Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
Viewport	22	283	232	203	0.6065891460.7%	Show methods

Class Viewport

Class Viewport	Line # 22	Total Statements 283	Complexity 232	Uncovered Elements 203	TOTAL Coverage 0.6065891460.7%
Viewport()   Viewport()	466466	3.03	1.01	0.00	1.0 1.0100%
addCalcIdParam(jalview.schemabinding.version2.CalcIdParam) : void   addCalcIdParam(jalview.schemabinding.version2.CalcIdParam) : void	484484	1.01	1.01	1.01	0.0 0.00%
addCalcIdParam(int,jalview.schemabinding.version2.CalcIdParam) : void   addCalcIdParam(int,jalview.schemabinding.version2.CalcIdParam) : void	499499	1.01	1.01	1.01	0.0 0.00%
addHiddenColumns(jalview.schemabinding.version2.HiddenColumns) : void   addHiddenColumns(jalview.schemabinding.version2.HiddenColumns) : void	513513	1.01	1.01	0.00	1.0 1.0100%
addHiddenColumns(int,jalview.schemabinding.version2.HiddenColumns) : void   addHiddenColumns(int,jalview.schemabinding.version2.HiddenColumns) : void	528528	1.01	1.01	1.01	0.0 0.00%
deleteCentreColumnLabels() : void   deleteCentreColumnLabels() : void	537537	1.01	1.01	1.01	0.0 0.00%
deleteConsThreshold() : void   deleteConsThreshold() : void	544544	1.01	1.01	1.01	0.0 0.00%
deleteConservationSelected() : void   deleteConservationSelected() : void	551551	1.01	1.01	1.01	0.0 0.00%
deleteFollowHighlight() : void   deleteFollowHighlight() : void	558558	1.01	1.01	1.01	0.0 0.00%
deleteFollowSelection() : void   deleteFollowSelection() : void	565565	1.01	1.01	1.01	0.0 0.00%
deleteFontSize() : void   deleteFontSize() : void	572572	1.01	1.01	1.01	0.0 0.00%
deleteFontStyle() : void   deleteFontStyle() : void	579579	1.01	1.01	1.01	0.0 0.00%
deleteGatheredViews() : void   deleteGatheredViews() : void	586586	1.01	1.01	1.01	0.0 0.00%
deleteHeight() : void   deleteHeight() : void	593593	1.01	1.01	1.01	0.0 0.00%
deleteIgnoreGapsinConsensus() : void   deleteIgnoreGapsinConsensus() : void	600600	1.01	1.01	1.01	0.0 0.00%
deleteNormaliseSequenceLogo() : void   deleteNormaliseSequenceLogo() : void	607607	1.01	1.01	1.01	0.0 0.00%
deletePidSelected() : void   deletePidSelected() : void	614614	1.01	1.01	1.01	0.0 0.00%
deletePidThreshold() : void   deletePidThreshold() : void	621621	1.01	1.01	1.01	0.0 0.00%
deleteRenderGaps() : void   deleteRenderGaps() : void	628628	1.01	1.01	1.01	0.0 0.00%
deleteRightAlignIds() : void   deleteRightAlignIds() : void	635635	1.01	1.01	1.01	0.0 0.00%
deleteScaleProteinAsCdna() : void   deleteScaleProteinAsCdna() : void	642642	1.01	1.01	1.01	0.0 0.00%
deleteShowAnnotation() : void   deleteShowAnnotation() : void	649649	1.01	1.01	1.01	0.0 0.00%
deleteShowBoxes() : void   deleteShowBoxes() : void	656656	1.01	1.01	1.01	0.0 0.00%
deleteShowColourText() : void   deleteShowColourText() : void	663663	1.01	1.01	1.01	0.0 0.00%
deleteShowConsensusHistogram() : void   deleteShowConsensusHistogram() : void	670670	1.01	1.01	1.01	0.0 0.00%
deleteShowDbRefTooltip() : void   deleteShowDbRefTooltip() : void	677677	1.01	1.01	1.01	0.0 0.00%
deleteShowFullId() : void   deleteShowFullId() : void	684684	1.01	1.01	1.01	0.0 0.00%
deleteShowGroupConsensus() : void   deleteShowGroupConsensus() : void	691691	1.01	1.01	1.01	0.0 0.00%
deleteShowGroupConservation() : void   deleteShowGroupConservation() : void	698698	1.01	1.01	1.01	0.0 0.00%
deleteShowNPfeatureTooltip() : void   deleteShowNPfeatureTooltip() : void	705705	1.01	1.01	1.01	0.0 0.00%
deleteShowSequenceFeatures() : void   deleteShowSequenceFeatures() : void	712712	1.01	1.01	1.01	0.0 0.00%
deleteShowSequenceLogo() : void   deleteShowSequenceLogo() : void	719719	1.01	1.01	1.01	0.0 0.00%
deleteShowText() : void   deleteShowText() : void	726726	1.01	1.01	1.01	0.0 0.00%
deleteShowUnconserved() : void   deleteShowUnconserved() : void	733733	1.01	1.01	1.01	0.0 0.00%
deleteStartRes() : void   deleteStartRes() : void	740740	1.01	1.01	1.01	0.0 0.00%
deleteStartSeq() : void   deleteStartSeq() : void	747747	1.01	1.01	1.01	0.0 0.00%
deleteTextCol1() : void   deleteTextCol1() : void	754754	1.01	1.01	1.01	0.0 0.00%
deleteTextCol2() : void   deleteTextCol2() : void	761761	1.01	1.01	1.01	0.0 0.00%
deleteTextColThreshold() : void   deleteTextColThreshold() : void	768768	1.01	1.01	1.01	0.0 0.00%
deleteWidth() : void   deleteWidth() : void	775775	1.01	1.01	1.01	0.0 0.00%
deleteWrapAlignment() : void   deleteWrapAlignment() : void	782782	1.01	1.01	1.01	0.0 0.00%
deleteXpos() : void   deleteXpos() : void	789789	1.01	1.01	1.01	0.0 0.00%
deleteYpos() : void   deleteYpos() : void	796796	1.01	1.01	1.01	0.0 0.00%
enumerateCalcIdParam() : java.util.Enumeration   enumerateCalcIdParam() : java.util.Enumeration	807807	1.01	1.01	1.01	0.0 0.00%
enumerateHiddenColumns() : java.util.Enumeration   enumerateHiddenColumns() : java.util.Enumeration	818818	1.01	1.01	1.01	0.0 0.00%
getAnnotationColours() : jalview.schemabinding.version2.AnnotationColours   getAnnotationColours() : jalview.schemabinding.version2.AnnotationColours	828828	1.01	1.01	0.00	1.0 1.0100%
getBgColour() : java.lang.String   getBgColour() : java.lang.String	838838	1.01	1.01	0.00	1.0 1.0100%
getCalcIdParam(int) : jalview.schemabinding.version2.CalcIdParam   getCalcIdParam(int) : jalview.schemabinding.version2.CalcIdParam	852852	3.03	3.03	5.05	0.0 0.00%
getCalcIdParam() : jalview.schemabinding.version2.CalcIdParam[]   getCalcIdParam() : jalview.schemabinding.version2.CalcIdParam[]	876876	2.02	1.01	0.00	1.0 1.0100%
getCalcIdParamCount() : int   getCalcIdParamCount() : int	888888	1.01	1.01	1.01	0.0 0.00%
getCentreColumnLabels() : boolean   getCentreColumnLabels() : boolean	898898	1.01	1.01	1.01	0.0 0.00%
getComplementId() : java.lang.String   getComplementId() : java.lang.String	911911	1.01	1.01	0.00	1.0 1.0100%
getConsThreshold() : int   getConsThreshold() : int	921921	1.01	1.01	0.00	1.0 1.0100%
getConservationSelected() : boolean   getConservationSelected() : boolean	931931	1.01	1.01	0.00	1.0 1.0100%
getFollowHighlight() : boolean   getFollowHighlight() : boolean	941941	1.01	1.01	0.00	1.0 1.0100%
getFollowSelection() : boolean   getFollowSelection() : boolean	951951	1.01	1.01	0.00	1.0 1.0100%
getFontName() : java.lang.String   getFontName() : java.lang.String	961961	1.01	1.01	0.00	1.0 1.0100%
getFontSize() : int   getFontSize() : int	971971	1.01	1.01	0.00	1.0 1.0100%
getFontStyle() : int   getFontStyle() : int	981981	1.01	1.01	0.00	1.0 1.0100%
getGatheredViews() : boolean   getGatheredViews() : boolean	991991	1.01	1.01	0.00	1.0 1.0100%
getHeight() : int   getHeight() : int	10011001	1.01	1.01	0.00	1.0 1.0100%
getHiddenColumns(int) : jalview.schemabinding.version2.HiddenColumns   getHiddenColumns(int) : jalview.schemabinding.version2.HiddenColumns	10151015	3.03	3.03	2.02	0.6 0.660%
getHiddenColumns() : jalview.schemabinding.version2.HiddenColumns[]   getHiddenColumns() : jalview.schemabinding.version2.HiddenColumns[]	10391039	2.02	1.01	0.00	1.0 1.0100%
getHiddenColumnsCount() : int   getHiddenColumnsCount() : int	10511051	1.01	1.01	0.00	1.0 1.0100%
getId() : java.lang.String   getId() : java.lang.String	10641064	1.01	1.01	0.00	1.0 1.0100%
getIgnoreGapsinConsensus() : boolean   getIgnoreGapsinConsensus() : boolean	10741074	1.01	1.01	0.00	1.0 1.0100%
getNormaliseSequenceLogo() : boolean   getNormaliseSequenceLogo() : boolean	10841084	1.01	1.01	0.00	1.0 1.0100%
getPidSelected() : boolean   getPidSelected() : boolean	10941094	1.01	1.01	0.00	1.0 1.0100%
getPidThreshold() : int   getPidThreshold() : int	11041104	1.01	1.01	0.00	1.0 1.0100%
getRenderGaps() : boolean   getRenderGaps() : boolean	11141114	1.01	1.01	0.00	1.0 1.0100%
getRightAlignIds() : boolean   getRightAlignIds() : boolean	11241124	1.01	1.01	0.00	1.0 1.0100%
getScaleProteinAsCdna() : boolean   getScaleProteinAsCdna() : boolean	11341134	1.01	1.01	0.00	1.0 1.0100%
getSequenceSetId() : java.lang.String   getSequenceSetId() : java.lang.String	11441144	1.01	1.01	0.00	1.0 1.0100%
getShowAnnotation() : boolean   getShowAnnotation() : boolean	11541154	1.01	1.01	0.00	1.0 1.0100%
getShowBoxes() : boolean   getShowBoxes() : boolean	11641164	1.01	1.01	0.00	1.0 1.0100%
getShowColourText() : boolean   getShowColourText() : boolean	11741174	1.01	1.01	0.00	1.0 1.0100%
getShowConsensusHistogram() : boolean   getShowConsensusHistogram() : boolean	11841184	1.01	1.01	0.00	1.0 1.0100%
getShowDbRefTooltip() : boolean   getShowDbRefTooltip() : boolean	11941194	1.01	1.01	0.00	1.0 1.0100%
getShowFullId() : boolean   getShowFullId() : boolean	12041204	1.01	1.01	0.00	1.0 1.0100%
getShowGroupConsensus() : boolean   getShowGroupConsensus() : boolean	12141214	1.01	1.01	0.00	1.0 1.0100%
getShowGroupConservation() : boolean   getShowGroupConservation() : boolean	12241224	1.01	1.01	0.00	1.0 1.0100%
getShowNPfeatureTooltip() : boolean   getShowNPfeatureTooltip() : boolean	12341234	1.01	1.01	0.00	1.0 1.0100%
getShowSequenceFeatures() : boolean   getShowSequenceFeatures() : boolean	12441244	1.01	1.01	0.00	1.0 1.0100%
getShowSequenceLogo() : boolean   getShowSequenceLogo() : boolean	12541254	1.01	1.01	0.00	1.0 1.0100%
getShowText() : boolean   getShowText() : boolean	12641264	1.01	1.01	0.00	1.0 1.0100%
getShowUnconserved() : boolean   getShowUnconserved() : boolean	12741274	1.01	1.01	0.00	1.0 1.0100%
getStartRes() : int   getStartRes() : int	12841284	1.01	1.01	0.00	1.0 1.0100%
getStartSeq() : int   getStartSeq() : int	12941294	1.01	1.01	0.00	1.0 1.0100%
getTextCol1() : int   getTextCol1() : int	13041304	1.01	1.01	0.00	1.0 1.0100%
getTextCol2() : int   getTextCol2() : int	13141314	1.01	1.01	0.00	1.0 1.0100%
getTextColThreshold() : int   getTextColThreshold() : int	13241324	1.01	1.01	0.00	1.0 1.0100%
getTitle() : java.lang.String   getTitle() : java.lang.String	13341334	1.01	1.01	0.00	1.0 1.0100%
getViewName() : java.lang.String   getViewName() : java.lang.String	13441344	1.01	1.01	0.00	1.0 1.0100%
getWidth() : int   getWidth() : int	13541354	1.01	1.01	0.00	1.0 1.0100%
getWrapAlignment() : boolean   getWrapAlignment() : boolean	13641364	1.01	1.01	0.00	1.0 1.0100%
getXpos() : int   getXpos() : int	13741374	1.01	1.01	0.00	1.0 1.0100%
getYpos() : int   getYpos() : int	13841384	1.01	1.01	0.00	1.0 1.0100%
hasCentreColumnLabels() : boolean   hasCentreColumnLabels() : boolean	13941394	1.01	1.01	0.00	1.0 1.0100%
hasConsThreshold() : boolean   hasConsThreshold() : boolean	14041404	1.01	1.01	0.00	1.0 1.0100%
hasConservationSelected() : boolean   hasConservationSelected() : boolean	14141414	1.01	1.01	0.00	1.0 1.0100%
