package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Viewport implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _conservationSelected.
- */
- private boolean _conservationSelected;
-
- /**
- * keeps track of state for field: _conservationSelected
- */
- private boolean _has_conservationSelected;
-
- /**
- * Field _pidSelected.
- */
- private boolean _pidSelected;
-
- /**
- * keeps track of state for field: _pidSelected
- */
- private boolean _has_pidSelected;
-
- /**
- * Field _bgColour.
- */
- private java.lang.String _bgColour;
-
- /**
- * Field _consThreshold.
- */
- private int _consThreshold;
-
- /**
- * keeps track of state for field: _consThreshold
- */
- private boolean _has_consThreshold;
-
- /**
- * Field _pidThreshold.
- */
- private int _pidThreshold;
-
- /**
- * keeps track of state for field: _pidThreshold
- */
- private boolean _has_pidThreshold;
-
- /**
- * Field _title.
- */
- private java.lang.String _title;
-
- /**
- * Field _showFullId.
- */
- private boolean _showFullId;
-
- /**
- * keeps track of state for field: _showFullId
- */
- private boolean _has_showFullId;
-
- /**
- * Field _rightAlignIds.
- */
- private boolean _rightAlignIds;
-
- /**
- * keeps track of state for field: _rightAlignIds
- */
- private boolean _has_rightAlignIds;
-
- /**
- * Field _showText.
- */
- private boolean _showText;
-
- /**
- * keeps track of state for field: _showText
- */
- private boolean _has_showText;
-
- /**
- * Field _showColourText.
- */
- private boolean _showColourText;
-
- /**
- * keeps track of state for field: _showColourText
- */
- private boolean _has_showColourText;
-
- /**
- * Field _showUnconserved.
- */
- private boolean _showUnconserved = false;
-
- /**
- * keeps track of state for field: _showUnconserved
- */
- private boolean _has_showUnconserved;
-
- /**
- * Field _showBoxes.
- */
- private boolean _showBoxes;
-
- /**
- * keeps track of state for field: _showBoxes
- */
- private boolean _has_showBoxes;
-
- /**
- * Field _wrapAlignment.
- */
- private boolean _wrapAlignment;
-
- /**
- * keeps track of state for field: _wrapAlignment
- */
- private boolean _has_wrapAlignment;
-
- /**
- * Field _renderGaps.
- */
- private boolean _renderGaps;
-
- /**
- * keeps track of state for field: _renderGaps
- */
- private boolean _has_renderGaps;
-
- /**
- * Field _showSequenceFeatures.
- */
- private boolean _showSequenceFeatures;
-
- /**
- * keeps track of state for field: _showSequenceFeatures
- */
- private boolean _has_showSequenceFeatures;
-
- /**
- * Field _showNPfeatureTooltip.
- */
- private boolean _showNPfeatureTooltip;
-
- /**
- * keeps track of state for field: _showNPfeatureTooltip
- */
- private boolean _has_showNPfeatureTooltip;
-
- /**
- * Field _showDbRefTooltip.
- */
- private boolean _showDbRefTooltip;
-
- /**
- * keeps track of state for field: _showDbRefTooltip
- */
- private boolean _has_showDbRefTooltip;
-
- /**
- * Field _followHighlight.
- */
- private boolean _followHighlight = true;
-
- /**
- * keeps track of state for field: _followHighlight
- */
- private boolean _has_followHighlight;
-
- /**
- * Field _followSelection.
- */
- private boolean _followSelection = true;
-
- /**
- * keeps track of state for field: _followSelection
- */
- private boolean _has_followSelection;
-
- /**
- * Field _showAnnotation.
- */
- private boolean _showAnnotation;
-
- /**
- * keeps track of state for field: _showAnnotation
- */
- private boolean _has_showAnnotation;
-
- /**
- * Field _centreColumnLabels.
- */
- private boolean _centreColumnLabels = false;
-
- /**
- * keeps track of state for field: _centreColumnLabels
- */
- private boolean _has_centreColumnLabels;
-
- /**
- * Field _showGroupConservation.
- */
- private boolean _showGroupConservation = false;
-
- /**
- * keeps track of state for field: _showGroupConservation
- */
- private boolean _has_showGroupConservation;
-
- /**
- * Field _showGroupConsensus.
- */
- private boolean _showGroupConsensus = false;
-
- /**
- * keeps track of state for field: _showGroupConsensus
- */
- private boolean _has_showGroupConsensus;
-
- /**
- * Field _showConsensusHistogram.
- */
- private boolean _showConsensusHistogram = true;
-
- /**
- * keeps track of state for field: _showConsensusHistogram
- */
- private boolean _has_showConsensusHistogram;
-
- /**
- * Field _showSequenceLogo.
- */
- private boolean _showSequenceLogo = false;
-
- /**
- * keeps track of state for field: _showSequenceLogo
- */
- private boolean _has_showSequenceLogo;
-
- /**
- * Field _normaliseSequenceLogo.
- */
- private boolean _normaliseSequenceLogo = false;
-
- /**
- * keeps track of state for field: _normaliseSequenceLogo
- */
- private boolean _has_normaliseSequenceLogo;
-
- /**
- * Field _ignoreGapsinConsensus.
- */
- private boolean _ignoreGapsinConsensus = true;
-
- /**
- * keeps track of state for field: _ignoreGapsinConsensus
- */
- private boolean _has_ignoreGapsinConsensus;
-
- /**
- * Field _startRes.
- */
- private int _startRes;
-
- /**
- * keeps track of state for field: _startRes
- */
- private boolean _has_startRes;
-
- /**
- * Field _startSeq.
- */
- private int _startSeq;
-
- /**
- * keeps track of state for field: _startSeq
- */
- private boolean _has_startSeq;
-
- /**
- * Field _fontName.
- */
- private java.lang.String _fontName;
-
- /**
- * Field _fontSize.
- */
- private int _fontSize;
-
- /**
- * keeps track of state for field: _fontSize
- */
- private boolean _has_fontSize;
-
- /**
- * Field _fontStyle.
- */
- private int _fontStyle;
-
- /**
- * keeps track of state for field: _fontStyle
- */
- private boolean _has_fontStyle;
-
- /**
- * Field _scaleProteinAsCdna.
- */
- private boolean _scaleProteinAsCdna = true;
-
- /**
- * keeps track of state for field: _scaleProteinAsCdna
- */
- private boolean _has_scaleProteinAsCdna;
-
- /**
- * Field _viewName.
- */
- private java.lang.String _viewName;
-
- /**
- * Field _sequenceSetId.
- */
- private java.lang.String _sequenceSetId;
-
- /**
- * Field _gatheredViews.
- */
- private boolean _gatheredViews;
-
- /**
- * keeps track of state for field: _gatheredViews
- */
- private boolean _has_gatheredViews;
-
- /**
- * Field _textCol1.
- */
- private int _textCol1;
-
- /**
- * keeps track of state for field: _textCol1
- */
- private boolean _has_textCol1;
-
- /**
- * Field _textCol2.
- */
- private int _textCol2;
-
- /**
- * keeps track of state for field: _textCol2
- */
- private boolean _has_textCol2;
-
- /**
- * Field _textColThreshold.
- */
- private int _textColThreshold;
-
- /**
- * keeps track of state for field: _textColThreshold
- */
- private boolean _has_textColThreshold;
-
- /**
- * unique id used by jalview to
- * synchronize
- * between stored and
- * instantiated views
- *
- */
- private java.lang.String _id;
-
- /**
- * The viewport id of this viewport's
- * (cdna/protein) coding complement, if any
- *
- */
- private java.lang.String _complementId;
-
- /**
- * Field _width.
- */
- private int _width;
-
- /**
- * keeps track of state for field: _width
- */
- private boolean _has_width;
-
- /**
- * Field _height.
- */
- private int _height;
-
- /**
- * keeps track of state for field: _height
- */
- private boolean _has_height;
-
- /**
- * Field _xpos.
- */
- private int _xpos;
-
- /**
- * keeps track of state for field: _xpos
- */
- private boolean _has_xpos;
-
- /**
- * Field _ypos.
- */
- private int _ypos;
-
- /**
- * keeps track of state for field: _ypos
- */
- private boolean _has_ypos;
-
- /**
- * Field _annotationColours.
- */
- private jalview.schemabinding.version2.AnnotationColours _annotationColours;
-
- /**
- * Field _hiddenColumnsList.
- */
- private java.util.Vector _hiddenColumnsList;
-
- /**
- * Field _calcIdParamList.
