		* @return
7694		* possible object is
7695		* {@link String }
7696		*
7697		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
7698	0	public String getCalcId() {...
7699	0	return calcId;
7700		}
7701
7702		/**
7703		* Sets the value of the calcId property.
7704		*
7705		* @param value
7706		* allowed object is
7707		* {@link String }
7708		*
7709		* @see #getCalcId()
7710		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
7711	0	public void setCalcId(String value) {...
7712	0	this.calcId = value;
7713		}
7714
7715		/**
7716		* should the calculation be performed
7717		* immediately after loading in order to refresh results
7718		*
7719		* @return
7720		* possible object is
7721		* {@link Boolean }
7722		*
7723		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
7724	0	public boolean isNeedsUpdate() {...
7725	0	if (needsUpdate == null) {
7726	0	return false;
7727		} else {
7728	0	return needsUpdate;
7729		}
7730		}
7731
7732		/**
7733		* Sets the value of the needsUpdate property.
7734		*
7735		* @param value
7736		* allowed object is
7737		* {@link Boolean }
7738		*
7739		* @see #isNeedsUpdate()
7740		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
7741	0	public void setNeedsUpdate(Boolean value) {...
7742	0	this.needsUpdate = value;
7743		}
7744
7745		/**
7746		* should the calculation be automatically
7747		* performed on edits
7748		*
7749		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
7750	0	public boolean isAutoUpdate() {...
7751	0	return autoUpdate;
7752		}
7753
7754		/**
7755		* Sets the value of the autoUpdate property.
7756		*
7757		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
7758	0	public void setAutoUpdate(boolean value) {...
7759	0	this.autoUpdate = value;
7760		}
7761
7762		}
7763
7764
7765		/**
7766		* <p>Java class for anonymous complex type</p>.
7767		*
7768		* <p>The following schema fragment specifies the expected content contained within this class.</p>
7769		*
7770		* <pre>
7771		* &lt;complexType&gt;
7772		* &lt;complexContent&gt;
7773		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
7774		* &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
7775		* &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
7776		* &lt;/restriction&gt;
7777		* &lt;/complexContent&gt;
7778		* &lt;/complexType&gt;
7779		* </pre>
7780		*
7781		*
7782		*/
7783		@XmlAccessorType(XmlAccessType.FIELD)
7784		@XmlType(name = "")
		100% Uncovered Elements: 0 (8) Complexity: 4 Complexity Density: 1
7785		public static class HiddenColumns {
7786
7787		@XmlAttribute(name = "start")
7788		protected Integer start;
7789		@XmlAttribute(name = "end")
7790		protected Integer end;
7791
7792		/**
7793		* Gets the value of the start property.
7794		*
7795		* @return
7796		* possible object is
7797		* {@link Integer }
7798		*
7799		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7800	54	public Integer getStart() {...
7801	54	return start;
7802		}
7803
7804		/**
7805		* Sets the value of the start property.
7806		*
7807		* @param value
7808		* allowed object is
7809		* {@link Integer }
7810		*
7811		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7812	6	public void setStart(Integer value) {...
7813	6	this.start = value;
7814		}
7815
7816		/**
7817		* Gets the value of the end property.
7818		*
7819		* @return
7820		* possible object is
7821		* {@link Integer }
7822		*
7823		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7824	54	public Integer getEnd() {...
7825	54	return end;
7826		}
7827
7828		/**
7829		* Sets the value of the end property.
7830		*
7831		* @param value
7832		* allowed object is
7833		* {@link Integer }
7834		*
7835		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7836	6	public void setEnd(Integer value) {...
7837	6	this.end = value;
7838		}
7839
7840		}
7841
7842
7843		/**
7844		* <p>Java class for anonymous complex type</p>.
7845		*
7846		* <p>The following schema fragment specifies the expected content contained within this class.</p>
7847		*
7848		* <pre>
7849		* &lt;complexType&gt;
7850		* &lt;complexContent&gt;
7851		* &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
7852		* &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
7853		* &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
7854		* &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
7855		* &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
7856		* &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
7857		* &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
7858		* &lt;/restriction&gt;
7859		* &lt;/complexContent&gt;
7860		* &lt;/complexType&gt;
7861		* </pre>
7862		*
7863		*
7864		*/
7865		@XmlAccessorType(XmlAccessType.FIELD)
7866		@XmlType(name = "")
		100% Uncovered Elements: 0 (36) Complexity: 18 Complexity Density: 1
7867		public static class Overview {
7868
7869		@XmlAttribute(name = "showHidden")
7870		protected Boolean showHidden;
7871		@XmlAttribute(name = "residueColour")
7872		protected Integer residueColour;
7873		@XmlAttribute(name = "gapColour")
7874		protected Integer gapColour;
7875		@XmlAttribute(name = "hiddenColour")
7876		protected Integer hiddenColour;
7877		@XmlAttribute(name = "title")
7878		protected String title;
7879		@XmlAttribute(name = "width")
7880		protected Integer width;
7881		@XmlAttribute(name = "height")
7882		protected Integer height;
7883		@XmlAttribute(name = "xpos")
7884		protected Integer xpos;
7885		@XmlAttribute(name = "ypos")
7886		protected Integer ypos;
7887
7888		/**
7889		* Gets the value of the showHidden property.