hasFollowHighlight() : boolean   hasFollowHighlight() : boolean	14241424	1.01	1.01	0.00	1.0 1.0100%
hasFollowSelection() : boolean   hasFollowSelection() : boolean	14341434	1.01	1.01	0.00	1.0 1.0100%
hasFontSize() : boolean   hasFontSize() : boolean	14441444	1.01	1.01	0.00	1.0 1.0100%
hasFontStyle() : boolean   hasFontStyle() : boolean	14541454	1.01	1.01	0.00	1.0 1.0100%
hasGatheredViews() : boolean   hasGatheredViews() : boolean	14641464	1.01	1.01	0.00	1.0 1.0100%
hasHeight() : boolean   hasHeight() : boolean	14741474	1.01	1.01	0.00	1.0 1.0100%
hasIgnoreGapsinConsensus() : boolean   hasIgnoreGapsinConsensus() : boolean	14841484	1.01	1.01	0.00	1.0 1.0100%
hasNormaliseSequenceLogo() : boolean   hasNormaliseSequenceLogo() : boolean	14941494	1.01	1.01	0.00	1.0 1.0100%
hasPidSelected() : boolean   hasPidSelected() : boolean	15041504	1.01	1.01	0.00	1.0 1.0100%
hasPidThreshold() : boolean   hasPidThreshold() : boolean	15141514	1.01	1.01	0.00	1.0 1.0100%
hasRenderGaps() : boolean   hasRenderGaps() : boolean	15241524	1.01	1.01	0.00	1.0 1.0100%
hasRightAlignIds() : boolean   hasRightAlignIds() : boolean	15341534	1.01	1.01	0.00	1.0 1.0100%
hasScaleProteinAsCdna() : boolean   hasScaleProteinAsCdna() : boolean	15441544	1.01	1.01	0.00	1.0 1.0100%
hasShowAnnotation() : boolean   hasShowAnnotation() : boolean	15541554	1.01	1.01	0.00	1.0 1.0100%
hasShowBoxes() : boolean   hasShowBoxes() : boolean	15641564	1.01	1.01	0.00	1.0 1.0100%
hasShowColourText() : boolean   hasShowColourText() : boolean	15741574	1.01	1.01	0.00	1.0 1.0100%
hasShowConsensusHistogram() : boolean   hasShowConsensusHistogram() : boolean	15841584	1.01	1.01	0.00	1.0 1.0100%
hasShowDbRefTooltip() : boolean   hasShowDbRefTooltip() : boolean	15941594	1.01	1.01	0.00	1.0 1.0100%
hasShowFullId() : boolean   hasShowFullId() : boolean	16041604	1.01	1.01	0.00	1.0 1.0100%
hasShowGroupConsensus() : boolean   hasShowGroupConsensus() : boolean	16141614	1.01	1.01	0.00	1.0 1.0100%
hasShowGroupConservation() : boolean   hasShowGroupConservation() : boolean	16241624	1.01	1.01	0.00	1.0 1.0100%
hasShowNPfeatureTooltip() : boolean   hasShowNPfeatureTooltip() : boolean	16341634	1.01	1.01	0.00	1.0 1.0100%
hasShowSequenceFeatures() : boolean   hasShowSequenceFeatures() : boolean	16441644	1.01	1.01	0.00	1.0 1.0100%
hasShowSequenceLogo() : boolean   hasShowSequenceLogo() : boolean	16541654	1.01	1.01	0.00	1.0 1.0100%
hasShowText() : boolean   hasShowText() : boolean	16641664	1.01	1.01	0.00	1.0 1.0100%
hasShowUnconserved() : boolean   hasShowUnconserved() : boolean	16741674	1.01	1.01	0.00	1.0 1.0100%
hasStartRes() : boolean   hasStartRes() : boolean	16841684	1.01	1.01	0.00	1.0 1.0100%
hasStartSeq() : boolean   hasStartSeq() : boolean	16941694	1.01	1.01	0.00	1.0 1.0100%
hasTextCol1() : boolean   hasTextCol1() : boolean	17041704	1.01	1.01	0.00	1.0 1.0100%
hasTextCol2() : boolean   hasTextCol2() : boolean	17141714	1.01	1.01	0.00	1.0 1.0100%
hasTextColThreshold() : boolean   hasTextColThreshold() : boolean	17241724	1.01	1.01	0.00	1.0 1.0100%
hasWidth() : boolean   hasWidth() : boolean	17341734	1.01	1.01	0.00	1.0 1.0100%
hasWrapAlignment() : boolean   hasWrapAlignment() : boolean	17441744	1.01	1.01	0.00	1.0 1.0100%
hasXpos() : boolean   hasXpos() : boolean	17541754	1.01	1.01	0.00	1.0 1.0100%
hasYpos() : boolean   hasYpos() : boolean	17641764	1.01	1.01	0.00	1.0 1.0100%
isCentreColumnLabels() : boolean   isCentreColumnLabels() : boolean	17741774	1.01	1.01	1.01	0.0 0.00%
isConservationSelected() : boolean   isConservationSelected() : boolean	17841784	1.01	1.01	1.01	0.0 0.00%
isFollowHighlight() : boolean   isFollowHighlight() : boolean	17941794	1.01	1.01	1.01	0.0 0.00%
isFollowSelection() : boolean   isFollowSelection() : boolean	18041804	1.01	1.01	1.01	0.0 0.00%
isGatheredViews() : boolean   isGatheredViews() : boolean	18141814	1.01	1.01	1.01	0.0 0.00%
isIgnoreGapsinConsensus() : boolean   isIgnoreGapsinConsensus() : boolean	18241824	1.01	1.01	1.01	0.0 0.00%
isNormaliseSequenceLogo() : boolean   isNormaliseSequenceLogo() : boolean	18341834	1.01	1.01	1.01	0.0 0.00%
isPidSelected() : boolean   isPidSelected() : boolean	18441844	1.01	1.01	1.01	0.0 0.00%
isRenderGaps() : boolean   isRenderGaps() : boolean	18541854	1.01	1.01	1.01	0.0 0.00%
isRightAlignIds() : boolean   isRightAlignIds() : boolean	18641864	1.01	1.01	1.01	0.0 0.00%
isScaleProteinAsCdna() : boolean   isScaleProteinAsCdna() : boolean	18741874	1.01	1.01	0.00	1.0 1.0100%
isShowAnnotation() : boolean   isShowAnnotation() : boolean	18841884	1.01	1.01	1.01	0.0 0.00%
isShowBoxes() : boolean   isShowBoxes() : boolean	18941894	1.01	1.01	1.01	0.0 0.00%
isShowColourText() : boolean   isShowColourText() : boolean	19041904	1.01	1.01	1.01	0.0 0.00%
isShowConsensusHistogram() : boolean   isShowConsensusHistogram() : boolean	19141914	1.01	1.01	1.01	0.0 0.00%
isShowDbRefTooltip() : boolean   isShowDbRefTooltip() : boolean	19241924	1.01	1.01	1.01	0.0 0.00%
isShowFullId() : boolean   isShowFullId() : boolean	19341934	1.01	1.01	1.01	0.0 0.00%
isShowGroupConsensus() : boolean   isShowGroupConsensus() : boolean	19441944	1.01	1.01	1.01	0.0 0.00%
isShowGroupConservation() : boolean   isShowGroupConservation() : boolean	19541954	1.01	1.01	1.01	0.0 0.00%
isShowNPfeatureTooltip() : boolean   isShowNPfeatureTooltip() : boolean	19641964	1.01	1.01	1.01	0.0 0.00%
isShowSequenceFeatures() : boolean   isShowSequenceFeatures() : boolean	19741974	1.01	1.01	1.01	0.0 0.00%
isShowSequenceLogo() : boolean   isShowSequenceLogo() : boolean	19841984	1.01	1.01	1.01	0.0 0.00%
isShowText() : boolean   isShowText() : boolean	19941994	1.01	1.01	1.01	0.0 0.00%
isShowUnconserved() : boolean   isShowUnconserved() : boolean	20042004	1.01	1.01	0.00	1.0 1.0100%
isValid() : boolean   isValid() : boolean	20142014	4.04	2.02	4.04	0.0 0.00%
isWrapAlignment() : boolean   isWrapAlignment() : boolean	20312031	1.01	1.01	1.01	0.0 0.00%
marshal(java.io.Writer) : void   marshal(java.io.Writer) : void	20462046	1.01	1.01	1.01	0.0 0.00%
marshal(org.xml.sax.ContentHandler) : void   marshal(org.xml.sax.ContentHandler) : void	20652065	1.01	1.01	1.01	0.0 0.00%
removeAllCalcIdParam() : void   removeAllCalcIdParam() : void	20752075	1.01	1.01	1.01	0.0 0.00%
removeAllHiddenColumns() : void   removeAllHiddenColumns() : void	20822082	1.01	1.01	1.01	0.0 0.00%
removeCalcIdParam(jalview.schemabinding.version2.CalcIdParam) : boolean   removeCalcIdParam(jalview.schemabinding.version2.CalcIdParam) : boolean	20932093	2.02	1.01	2.02	0.0 0.00%
removeCalcIdParamAt(int) : jalview.schemabinding.version2.CalcIdParam   removeCalcIdParamAt(int) : jalview.schemabinding.version2.CalcIdParam	21062106	2.02	1.01	2.02	0.0 0.00%
removeHiddenColumns(jalview.schemabinding.version2.HiddenColumns) : boolean   removeHiddenColumns(jalview.schemabinding.version2.HiddenColumns) : boolean	21192119	2.02	1.01	2.02	0.0 0.00%
removeHiddenColumnsAt(int) : jalview.schemabinding.version2.HiddenColumns   removeHiddenColumnsAt(int) : jalview.schemabinding.version2.HiddenColumns	21322132	2.02	1.01	2.02	0.0 0.00%
setAnnotationColours(jalview.schemabinding.version2.AnnotationColours) : void   setAnnotationColours(jalview.schemabinding.version2.AnnotationColours) : void	21452145	1.01	1.01	0.00	1.0 1.0100%
setBgColour(java.lang.String) : void   setBgColour(java.lang.String) : void	21572157	1.01	1.01	0.00	1.0 1.0100%
setCalcIdParam(int,jalview.schemabinding.version2.CalcIdParam) : void   setCalcIdParam(int,jalview.schemabinding.version2.CalcIdParam) : void	21702170	3.03	3.03	5.05	0.0 0.00%
setCalcIdParam(jalview.schemabinding.version2.CalcIdParam[]) : void   setCalcIdParam(jalview.schemabinding.version2.CalcIdParam[]) : void	21902190	3.03	2.02	5.05	0.0 0.00%
setCentreColumnLabels(boolean) : void   setCentreColumnLabels(boolean) : void	22082208	2.02	1.01	2.02	0.0 0.00%
setComplementId(java.lang.String) : void   setComplementId(java.lang.String) : void	22232223	1.01	1.01	1.01	0.0 0.00%
setConsThreshold(int) : void   setConsThreshold(int) : void	22342234	2.02	1.01	0.00	1.0 1.0100%
setConservationSelected(boolean) : void   setConservationSelected(boolean) : void	22462246	2.02	1.01	0.00	1.0 1.0100%
setFollowHighlight(boolean) : void   setFollowHighlight(boolean) : void	22582258	2.02	1.01	0.00	1.0 1.0100%
setFollowSelection(boolean) : void   setFollowSelection(boolean) : void	22702270	2.02	1.01	0.00	1.0 1.0100%
setFontName(java.lang.String) : void   setFontName(java.lang.String) : void	22822282	1.01	1.01	0.00	1.0 1.0100%
setFontSize(int) : void   setFontSize(int) : void	22932293	2.02	1.01	0.00	1.0 1.0100%
setFontStyle(int) : void   setFontStyle(int) : void	23052305	2.02	1.01	0.00	1.0 1.0100%
setGatheredViews(boolean) : void   setGatheredViews(boolean) : void	23172317	2.02	1.01	0.00	1.0 1.0100%
setHeight(int) : void   setHeight(int) : void	23292329	2.02	1.01	0.00	1.0 1.0100%
setHiddenColumns(int,jalview.schemabinding.version2.HiddenColumns) : void   setHiddenColumns(int,jalview.schemabinding.version2.HiddenColumns) : void	23432343	3.03	3.03	5.05	0.0 0.00%
setHiddenColumns(jalview.schemabinding.version2.HiddenColumns[]) : void   setHiddenColumns(jalview.schemabinding.version2.HiddenColumns[]) : void	23632363	3.03	2.02	5.05	0.0 0.00%
setId(java.lang.String) : void   setId(java.lang.String) : void	23842384	1.01	1.01	0.00	1.0 1.0100%
setIgnoreGapsinConsensus(boolean) : void   setIgnoreGapsinConsensus(boolean) : void	23952395	2.02	1.01	0.00	1.0 1.0100%
setNormaliseSequenceLogo(boolean) : void   setNormaliseSequenceLogo(boolean) : void	24072407	2.02	1.01	0.00	1.0 1.0100%
setPidSelected(boolean) : void   setPidSelected(boolean) : void	24192419	2.02	1.01	0.00	1.0 1.0100%
setPidThreshold(int) : void   setPidThreshold(int) : void	24312431	2.02	1.01	0.00	1.0 1.0100%
setRenderGaps(boolean) : void   setRenderGaps(boolean) : void	24432443	2.02	1.01	0.00	1.0 1.0100%
setRightAlignIds(boolean) : void   setRightAlignIds(boolean) : void	24552455	2.02	1.01	0.00	1.0 1.0100%
setScaleProteinAsCdna(boolean) : void   setScaleProteinAsCdna(boolean) : void	24672467	2.02	1.01	0.00	1.0 1.0100%
setSequenceSetId(java.lang.String) : void   setSequenceSetId(java.lang.String) : void	24792479	1.01	1.01	0.00	1.0 1.0100%
setShowAnnotation(boolean) : void   setShowAnnotation(boolean) : void	24902490	2.02	1.01	0.00	1.0 1.0100%
setShowBoxes(boolean) : void   setShowBoxes(boolean) : void	25022502	2.02	1.01	0.00	1.0 1.0100%