- */
- private java.util.Vector _calcIdParamList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Viewport() {
- super();
- this._hiddenColumnsList = new java.util.Vector();
- this._calcIdParamList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vCalcIdParam
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addCalcIdParam(
- final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
- throws java.lang.IndexOutOfBoundsException {
- this._calcIdParamList.addElement(vCalcIdParam);
- }
-
- /**
- *
- *
- * @param index
- * @param vCalcIdParam
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addCalcIdParam(
- final int index,
- final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
- throws java.lang.IndexOutOfBoundsException {
- this._calcIdParamList.add(index, vCalcIdParam);
- }
-
- /**
- *
- *
- * @param vHiddenColumns
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addHiddenColumns(
- final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
- throws java.lang.IndexOutOfBoundsException {
- this._hiddenColumnsList.addElement(vHiddenColumns);
- }
-
- /**
- *
- *
- * @param index
- * @param vHiddenColumns
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addHiddenColumns(
- final int index,
- final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
- throws java.lang.IndexOutOfBoundsException {
- this._hiddenColumnsList.add(index, vHiddenColumns);
- }
+public class Viewport implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _conservationSelected.
+ */
+ private boolean _conservationSelected;
+
+ /**
+ * keeps track of state for field: _conservationSelected
+ */
+ private boolean _has_conservationSelected;
+
+ /**
+ * Field _pidSelected.
+ */
+ private boolean _pidSelected;
+
+ /**
+ * keeps track of state for field: _pidSelected
+ */
+ private boolean _has_pidSelected;
+
+ /**
+ * Field _bgColour.
+ */
+ private java.lang.String _bgColour;
+
+ /**
+ * Field _consThreshold.
+ */
+ private int _consThreshold;
+
+ /**
+ * keeps track of state for field: _consThreshold
+ */
+ private boolean _has_consThreshold;
+
+ /**
+ * Field _pidThreshold.
+ */
+ private int _pidThreshold;
+
+ /**
+ * keeps track of state for field: _pidThreshold
+ */
+ private boolean _has_pidThreshold;
+
+ /**
+ * Field _title.
+ */
+ private java.lang.String _title;
+
+ /**
+ * Field _showFullId.
+ */
+ private boolean _showFullId;
+
+ /**
+ * keeps track of state for field: _showFullId
+ */
+ private boolean _has_showFullId;
+
+ /**
+ * Field _rightAlignIds.
+ */
+ private boolean _rightAlignIds;
+
+ /**
+ * keeps track of state for field: _rightAlignIds
+ */
+ private boolean _has_rightAlignIds;
+
+ /**
+ * Field _showText.
+ */
+ private boolean _showText;
+
+ /**
+ * keeps track of state for field: _showText
+ */
+ private boolean _has_showText;
+
+ /**
+ * Field _showColourText.
+ */
+ private boolean _showColourText;
+
+ /**
+ * keeps track of state for field: _showColourText
+ */
+ private boolean _has_showColourText;
+
+ /**
+ * Field _showUnconserved.
+ */
+ private boolean _showUnconserved = false;
+
+ /**
+ * keeps track of state for field: _showUnconserved
+ */
+ private boolean _has_showUnconserved;
+
+ /**
+ * Field _showBoxes.
+ */
+ private boolean _showBoxes;
+
+ /**
+ * keeps track of state for field: _showBoxes
+ */
+ private boolean _has_showBoxes;
+
+ /**
+ * Field _wrapAlignment.
+ */
+ private boolean _wrapAlignment;
+
+ /**
+ * keeps track of state for field: _wrapAlignment
+ */
+ private boolean _has_wrapAlignment;
+
+ /**
+ * Field _renderGaps.
+ */
+ private boolean _renderGaps;
+
+ /**
+ * keeps track of state for field: _renderGaps
+ */
+ private boolean _has_renderGaps;
+
+ /**
+ * Field _showSequenceFeatures.
+ */
+ private boolean _showSequenceFeatures;
+
+ /**
+ * keeps track of state for field: _showSequenceFeatures
+ */
+ private boolean _has_showSequenceFeatures;
+
+ /**
+ * Field _showNPfeatureTooltip.
+ */
+ private boolean _showNPfeatureTooltip;
+
+ /**
+ * keeps track of state for field: _showNPfeatureTooltip
+ */
+ private boolean _has_showNPfeatureTooltip;
+
+ /**
+ * Field _showDbRefTooltip.
+ */
+ private boolean _showDbRefTooltip;
+
+ /**
+ * keeps track of state for field: _showDbRefTooltip
+ */
+ private boolean _has_showDbRefTooltip;
+
+ /**
+ * Field _followHighlight.
+ */
+ private boolean _followHighlight = true;
+
+ /**
+ * keeps track of state for field: _followHighlight
+ */
+ private boolean _has_followHighlight;
+
+ /**
+ * Field _followSelection.
+ */
+ private boolean _followSelection = true;
+
+ /**
+ * keeps track of state for field: _followSelection
+ */
+ private boolean _has_followSelection;
+
+ /**
+ * Field _showAnnotation.
+ */
+ private boolean _showAnnotation;
+
+ /**
+ * keeps track of state for field: _showAnnotation
+ */
+ private boolean _has_showAnnotation;
+
+ /**
+ * Field _centreColumnLabels.
+ */
+ private boolean _centreColumnLabels = false;
+
+ /**
+ * keeps track of state for field: _centreColumnLabels
+ */
+ private boolean _has_centreColumnLabels;
+
+ /**
+ * Field _showGroupConservation.
+ */
+ private boolean _showGroupConservation = false;
+
+ /**
+ * keeps track of state for field: _showGroupConservation
+ */
+ private boolean _has_showGroupConservation;
+
+ /**
+ * Field _showGroupConsensus.
+ */
+ private boolean _showGroupConsensus = false;
+
+ /**
+ * keeps track of state for field: _showGroupConsensus
+ */
+ private boolean _has_showGroupConsensus;
+
+ /**
+ * Field _showConsensusHistogram.
+ */
+ private boolean _showConsensusHistogram = true;
+
+ /**
+ * keeps track of state for field: _showConsensusHistogram
+ */
+ private boolean _has_showConsensusHistogram;
+
+ /**
+ * Field _showSequenceLogo.
+ */
+ private boolean _showSequenceLogo = false;
+
+ /**
+ * keeps track of state for field: _showSequenceLogo
+ */
+ private boolean _has_showSequenceLogo;
+
+ /**
+ * Field _normaliseSequenceLogo.
+ */
+ private boolean _normaliseSequenceLogo = false;
+
+ /**
+ * keeps track of state for field: _normaliseSequenceLogo
+ */
+ private boolean _has_normaliseSequenceLogo;
+
+ /**
+ * Field _ignoreGapsinConsensus.
+ */
+ private boolean _ignoreGapsinConsensus = true;
+
+ /**
+ * keeps track of state for field: _ignoreGapsinConsensus
+ */
+ private boolean _has_ignoreGapsinConsensus;
+
+ /**
+ * Field _startRes.
+ */
+ private int _startRes;
+
+ /**
+ * keeps track of state for field: _startRes
+ */
+ private boolean _has_startRes;
+
+ /**
+ * Field _startSeq.
+ */
+ private int _startSeq;
+
+ /**
+ * keeps track of state for field: _startSeq
+ */
+ private boolean _has_startSeq;
+
+ /**
+ * Field _fontName.
+ */
+ private java.lang.String _fontName;
+
+ /**
+ * Field _fontSize.
+ */
+ private int _fontSize;
+
+ /**
+ * keeps track of state for field: _fontSize
+ */
+ private boolean _has_fontSize;
+
+ /**
+ * Field _fontStyle.
+ */
+ private int _fontStyle;
+
+ /**
+ * keeps track of state for field: _fontStyle
+ */
+ private boolean _has_fontStyle;
+
+ /**
+ * Field _scaleProteinAsCdna.
+ */
+ private boolean _scaleProteinAsCdna = true;
+
+ /**
+ * keeps track of state for field: _scaleProteinAsCdna
+ */
+ private boolean _has_scaleProteinAsCdna;
+
+ /**
+ * Field _viewName.
+ */
+ private java.lang.String _viewName;
+
+ /**
+ * Field _sequenceSetId.
+ */
+ private java.lang.String _sequenceSetId;
+
+ /**
+ * Field _gatheredViews.
+ */
+ private boolean _gatheredViews;
+
+ /**
+ * keeps track of state for field: _gatheredViews
+ */
+ private boolean _has_gatheredViews;
+
+ /**
+ * Field _textCol1.
+ */
+ private int _textCol1;
+
+ /**
+ * keeps track of state for field: _textCol1
+ */
+ private boolean _has_textCol1;
+
+ /**
+ * Field _textCol2.
+ */
+ private int _textCol2;
+
+ /**
+ * keeps track of state for field: _textCol2
+ */
+ private boolean _has_textCol2;
+
+ /**
+ * Field _textColThreshold.
+ */
+ private int _textColThreshold;
+
+ /**
+ * keeps track of state for field: _textColThreshold
+ */
+ private boolean _has_textColThreshold;
+
+ /**
+ * unique id used by jalview to synchronize between stored and instantiated
+ * views
+ *
+ */
+ private java.lang.String _id;
+
+ /**
+ * The viewport id of this viewport's (cdna/protein) coding complement, if any
+ *
+ */
+ private java.lang.String _complementId;
+
+ /**
+ * Field _width.