7890		*
7891		* @return
7892		* possible object is
7893		* {@link Boolean }
7894		*
7895		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7896	11	public Boolean isShowHidden() {...
7897	11	return showHidden;
7898		}
7899
7900		/**
7901		* Sets the value of the showHidden property.
7902		*
7903		* @param value
7904		* allowed object is
7905		* {@link Boolean }
7906		*
7907		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7908	14	public void setShowHidden(Boolean value) {...
7909	14	this.showHidden = value;
7910		}
7911
7912		/**
7913		* Gets the value of the residueColour property.
7914		*
7915		* @return
7916		* possible object is
7917		* {@link Integer }
7918		*
7919		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7920	11	public Integer getResidueColour() {...
7921	11	return residueColour;
7922		}
7923
7924		/**
7925		* Sets the value of the residueColour property.
7926		*
7927		* @param value
7928		* allowed object is
7929		* {@link Integer }
7930		*
7931		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7932	14	public void setResidueColour(Integer value) {...
7933	14	this.residueColour = value;
7934		}
7935
7936		/**
7937		* Gets the value of the gapColour property.
7938		*
7939		* @return
7940		* possible object is
7941		* {@link Integer }
7942		*
7943		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7944	11	public Integer getGapColour() {...
7945	11	return gapColour;
7946		}
7947
7948		/**
7949		* Sets the value of the gapColour property.
7950		*
7951		* @param value
7952		* allowed object is
7953		* {@link Integer }
7954		*
7955		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7956	14	public void setGapColour(Integer value) {...
7957	14	this.gapColour = value;
7958		}
7959
7960		/**
7961		* Gets the value of the hiddenColour property.
7962		*
7963		* @return
7964		* possible object is
7965		* {@link Integer }
7966		*
7967		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7968	11	public Integer getHiddenColour() {...
7969	11	return hiddenColour;
7970		}
7971
7972		/**
7973		* Sets the value of the hiddenColour property.
7974		*
7975		* @param value
7976		* allowed object is
7977		* {@link Integer }
7978		*
7979		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7980	14	public void setHiddenColour(Integer value) {...
7981	14	this.hiddenColour = value;
7982		}
7983
7984		/**
7985		* Gets the value of the title property.
7986		*
7987		* @return
7988		* possible object is
7989		* {@link String }
7990		*
7991		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
7992	11	public String getTitle() {...
7993	11	return title;
7994		}
7995
7996		/**
7997		* Sets the value of the title property.
7998		*
7999		* @param value
8000		* allowed object is
8001		* {@link String }
8002		*
8003		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
8004	14	public void setTitle(String value) {...
8005	14	this.title = value;
8006		}
8007
8008		/**
8009		* Gets the value of the width property.
8010		*
8011		* @return
8012		* possible object is
8013		* {@link Integer }
8014		*
8015		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
8016	11	public Integer getWidth() {...
8017	11	return width;
8018		}
8019
8020		/**
8021		* Sets the value of the width property.
8022		*
8023		* @param value
8024		* allowed object is
8025		* {@link Integer }
8026		*
8027		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
8028	14	public void setWidth(Integer value) {...
8029	14	this.width = value;
8030		}
8031
8032		/**
8033		* Gets the value of the height property.
8034		*
8035		* @return
8036		* possible object is
8037		* {@link Integer }
8038		*
8039		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
8040	11	public Integer getHeight() {...
8041	11	return height;
8042		}
8043
8044		/**
8045		* Sets the value of the height property.
8046		*
8047		* @param value
8048		* allowed object is
8049		* {@link Integer }
8050		*
8051		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
8052	14	public void setHeight(Integer value) {...
8053	14	this.height = value;
8054		}
8055
8056		/**
8057		* Gets the value of the xpos property.
8058		*
8059		* @return
8060		* possible object is
8061		* {@link Integer }
8062		*
8063		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
8064	11	public Integer getXpos() {...
8065	11	return xpos;
8066		}
8067
8068		/**
8069		* Sets the value of the xpos property.
8070		*
8071		* @param value
8072		* allowed object is
8073		* {@link Integer }
8074		*
8075		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
8076	14	public void setXpos(Integer value) {...
8077	14	this.xpos = value;
8078		}
8079
8080		/**
8081		* Gets the value of the ypos property.
8082		*
8083		* @return
8084		* possible object is
8085		* {@link Integer }
8086		*
8087		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
8088	11	public Integer getYpos() {...
8089	11	return ypos;
8090		}
8091
8092		/**
8093		* Sets the value of the ypos property.
8094		*
8095		* @param value
8096		* allowed object is
8097		* {@link Integer }
8098		*
8099		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
8100	14	public void setYpos(Integer value) {...
8101	14	this.ypos = value;
8102		}
8103
8104		}
8105
8106		}
8107
8108		}