setShowColourText(boolean) : void   setShowColourText(boolean) : void	25142514	2.02	1.01	0.00	1.0 1.0100%
setShowConsensusHistogram(boolean) : void   setShowConsensusHistogram(boolean) : void	25262526	2.02	1.01	0.00	1.0 1.0100%
setShowDbRefTooltip(boolean) : void   setShowDbRefTooltip(boolean) : void	25382538	2.02	1.01	0.00	1.0 1.0100%
setShowFullId(boolean) : void   setShowFullId(boolean) : void	25502550	2.02	1.01	0.00	1.0 1.0100%
setShowGroupConsensus(boolean) : void   setShowGroupConsensus(boolean) : void	25622562	2.02	1.01	0.00	1.0 1.0100%
setShowGroupConservation(boolean) : void   setShowGroupConservation(boolean) : void	25742574	2.02	1.01	0.00	1.0 1.0100%
setShowNPfeatureTooltip(boolean) : void   setShowNPfeatureTooltip(boolean) : void	25862586	2.02	1.01	0.00	1.0 1.0100%
setShowSequenceFeatures(boolean) : void   setShowSequenceFeatures(boolean) : void	25982598	2.02	1.01	0.00	1.0 1.0100%
setShowSequenceLogo(boolean) : void   setShowSequenceLogo(boolean) : void	26102610	2.02	1.01	0.00	1.0 1.0100%
setShowText(boolean) : void   setShowText(boolean) : void	26222622	2.02	1.01	0.00	1.0 1.0100%
setShowUnconserved(boolean) : void   setShowUnconserved(boolean) : void	26342634	2.02	1.01	0.00	1.0 1.0100%
setStartRes(int) : void   setStartRes(int) : void	26462646	2.02	1.01	0.00	1.0 1.0100%
setStartSeq(int) : void   setStartSeq(int) : void	26582658	2.02	1.01	0.00	1.0 1.0100%
setTextCol1(int) : void   setTextCol1(int) : void	26702670	2.02	1.01	0.00	1.0 1.0100%
setTextCol2(int) : void   setTextCol2(int) : void	26822682	2.02	1.01	0.00	1.0 1.0100%
setTextColThreshold(int) : void   setTextColThreshold(int) : void	26942694	2.02	1.01	0.00	1.0 1.0100%
setTitle(java.lang.String) : void   setTitle(java.lang.String) : void	27062706	1.01	1.01	0.00	1.0 1.0100%
setViewName(java.lang.String) : void   setViewName(java.lang.String) : void	27172717	1.01	1.01	0.00	1.0 1.0100%
setWidth(int) : void   setWidth(int) : void	27282728	2.02	1.01	0.00	1.0 1.0100%
setWrapAlignment(boolean) : void   setWrapAlignment(boolean) : void	27402740	2.02	1.01	0.00	1.0 1.0100%
setXpos(int) : void   setXpos(int) : void	27522752	2.02	1.01	0.00	1.0 1.0100%
setYpos(int) : void   setYpos(int) : void	27642764	2.02	1.01	0.00	1.0 1.0100%
unmarshal(java.io.Reader) : jalview.schemabinding.version2.Viewport   unmarshal(java.io.Reader) : jalview.schemabinding.version2.Viewport	27812781	1.01	1.01	1.01	0.0 0.00%
validate() : void   validate() : void	27972797	2.02	1.01	2.02	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.59108526	jalview.io.Jalview2xmlTests.testStoreAndRecoverExpandedviewsjalview.io.Jalview2xmlTests.testStoreAndRecoverExpandedviews	1PASS
	0.59108526	jalview.io.Jalview2xmlTests.testStoreAndRecoverColourThresholdsjalview.io.Jalview2xmlTests.testStoreAndRecoverColourThresholds	1PASS
	0.59108526	jalview.io.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettingsjalview.io.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettings	1PASS
	0.58914727	jalview.io.Jalview2xmlTests.testColourByAnnotScoresjalview.io.Jalview2xmlTests.testColourByAnnotScores	1PASS
	0.5852713	jalview.io.Jalview2xmlTests.testRNAStructureRecoveryjalview.io.Jalview2xmlTests.testRNAStructureRecovery	1PASS
	0.5852713	jalview.io.Jalview2xmlTests.testTCoffeeScoresjalview.io.Jalview2xmlTests.testTCoffeeScores	1PASS
	0.57945734	jalview.io.Jalview2xmlTests.testStoreAndRecoverPDBEntryjalview.io.Jalview2xmlTests.testStoreAndRecoverPDBEntry	1PASS
	0.57945734	jalview.io.AnnotatedPDBFileInputTest.testJalviewProjectRelocationAnnotationjalview.io.AnnotatedPDBFileInputTest.testJalviewProjectRelocationAnnotation	1PASS
	0.57945734	jalview.io.Jalview2xmlTests.testStoreAndRecoverGroupRepSeqsjalview.io.Jalview2xmlTests.testStoreAndRecoverGroupRepSeqs	1PASS
	0.57945734	jalview.io.Jalview2xmlTests.testSaveLoadFeatureColoursAndFiltersjalview.io.Jalview2xmlTests.testSaveLoadFeatureColoursAndFilters	1PASS
	0.4651163	jalview.gui.AlignFrameTest.testNewView_colourThresholdsjalview.gui.AlignFrameTest.testNewView_colourThresholds	1PASS
	0.45348838	jalview.gui.AlignViewportTest.testDeregisterMapping_onCloseViewjalview.gui.AlignViewportTest.testDeregisterMapping_onCloseView	1PASS
	0.4496124	jalview.io.Jalview2xmlTests.testCopyViewSettingsjalview.io.Jalview2xmlTests.testCopyViewSettings	1PASS
	0.4496124	jalview.io.Jalview2xmlTests.gatherViewsHerejalview.io.Jalview2xmlTests.gatherViewsHere	1PASS
	0.4496124	jalview.io.Jalview2xmlTests.viewRefPdbAnnotationjalview.io.Jalview2xmlTests.viewRefPdbAnnotation	1PASS
	0.4496124	jalview.io.Jalview2xmlTests.noDuplicatePdbMappingsMadejalview.io.Jalview2xmlTests.noDuplicatePdbMappingsMade	1PASS

 

Source view

1		/*
2		* This class was automatically generated with
3		* <a href="http://www.castor.org">Castor 1.1</a>, using an XML
4		* Schema.
5		* $Id$
6		*/
7
8		package jalview.schemabinding.version2;
9
10		//---------------------------------/
11		//- Imported classes and packages -/
12		//---------------------------------/
13
14		import org.exolab.castor.xml.Marshaller;
15		import org.exolab.castor.xml.Unmarshaller;
16
17		/**
18		* Class Viewport.
19		*
20		* @version $Revision$ $Date$
21		*/
		60.7% Uncovered Elements: 203 (516) Complexity: 232 Complexity Density: 0.82
22		public class Viewport implements java.io.Serializable
23		{
24
25		// --------------------------/
26		// - Class/Member Variables -/
27		// --------------------------/
28
29		/**
30		* Field _conservationSelected.
31		*/
32		private boolean _conservationSelected;
33
34		/**
35		* keeps track of state for field: _conservationSelected
36		*/
37		private boolean _has_conservationSelected;
38
39		/**
40		* Field _pidSelected.
41		*/
42		private boolean _pidSelected;
43
44		/**
45		* keeps track of state for field: _pidSelected
46		*/
47		private boolean _has_pidSelected;
48
49		/**
50		* Field _bgColour.
51		*/
52		private java.lang.String _bgColour;
53
54		/**
55		* Field _consThreshold.
56		*/
57		private int _consThreshold;
58
59		/**
60		* keeps track of state for field: _consThreshold
61		*/
62		private boolean _has_consThreshold;
63
64		/**
65		* Field _pidThreshold.
66		*/
67		private int _pidThreshold;
68
69		/**
70		* keeps track of state for field: _pidThreshold
71		*/
72		private boolean _has_pidThreshold;
73
74		/**
75		* Field _title.
76		*/
77		private java.lang.String _title;
78
79		/**
80		* Field _showFullId.
81		*/
82		private boolean _showFullId;
83
84		/**
85		* keeps track of state for field: _showFullId
86		*/
87		private boolean _has_showFullId;
88
89		/**
90		* Field _rightAlignIds.
91		*/
92		private boolean _rightAlignIds;
93
94		/**
95		* keeps track of state for field: _rightAlignIds
96		*/
97		private boolean _has_rightAlignIds;
98
99		/**
100		* Field _showText.
101		*/
102		private boolean _showText;
103
104		/**
105		* keeps track of state for field: _showText
106		*/
107		private boolean _has_showText;
108
109		/**
110		* Field _showColourText.
111		*/
112		private boolean _showColourText;
113
114		/**
115		* keeps track of state for field: _showColourText
116		*/
117		private boolean _has_showColourText;
118
119		/**
120		* Field _showUnconserved.
121		*/
122		private boolean _showUnconserved = false;
123
124		/**
125		* keeps track of state for field: _showUnconserved
126		*/
127		private boolean _has_showUnconserved;
128
129		/**
130		* Field _showBoxes.
131		*/
132		private boolean _showBoxes;
133
134		/**
135		* keeps track of state for field: _showBoxes
136		*/
137		private boolean _has_showBoxes;
138
139		/**
140		* Field _wrapAlignment.
141		*/
142		private boolean _wrapAlignment;
143
144		/**
145		* keeps track of state for field: _wrapAlignment
146		*/
147		private boolean _has_wrapAlignment;
148
149		/**
150		* Field _renderGaps.
151		*/
152		private boolean _renderGaps;
153
154		/**
155		* keeps track of state for field: _renderGaps
156		*/
157		private boolean _has_renderGaps;
158
159		/**
160		* Field _showSequenceFeatures.
161		*/
162		private boolean _showSequenceFeatures;
163
164		/**
165		* keeps track of state for field: _showSequenceFeatures
166		*/
167		private boolean _has_showSequenceFeatures;
168
169		/**
170		* Field _showNPfeatureTooltip.
171		*/
172		private boolean _showNPfeatureTooltip;
173
174		/**
175		* keeps track of state for field: _showNPfeatureTooltip
176		*/
177		private boolean _has_showNPfeatureTooltip;
178
179		/**
180		* Field _showDbRefTooltip.
181		*/
182		private boolean _showDbRefTooltip;
183
184		/**
185		* keeps track of state for field: _showDbRefTooltip
186		*/
187		private boolean _has_showDbRefTooltip;
188
189		/**
190		* Field _followHighlight.
191		*/
192		private boolean _followHighlight = true;
193
194		/**
195		* keeps track of state for field: _followHighlight
196		*/
197		private boolean _has_followHighlight;
198
199		/**
200		* Field _followSelection.
201		*/
202		private boolean _followSelection = true;
203
204		/**
205		* keeps track of state for field: _followSelection
206		*/
207		private boolean _has_followSelection;
208
209		/**
210		* Field _showAnnotation.
211		*/
212		private boolean _showAnnotation;
213
214		/**
215		* keeps track of state for field: _showAnnotation
216		*/
217		private boolean _has_showAnnotation;
218
219		/**
220		* Field _centreColumnLabels.
221		*/
222		private boolean _centreColumnLabels = false;
223
224		/**
225		* keeps track of state for field: _centreColumnLabels
226		*/
227		private boolean _has_centreColumnLabels;
228
229		/**
230		* Field _showGroupConservation.
231		*/
232		private boolean _showGroupConservation = false;
233
234		/**
235		* keeps track of state for field: _showGroupConservation
236		*/
237		private boolean _has_showGroupConservation;
238
239		/**
240		* Field _showGroupConsensus.
241		*/
242		private boolean _showGroupConsensus = false;
243
244		/**
245		* keeps track of state for field: _showGroupConsensus
246		*/
247		private boolean _has_showGroupConsensus;
248
249		/**
250		* Field _showConsensusHistogram.
251		*/
252		private boolean _showConsensusHistogram = true;
253
254		/**
255		* keeps track of state for field: _showConsensusHistogram
256		*/
257		private boolean _has_showConsensusHistogram;
258
259		/**
260		* Field _showSequenceLogo.
261		*/
262		private boolean _showSequenceLogo = false;
263
264		/**
265		* keeps track of state for field: _showSequenceLogo
266		*/
267		private boolean _has_showSequenceLogo;
268
269		/**
270		* Field _normaliseSequenceLogo.