+ */
+ private int _width;
+
+ /**
+ * keeps track of state for field: _width
+ */
+ private boolean _has_width;
+
+ /**
+ * Field _height.
+ */
+ private int _height;
+
+ /**
+ * keeps track of state for field: _height
+ */
+ private boolean _has_height;
+
+ /**
+ * Field _xpos.
+ */
+ private int _xpos;
+
+ /**
+ * keeps track of state for field: _xpos
+ */
+ private boolean _has_xpos;
+
+ /**
+ * Field _ypos.
+ */
+ private int _ypos;
+
+ /**
+ * keeps track of state for field: _ypos
+ */
+ private boolean _has_ypos;
+
+ /**
+ * Field _annotationColours.
+ */
+ private jalview.schemabinding.version2.AnnotationColours _annotationColours;
+
+ /**
+ * Field _hiddenColumnsList.
+ */
+ private java.util.Vector _hiddenColumnsList;
+
+ /**
+ * Field _calcIdParamList.
+ */
+ private java.util.Vector _calcIdParamList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Viewport()
+ {
+ super();
+ this._hiddenColumnsList = new java.util.Vector();
+ this._calcIdParamList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vCalcIdParam
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addCalcIdParam(
+ final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._calcIdParamList.addElement(vCalcIdParam);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vCalcIdParam
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addCalcIdParam(final int index,
+ final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._calcIdParamList.add(index, vCalcIdParam);
+ }
+
+ /**
+ *
+ *
+ * @param vHiddenColumns
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addHiddenColumns(
+ final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._hiddenColumnsList.addElement(vHiddenColumns);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vHiddenColumns
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addHiddenColumns(final int index,
+ final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._hiddenColumnsList.add(index, vHiddenColumns);
+ }
+
+ /**
+ */
+ public void deleteCentreColumnLabels()
+ {
+ this._has_centreColumnLabels = false;
+ }
+
+ /**
+ */
+ public void deleteConsThreshold()
+ {
+ this._has_consThreshold = false;
+ }
+
+ /**
+ */
+ public void deleteConservationSelected()
+ {
+ this._has_conservationSelected = false;
+ }
+
+ /**
+ */
+ public void deleteFollowHighlight()
+ {
+ this._has_followHighlight = false;
+ }
+
+ /**
+ */
+ public void deleteFollowSelection()
+ {
+ this._has_followSelection = false;
+ }
+
+ /**
+ */
+ public void deleteFontSize()
+ {
+ this._has_fontSize = false;
+ }
+
+ /**
+ */
+ public void deleteFontStyle()
+ {
+ this._has_fontStyle = false;
+ }
+
+ /**
+ */
+ public void deleteGatheredViews()
+ {
+ this._has_gatheredViews = false;
+ }
+
+ /**
+ */
+ public void deleteHeight()
+ {
+ this._has_height = false;
+ }
- /**
+ /**
*/
- public void deleteCentreColumnLabels(
- ) {
- this._has_centreColumnLabels= false;
- }
-
- /**
- */
- public void deleteConsThreshold(
- ) {
- this._has_consThreshold= false;
- }
-
- /**
- */
- public void deleteConservationSelected(
- ) {
- this._has_conservationSelected= false;
- }
-
- /**
- */
- public void deleteFollowHighlight(
- ) {
- this._has_followHighlight= false;
- }
-
- /**
- */
- public void deleteFollowSelection(
- ) {
- this._has_followSelection= false;
- }
-
- /**
- */
- public void deleteFontSize(
- ) {
- this._has_fontSize= false;
- }
-
- /**
- */
- public void deleteFontStyle(
- ) {
- this._has_fontStyle= false;
- }
-
- /**
- */
- public void deleteGatheredViews(
- ) {
- this._has_gatheredViews= false;
- }
-
- /**
- */
- public void deleteHeight(
- ) {
- this._has_height= false;
- }
-
- /**
- */
- public void deleteIgnoreGapsinConsensus(
- ) {
- this._has_ignoreGapsinConsensus= false;
- }
-
- /**
- */
- public void deleteNormaliseSequenceLogo(
- ) {
- this._has_normaliseSequenceLogo= false;
- }
-
- /**
- */
- public void deletePidSelected(
- ) {
- this._has_pidSelected= false;
- }
-
- /**
- */
- public void deletePidThreshold(
- ) {
- this._has_pidThreshold= false;
- }
-
- /**
- */
- public void deleteRenderGaps(
- ) {
- this._has_renderGaps= false;
- }
+ public void deleteIgnoreGapsinConsensus()
+ {
+ this._has_ignoreGapsinConsensus = false;
+ }
- /**
+ /**
*/
- public void deleteRightAlignIds(
- ) {
- this._has_rightAlignIds= false;
- }
-
- /**
- */
- public void deleteScaleProteinAsCdna(
- ) {
- this._has_scaleProteinAsCdna= false;
- }
+ public void deleteNormaliseSequenceLogo()
+ {
+ this._has_normaliseSequenceLogo = false;
+ }
- /**
+ /**
*/
- public void deleteShowAnnotation(
- ) {
- this._has_showAnnotation= false;
- }
+ public void deletePidSelected()
+ {
+ this._has_pidSelected = false;
+ }
- /**
+ /**
*/
- public void deleteShowBoxes(
- ) {
- this._has_showBoxes= false;
- }
+ public void deletePidThreshold()
+ {
+ this._has_pidThreshold = false;
+ }
- /**
+ /**
*/
- public void deleteShowColourText(
- ) {
- this._has_showColourText= false;
- }
+ public void deleteRenderGaps()
+ {
+ this._has_renderGaps = false;
+ }
- /**
+ /**
*/
- public void deleteShowConsensusHistogram(
- ) {
- this._has_showConsensusHistogram= false;
- }
+ public void deleteRightAlignIds()
+ {
+ this._has_rightAlignIds = false;
+ }
- /**
+ /**
*/
- public void deleteShowDbRefTooltip(
- ) {
- this._has_showDbRefTooltip= false;
- }
+ public void deleteScaleProteinAsCdna()
+ {
+ this._has_scaleProteinAsCdna = false;
+ }
- /**
+ /**
*/
- public void deleteShowFullId(
- ) {
- this._has_showFullId= false;
- }
+ public void deleteShowAnnotation()
+ {
+ this._has_showAnnotation = false;
+ }
- /**
+ /**
*/
- public void deleteShowGroupConsensus(
- ) {
- this._has_showGroupConsensus= false;
- }
+ public void deleteShowBoxes()
+ {
+ this._has_showBoxes = false;
+ }
- /**
+ /**
*/
- public void deleteShowGroupConservation(
- ) {
- this._has_showGroupConservation= false;
- }
+ public void deleteShowColourText()
+ {
+ this._has_showColourText = false;
+ }
- /**
+ /**
*/
- public void deleteShowNPfeatureTooltip(
- ) {
- this._has_showNPfeatureTooltip= false;
- }
+ public void deleteShowConsensusHistogram()
+ {
+ this._has_showConsensusHistogram = false;
+ }
- /**
+ /**
*/
- public void deleteShowSequenceFeatures(
- ) {
- this._has_showSequenceFeatures= false;
- }
+ public void deleteShowDbRefTooltip()
+ {
+ this._has_showDbRefTooltip = false;
+ }
- /**
+ /**
*/
- public void deleteShowSequenceLogo(
- ) {
- this._has_showSequenceLogo= false;
- }
+ public void deleteShowFullId()
+ {
+ this._has_showFullId = false;
+ }
- /**
+ /**
*/
- public void deleteShowText(
- ) {
- this._has_showText= false;
- }
+ public void deleteShowGroupConsensus()
+ {
+ this._has_showGroupConsensus = false;
+ }
- /**
+ /**
*/
- public void deleteShowUnconserved(
- ) {
- this._has_showUnconserved= false;
- }
+ public void deleteShowGroupConservation()
+ {
+ this._has_showGroupConservation = false;
+ }
- /**
+ /**
*/
- public void deleteStartRes(
- ) {
- this._has_startRes= false;
- }
+ public void deleteShowNPfeatureTooltip()
+ {
+ this._has_showNPfeatureTooltip = false;
+ }
- /**
+ /**
*/
- public void deleteStartSeq(
- ) {
- this._has_startSeq= false;
- }
+ public void deleteShowSequenceFeatures()
+ {
+ this._has_showSequenceFeatures = false;
+ }
- /**
+ /**
*/
- public void deleteTextCol1(
- ) {
- this._has_textCol1= false;
- }
+ public void deleteShowSequenceLogo()
+ {
+ this._has_showSequenceLogo = false;
+ }
- /**
+ /**
*/
- public void deleteTextCol2(
- ) {
- this._has_textCol2= false;
- }
+ public void deleteShowText()
+ {
+ this._has_showText = false;
+ }
- /**
+ /**
*/
- public void deleteTextColThreshold(
- ) {
- this._has_textColThreshold= false;
- }
+ public void deleteShowUnconserved()
+ {
+ this._has_showUnconserved = false;
+ }
- /**
+ /**
*/
- public void deleteWidth(
- ) {
- this._has_width= false;
- }
-
- /**
- */
- public void deleteWrapAlignment(
- ) {
- this._has_wrapAlignment= false;
- }
-
- /**
- */
- public void deleteXpos(
- ) {
- this._has_xpos= false;
- }
-
- /**
- */
- public void deleteYpos(
- ) {
- this._has_ypos= false;
- }
-
- /**
- * Method enumerateCalcIdParam.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.CalcIdParam elements
- */
- public java.util.Enumeration enumerateCalcIdParam(
- ) {
- return this._calcIdParamList.elements();
- }
-
- /**
- * Method enumerateHiddenColumns.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.HiddenColumns elements
- */
- public java.util.Enumeration enumerateHiddenColumns(
- ) {
- return this._hiddenColumnsList.elements();
- }
-
- /**
- * Returns the value of field 'annotationColours'.