271		*/
272		private boolean _normaliseSequenceLogo = false;
273
274		/**
275		* keeps track of state for field: _normaliseSequenceLogo
276		*/
277		private boolean _has_normaliseSequenceLogo;
278
279		/**
280		* Field _ignoreGapsinConsensus.
281		*/
282		private boolean _ignoreGapsinConsensus = true;
283
284		/**
285		* keeps track of state for field: _ignoreGapsinConsensus
286		*/
287		private boolean _has_ignoreGapsinConsensus;
288
289		/**
290		* Field _startRes.
291		*/
292		private int _startRes;
293
294		/**
295		* keeps track of state for field: _startRes
296		*/
297		private boolean _has_startRes;
298
299		/**
300		* Field _startSeq.
301		*/
302		private int _startSeq;
303
304		/**
305		* keeps track of state for field: _startSeq
306		*/
307		private boolean _has_startSeq;
308
309		/**
310		* Field _fontName.
311		*/
312		private java.lang.String _fontName;
313
314		/**
315		* Field _fontSize.
316		*/
317		private int _fontSize;
318
319		/**
320		* keeps track of state for field: _fontSize
321		*/
322		private boolean _has_fontSize;
323
324		/**
325		* Field _fontStyle.
326		*/
327		private int _fontStyle;
328
329		/**
330		* keeps track of state for field: _fontStyle
331		*/
332		private boolean _has_fontStyle;
333
334		/**
335		* Field _scaleProteinAsCdna.
336		*/
337		private boolean _scaleProteinAsCdna = true;
338
339		/**
340		* keeps track of state for field: _scaleProteinAsCdna
341		*/
342		private boolean _has_scaleProteinAsCdna;
343
344		/**
345		* Field _viewName.
346		*/
347		private java.lang.String _viewName;
348
349		/**
350		* Field _sequenceSetId.
351		*/
352		private java.lang.String _sequenceSetId;
353
354		/**
355		* Field _gatheredViews.
356		*/
357		private boolean _gatheredViews;
358
359		/**
360		* keeps track of state for field: _gatheredViews
361		*/
362		private boolean _has_gatheredViews;
363
364		/**
365		* Field _textCol1.
366		*/
367		private int _textCol1;
368
369		/**
370		* keeps track of state for field: _textCol1
371		*/
372		private boolean _has_textCol1;
373
374		/**
375		* Field _textCol2.
376		*/
377		private int _textCol2;
378
379		/**
380		* keeps track of state for field: _textCol2
381		*/
382		private boolean _has_textCol2;
383
384		/**
385		* Field _textColThreshold.
386		*/
387		private int _textColThreshold;
388
389		/**
390		* keeps track of state for field: _textColThreshold
391		*/
392		private boolean _has_textColThreshold;
393
394		/**
395		* unique id used by jalview to synchronize between stored and instantiated
396		* views
397		*
398		*/
399		private java.lang.String _id;
400
401		/**
402		* The viewport id of this viewport's (cdna/protein) coding complement, if any
403		*
404		*/
405		private java.lang.String _complementId;
406
407		/**
408		* Field _width.
409		*/
410		private int _width;
411
412		/**
413		* keeps track of state for field: _width
414		*/
415		private boolean _has_width;
416
417		/**
418		* Field _height.
419		*/
420		private int _height;
421
422		/**
423		* keeps track of state for field: _height
424		*/
425		private boolean _has_height;
426
427		/**
428		* Field _xpos.
429		*/
430		private int _xpos;
431
432		/**
433		* keeps track of state for field: _xpos
434		*/
435		private boolean _has_xpos;
436
437		/**
438		* Field _ypos.
439		*/
440		private int _ypos;
441
442		/**
443		* keeps track of state for field: _ypos
444		*/
445		private boolean _has_ypos;
446
447		/**
448		* Field _annotationColours.
449		*/
450		private jalview.schemabinding.version2.AnnotationColours _annotationColours;
451
452		/**
453		* Field _hiddenColumnsList.
454		*/
455		private java.util.Vector _hiddenColumnsList;
456
457		/**
458		* Field _calcIdParamList.
459		*/
460		private java.util.Vector _calcIdParamList;
461
462		// ----------------/
463		// - Constructors -/
464		// ----------------/
465
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
466	91	public Viewport()...
467		{
468	91	super();
469	91	this._hiddenColumnsList = new java.util.Vector();
470	91	this._calcIdParamList = new java.util.Vector();
471		}
472
473		// -----------/
474		// - Methods -/
475		// -----------/
476
477		/**
478		*
479		*
480		* @param vCalcIdParam
481		* @throws java.lang.IndexOutOfBoundsException
482		* if the index given is outside the bounds of the collection
483		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
484	0	public void addCalcIdParam(...
485		final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
486		throws java.lang.IndexOutOfBoundsException
487		{
488	0	this._calcIdParamList.addElement(vCalcIdParam);
489		}
490
491		/**
492		*
493		*
494		* @param index
495		* @param vCalcIdParam
496		* @throws java.lang.IndexOutOfBoundsException
497		* if the index given is outside the bounds of the collection
498		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
499	0	public void addCalcIdParam(final int index,...
500		final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
501		throws java.lang.IndexOutOfBoundsException
502		{
503	0	this._calcIdParamList.add(index, vCalcIdParam);
504		}
505
506		/**
507		*
508		*
509		* @param vHiddenColumns
510		* @throws java.lang.IndexOutOfBoundsException
511		* if the index given is outside the bounds of the collection
512		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
513	42	public void addHiddenColumns(...
514		final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
515		throws java.lang.IndexOutOfBoundsException
516		{
517	42	this._hiddenColumnsList.addElement(vHiddenColumns);
518		}
519
520		/**
521		*
522		*
523		* @param index
524		* @param vHiddenColumns
525		* @throws java.lang.IndexOutOfBoundsException
526		* if the index given is outside the bounds of the collection
527		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
528	0	public void addHiddenColumns(final int index,...
529		final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
530		throws java.lang.IndexOutOfBoundsException
531		{
532	0	this._hiddenColumnsList.add(index, vHiddenColumns);
533		}
534
535		/**
536		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
537	0	public void deleteCentreColumnLabels()...
538		{
539	0	this._has_centreColumnLabels = false;
540		}
541
542		/**
543		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
544	0	public void deleteConsThreshold()...
545		{
546	0	this._has_consThreshold = false;
547		}
548
549		/**
550		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
551	0	public void deleteConservationSelected()...
552		{
553	0	this._has_conservationSelected = false;
554		}
555
556		/**
557		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
558	0	public void deleteFollowHighlight()...
559		{
560	0	this._has_followHighlight = false;
561		}
562
563		/**
564		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
565	0	public void deleteFollowSelection()...
566		{
567	0	this._has_followSelection = false;
568		}
569
570		/**
571		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
572	0	public void deleteFontSize()...
573		{
574	0	this._has_fontSize = false;
575		}
576
577		/**
578		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
579	0	public void deleteFontStyle()...
580		{
581	0	this._has_fontStyle = false;
582		}
583
584		/**
585		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
586	0	public void deleteGatheredViews()...
587		{
588	0	this._has_gatheredViews = false;
589		}
590
591		/**
592		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
593	0	public void deleteHeight()...
594		{
595	0	this._has_height = false;
596		}
597
598		/**
599		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
600	0	public void deleteIgnoreGapsinConsensus()...
601		{
602	0	this._has_ignoreGapsinConsensus = false;
603		}
604
605		/**
606		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
607	0	public void deleteNormaliseSequenceLogo()...
608		{
609	0	this._has_normaliseSequenceLogo = false;
610		}
611
612		/**
613		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
614	0	public void deletePidSelected()...
615		{
616	0	this._has_pidSelected = false;
617		}
618
619		/**
620		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
621	0	public void deletePidThreshold()...
622		{
623	0	this._has_pidThreshold = false;
624		}
625
626		/**
627		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
628	0	public void deleteRenderGaps()...
629		{
630	0	this._has_renderGaps = false;
631		}
632
633		/**
634		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
635	0	public void deleteRightAlignIds()...
636		{
637	0	this._has_rightAlignIds = false;
638		}
639
640		/**
641		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
642	0	public void deleteScaleProteinAsCdna()...
643		{
644	0	this._has_scaleProteinAsCdna = false;
645		}
646
647		/**
648		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
649	0	public void deleteShowAnnotation()...
650		{
651	0	this._has_showAnnotation = false;
652		}
653
654		/**
655		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
656	0	public void deleteShowBoxes()...
657		{
658	0	this._has_showBoxes = false;
659		}
660
661		/**
662		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
663	0	public void deleteShowColourText()...
664		{
665	0	this._has_showColourText = false;
666		}
667
668		/**
669		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
670	0	public void deleteShowConsensusHistogram()...
671		{
672	0	this._has_showConsensusHistogram = false;
673		}
674
675		/**
676		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
677	0	public void deleteShowDbRefTooltip()...
678		{
679	0	this._has_showDbRefTooltip = false;
680		}
681
682		/**
683		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
684	0	public void deleteShowFullId()...
685		{
686	0	this._has_showFullId = false;
687		}
688
689		/**
690		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
691	0	public void deleteShowGroupConsensus()...
692		{
693	0	this._has_showGroupConsensus = false;
694		}
695
696		/**
697		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
698	0	public void deleteShowGroupConservation()...
699		{
700	0	this._has_showGroupConservation = false;
701		}
702
703		/**
704		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
705	0	public void deleteShowNPfeatureTooltip()...
706		{
707	0	this._has_showNPfeatureTooltip = false;
708		}
709
710		/**
711		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
712	0	public void deleteShowSequenceFeatures()...
713		{
714	0	this._has_showSequenceFeatures = false;
715		}
716
717		/**
718		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
719	0	public void deleteShowSequenceLogo()...
720		{
721	0	this._has_showSequenceLogo = false;
722		}
723
724		/**
725		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
726	0	public void deleteShowText()...
727		{
728	0	this._has_showText = false;
729		}
730
731		/**
732		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
733	0	public void deleteShowUnconserved()...
734		{
735	0	this._has_showUnconserved = false;
736		}
737
738		/**
739		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
740	0	public void deleteStartRes()...
741		{
742	0	this._has_startRes = false;
743		}
744
745		/**
746		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
747	0	public void deleteStartSeq()...
748		{
749	0	this._has_startSeq = false;
750		}
751
752		/**
753		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
754	0	public void deleteTextCol1()...
755		{
756	0	this._has_textCol1 = false;
757		}
758
759		/**
760		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
761	0	public void deleteTextCol2()...
762		{
763	0	this._has_textCol2 = false;
764		}
765
766		/**
767		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
768	0	public void deleteTextColThreshold()...
769		{
770	0	this._has_textColThreshold = false;
771		}
772
773		/**
774		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
775	0	public void deleteWidth()...
776		{
777	0	this._has_width = false;
778		}
779
780		/**
781		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
782	0	public void deleteWrapAlignment()...
783		{
784	0	this._has_wrapAlignment = false;
785		}
786
787		/**
788		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
789	0	public void deleteXpos()...
790		{
791	0	this._has_xpos = false;
792		}
793
794		/**
795		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
796	0	public void deleteYpos()...
797		{
798	0	this._has_ypos = false;
799		}
800
801		/**
802		* Method enumerateCalcIdParam.
803		*
804		* @return an Enumeration over all jalview.schemabinding.version2.CalcIdParam
805		* elements
806		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
807	0	public java.util.Enumeration enumerateCalcIdParam()...
808		{
809	0	return this._calcIdParamList.elements();
810		}
811
812		/**
813		* Method enumerateHiddenColumns.
814		*
815		* @return an Enumeration over all
816		* jalview.schemabinding.version2.HiddenColumns elements
817		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
818	0	public java.util.Enumeration enumerateHiddenColumns()...
819		{
820	0	return this._hiddenColumnsList.elements();
821		}
822
823		/**
824		* Returns the value of field 'annotationColours'.
825		*
826		* @return the value of field 'AnnotationColours'.
827		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
828	39	public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()...
829		{
830	39	return this._annotationColours;
831		}
832
833		/**
834		* Returns the value of field 'bgColour'.
835		*
836		* @return the value of field 'BgColour'.
837		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
838	325	public java.lang.String getBgColour()...
839		{
840	325	return this._bgColour;
841		}
842
843		/**
844		* Method getCalcIdParam.
845		*
846		* @param index
847		* @throws java.lang.IndexOutOfBoundsException
848		* if the index given is outside the bounds of the collection
849		* @return the value of the jalview.schemabinding.version2.CalcIdParam at the
850		* given index
851		*/
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 1
852	0	public jalview.schemabinding.version2.CalcIdParam getCalcIdParam(...
853		final int index) throws java.lang.IndexOutOfBoundsException
854		{
855		// check bounds for index
856	0	if (index < 0 || index >= this._calcIdParamList.size())
857		{
858	0	throw new IndexOutOfBoundsException("getCalcIdParam: Index value '"
859		+ index + "' not in range [0.."
860		+ (this._calcIdParamList.size() - 1) + "]");
861		}
862
863	0	return (jalview.schemabinding.version2.CalcIdParam) _calcIdParamList
864		.get(index);
865		}
866
867		/**
868		* Method getCalcIdParam.Returns the contents of the collection in an Array.
869		* <p>
870		* Note: Just in case the collection contents are changing in another thread,
871		* we pass a 0-length Array of the correct type into the API call. This way we
872		* <i>know</i> that the Array returned is of exactly the correct length.
873		*
874		* @return this collection as an Array
875		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
876	182	public jalview.schemabinding.version2.CalcIdParam[] getCalcIdParam()...
877		{
878	182	jalview.schemabinding.version2.CalcIdParam[] array = new jalview.schemabinding.version2.CalcIdParam[0];
879	182	return (jalview.schemabinding.version2.CalcIdParam[]) this._calcIdParamList
880		.toArray(array);
881		}
882
883		/**
884		* Method getCalcIdParamCount.
885		*
886		* @return the size of this collection
887		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
888	0	public int getCalcIdParamCount()...
889		{
890	0	return this._calcIdParamList.size();
891		}
892
893		/**
894		* Returns the value of field 'centreColumnLabels'.
895		*
896		* @return the value of field 'CentreColumnLabels'.
897		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
898	0	public boolean getCentreColumnLabels()...
899		{
900	0	return this._centreColumnLabels;
901		}
902
903		/**
904		* Returns the value of field 'complementId'. The field 'complementId' has the
905		* following description: The viewport id of this viewport's (cdna/protein)
906		* coding complement, if any
907		*
908		*
909		* @return the value of field 'ComplementId'.
910		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
911	110	public java.lang.String getComplementId()...
912		{
913	110	return this._complementId;
914		}
915
916		/**
917		* Returns the value of field 'consThreshold'.
918		*
919		* @return the value of field 'ConsThreshold'.
920		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
921	76	public int getConsThreshold()...
922		{
923	76	return this._consThreshold;
924		}
925
926		/**
927		* Returns the value of field 'conservationSelected'.
928		*
929		* @return the value of field 'ConservationSelected'.
930		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
931	182	public boolean getConservationSelected()...
932		{
933	182	return this._conservationSelected;
934		}
935
936		/**
937		* Returns the value of field 'followHighlight'.
938		*
939		* @return the value of field 'FollowHighlight'.
940		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
941	110	public boolean getFollowHighlight()...
942		{
943	110	return this._followHighlight;
944		}
945
946		/**
947		* Returns the value of field 'followSelection'.
948		*
949		* @return the value of field 'FollowSelection'.
950		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
951	110	public boolean getFollowSelection()...
952		{
953	110	return this._followSelection;
954		}
955
956		/**
957		* Returns the value of field 'fontName'.
958		*
959		* @return the value of field 'FontName'.
960		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
961	110	public java.lang.String getFontName()...
962		{
963	110	return this._fontName;
964		}
965
966		/**
967		* Returns the value of field 'fontSize'.
968		*
969		* @return the value of field 'FontSize'.
970		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
971	110	public int getFontSize()...
972		{
973	110	return this._fontSize;
974		}
975
976		/**
977		* Returns the value of field 'fontStyle'.
978		*
979		* @return the value of field 'FontStyle'.
980		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
981	110	public int getFontStyle()...
982		{
983	110	return this._fontStyle;
984		}
985
986		/**
987		* Returns the value of field 'gatheredViews'.
988		*
989		* @return the value of field 'GatheredViews'.
990		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
991	110	public boolean getGatheredViews()...
992		{
993	110	return this._gatheredViews;
994		}
995
996		/**
997		* Returns the value of field 'height'.
998		*
999		* @return the value of field 'Height'.
1000		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1001	254	public int getHeight()...
1002		{
1003	254	return this._height;
1004		}
1005
1006		/**
1007		* Method getHiddenColumns.
1008		*
1009		* @param index
1010		* @throws java.lang.IndexOutOfBoundsException
1011		* if the index given is outside the bounds of the collection
1012		* @return the value of the jalview.schemabinding.version2.HiddenColumns at
1013		* the given index
1014		*/
		60% Uncovered Elements: 2 (5) Complexity: 3 Complexity Density: 1
1015	72	public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(...
1016		final int index) throws java.lang.IndexOutOfBoundsException
1017		{
1018		// check bounds for index
1019	72	if (index < 0 || index >= this._hiddenColumnsList.size())
1020		{
1021	0	throw new IndexOutOfBoundsException("getHiddenColumns: Index value '"
1022		+ index + "' not in range [0.."
1023		+ (this._hiddenColumnsList.size() - 1) + "]");
1024		}
1025
1026	72	return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList
1027		.get(index);
1028		}
1029
1030		/**
1031		* Method getHiddenColumns.Returns the contents of the collection in an Array.
1032		* <p>
1033		* Note: Just in case the collection contents are changing in another thread,
1034		* we pass a 0-length Array of the correct type into the API call. This way we
1035		* <i>know</i> that the Array returned is of exactly the correct length.
1036		*
1037		* @return this collection as an Array
1038		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
1039	38	public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()...
1040		{
1041	38	jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
1042	38	return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList
1043		.toArray(array);
1044		}
1045
1046		/**
1047		* Method getHiddenColumnsCount.
1048		*
1049		* @return the size of this collection
1050		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1051	132	public int getHiddenColumnsCount()...
1052		{
1053	132	return this._hiddenColumnsList.size();
1054		}
1055
1056		/**
1057		* Returns the value of field 'id'. The field 'id' has the following
1058		* description: unique id used by jalview to synchronize between stored and
1059		* instantiated views
1060		*
1061		*
1062		* @return the value of field 'Id'.
1063		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1064	179	public java.lang.String getId()...
1065		{
1066	179	return this._id;
1067		}
1068
1069		/**
1070		* Returns the value of field 'ignoreGapsinConsensus'.
1071		*
1072		* @return the value of field 'IgnoreGapsinConsensus'.
1073		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1074	182	public boolean getIgnoreGapsinConsensus()...
1075		{
1076	182	return this._ignoreGapsinConsensus;
1077		}
1078
1079		/**
1080		* Returns the value of field 'normaliseSequenceLogo'.
1081		*
1082		* @return the value of field 'NormaliseSequenceLogo'.
1083		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1084	60	public boolean getNormaliseSequenceLogo()...
1085		{
1086	60	return this._normaliseSequenceLogo;
1087		}
1088
1089		/**
1090		* Returns the value of field 'pidSelected'.
1091		*
1092		* @return the value of field 'PidSelected'.
1093		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1094	110	public boolean getPidSelected()...
1095		{
1096	110	return this._pidSelected;
1097		}
1098
1099		/**
1100		* Returns the value of field 'pidThreshold'.
1101		*
1102		* @return the value of field 'PidThreshold'.
1103		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1104	152	public int getPidThreshold()...
1105		{
1106	152	return this._pidThreshold;
1107		}
1108
1109		/**
1110		* Returns the value of field 'renderGaps'.
1111		*
1112		* @return the value of field 'RenderGaps'.
1113		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1114	110	public boolean getRenderGaps()...
1115		{
1116	110	return this._renderGaps;
1117		}
1118
1119		/**
1120		* Returns the value of field 'rightAlignIds'.
1121		*
1122		* @return the value of field 'RightAlignIds'.
1123		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1124	110	public boolean getRightAlignIds()...
1125		{
1126	110	return this._rightAlignIds;
1127		}
1128
1129		/**
1130		* Returns the value of field 'scaleProteinAsCdna'.
1131		*
1132		* @return the value of field 'ScaleProteinAsCdna'.
1133		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1134	38	public boolean getScaleProteinAsCdna()...
1135		{
1136	38	return this._scaleProteinAsCdna;
1137		}
1138
1139		/**
1140		* Returns the value of field 'sequenceSetId'.
1141		*
1142		* @return the value of field 'SequenceSetId'.
1143		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1144	182	public java.lang.String getSequenceSetId()...
1145		{
1146	182	return this._sequenceSetId;
1147		}
1148
1149		/**
1150		* Returns the value of field 'showAnnotation'.
1151		*
1152		* @return the value of field 'ShowAnnotation'.
1153		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1154	182	public boolean getShowAnnotation()...
1155		{
1156	182	return this._showAnnotation;
1157		}
1158
1159		/**
1160		* Returns the value of field 'showBoxes'.
1161		*
1162		* @return the value of field 'ShowBoxes'.
1163		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1164	110	public boolean getShowBoxes()...
1165		{
1166	110	return this._showBoxes;
1167		}
1168
1169		/**
1170		* Returns the value of field 'showColourText'.
1171		*
1172		* @return the value of field 'ShowColourText'.
1173		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1174	110	public boolean getShowColourText()...
1175		{
1176	110	return this._showColourText;
1177		}
1178
1179		/**
1180		* Returns the value of field 'showConsensusHistogram'.
1181		*
1182		* @return the value of field 'ShowConsensusHistogram'.
1183		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1184	110	public boolean getShowConsensusHistogram()...
1185		{
1186	110	return this._showConsensusHistogram;
1187		}
1188
1189		/**
1190		* Returns the value of field 'showDbRefTooltip'.
1191		*
1192		* @return the value of field 'ShowDbRefTooltip'.
1193		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1194	110	public boolean getShowDbRefTooltip()...
1195		{
1196	110	return this._showDbRefTooltip;
1197		}
1198
1199		/**
1200		* Returns the value of field 'showFullId'.
1201		*
1202		* @return the value of field 'ShowFullId'.
1203		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1204	110	public boolean getShowFullId()...
1205		{
1206	110	return this._showFullId;
1207		}
1208
1209		/**
1210		* Returns the value of field 'showGroupConsensus'.
1211		*
1212		* @return the value of field 'ShowGroupConsensus'.
1213		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1214	110	public boolean getShowGroupConsensus()...
1215		{
1216	110	return this._showGroupConsensus;
1217		}
1218
1219		/**
1220		* Returns the value of field 'showGroupConservation'.
1221		*
1222		* @return the value of field 'ShowGroupConservation'.
1223		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1224	110	public boolean getShowGroupConservation()...
1225		{
1226	110	return this._showGroupConservation;
1227		}
1228
1229		/**
1230		* Returns the value of field 'showNPfeatureTooltip'.
1231		*
1232		* @return the value of field 'ShowNPfeatureTooltip'.
1233		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1234	38	public boolean getShowNPfeatureTooltip()...
1235		{
1236	38	return this._showNPfeatureTooltip;
1237		}
1238
1239		/**
1240		* Returns the value of field 'showSequenceFeatures'.
1241		*
1242		* @return the value of field 'ShowSequenceFeatures'.
1243		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1244	110	public boolean getShowSequenceFeatures()...
1245		{
1246	110	return this._showSequenceFeatures;
1247		}
1248
1249		/**
1250		* Returns the value of field 'showSequenceLogo'.
1251		*
1252		* @return the value of field 'ShowSequenceLogo'.
1253		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1254	110	public boolean getShowSequenceLogo()...
1255		{
1256	110	return this._showSequenceLogo;
1257		}
1258
1259		/**
1260		* Returns the value of field 'showText'.
1261		*
1262		* @return the value of field 'ShowText'.
1263		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1264	110	public boolean getShowText()...
1265		{
1266	110	return this._showText;
1267		}
1268
1269		/**
1270		* Returns the value of field 'showUnconserved'.
1271		*
1272		* @return the value of field 'ShowUnconserved'.
1273		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1274	38	public boolean getShowUnconserved()...
1275		{
1276	38	return this._showUnconserved;
1277		}
1278
1279		/**
1280		* Returns the value of field 'startRes'.
1281		*
1282		* @return the value of field 'StartRes'.
1283		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1284	110	public int getStartRes()...
1285		{
1286	110	return this._startRes;
1287		}
1288
1289		/**
1290		* Returns the value of field 'startSeq'.
1291		*
1292		* @return the value of field 'StartSeq'.
1293		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1294	38	public int getStartSeq()...
1295		{
1296	38	return this._startSeq;
1297		}
1298
1299		/**
1300		* Returns the value of field 'textCol1'.
1301		*
1302		* @return the value of field 'TextCol1'.
1303		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1304	110	public int getTextCol1()...
1305		{
1306	110	return this._textCol1;
1307		}
1308
1309		/**
1310		* Returns the value of field 'textCol2'.
1311		*
1312		* @return the value of field 'TextCol2'.
1313		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1314	110	public int getTextCol2()...
1315		{
1316	110	return this._textCol2;
1317		}
1318
1319		/**
1320		* Returns the value of field 'textColThreshold'.
1321		*
1322		* @return the value of field 'TextColThreshold'.
1323		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1324	110	public int getTextColThreshold()...
1325		{
1326	110	return this._textColThreshold;
1327		}
1328
1329		/**
1330		* Returns the value of field 'title'.
1331		*
1332		* @return the value of field 'Title'.
1333		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1334	182	public java.lang.String getTitle()...
1335		{
1336	182	return this._title;
1337		}
1338
1339		/**
1340		* Returns the value of field 'viewName'.
1341		*
1342		* @return the value of field 'ViewName'.
1343		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1344	172	public java.lang.String getViewName()...
1345		{
1346	172	return this._viewName;
1347		}
1348
1349		/**
1350		* Returns the value of field 'width'.
1351		*
1352		* @return the value of field 'Width'.
1353		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1354	254	public int getWidth()...
1355		{
1356	254	return this._width;
1357		}
1358
1359		/**
1360		* Returns the value of field 'wrapAlignment'.
1361		*
1362		* @return the value of field 'WrapAlignment'.
1363		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1364	110	public boolean getWrapAlignment()...
1365		{
1366	110	return this._wrapAlignment;
1367		}
1368
1369		/**
1370		* Returns the value of field 'xpos'.
1371		*
1372		* @return the value of field 'Xpos'.
1373		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1374	110	public int getXpos()...
1375		{
1376	110	return this._xpos;
1377		}
1378
1379		/**
1380		* Returns the value of field 'ypos'.
1381		*
1382		* @return the value of field 'Ypos'.
1383		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1384	110	public int getYpos()...