- *
- * @return the value of field 'AnnotationColours'.
- */
- public jalview.schemabinding.version2.AnnotationColours getAnnotationColours(
- ) {
- return this._annotationColours;
- }
-
- /**
- * Returns the value of field 'bgColour'.
- *
- * @return the value of field 'BgColour'.
- */
- public java.lang.String getBgColour(
- ) {
- return this._bgColour;
- }
-
- /**
- * Method getCalcIdParam.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.CalcIdParam at the given index
- */
- public jalview.schemabinding.version2.CalcIdParam getCalcIdParam(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._calcIdParamList.size()) {
- throw new IndexOutOfBoundsException("getCalcIdParam: Index value '" + index + "' not in range [0.." + (this._calcIdParamList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.CalcIdParam) _calcIdParamList.get(index);
- }
-
- /**
- * Method getCalcIdParam.Returns the contents of the collection
- * in an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.CalcIdParam[] getCalcIdParam(
- ) {
- jalview.schemabinding.version2.CalcIdParam[] array = new jalview.schemabinding.version2.CalcIdParam[0];
- return (jalview.schemabinding.version2.CalcIdParam[]) this._calcIdParamList.toArray(array);
- }
-
- /**
- * Method getCalcIdParamCount.
- *
- * @return the size of this collection
- */
- public int getCalcIdParamCount(
- ) {
- return this._calcIdParamList.size();
- }
-
- /**
- * Returns the value of field 'centreColumnLabels'.
- *
- * @return the value of field 'CentreColumnLabels'.
- */
- public boolean getCentreColumnLabels(
- ) {
- return this._centreColumnLabels;
- }
-
- /**
- * Returns the value of field 'complementId'. The field
- * 'complementId' has the following description: The viewport
- * id of this viewport's
- * (cdna/protein) coding complement, if any
- *
- *
- * @return the value of field 'ComplementId'.
- */
- public java.lang.String getComplementId(
- ) {
- return this._complementId;
- }
-
- /**
- * Returns the value of field 'consThreshold'.
- *
- * @return the value of field 'ConsThreshold'.
- */
- public int getConsThreshold(
- ) {
- return this._consThreshold;
- }
-
- /**
- * Returns the value of field 'conservationSelected'.
- *
- * @return the value of field 'ConservationSelected'.
- */
- public boolean getConservationSelected(
- ) {
- return this._conservationSelected;
- }
-
- /**
- * Returns the value of field 'followHighlight'.
- *
- * @return the value of field 'FollowHighlight'.
- */
- public boolean getFollowHighlight(
- ) {
- return this._followHighlight;
- }
-
- /**
- * Returns the value of field 'followSelection'.
- *
- * @return the value of field 'FollowSelection'.
- */
- public boolean getFollowSelection(
- ) {
- return this._followSelection;
- }
-
- /**
- * Returns the value of field 'fontName'.
- *
- * @return the value of field 'FontName'.
- */
- public java.lang.String getFontName(
- ) {
- return this._fontName;
- }
-
- /**
- * Returns the value of field 'fontSize'.
- *
- * @return the value of field 'FontSize'.
- */
- public int getFontSize(
- ) {
- return this._fontSize;
- }
-
- /**
- * Returns the value of field 'fontStyle'.
- *
- * @return the value of field 'FontStyle'.
- */
- public int getFontStyle(
- ) {
- return this._fontStyle;
- }
-
- /**
- * Returns the value of field 'gatheredViews'.
- *
- * @return the value of field 'GatheredViews'.
- */
- public boolean getGatheredViews(
- ) {
- return this._gatheredViews;
- }
-
- /**
- * Returns the value of field 'height'.
- *
- * @return the value of field 'Height'.
- */
- public int getHeight(
- ) {
- return this._height;
- }
-
- /**
- * Method getHiddenColumns.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.HiddenColumns at the given
- * index
- */
- public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._hiddenColumnsList.size()) {
- throw new IndexOutOfBoundsException("getHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.get(index);
- }
-
- /**
- * Method getHiddenColumns.Returns the contents of the
- * collection in an Array. <p>Note: Just in case the
- * collection contents are changing in another thread, we pass
- * a 0-length Array of the correct type into the API call.
- * This way we <i>know</i> that the Array returned is of
- * exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns(
- ) {
- jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
- return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList.toArray(array);
- }
-
- /**
- * Method getHiddenColumnsCount.
- *
- * @return the size of this collection
- */
- public int getHiddenColumnsCount(
- ) {
- return this._hiddenColumnsList.size();
- }
-
- /**
- * Returns the value of field 'id'. The field 'id' has the
- * following description: unique id used by jalview to
- * synchronize
- * between stored and
- * instantiated views
- *
- *
- * @return the value of field 'Id'.
- */
- public java.lang.String getId(
- ) {
- return this._id;
- }
-
- /**
- * Returns the value of field 'ignoreGapsinConsensus'.
- *
- * @return the value of field 'IgnoreGapsinConsensus'.
- */
- public boolean getIgnoreGapsinConsensus(
- ) {
- return this._ignoreGapsinConsensus;
- }
-
- /**
- * Returns the value of field 'normaliseSequenceLogo'.
- *
- * @return the value of field 'NormaliseSequenceLogo'.
- */
- public boolean getNormaliseSequenceLogo(
- ) {
- return this._normaliseSequenceLogo;
- }
-
- /**
- * Returns the value of field 'pidSelected'.
- *
- * @return the value of field 'PidSelected'.
- */
- public boolean getPidSelected(
- ) {
- return this._pidSelected;
- }
-
- /**
- * Returns the value of field 'pidThreshold'.
- *
- * @return the value of field 'PidThreshold'.
- */
- public int getPidThreshold(
- ) {
- return this._pidThreshold;
- }
-
- /**
- * Returns the value of field 'renderGaps'.
- *
- * @return the value of field 'RenderGaps'.
- */
- public boolean getRenderGaps(
- ) {
- return this._renderGaps;
- }
-
- /**
- * Returns the value of field 'rightAlignIds'.
- *
- * @return the value of field 'RightAlignIds'.
- */
- public boolean getRightAlignIds(
- ) {
- return this._rightAlignIds;
- }
-
- /**
- * Returns the value of field 'scaleProteinAsCdna'.
- *
- * @return the value of field 'ScaleProteinAsCdna'.
- */
- public boolean getScaleProteinAsCdna(
- ) {
- return this._scaleProteinAsCdna;
- }
-
- /**
- * Returns the value of field 'sequenceSetId'.
- *
- * @return the value of field 'SequenceSetId'.
- */
- public java.lang.String getSequenceSetId(
- ) {
- return this._sequenceSetId;
- }
-
- /**
- * Returns the value of field 'showAnnotation'.
- *
- * @return the value of field 'ShowAnnotation'.
- */
- public boolean getShowAnnotation(
- ) {
- return this._showAnnotation;
- }
-
- /**
- * Returns the value of field 'showBoxes'.
- *
- * @return the value of field 'ShowBoxes'.
- */
- public boolean getShowBoxes(
- ) {
- return this._showBoxes;
- }
-
- /**
- * Returns the value of field 'showColourText'.
- *
- * @return the value of field 'ShowColourText'.
- */
- public boolean getShowColourText(
- ) {
- return this._showColourText;
- }
-
- /**
- * Returns the value of field 'showConsensusHistogram'.
- *
- * @return the value of field 'ShowConsensusHistogram'.
- */
- public boolean getShowConsensusHistogram(
- ) {
- return this._showConsensusHistogram;
- }
-
- /**
- * Returns the value of field 'showDbRefTooltip'.
- *
- * @return the value of field 'ShowDbRefTooltip'.