1385		{
1386	110	return this._ypos;
1387		}
1388
1389		/**
1390		* Method hasCentreColumnLabels.
1391		*
1392		* @return true if at least one CentreColumnLabels has been adde
1393		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1394	110	public boolean hasCentreColumnLabels()...
1395		{
1396	110	return this._has_centreColumnLabels;
1397		}
1398
1399		/**
1400		* Method hasConsThreshold.
1401		*
1402		* @return true if at least one ConsThreshold has been added
1403		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1404	38	public boolean hasConsThreshold()...
1405		{
1406	38	return this._has_consThreshold;
1407		}
1408
1409		/**
1410		* Method hasConservationSelected.
1411		*
1412		* @return true if at least one ConservationSelected has been added
1413		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1414	38	public boolean hasConservationSelected()...
1415		{
1416	38	return this._has_conservationSelected;
1417		}
1418
1419		/**
1420		* Method hasFollowHighlight.
1421		*
1422		* @return true if at least one FollowHighlight has been added
1423		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1424	110	public boolean hasFollowHighlight()...
1425		{
1426	110	return this._has_followHighlight;
1427		}
1428
1429		/**
1430		* Method hasFollowSelection.
1431		*
1432		* @return true if at least one FollowSelection has been added
1433		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1434	110	public boolean hasFollowSelection()...
1435		{
1436	110	return this._has_followSelection;
1437		}
1438
1439		/**
1440		* Method hasFontSize.
1441		*
1442		* @return true if at least one FontSize has been added
1443		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1444	38	public boolean hasFontSize()...
1445		{
1446	38	return this._has_fontSize;
1447		}
1448
1449		/**
1450		* Method hasFontStyle.
1451		*
1452		* @return true if at least one FontStyle has been added
1453		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1454	38	public boolean hasFontStyle()...
1455		{
1456	38	return this._has_fontStyle;
1457		}
1458
1459		/**
1460		* Method hasGatheredViews.
1461		*
1462		* @return true if at least one GatheredViews has been added
1463		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1464	38	public boolean hasGatheredViews()...
1465		{
1466	38	return this._has_gatheredViews;
1467		}
1468
1469		/**
1470		* Method hasHeight.
1471		*
1472		* @return true if at least one Height has been added
1473		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1474	38	public boolean hasHeight()...
1475		{
1476	38	return this._has_height;
1477		}
1478
1479		/**
1480		* Method hasIgnoreGapsinConsensus.
1481		*
1482		* @return true if at least one IgnoreGapsinConsensus has been added
1483		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1484	110	public boolean hasIgnoreGapsinConsensus()...
1485		{
1486	110	return this._has_ignoreGapsinConsensus;
1487		}
1488
1489		/**
1490		* Method hasNormaliseSequenceLogo.
1491		*
1492		* @return true if at least one NormaliseSequenceLogo has been added
1493		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1494	110	public boolean hasNormaliseSequenceLogo()...
1495		{
1496	110	return this._has_normaliseSequenceLogo;
1497		}
1498
1499		/**
1500		* Method hasPidSelected.
1501		*
1502		* @return true if at least one PidSelected has been added
1503		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1504	38	public boolean hasPidSelected()...
1505		{
1506	38	return this._has_pidSelected;
1507		}
1508
1509		/**
1510		* Method hasPidThreshold.
1511		*
1512		* @return true if at least one PidThreshold has been added
1513		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1514	38	public boolean hasPidThreshold()...
1515		{
1516	38	return this._has_pidThreshold;
1517		}
1518
1519		/**
1520		* Method hasRenderGaps.
1521		*
1522		* @return true if at least one RenderGaps has been added
1523		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1524	38	public boolean hasRenderGaps()...
1525		{
1526	38	return this._has_renderGaps;
1527		}
1528
1529		/**
1530		* Method hasRightAlignIds.
1531		*
1532		* @return true if at least one RightAlignIds has been added
1533		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1534	38	public boolean hasRightAlignIds()...
1535		{
1536	38	return this._has_rightAlignIds;
1537		}
1538
1539		/**
1540		* Method hasScaleProteinAsCdna.
1541		*
1542		* @return true if at least one ScaleProteinAsCdna has been adde
1543		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1544	38	public boolean hasScaleProteinAsCdna()...
1545		{
1546	38	return this._has_scaleProteinAsCdna;
1547		}
1548
1549		/**
1550		* Method hasShowAnnotation.
1551		*
1552		* @return true if at least one ShowAnnotation has been added
1553		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1554	38	public boolean hasShowAnnotation()...
1555		{
1556	38	return this._has_showAnnotation;
1557		}
1558
1559		/**
1560		* Method hasShowBoxes.
1561		*
1562		* @return true if at least one ShowBoxes has been added
1563		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1564	38	public boolean hasShowBoxes()...
1565		{
1566	38	return this._has_showBoxes;
1567		}
1568
1569		/**
1570		* Method hasShowColourText.
1571		*
1572		* @return true if at least one ShowColourText has been added
1573		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1574	38	public boolean hasShowColourText()...
1575		{
1576	38	return this._has_showColourText;
1577		}
1578
1579		/**
1580		* Method hasShowConsensusHistogram.
1581		*
1582		* @return true if at least one ShowConsensusHistogram has been added
1583		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1584	110	public boolean hasShowConsensusHistogram()...
1585		{
1586	110	return this._has_showConsensusHistogram;
1587		}
1588
1589		/**
1590		* Method hasShowDbRefTooltip.
1591		*
1592		* @return true if at least one ShowDbRefTooltip has been added
1593		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1594	110	public boolean hasShowDbRefTooltip()...
1595		{
1596	110	return this._has_showDbRefTooltip;
1597		}
1598
1599		/**
1600		* Method hasShowFullId.
1601		*
1602		* @return true if at least one ShowFullId has been added
1603		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1604	38	public boolean hasShowFullId()...
1605		{
1606	38	return this._has_showFullId;
1607		}
1608
1609		/**
1610		* Method hasShowGroupConsensus.
1611		*
1612		* @return true if at least one ShowGroupConsensus has been adde
1613		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1614	110	public boolean hasShowGroupConsensus()...
1615		{
1616	110	return this._has_showGroupConsensus;
1617		}
1618
1619		/**
1620		* Method hasShowGroupConservation.
1621		*
1622		* @return true if at least one ShowGroupConservation has been added
1623		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1624	110	public boolean hasShowGroupConservation()...
1625		{
1626	110	return this._has_showGroupConservation;
1627		}
1628
1629		/**
1630		* Method hasShowNPfeatureTooltip.
1631		*
1632		* @return true if at least one ShowNPfeatureTooltip has been added
1633		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1634	182	public boolean hasShowNPfeatureTooltip()...
1635		{
1636	182	return this._has_showNPfeatureTooltip;
1637		}
1638
1639		/**
1640		* Method hasShowSequenceFeatures.
1641		*
1642		* @return true if at least one ShowSequenceFeatures has been added
1643		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1644	38	public boolean hasShowSequenceFeatures()...
1645		{
1646	38	return this._has_showSequenceFeatures;
1647		}
1648
1649		/**
1650		* Method hasShowSequenceLogo.
1651		*
1652		* @return true if at least one ShowSequenceLogo has been added
1653		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1654	110	public boolean hasShowSequenceLogo()...
1655		{
1656	110	return this._has_showSequenceLogo;
1657		}
1658
1659		/**
1660		* Method hasShowText.
1661		*
1662		* @return true if at least one ShowText has been added
1663		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1664	38	public boolean hasShowText()...
1665		{
1666	38	return this._has_showText;
1667		}
1668
1669		/**
1670		* Method hasShowUnconserved.
1671		*
1672		* @return true if at least one ShowUnconserved has been added
1673		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1674	110	public boolean hasShowUnconserved()...
1675		{
1676	110	return this._has_showUnconserved;
1677		}
1678
1679		/**
1680		* Method hasStartRes.
1681		*
1682		* @return true if at least one StartRes has been added
1683		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1684	38	public boolean hasStartRes()...
1685		{
1686	38	return this._has_startRes;
1687		}
1688
1689		/**
1690		* Method hasStartSeq.
1691		*
1692		* @return true if at least one StartSeq has been added
1693		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1694	38	public boolean hasStartSeq()...
1695		{
1696	38	return this._has_startSeq;
1697		}
1698
1699		/**
1700		* Method hasTextCol1.
1701		*
1702		* @return true if at least one TextCol1 has been added
1703		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1704	38	public boolean hasTextCol1()...
1705		{
1706	38	return this._has_textCol1;
1707		}
1708
1709		/**
1710		* Method hasTextCol2.
1711		*
1712		* @return true if at least one TextCol2 has been added
1713		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1714	38	public boolean hasTextCol2()...
1715		{
1716	38	return this._has_textCol2;
1717		}
1718
1719		/**
1720		* Method hasTextColThreshold.
1721		*
1722		* @return true if at least one TextColThreshold has been added
1723		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1724	38	public boolean hasTextColThreshold()...
1725		{
1726	38	return this._has_textColThreshold;
1727		}
1728
1729		/**
1730		* Method hasWidth.
1731		*
1732		* @return true if at least one Width has been added
1733		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1734	38	public boolean hasWidth()...
1735		{
1736	38	return this._has_width;
1737		}
1738
1739		/**
1740		* Method hasWrapAlignment.
1741		*
1742		* @return true if at least one WrapAlignment has been added
1743		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1744	38	public boolean hasWrapAlignment()...
1745		{
1746	38	return this._has_wrapAlignment;
1747		}
1748
1749		/**
1750		* Method hasXpos.
1751		*
1752		* @return true if at least one Xpos has been added
1753		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1754	38	public boolean hasXpos()...
1755		{
1756	38	return this._has_xpos;
1757		}
1758
1759		/**
1760		* Method hasYpos.
1761		*
1762		* @return true if at least one Ypos has been added
1763		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1764	38	public boolean hasYpos()...
1765		{
1766	38	return this._has_ypos;
1767		}
1768
1769		/**
1770		* Returns the value of field 'centreColumnLabels'.
1771		*
1772		* @return the value of field 'CentreColumnLabels'.
1773		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1774	0	public boolean isCentreColumnLabels()...
1775		{
1776	0	return this._centreColumnLabels;
1777		}
1778
1779		/**
1780		* Returns the value of field 'conservationSelected'.
1781		*
1782		* @return the value of field 'ConservationSelected'.
1783		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1784	0	public boolean isConservationSelected()...
1785		{
1786	0	return this._conservationSelected;
1787		}
1788
1789		/**
1790		* Returns the value of field 'followHighlight'.
1791		*
1792		* @return the value of field 'FollowHighlight'.
1793		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1794	0	public boolean isFollowHighlight()...
1795		{
1796	0	return this._followHighlight;
1797		}
1798
1799		/**
1800		* Returns the value of field 'followSelection'.
1801		*
1802		* @return the value of field 'FollowSelection'.
1803		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1804	0	public boolean isFollowSelection()...
1805		{
1806	0	return this._followSelection;
1807		}
1808
1809		/**
1810		* Returns the value of field 'gatheredViews'.
1811		*
1812		* @return the value of field 'GatheredViews'.
1813		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1814	0	public boolean isGatheredViews()...
1815		{
1816	0	return this._gatheredViews;
1817		}
1818
1819		/**
1820		* Returns the value of field 'ignoreGapsinConsensus'.
1821		*
1822		* @return the value of field 'IgnoreGapsinConsensus'.
1823		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1824	0	public boolean isIgnoreGapsinConsensus()...
1825		{
1826	0	return this._ignoreGapsinConsensus;
1827		}
1828
1829		/**
1830		* Returns the value of field 'normaliseSequenceLogo'.
1831		*
1832		* @return the value of field 'NormaliseSequenceLogo'.
1833		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1834	0	public boolean isNormaliseSequenceLogo()...
1835		{
1836	0	return this._normaliseSequenceLogo;
1837		}
1838
1839		/**
1840		* Returns the value of field 'pidSelected'.
1841		*
1842		* @return the value of field 'PidSelected'.
1843		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1844	0	public boolean isPidSelected()...
1845		{
1846	0	return this._pidSelected;
1847		}
1848
1849		/**
1850		* Returns the value of field 'renderGaps'.
1851		*
1852		* @return the value of field 'RenderGaps'.
1853		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1854	0	public boolean isRenderGaps()...
1855		{
1856	0	return this._renderGaps;
1857		}
1858
1859		/**
1860		* Returns the value of field 'rightAlignIds'.
1861		*
1862		* @return the value of field 'RightAlignIds'.
1863		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1864	0	public boolean isRightAlignIds()...
1865		{
1866	0	return this._rightAlignIds;
1867		}
1868
1869		/**
1870		* Returns the value of field 'scaleProteinAsCdna'.
1871		*
1872		* @return the value of field 'ScaleProteinAsCdna'.
1873		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1874	72	public boolean isScaleProteinAsCdna()...
1875		{
1876	72	return this._scaleProteinAsCdna;
1877		}
1878
1879		/**
1880		* Returns the value of field 'showAnnotation'.
1881		*
1882		* @return the value of field 'ShowAnnotation'.
1883		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1884	0	public boolean isShowAnnotation()...
1885		{
1886	0	return this._showAnnotation;
1887		}
1888
1889		/**
1890		* Returns the value of field 'showBoxes'.
1891		*
1892		* @return the value of field 'ShowBoxes'.
1893		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1894	0	public boolean isShowBoxes()...
1895		{
1896	0	return this._showBoxes;
1897		}
1898
1899		/**
1900		* Returns the value of field 'showColourText'.
1901		*
1902		* @return the value of field 'ShowColourText'.
1903		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1904	0	public boolean isShowColourText()...
1905		{
1906	0	return this._showColourText;
1907		}
1908
1909		/**
1910		* Returns the value of field 'showConsensusHistogram'.
1911		*
1912		* @return the value of field 'ShowConsensusHistogram'.
1913		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1914	0	public boolean isShowConsensusHistogram()...
1915		{
1916	0	return this._showConsensusHistogram;
1917		}
1918
1919		/**
1920		* Returns the value of field 'showDbRefTooltip'.
1921		*
1922		* @return the value of field 'ShowDbRefTooltip'.
1923		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1924	0	public boolean isShowDbRefTooltip()...
1925		{
1926	0	return this._showDbRefTooltip;
1927		}
1928
1929		/**
1930		* Returns the value of field 'showFullId'.
1931		*
1932		* @return the value of field 'ShowFullId'.
1933		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1934	0	public boolean isShowFullId()...
1935		{
1936	0	return this._showFullId;
1937		}
1938
1939		/**
1940		* Returns the value of field 'showGroupConsensus'.
1941		*
1942		* @return the value of field 'ShowGroupConsensus'.
1943		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1944	0	public boolean isShowGroupConsensus()...
1945		{
1946	0	return this._showGroupConsensus;
1947		}
1948
1949		/**
1950		* Returns the value of field 'showGroupConservation'.
1951		*
1952		* @return the value of field 'ShowGroupConservation'.
1953		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1954	0	public boolean isShowGroupConservation()...
1955		{
1956	0	return this._showGroupConservation;
1957		}
1958
1959		/**
1960		* Returns the value of field 'showNPfeatureTooltip'.
1961		*
1962		* @return the value of field 'ShowNPfeatureTooltip'.
1963		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1964	0	public boolean isShowNPfeatureTooltip()...
1965		{
1966	0	return this._showNPfeatureTooltip;
1967		}
1968
1969		/**
1970		* Returns the value of field 'showSequenceFeatures'.
1971		*
1972		* @return the value of field 'ShowSequenceFeatures'.
1973		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1974	0	public boolean isShowSequenceFeatures()...
1975		{
1976	0	return this._showSequenceFeatures;
1977		}
1978
1979		/**
1980		* Returns the value of field 'showSequenceLogo'.
1981		*
1982		* @return the value of field 'ShowSequenceLogo'.
1983		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1984	0	public boolean isShowSequenceLogo()...
1985		{
1986	0	return this._showSequenceLogo;
1987		}
1988
1989		/**
1990		* Returns the value of field 'showText'.
1991		*
1992		* @return the value of field 'ShowText'.
1993		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1994	0	public boolean isShowText()...
1995		{
1996	0	return this._showText;
1997		}
1998
1999		/**
2000		* Returns the value of field 'showUnconserved'.
2001		*
2002		* @return the value of field 'ShowUnconserved'.
2003		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2004	72	public boolean isShowUnconserved()...
2005		{
2006	72	return this._showUnconserved;
2007		}
2008
2009		/**
2010		* Method isValid.
2011		*
2012		* @return true if this object is valid according to the schema
2013		*/
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 0.5
2014	0	public boolean isValid()...
2015		{
2016	0	try
2017		{
2018	0	validate();
2019		} catch (org.exolab.castor.xml.ValidationException vex)
2020		{
2021	0	return false;
2022		}
2023	0	return true;
2024		}
2025
2026		/**
2027		* Returns the value of field 'wrapAlignment'.
2028		*
2029		* @return the value of field 'WrapAlignment'.
2030		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2031	0	public boolean isWrapAlignment()...
2032		{
2033	0	return this._wrapAlignment;
2034		}
2035
2036		/**
2037		*
2038		*
2039		* @param out
2040		* @throws org.exolab.castor.xml.MarshalException
2041		* if object is null or if any SAXException is thrown during
2042		* marshaling
2043		* @throws org.exolab.castor.xml.ValidationException
2044		* if this object is an invalid instance according to the schema
2045		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2046	0	public void marshal(final java.io.Writer out)...
2047		throws org.exolab.castor.xml.MarshalException,
2048		org.exolab.castor.xml.ValidationException
2049		{
2050	0	Marshaller.marshal(this, out);
2051		}
2052
2053		/**
2054		*
2055		*
2056		* @param handler
2057		* @throws java.io.IOException
2058		* if an IOException occurs during marshaling
2059		* @throws org.exolab.castor.xml.ValidationException
2060		* if this object is an invalid instance according to the schema
2061		* @throws org.exolab.castor.xml.MarshalException
2062		* if object is null or if any SAXException is thrown during
2063		* marshaling
2064		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2065	0	public void marshal(final org.xml.sax.ContentHandler handler)...
2066		throws java.io.IOException,
2067		org.exolab.castor.xml.MarshalException,
2068		org.exolab.castor.xml.ValidationException
2069		{
2070	0	Marshaller.marshal(this, handler);
2071		}
2072
2073		/**
2074		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2075	0	public void removeAllCalcIdParam()...
2076		{
2077	0	this._calcIdParamList.clear();
2078		}
2079
2080		/**
2081		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2082	0	public void removeAllHiddenColumns()...
2083		{
2084	0	this._hiddenColumnsList.clear();
2085		}
2086
2087		/**
2088		* Method removeCalcIdParam.
2089		*
2090		* @param vCalcIdParam
2091		* @return true if the object was removed from the collection.
2092		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
2093	0	public boolean removeCalcIdParam(...
2094		final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
2095		{
2096	0	boolean removed = _calcIdParamList.remove(vCalcIdParam);
2097	0	return removed;
2098		}
2099
2100		/**
2101		* Method removeCalcIdParamAt.
2102		*
2103		* @param index
2104		* @return the element removed from the collection
2105		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
2106	0	public jalview.schemabinding.version2.CalcIdParam removeCalcIdParamAt(...
2107		final int index)
2108		{
2109	0	java.lang.Object obj = this._calcIdParamList.remove(index);
2110	0	return (jalview.schemabinding.version2.CalcIdParam) obj;
2111		}
2112
2113		/**
2114		* Method removeHiddenColumns.
2115		*
2116		* @param vHiddenColumns
2117		* @return true if the object was removed from the collection.
2118		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
2119	0	public boolean removeHiddenColumns(...
2120		final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
2121		{
2122	0	boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
2123	0	return removed;
2124		}
2125
2126		/**
2127		* Method removeHiddenColumnsAt.
2128		*
2129		* @param index
2130		* @return the element removed from the collection
2131		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
2132	0	public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(...
2133		final int index)
2134		{
2135	0	java.lang.Object obj = this._hiddenColumnsList.remove(index);
2136	0	return (jalview.schemabinding.version2.HiddenColumns) obj;
2137		}
2138
2139		/**
2140		* Sets the value of field 'annotationColours'.
2141		*
2142		* @param annotationColours
2143		* the value of field 'annotationColours'.
2144		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2145	2	public void setAnnotationColours(...
2146		final jalview.schemabinding.version2.AnnotationColours annotationColours)
2147		{
2148	2	this._annotationColours = annotationColours;
2149		}
2150
2151		/**
2152		* Sets the value of field 'bgColour'.
2153		*
2154		* @param bgColour
2155		* the value of field 'bgColour'.
2156		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2157	91	public void setBgColour(final java.lang.String bgColour)...
2158		{
2159	91	this._bgColour = bgColour;
2160		}
2161
2162		/**
2163		*
2164		*
2165		* @param index
2166		* @param vCalcIdParam
2167		* @throws java.lang.IndexOutOfBoundsException
2168		* if the index given is outside the bounds of the collection
2169		*/
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 1
2170	0	public void setCalcIdParam(final int index,...
2171		final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
2172		throws java.lang.IndexOutOfBoundsException
2173		{
2174		// check bounds for index
2175	0	if (index < 0 || index >= this._calcIdParamList.size())
2176		{
2177	0	throw new IndexOutOfBoundsException("setCalcIdParam: Index value '"
2178		+ index + "' not in range [0.."
2179		+ (this._calcIdParamList.size() - 1) + "]");
2180		}
2181
2182	0	this._calcIdParamList.set(index, vCalcIdParam);
2183		}
2184
2185		/**
2186		*
2187		*
2188		* @param vCalcIdParamArray
2189		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
2190	0	public void setCalcIdParam(...
2191		final jalview.schemabinding.version2.CalcIdParam[] vCalcIdParamArray)
2192		{
2193		// -- copy array
2194	0	_calcIdParamList.clear();
2195
2196	0	for (int i = 0; i < vCalcIdParamArray.length; i++)
2197		{
2198	0	this._calcIdParamList.add(vCalcIdParamArray[i]);
2199		}
2200		}
2201
2202		/**
2203		* Sets the value of field 'centreColumnLabels'.
2204		*
2205		* @param centreColumnLabels
2206		* the value of field 'centreColumnLabels'.
2207		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
2208	0	public void setCentreColumnLabels(final boolean centreColumnLabels)...
2209		{
2210	0	this._centreColumnLabels = centreColumnLabels;
2211	0	this._has_centreColumnLabels = true;
2212		}
2213
2214		/**
2215		* Sets the value of field 'complementId'. The field 'complementId' has the
2216		* following description: The viewport id of this viewport's (cdna/protein)
2217		* coding complement, if any
2218		*
2219		*
2220		* @param complementId
2221		* the value of field 'complementId'.
2222		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2223	0	public void setComplementId(final java.lang.String complementId)...
2224		{
2225	0	this._complementId = complementId;
2226		}
2227
2228		/**
2229		* Sets the value of field 'consThreshold'.
2230		*
2231		* @param consThreshold
2232		* the value of field 'consThreshold'.
2233		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2234	3	public void setConsThreshold(final int consThreshold)...
2235		{
2236	3	this._consThreshold = consThreshold;
2237	3	this._has_consThreshold = true;
2238		}
2239
2240		/**
2241		* Sets the value of field 'conservationSelected'.
2242		*
2243		* @param conservationSelected
2244		* the value of field 'conservationSelected'.
2245		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2246	91	public void setConservationSelected(final boolean conservationSelected)...
2247		{
2248	91	this._conservationSelected = conservationSelected;
2249	91	this._has_conservationSelected = true;
2250		}
2251
2252		/**
2253		* Sets the value of field 'followHighlight'.
2254		*
2255		* @param followHighlight
2256		* the value of field 'followHighlight'.
2257		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2258	91	public void setFollowHighlight(final boolean followHighlight)...
2259		{
2260	91	this._followHighlight = followHighlight;
2261	91	this._has_followHighlight = true;
2262		}
2263
2264		/**
2265		* Sets the value of field 'followSelection'.
2266		*
2267		* @param followSelection
2268		* the value of field 'followSelection'.
2269		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2270	91	public void setFollowSelection(final boolean followSelection)...
2271		{
2272	91	this._followSelection = followSelection;
2273	91	this._has_followSelection = true;
2274		}
2275
2276		/**
2277		* Sets the value of field 'fontName'.
2278		*
2279		* @param fontName
2280		* the value of field 'fontName'.
2281		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2282	91	public void setFontName(final java.lang.String fontName)...
2283		{
2284	91	this._fontName = fontName;
2285		}
2286
2287		/**
2288		* Sets the value of field 'fontSize'.
2289		*
2290		* @param fontSize
2291		* the value of field 'fontSize'.
2292		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2293	91	public void setFontSize(final int fontSize)...
2294		{
2295	91	this._fontSize = fontSize;
2296	91	this._has_fontSize = true;
2297		}
2298
2299		/**
2300		* Sets the value of field 'fontStyle'.
2301		*
2302		* @param fontStyle
2303		* the value of field 'fontStyle'.
2304		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2305	91	public void setFontStyle(final int fontStyle)...
2306		{
2307	91	this._fontStyle = fontStyle;
2308	91	this._has_fontStyle = true;
2309		}
2310
2311		/**
2312		* Sets the value of field 'gatheredViews'.
2313		*
2314		* @param gatheredViews
2315		* the value of field 'gatheredViews'.
2316		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2317	91	public void setGatheredViews(final boolean gatheredViews)...
2318		{
2319	91	this._gatheredViews = gatheredViews;
2320	91	this._has_gatheredViews = true;
2321		}
2322
2323		/**
2324		* Sets the value of field 'height'.
2325		*
2326		* @param height
2327		* the value of field 'height'.
2328		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2329	91	public void setHeight(final int height)...
2330		{
2331	91	this._height = height;
2332	91	this._has_height = true;
2333		}
2334
2335		/**
2336		*
2337		*
2338		* @param index
2339		* @param vHiddenColumns
2340		* @throws java.lang.IndexOutOfBoundsException
2341		* if the index given is outside the bounds of the collection
2342		*/
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 1
2343	0	public void setHiddenColumns(final int index,...
2344		final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
2345		throws java.lang.IndexOutOfBoundsException
2346		{
2347		// check bounds for index
2348	0	if (index < 0 || index >= this._hiddenColumnsList.size())
2349		{
2350	0	throw new IndexOutOfBoundsException("setHiddenColumns: Index value '"
2351		+ index + "' not in range [0.."
2352		+ (this._hiddenColumnsList.size() - 1) + "]");
2353		}
2354
2355	0	this._hiddenColumnsList.set(index, vHiddenColumns);
2356		}
2357
2358		/**
2359		*
2360		*
2361		* @param vHiddenColumnsArray
2362		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
2363	0	public void setHiddenColumns(...