- */
- public boolean getShowDbRefTooltip(
- ) {
- return this._showDbRefTooltip;
- }
-
- /**
- * Returns the value of field 'showFullId'.
- *
- * @return the value of field 'ShowFullId'.
- */
- public boolean getShowFullId(
- ) {
- return this._showFullId;
- }
-
- /**
- * Returns the value of field 'showGroupConsensus'.
- *
- * @return the value of field 'ShowGroupConsensus'.
- */
- public boolean getShowGroupConsensus(
- ) {
- return this._showGroupConsensus;
- }
-
- /**
- * Returns the value of field 'showGroupConservation'.
- *
- * @return the value of field 'ShowGroupConservation'.
- */
- public boolean getShowGroupConservation(
- ) {
- return this._showGroupConservation;
- }
-
- /**
- * Returns the value of field 'showNPfeatureTooltip'.
- *
- * @return the value of field 'ShowNPfeatureTooltip'.
- */
- public boolean getShowNPfeatureTooltip(
- ) {
- return this._showNPfeatureTooltip;
- }
-
- /**
- * Returns the value of field 'showSequenceFeatures'.
- *
- * @return the value of field 'ShowSequenceFeatures'.
- */
- public boolean getShowSequenceFeatures(
- ) {
- return this._showSequenceFeatures;
- }
-
- /**
- * Returns the value of field 'showSequenceLogo'.
- *
- * @return the value of field 'ShowSequenceLogo'.
- */
- public boolean getShowSequenceLogo(
- ) {
- return this._showSequenceLogo;
- }
-
- /**
- * Returns the value of field 'showText'.
- *
- * @return the value of field 'ShowText'.
- */
- public boolean getShowText(
- ) {
- return this._showText;
- }
-
- /**
- * Returns the value of field 'showUnconserved'.
- *
- * @return the value of field 'ShowUnconserved'.
- */
- public boolean getShowUnconserved(
- ) {
- return this._showUnconserved;
- }
-
- /**
- * Returns the value of field 'startRes'.
- *
- * @return the value of field 'StartRes'.
- */
- public int getStartRes(
- ) {
- return this._startRes;
- }
-
- /**
- * Returns the value of field 'startSeq'.
- *
- * @return the value of field 'StartSeq'.
- */
- public int getStartSeq(
- ) {
- return this._startSeq;
- }
-
- /**
- * Returns the value of field 'textCol1'.
- *
- * @return the value of field 'TextCol1'.
- */
- public int getTextCol1(
- ) {
- return this._textCol1;
- }
-
- /**
- * Returns the value of field 'textCol2'.
- *
- * @return the value of field 'TextCol2'.
- */
- public int getTextCol2(
- ) {
- return this._textCol2;
- }
-
- /**
- * Returns the value of field 'textColThreshold'.
- *
- * @return the value of field 'TextColThreshold'.
- */
- public int getTextColThreshold(
- ) {
- return this._textColThreshold;
- }
-
- /**
- * Returns the value of field 'title'.
- *
- * @return the value of field 'Title'.
- */
- public java.lang.String getTitle(
- ) {
- return this._title;
- }
-
- /**
- * Returns the value of field 'viewName'.
- *
- * @return the value of field 'ViewName'.
- */
- public java.lang.String getViewName(
- ) {
- return this._viewName;
- }
-
- /**
- * Returns the value of field 'width'.
- *
- * @return the value of field 'Width'.
- */
- public int getWidth(
- ) {
- return this._width;
- }
-
- /**
- * Returns the value of field 'wrapAlignment'.
- *
- * @return the value of field 'WrapAlignment'.
- */
- public boolean getWrapAlignment(
- ) {
- return this._wrapAlignment;
- }
-
- /**
- * Returns the value of field 'xpos'.
- *
- * @return the value of field 'Xpos'.
- */
- public int getXpos(
- ) {
- return this._xpos;
- }
-
- /**
- * Returns the value of field 'ypos'.
- *
- * @return the value of field 'Ypos'.
- */
- public int getYpos(
- ) {
- return this._ypos;
- }
-
- /**
- * Method hasCentreColumnLabels.
- *
- * @return true if at least one CentreColumnLabels has been adde
- */
- public boolean hasCentreColumnLabels(
- ) {
- return this._has_centreColumnLabels;
- }
-
- /**
- * Method hasConsThreshold.
- *
- * @return true if at least one ConsThreshold has been added
- */
- public boolean hasConsThreshold(
- ) {
- return this._has_consThreshold;
- }
-
- /**
- * Method hasConservationSelected.
- *
- * @return true if at least one ConservationSelected has been
- * added
- */
- public boolean hasConservationSelected(
- ) {
- return this._has_conservationSelected;
- }
-
- /**
- * Method hasFollowHighlight.
- *
- * @return true if at least one FollowHighlight has been added
- */
- public boolean hasFollowHighlight(
- ) {
- return this._has_followHighlight;
- }
-
- /**
- * Method hasFollowSelection.
- *
- * @return true if at least one FollowSelection has been added
- */
- public boolean hasFollowSelection(
- ) {
- return this._has_followSelection;
- }
-
- /**
- * Method hasFontSize.
- *
- * @return true if at least one FontSize has been added
- */
- public boolean hasFontSize(
- ) {
- return this._has_fontSize;
- }
-
- /**
- * Method hasFontStyle.
- *
- * @return true if at least one FontStyle has been added
- */
- public boolean hasFontStyle(
- ) {
- return this._has_fontStyle;
- }
-
- /**
- * Method hasGatheredViews.
- *
- * @return true if at least one GatheredViews has been added
- */
- public boolean hasGatheredViews(
- ) {
- return this._has_gatheredViews;
- }
-
- /**
- * Method hasHeight.
- *
- * @return true if at least one Height has been added
- */
- public boolean hasHeight(
- ) {
- return this._has_height;
- }
-
- /**
- * Method hasIgnoreGapsinConsensus.
- *
- * @return true if at least one IgnoreGapsinConsensus has been
- * added
- */
- public boolean hasIgnoreGapsinConsensus(
- ) {
- return this._has_ignoreGapsinConsensus;
- }
-
- /**
- * Method hasNormaliseSequenceLogo.
- *
- * @return true if at least one NormaliseSequenceLogo has been
- * added
- */
- public boolean hasNormaliseSequenceLogo(
- ) {
- return this._has_normaliseSequenceLogo;
- }
-
- /**
- * Method hasPidSelected.
- *
- * @return true if at least one PidSelected has been added
- */
- public boolean hasPidSelected(
- ) {
- return this._has_pidSelected;
- }
-
- /**
- * Method hasPidThreshold.
- *
- * @return true if at least one PidThreshold has been added
- */
- public boolean hasPidThreshold(
- ) {
- return this._has_pidThreshold;
- }
-
- /**
- * Method hasRenderGaps.
- *
- * @return true if at least one RenderGaps has been added
- */
- public boolean hasRenderGaps(
- ) {
- return this._has_renderGaps;
- }
-
- /**
- * Method hasRightAlignIds.
- *
- * @return true if at least one RightAlignIds has been added
- */
- public boolean hasRightAlignIds(
- ) {
- return this._has_rightAlignIds;
- }
-
- /**
- * Method hasScaleProteinAsCdna.
- *
- * @return true if at least one ScaleProteinAsCdna has been adde
- */
- public boolean hasScaleProteinAsCdna(
- ) {
- return this._has_scaleProteinAsCdna;
- }
-
- /**
- * Method hasShowAnnotation.
- *
- * @return true if at least one ShowAnnotation has been added
- */
- public boolean hasShowAnnotation(
- ) {
- return this._has_showAnnotation;
- }
-
- /**
- * Method hasShowBoxes.
- *
- * @return true if at least one ShowBoxes has been added
- */
- public boolean hasShowBoxes(
- ) {
- return this._has_showBoxes;
- }
-
- /**
- * Method hasShowColourText.
- *
- * @return true if at least one ShowColourText has been added
- */
- public boolean hasShowColourText(
- ) {
- return this._has_showColourText;
- }
-
- /**
- * Method hasShowConsensusHistogram.
- *
- * @return true if at least one ShowConsensusHistogram has been
- * added
- */
- public boolean hasShowConsensusHistogram(
- ) {
- return this._has_showConsensusHistogram;
- }
-
- /**
- * Method hasShowDbRefTooltip.
- *
- * @return true if at least one ShowDbRefTooltip has been added
- */
- public boolean hasShowDbRefTooltip(
- ) {
- return this._has_showDbRefTooltip;
- }
-
- /**
- * Method hasShowFullId.
- *
- * @return true if at least one ShowFullId has been added
- */
- public boolean hasShowFullId(
- ) {
- return this._has_showFullId;
- }
-
- /**
- * Method hasShowGroupConsensus.
- *
- * @return true if at least one ShowGroupConsensus has been adde
- */
- public boolean hasShowGroupConsensus(
- ) {
- return this._has_showGroupConsensus;
- }
-
- /**
- * Method hasShowGroupConservation.
- *
- * @return true if at least one ShowGroupConservation has been
- * added
- */
- public boolean hasShowGroupConservation(
- ) {
- return this._has_showGroupConservation;
- }
-
- /**
- * Method hasShowNPfeatureTooltip.
- *
- * @return true if at least one ShowNPfeatureTooltip has been
- * added
- */
- public boolean hasShowNPfeatureTooltip(
- ) {
- return this._has_showNPfeatureTooltip;
- }
-
- /**
- * Method hasShowSequenceFeatures.
- *
- * @return true if at least one ShowSequenceFeatures has been
- * added
- */
- public boolean hasShowSequenceFeatures(
- ) {
- return this._has_showSequenceFeatures;
- }
-
- /**
- * Method hasShowSequenceLogo.
- *
- * @return true if at least one ShowSequenceLogo has been added
- */
- public boolean hasShowSequenceLogo(
- ) {
- return this._has_showSequenceLogo;
- }
-
- /**
- * Method hasShowText.
- *
- * @return true if at least one ShowText has been added
- */
- public boolean hasShowText(
- ) {
- return this._has_showText;
- }
-
- /**
- * Method hasShowUnconserved.
- *
- * @return true if at least one ShowUnconserved has been added
- */
- public boolean hasShowUnconserved(
- ) {
- return this._has_showUnconserved;
- }
-
- /**
- * Method hasStartRes.
- *
- * @return true if at least one StartRes has been added
- */
- public boolean hasStartRes(
- ) {
- return this._has_startRes;
- }
-
- /**
- * Method hasStartSeq.
- *
- * @return true if at least one StartSeq has been added
- */
- public boolean hasStartSeq(
- ) {
- return this._has_startSeq;
- }
-
- /**
- * Method hasTextCol1.
- *
- * @return true if at least one TextCol1 has been added
- */
- public boolean hasTextCol1(
- ) {
- return this._has_textCol1;
- }
-
- /**
- * Method hasTextCol2.
- *
- * @return true if at least one TextCol2 has been added
- */
- public boolean hasTextCol2(
- ) {
- return this._has_textCol2;
- }
-
- /**
- * Method hasTextColThreshold.
- *
- * @return true if at least one TextColThreshold has been added
- */
- public boolean hasTextColThreshold(
- ) {
- return this._has_textColThreshold;
- }
-
- /**
- * Method hasWidth.
- *
- * @return true if at least one Width has been added
- */
- public boolean hasWidth(
- ) {
- return this._has_width;
- }
-
- /**
- * Method hasWrapAlignment.
- *
- * @return true if at least one WrapAlignment has been added
- */
- public boolean hasWrapAlignment(
- ) {
- return this._has_wrapAlignment;
- }
-
- /**
- * Method hasXpos.
- *
- * @return true if at least one Xpos has been added
- */
- public boolean hasXpos(
- ) {
- return this._has_xpos;
- }
-
- /**
- * Method hasYpos.
- *
- * @return true if at least one Ypos has been added
- */
- public boolean hasYpos(
- ) {
- return this._has_ypos;
- }
-
- /**
- * Returns the value of field 'centreColumnLabels'.
- *
- * @return the value of field 'CentreColumnLabels'.
- */
- public boolean isCentreColumnLabels(
- ) {
- return this._centreColumnLabels;
- }
-
- /**
- * Returns the value of field 'conservationSelected'.
- *
- * @return the value of field 'ConservationSelected'.
- */
- public boolean isConservationSelected(
- ) {
- return this._conservationSelected;
- }
-
- /**
- * Returns the value of field 'followHighlight'.
- *
- * @return the value of field 'FollowHighlight'.
- */
- public boolean isFollowHighlight(
- ) {
- return this._followHighlight;
- }
-
- /**
- * Returns the value of field 'followSelection'.
- *
- * @return the value of field 'FollowSelection'.
- */
- public boolean isFollowSelection(
- ) {
- return this._followSelection;
- }
-
- /**
- * Returns the value of field 'gatheredViews'.
- *
- * @return the value of field 'GatheredViews'.
- */
- public boolean isGatheredViews(
- ) {
- return this._gatheredViews;
- }
-
- /**
- * Returns the value of field 'ignoreGapsinConsensus'.
- *
- * @return the value of field 'IgnoreGapsinConsensus'.
- */
- public boolean isIgnoreGapsinConsensus(
- ) {
- return this._ignoreGapsinConsensus;
- }
-
- /**
- * Returns the value of field 'normaliseSequenceLogo'.
- *
- * @return the value of field 'NormaliseSequenceLogo'.
- */
- public boolean isNormaliseSequenceLogo(
- ) {
- return this._normaliseSequenceLogo;
- }
-
- /**
- * Returns the value of field 'pidSelected'.
- *
- * @return the value of field 'PidSelected'.
- */
- public boolean isPidSelected(
- ) {
- return this._pidSelected;
- }
-
- /**
- * Returns the value of field 'renderGaps'.
- *
- * @return the value of field 'RenderGaps'.
- */
- public boolean isRenderGaps(
- ) {
- return this._renderGaps;
- }
-
- /**
- * Returns the value of field 'rightAlignIds'.
- *
- * @return the value of field 'RightAlignIds'.
- */
- public boolean isRightAlignIds(
- ) {
- return this._rightAlignIds;
- }
-
- /**
- * Returns the value of field 'scaleProteinAsCdna'.
- *
- * @return the value of field 'ScaleProteinAsCdna'.
- */
- public boolean isScaleProteinAsCdna(
- ) {
- return this._scaleProteinAsCdna;
- }
-
- /**
- * Returns the value of field 'showAnnotation'.
- *
- * @return the value of field 'ShowAnnotation'.
- */
- public boolean isShowAnnotation(
- ) {
- return this._showAnnotation;
- }
-
- /**
- * Returns the value of field 'showBoxes'.
- *
- * @return the value of field 'ShowBoxes'.
- */
- public boolean isShowBoxes(
- ) {
- return this._showBoxes;
- }
-
- /**
- * Returns the value of field 'showColourText'.
- *
- * @return the value of field 'ShowColourText'.
- */
- public boolean isShowColourText(
- ) {
- return this._showColourText;
- }
-
- /**
- * Returns the value of field 'showConsensusHistogram'.
- *
- * @return the value of field 'ShowConsensusHistogram'.
- */
- public boolean isShowConsensusHistogram(
- ) {
- return this._showConsensusHistogram;
- }
-
- /**
- * Returns the value of field 'showDbRefTooltip'.
- *
- * @return the value of field 'ShowDbRefTooltip'.
- */
- public boolean isShowDbRefTooltip(
- ) {
- return this._showDbRefTooltip;
- }
-
- /**
- * Returns the value of field 'showFullId'.
- *
- * @return the value of field 'ShowFullId'.
- */
- public boolean isShowFullId(
- ) {
- return this._showFullId;
- }
-
- /**
- * Returns the value of field 'showGroupConsensus'.
- *
- * @return the value of field 'ShowGroupConsensus'.
- */
- public boolean isShowGroupConsensus(
- ) {
- return this._showGroupConsensus;
- }
-
- /**
- * Returns the value of field 'showGroupConservation'.
- *
- * @return the value of field 'ShowGroupConservation'.
- */
- public boolean isShowGroupConservation(
- ) {
- return this._showGroupConservation;
- }
-
- /**
- * Returns the value of field 'showNPfeatureTooltip'.
- *
- * @return the value of field 'ShowNPfeatureTooltip'.
- */
- public boolean isShowNPfeatureTooltip(
- ) {
- return this._showNPfeatureTooltip;
- }
-
- /**
- * Returns the value of field 'showSequenceFeatures'.
- *
- * @return the value of field 'ShowSequenceFeatures'.
- */
- public boolean isShowSequenceFeatures(
- ) {
- return this._showSequenceFeatures;
- }
-
- /**
- * Returns the value of field 'showSequenceLogo'.
- *
- * @return the value of field 'ShowSequenceLogo'.
- */
- public boolean isShowSequenceLogo(
- ) {
- return this._showSequenceLogo;
- }
-
- /**
- * Returns the value of field 'showText'.
- *
- * @return the value of field 'ShowText'.
- */
- public boolean isShowText(
- ) {
- return this._showText;
- }
-
- /**
- * Returns the value of field 'showUnconserved'.
- *
- * @return the value of field 'ShowUnconserved'.
- */
- public boolean isShowUnconserved(
- ) {
- return this._showUnconserved;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- * Returns the value of field 'wrapAlignment'.
- *
- * @return the value of field 'WrapAlignment'.
- */
- public boolean isWrapAlignment(
- ) {
- return this._wrapAlignment;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllCalcIdParam(
- ) {
- this._calcIdParamList.clear();
- }
-
- /**
- */
- public void removeAllHiddenColumns(
- ) {
- this._hiddenColumnsList.clear();
- }
-
- /**
- * Method removeCalcIdParam.