2364		final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray)
2365		{
2366		// -- copy array
2367	0	_hiddenColumnsList.clear();
2368
2369	0	for (int i = 0; i < vHiddenColumnsArray.length; i++)
2370		{
2371	0	this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
2372		}
2373		}
2374
2375		/**
2376		* Sets the value of field 'id'. The field 'id' has the following description:
2377		* unique id used by jalview to synchronize between stored and instantiated
2378		* views
2379		*
2380		*
2381		* @param id
2382		* the value of field 'id'.
2383		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2384	94	public void setId(final java.lang.String id)...
2385		{
2386	94	this._id = id;
2387		}
2388
2389		/**
2390		* Sets the value of field 'ignoreGapsinConsensus'.
2391		*
2392		* @param ignoreGapsinConsensus
2393		* the value of field 'ignoreGapsinConsensus'.
2394		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2395	91	public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus)...
2396		{
2397	91	this._ignoreGapsinConsensus = ignoreGapsinConsensus;
2398	91	this._has_ignoreGapsinConsensus = true;
2399		}
2400
2401		/**
2402		* Sets the value of field 'normaliseSequenceLogo'.
2403		*
2404		* @param normaliseSequenceLogo
2405		* the value of field 'normaliseSequenceLogo'.
2406		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2407	41	public void setNormaliseSequenceLogo(final boolean normaliseSequenceLogo)...
2408		{
2409	41	this._normaliseSequenceLogo = normaliseSequenceLogo;
2410	41	this._has_normaliseSequenceLogo = true;
2411		}
2412
2413		/**
2414		* Sets the value of field 'pidSelected'.
2415		*
2416		* @param pidSelected
2417		* the value of field 'pidSelected'.
2418		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2419	91	public void setPidSelected(final boolean pidSelected)...
2420		{
2421	91	this._pidSelected = pidSelected;
2422	91	this._has_pidSelected = true;
2423		}
2424
2425		/**
2426		* Sets the value of field 'pidThreshold'.
2427		*
2428		* @param pidThreshold
2429		* the value of field 'pidThreshold'.
2430		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2431	9	public void setPidThreshold(final int pidThreshold)...
2432		{
2433	9	this._pidThreshold = pidThreshold;
2434	9	this._has_pidThreshold = true;
2435		}
2436
2437		/**
2438		* Sets the value of field 'renderGaps'.
2439		*
2440		* @param renderGaps
2441		* the value of field 'renderGaps'.
2442		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2443	91	public void setRenderGaps(final boolean renderGaps)...
2444		{
2445	91	this._renderGaps = renderGaps;
2446	91	this._has_renderGaps = true;
2447		}
2448
2449		/**
2450		* Sets the value of field 'rightAlignIds'.
2451		*
2452		* @param rightAlignIds
2453		* the value of field 'rightAlignIds'.
2454		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2455	91	public void setRightAlignIds(final boolean rightAlignIds)...
2456		{
2457	91	this._rightAlignIds = rightAlignIds;
2458	91	this._has_rightAlignIds = true;
2459		}
2460
2461		/**
2462		* Sets the value of field 'scaleProteinAsCdna'.
2463		*
2464		* @param scaleProteinAsCdna
2465		* the value of field 'scaleProteinAsCdna'.
2466		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2467	41	public void setScaleProteinAsCdna(final boolean scaleProteinAsCdna)...
2468		{
2469	41	this._scaleProteinAsCdna = scaleProteinAsCdna;
2470	41	this._has_scaleProteinAsCdna = true;
2471		}
2472
2473		/**
2474		* Sets the value of field 'sequenceSetId'.
2475		*
2476		* @param sequenceSetId
2477		* the value of field 'sequenceSetId'.
2478		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2479	91	public void setSequenceSetId(final java.lang.String sequenceSetId)...
2480		{
2481	91	this._sequenceSetId = sequenceSetId;
2482		}
2483
2484		/**
2485		* Sets the value of field 'showAnnotation'.
2486		*
2487		* @param showAnnotation
2488		* the value of field 'showAnnotation'.
2489		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2490	91	public void setShowAnnotation(final boolean showAnnotation)...
2491		{
2492	91	this._showAnnotation = showAnnotation;
2493	91	this._has_showAnnotation = true;
2494		}
2495
2496		/**
2497		* Sets the value of field 'showBoxes'.
2498		*
2499		* @param showBoxes
2500		* the value of field 'showBoxes'.
2501		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2502	91	public void setShowBoxes(final boolean showBoxes)...
2503		{
2504	91	this._showBoxes = showBoxes;
2505	91	this._has_showBoxes = true;
2506		}
2507
2508		/**
2509		* Sets the value of field 'showColourText'.
2510		*
2511		* @param showColourText
2512		* the value of field 'showColourText'.
2513		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2514	91	public void setShowColourText(final boolean showColourText)...
2515		{
2516	91	this._showColourText = showColourText;
2517	91	this._has_showColourText = true;
2518		}
2519
2520		/**
2521		* Sets the value of field 'showConsensusHistogram'.
2522		*
2523		* @param showConsensusHistogram
2524		* the value of field 'showConsensusHistogram'.
2525		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2526	91	public void setShowConsensusHistogram(final boolean showConsensusHistogram)...
2527		{
2528	91	this._showConsensusHistogram = showConsensusHistogram;
2529	91	this._has_showConsensusHistogram = true;
2530		}
2531
2532		/**
2533		* Sets the value of field 'showDbRefTooltip'.
2534		*
2535		* @param showDbRefTooltip
2536		* the value of field 'showDbRefTooltip'
2537		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2538	91	public void setShowDbRefTooltip(final boolean showDbRefTooltip)...
2539		{
2540	91	this._showDbRefTooltip = showDbRefTooltip;
2541	91	this._has_showDbRefTooltip = true;
2542		}
2543
2544		/**
2545		* Sets the value of field 'showFullId'.
2546		*
2547		* @param showFullId
2548		* the value of field 'showFullId'.
2549		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2550	91	public void setShowFullId(final boolean showFullId)...
2551		{
2552	91	this._showFullId = showFullId;
2553	91	this._has_showFullId = true;
2554		}
2555
2556		/**
2557		* Sets the value of field 'showGroupConsensus'.
2558		*
2559		* @param showGroupConsensus
2560		* the value of field 'showGroupConsensus'.
2561		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2562	91	public void setShowGroupConsensus(final boolean showGroupConsensus)...
2563		{
2564	91	this._showGroupConsensus = showGroupConsensus;
2565	91	this._has_showGroupConsensus = true;
2566		}
2567
2568		/**
2569		* Sets the value of field 'showGroupConservation'.
2570		*
2571		* @param showGroupConservation
2572		* the value of field 'showGroupConservation'.
2573		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2574	91	public void setShowGroupConservation(final boolean showGroupConservation)...
2575		{
2576	91	this._showGroupConservation = showGroupConservation;
2577	91	this._has_showGroupConservation = true;
2578		}
2579
2580		/**
2581		* Sets the value of field 'showNPfeatureTooltip'.
2582		*
2583		* @param showNPfeatureTooltip
2584		* the value of field 'showNPfeatureTooltip'.
2585		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2586	91	public void setShowNPfeatureTooltip(final boolean showNPfeatureTooltip)...
2587		{
2588	91	this._showNPfeatureTooltip = showNPfeatureTooltip;
2589	91	this._has_showNPfeatureTooltip = true;
2590		}
2591
2592		/**
2593		* Sets the value of field 'showSequenceFeatures'.
2594		*
2595		* @param showSequenceFeatures
2596		* the value of field 'showSequenceFeatures'.
2597		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2598	91	public void setShowSequenceFeatures(final boolean showSequenceFeatures)...
2599		{
2600	91	this._showSequenceFeatures = showSequenceFeatures;
2601	91	this._has_showSequenceFeatures = true;
2602		}
2603
2604		/**
2605		* Sets the value of field 'showSequenceLogo'.
2606		*
2607		* @param showSequenceLogo
2608		* the value of field 'showSequenceLogo'
2609		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2610	91	public void setShowSequenceLogo(final boolean showSequenceLogo)...
2611		{
2612	91	this._showSequenceLogo = showSequenceLogo;
2613	91	this._has_showSequenceLogo = true;
2614		}
2615
2616		/**
2617		* Sets the value of field 'showText'.
2618		*
2619		* @param showText
2620		* the value of field 'showText'.
2621		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2622	91	public void setShowText(final boolean showText)...
2623		{
2624	91	this._showText = showText;
2625	91	this._has_showText = true;
2626		}
2627
2628		/**
2629		* Sets the value of field 'showUnconserved'.
2630		*
2631		* @param showUnconserved
2632		* the value of field 'showUnconserved'.
2633		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2634	91	public void setShowUnconserved(final boolean showUnconserved)...
2635		{
2636	91	this._showUnconserved = showUnconserved;
2637	91	this._has_showUnconserved = true;
2638		}
2639
2640		/**
2641		* Sets the value of field 'startRes'.
2642		*
2643		* @param startRes
2644		* the value of field 'startRes'.
2645		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2646	91	public void setStartRes(final int startRes)...
2647		{
2648	91	this._startRes = startRes;
2649	91	this._has_startRes = true;
2650		}
2651
2652		/**
2653		* Sets the value of field 'startSeq'.
2654		*
2655		* @param startSeq
2656		* the value of field 'startSeq'.
2657		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2658	91	public void setStartSeq(final int startSeq)...
2659		{
2660	91	this._startSeq = startSeq;
2661	91	this._has_startSeq = true;
2662		}
2663
2664		/**
2665		* Sets the value of field 'textCol1'.
2666		*
2667		* @param textCol1
2668		* the value of field 'textCol1'.
2669		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2670	91	public void setTextCol1(final int textCol1)...
2671		{
2672	91	this._textCol1 = textCol1;
2673	91	this._has_textCol1 = true;
2674		}
2675
2676		/**
2677		* Sets the value of field 'textCol2'.
2678		*
2679		* @param textCol2
2680		* the value of field 'textCol2'.
2681		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2682	91	public void setTextCol2(final int textCol2)...
2683		{
2684	91	this._textCol2 = textCol2;
2685	91	this._has_textCol2 = true;
2686		}
2687
2688		/**
2689		* Sets the value of field 'textColThreshold'.
2690		*
2691		* @param textColThreshold
2692		* the value of field 'textColThreshold'
2693		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2694	91	public void setTextColThreshold(final int textColThreshold)...
2695		{
2696	91	this._textColThreshold = textColThreshold;
2697	91	this._has_textColThreshold = true;
2698		}
2699
2700		/**
2701		* Sets the value of field 'title'.
2702		*
2703		* @param title
2704		* the value of field 'title'.
2705		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2706	91	public void setTitle(final java.lang.String title)...
2707		{
2708	91	this._title = title;
2709		}
2710
2711		/**
2712		* Sets the value of field 'viewName'.
2713		*
2714		* @param viewName
2715		* the value of field 'viewName'.
2716		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
2717	84	public void setViewName(final java.lang.String viewName)...
2718		{
2719	84	this._viewName = viewName;
2720		}
2721
2722		/**
2723		* Sets the value of field 'width'.
2724		*
2725		* @param width
2726		* the value of field 'width'.
2727		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2728	91	public void setWidth(final int width)...
2729		{
2730	91	this._width = width;
2731	91	this._has_width = true;
2732		}
2733
2734		/**
2735		* Sets the value of field 'wrapAlignment'.
2736		*
2737		* @param wrapAlignment
2738		* the value of field 'wrapAlignment'.
2739		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2740	91	public void setWrapAlignment(final boolean wrapAlignment)...
2741		{
2742	91	this._wrapAlignment = wrapAlignment;
2743	91	this._has_wrapAlignment = true;
2744		}
2745
2746		/**
2747		* Sets the value of field 'xpos'.
2748		*
2749		* @param xpos
2750		* the value of field 'xpos'.
2751		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2752	91	public void setXpos(final int xpos)...
2753		{
2754	91	this._xpos = xpos;
2755	91	this._has_xpos = true;
2756		}
2757
2758		/**
2759		* Sets the value of field 'ypos'.
2760		*
2761		* @param ypos
2762		* the value of field 'ypos'.
2763		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
2764	91	public void setYpos(final int ypos)...
2765		{
2766	91	this._ypos = ypos;
2767	91	this._has_ypos = true;
2768		}
2769
2770		/**
2771		* Method unmarshal.
2772		*
2773		* @param reader
2774		* @throws org.exolab.castor.xml.MarshalException
2775		* if object is null or if any SAXException is thrown during
2776		* marshaling
2777		* @throws org.exolab.castor.xml.ValidationException
2778		* if this object is an invalid instance according to the schema
2779		* @return the unmarshaled jalview.schemabinding.version2.Viewport
2780		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2781	0	public static jalview.schemabinding.version2.Viewport unmarshal(...
2782		final java.io.Reader reader)
2783		throws org.exolab.castor.xml.MarshalException,
2784		org.exolab.castor.xml.ValidationException
2785		{
2786	0	return (jalview.schemabinding.version2.Viewport) Unmarshaller
2787		.unmarshal(jalview.schemabinding.version2.Viewport.class,
2788		reader);
2789		}
2790
2791		/**
2792		*
2793		*
2794		* @throws org.exolab.castor.xml.ValidationException
2795		* if this object is an invalid instance according to the schema
2796		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
2797	0	public void validate() throws org.exolab.castor.xml.ValidationException...
2798		{
2799	0	org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
2800	0	validator.validate(this);
2801		}
2802
2803		}