- *
- * @param vCalcIdParam
- * @return true if the object was removed from the collection.
- */
- public boolean removeCalcIdParam(
- final jalview.schemabinding.version2.CalcIdParam vCalcIdParam) {
- boolean removed = _calcIdParamList.remove(vCalcIdParam);
- return removed;
- }
-
- /**
- * Method removeCalcIdParamAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.CalcIdParam removeCalcIdParamAt(
- final int index) {
- java.lang.Object obj = this._calcIdParamList.remove(index);
- return (jalview.schemabinding.version2.CalcIdParam) obj;
- }
-
- /**
- * Method removeHiddenColumns.
- *
- * @param vHiddenColumns
- * @return true if the object was removed from the collection.
- */
- public boolean removeHiddenColumns(
- final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) {
- boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
- return removed;
- }
-
- /**
- * Method removeHiddenColumnsAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
- final int index) {
- java.lang.Object obj = this._hiddenColumnsList.remove(index);
- return (jalview.schemabinding.version2.HiddenColumns) obj;
- }
-
- /**
- * Sets the value of field 'annotationColours'.
- *
- * @param annotationColours the value of field
- * 'annotationColours'.
- */
- public void setAnnotationColours(
- final jalview.schemabinding.version2.AnnotationColours annotationColours) {
- this._annotationColours = annotationColours;
- }
-
- /**
- * Sets the value of field 'bgColour'.
- *
- * @param bgColour the value of field 'bgColour'.
- */
- public void setBgColour(
- final java.lang.String bgColour) {
- this._bgColour = bgColour;
- }
-
- /**
- *
- *
- * @param index
- * @param vCalcIdParam
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setCalcIdParam(
- final int index,
- final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._calcIdParamList.size()) {
- throw new IndexOutOfBoundsException("setCalcIdParam: Index value '" + index + "' not in range [0.." + (this._calcIdParamList.size() - 1) + "]");
- }
-
- this._calcIdParamList.set(index, vCalcIdParam);
- }
-
- /**
- *
- *
- * @param vCalcIdParamArray
- */
- public void setCalcIdParam(
- final jalview.schemabinding.version2.CalcIdParam[] vCalcIdParamArray) {
- //-- copy array
- _calcIdParamList.clear();
-
- for (int i = 0; i < vCalcIdParamArray.length; i++) {
- this._calcIdParamList.add(vCalcIdParamArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'centreColumnLabels'.
- *
- * @param centreColumnLabels the value of field
- * 'centreColumnLabels'.
- */
- public void setCentreColumnLabels(
- final boolean centreColumnLabels) {
- this._centreColumnLabels = centreColumnLabels;
- this._has_centreColumnLabels = true;
- }
-
- /**
- * Sets the value of field 'complementId'. The field
- * 'complementId' has the following description: The viewport
- * id of this viewport's
- * (cdna/protein) coding complement, if any
- *
- *
- * @param complementId the value of field 'complementId'.
- */
- public void setComplementId(
- final java.lang.String complementId) {
- this._complementId = complementId;
- }
-
- /**
- * Sets the value of field 'consThreshold'.
- *
- * @param consThreshold the value of field 'consThreshold'.
- */
- public void setConsThreshold(
- final int consThreshold) {
- this._consThreshold = consThreshold;
- this._has_consThreshold = true;
- }
-
- /**
- * Sets the value of field 'conservationSelected'.
- *
- * @param conservationSelected the value of field
- * 'conservationSelected'.
- */
- public void setConservationSelected(
- final boolean conservationSelected) {
- this._conservationSelected = conservationSelected;
- this._has_conservationSelected = true;
- }
-
- /**
- * Sets the value of field 'followHighlight'.
- *
- * @param followHighlight the value of field 'followHighlight'.
- */
- public void setFollowHighlight(
- final boolean followHighlight) {
- this._followHighlight = followHighlight;
- this._has_followHighlight = true;
- }
-
- /**
- * Sets the value of field 'followSelection'.
- *
- * @param followSelection the value of field 'followSelection'.
- */
- public void setFollowSelection(
- final boolean followSelection) {
- this._followSelection = followSelection;
- this._has_followSelection = true;
- }
-
- /**
- * Sets the value of field 'fontName'.
- *
- * @param fontName the value of field 'fontName'.
- */
- public void setFontName(
- final java.lang.String fontName) {
- this._fontName = fontName;
- }
-
- /**
- * Sets the value of field 'fontSize'.
- *
- * @param fontSize the value of field 'fontSize'.
- */
- public void setFontSize(
- final int fontSize) {
- this._fontSize = fontSize;
- this._has_fontSize = true;
- }
-
- /**
- * Sets the value of field 'fontStyle'.
- *
- * @param fontStyle the value of field 'fontStyle'.
- */
- public void setFontStyle(
- final int fontStyle) {
- this._fontStyle = fontStyle;
- this._has_fontStyle = true;
- }
-
- /**
- * Sets the value of field 'gatheredViews'.
- *
- * @param gatheredViews the value of field 'gatheredViews'.
- */
- public void setGatheredViews(
- final boolean gatheredViews) {
- this._gatheredViews = gatheredViews;
- this._has_gatheredViews = true;
- }
-
- /**
- * Sets the value of field 'height'.
- *
- * @param height the value of field 'height'.
- */
- public void setHeight(
- final int height) {
- this._height = height;
- this._has_height = true;
- }
-
- /**
- *
- *
- * @param index
- * @param vHiddenColumns
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setHiddenColumns(
- final int index,
- final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._hiddenColumnsList.size()) {
- throw new IndexOutOfBoundsException("setHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
- }
-
- this._hiddenColumnsList.set(index, vHiddenColumns);
- }
-
- /**
- *
- *
- * @param vHiddenColumnsArray
- */
- public void setHiddenColumns(
- final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray) {
- //-- copy array
- _hiddenColumnsList.clear();
-
- for (int i = 0; i < vHiddenColumnsArray.length; i++) {
- this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'id'. The field 'id' has the
- * following description: unique id used by jalview to
- * synchronize
- * between stored and
- * instantiated views
- *
- *
- * @param id the value of field 'id'.
- */
- public void setId(
- final java.lang.String id) {
- this._id = id;
- }
-
- /**
- * Sets the value of field 'ignoreGapsinConsensus'.
- *
- * @param ignoreGapsinConsensus the value of field
- * 'ignoreGapsinConsensus'.
- */
- public void setIgnoreGapsinConsensus(
- final boolean ignoreGapsinConsensus) {
- this._ignoreGapsinConsensus = ignoreGapsinConsensus;
- this._has_ignoreGapsinConsensus = true;
- }
-
- /**
- * Sets the value of field 'normaliseSequenceLogo'.
- *
- * @param normaliseSequenceLogo the value of field
- * 'normaliseSequenceLogo'.
- */
- public void setNormaliseSequenceLogo(
- final boolean normaliseSequenceLogo) {
- this._normaliseSequenceLogo = normaliseSequenceLogo;
- this._has_normaliseSequenceLogo = true;
- }
-
- /**
- * Sets the value of field 'pidSelected'.
- *
- * @param pidSelected the value of field 'pidSelected'.
- */
- public void setPidSelected(
- final boolean pidSelected) {
- this._pidSelected = pidSelected;
- this._has_pidSelected = true;
- }
-
- /**
- * Sets the value of field 'pidThreshold'.
- *
- * @param pidThreshold the value of field 'pidThreshold'.
- */
- public void setPidThreshold(
- final int pidThreshold) {
- this._pidThreshold = pidThreshold;
- this._has_pidThreshold = true;
- }
-
- /**
- * Sets the value of field 'renderGaps'.
- *
- * @param renderGaps the value of field 'renderGaps'.
- */
- public void setRenderGaps(
- final boolean renderGaps) {
- this._renderGaps = renderGaps;
- this._has_renderGaps = true;
- }
-
- /**
- * Sets the value of field 'rightAlignIds'.
- *
- * @param rightAlignIds the value of field 'rightAlignIds'.
- */
- public void setRightAlignIds(
- final boolean rightAlignIds) {
- this._rightAlignIds = rightAlignIds;
- this._has_rightAlignIds = true;
- }
-
- /**
- * Sets the value of field 'scaleProteinAsCdna'.
- *
- * @param scaleProteinAsCdna the value of field
- * 'scaleProteinAsCdna'.
- */
- public void setScaleProteinAsCdna(
- final boolean scaleProteinAsCdna) {
- this._scaleProteinAsCdna = scaleProteinAsCdna;
- this._has_scaleProteinAsCdna = true;
- }
-
- /**
- * Sets the value of field 'sequenceSetId'.
- *
- * @param sequenceSetId the value of field 'sequenceSetId'.
- */
- public void setSequenceSetId(
- final java.lang.String sequenceSetId) {
- this._sequenceSetId = sequenceSetId;
- }
-
- /**
- * Sets the value of field 'showAnnotation'.
- *
- * @param showAnnotation the value of field 'showAnnotation'.
- */
- public void setShowAnnotation(
- final boolean showAnnotation) {
- this._showAnnotation = showAnnotation;
- this._has_showAnnotation = true;
- }
-
- /**
- * Sets the value of field 'showBoxes'.
- *
- * @param showBoxes the value of field 'showBoxes'.
- */
- public void setShowBoxes(
- final boolean showBoxes) {
- this._showBoxes = showBoxes;
- this._has_showBoxes = true;
- }
-
- /**
- * Sets the value of field 'showColourText'.
- *
- * @param showColourText the value of field 'showColourText'.
- */
- public void setShowColourText(
- final boolean showColourText) {
- this._showColourText = showColourText;
- this._has_showColourText = true;
- }
-
- /**
- * Sets the value of field 'showConsensusHistogram'.
- *
- * @param showConsensusHistogram the value of field
- * 'showConsensusHistogram'.
- */
- public void setShowConsensusHistogram(
- final boolean showConsensusHistogram) {
- this._showConsensusHistogram = showConsensusHistogram;
- this._has_showConsensusHistogram = true;
- }
-
- /**
- * Sets the value of field 'showDbRefTooltip'.
- *
- * @param showDbRefTooltip the value of field 'showDbRefTooltip'
- */
- public void setShowDbRefTooltip(
- final boolean showDbRefTooltip) {
- this._showDbRefTooltip = showDbRefTooltip;
- this._has_showDbRefTooltip = true;
- }
-
- /**
- * Sets the value of field 'showFullId'.
- *
- * @param showFullId the value of field 'showFullId'.
- */
- public void setShowFullId(
- final boolean showFullId) {
- this._showFullId = showFullId;
- this._has_showFullId = true;
- }
-
- /**
- * Sets the value of field 'showGroupConsensus'.
- *
- * @param showGroupConsensus the value of field
- * 'showGroupConsensus'.
- */
- public void setShowGroupConsensus(
- final boolean showGroupConsensus) {
- this._showGroupConsensus = showGroupConsensus;
- this._has_showGroupConsensus = true;
- }
-
- /**
- * Sets the value of field 'showGroupConservation'.
- *
- * @param showGroupConservation the value of field
- * 'showGroupConservation'.
- */
- public void setShowGroupConservation(
- final boolean showGroupConservation) {
- this._showGroupConservation = showGroupConservation;
- this._has_showGroupConservation = true;
- }
-
- /**
- * Sets the value of field 'showNPfeatureTooltip'.
- *
- * @param showNPfeatureTooltip the value of field
- * 'showNPfeatureTooltip'.
- */
- public void setShowNPfeatureTooltip(
- final boolean showNPfeatureTooltip) {
- this._showNPfeatureTooltip = showNPfeatureTooltip;
- this._has_showNPfeatureTooltip = true;
- }
-
- /**
- * Sets the value of field 'showSequenceFeatures'.
- *
- * @param showSequenceFeatures the value of field
- * 'showSequenceFeatures'.
- */
- public void setShowSequenceFeatures(
- final boolean showSequenceFeatures) {
- this._showSequenceFeatures = showSequenceFeatures;
- this._has_showSequenceFeatures = true;
- }
-
- /**
- * Sets the value of field 'showSequenceLogo'.
- *
- * @param showSequenceLogo the value of field 'showSequenceLogo'
- */
- public void setShowSequenceLogo(
- final boolean showSequenceLogo) {
- this._showSequenceLogo = showSequenceLogo;
- this._has_showSequenceLogo = true;
- }
-
- /**
- * Sets the value of field 'showText'.
- *
- * @param showText the value of field 'showText'.
- */
- public void setShowText(
- final boolean showText) {
- this._showText = showText;
- this._has_showText = true;
- }
-
- /**
- * Sets the value of field 'showUnconserved'.
- *
- * @param showUnconserved the value of field 'showUnconserved'.
- */
- public void setShowUnconserved(
- final boolean showUnconserved) {
- this._showUnconserved = showUnconserved;
- this._has_showUnconserved = true;
- }
-
- /**
- * Sets the value of field 'startRes'.
- *
- * @param startRes the value of field 'startRes'.
- */
- public void setStartRes(
- final int startRes) {
- this._startRes = startRes;
- this._has_startRes = true;
- }
-
- /**
- * Sets the value of field 'startSeq'.
- *
- * @param startSeq the value of field 'startSeq'.
- */
- public void setStartSeq(
- final int startSeq) {
- this._startSeq = startSeq;
- this._has_startSeq = true;
- }
-
- /**
- * Sets the value of field 'textCol1'.
- *
- * @param textCol1 the value of field 'textCol1'.
- */
- public void setTextCol1(
- final int textCol1) {
- this._textCol1 = textCol1;
- this._has_textCol1 = true;
- }
-
- /**
- * Sets the value of field 'textCol2'.
- *
- * @param textCol2 the value of field 'textCol2'.
- */
- public void setTextCol2(
- final int textCol2) {
- this._textCol2 = textCol2;
- this._has_textCol2 = true;
- }
-
- /**
- * Sets the value of field 'textColThreshold'.
- *
- * @param textColThreshold the value of field 'textColThreshold'
- */
- public void setTextColThreshold(
- final int textColThreshold) {
- this._textColThreshold = textColThreshold;
- this._has_textColThreshold = true;
- }
-
- /**
- * Sets the value of field 'title'.
- *
- * @param title the value of field 'title'.
- */
- public void setTitle(
- final java.lang.String title) {
- this._title = title;
- }
-
- /**
- * Sets the value of field 'viewName'.
- *
- * @param viewName the value of field 'viewName'.
- */
- public void setViewName(
- final java.lang.String viewName) {
- this._viewName = viewName;
- }
-
- /**
- * Sets the value of field 'width'.
- *
- * @param width the value of field 'width'.
- */
- public void setWidth(
- final int width) {
- this._width = width;
- this._has_width = true;
- }
-
- /**
- * Sets the value of field 'wrapAlignment'.
- *
- * @param wrapAlignment the value of field 'wrapAlignment'.
- */
- public void setWrapAlignment(
- final boolean wrapAlignment) {
- this._wrapAlignment = wrapAlignment;
- this._has_wrapAlignment = true;
- }
-
- /**
- * Sets the value of field 'xpos'.
- *
- * @param xpos the value of field 'xpos'.
- */
- public void setXpos(
- final int xpos) {
- this._xpos = xpos;
- this._has_xpos = true;
- }
-
- /**
- * Sets the value of field 'ypos'.
- *
- * @param ypos the value of field 'ypos'.
- */
- public void setYpos(
- final int ypos) {
- this._ypos = ypos;
- this._has_ypos = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.Viewport
- */
- public static jalview.schemabinding.version2.Viewport unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(jalview.schemabinding.version2.Viewport.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+ public void deleteStartRes()
+ {
+ this._has_startRes = false;
+ }
+
+ /**
+ */
+ public void deleteStartSeq()
+ {
+ this._has_startSeq = false;
+ }
+
+ /**
+ */
+ public void deleteTextCol1()
+ {
+ this._has_textCol1 = false;
+ }
+
+ /**
+ */
+ public void deleteTextCol2()
+ {
+ this._has_textCol2 = false;
+ }
+
+ /**
+ */
+ public void deleteTextColThreshold()
+ {
+ this._has_textColThreshold = false;
+ }
+
+ /**
+ */
+ public void deleteWidth()
+ {
+ this._has_width = false;
+ }
+
+ /**
+ */
+ public void deleteWrapAlignment()
+ {
+ this._has_wrapAlignment = false;
+ }
+
+ /**
+ */
+ public void deleteXpos()
+ {
+ this._has_xpos = false;
+ }
+
+ /**
+ */
+ public void deleteYpos()
+ {
+ this._has_ypos = false;
+ }
+
+ /**
+ * Method enumerateCalcIdParam.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.CalcIdParam
+ * elements
+ */
+ public java.util.Enumeration enumerateCalcIdParam()
+ {
+ return this._calcIdParamList.elements();
+ }
+
+ /**
+ * Method enumerateHiddenColumns.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.HiddenColumns elements
+ */
+ public java.util.Enumeration enumerateHiddenColumns()
+ {
+ return this._hiddenColumnsList.elements();
+ }
+
+ /**
+ * Returns the value of field 'annotationColours'.
+ *
+ * @return the value of field 'AnnotationColours'.
+ */
+ public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()
+ {
+ return this._annotationColours;
+ }
+
+ /**
+ * Returns the value of field 'bgColour'.
+ *
+ * @return the value of field 'BgColour'.
+ */
+ public java.lang.String getBgColour()
+ {
+ return this._bgColour;
+ }
+
+ /**
+ * Method getCalcIdParam.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.CalcIdParam at the
+ * given index
+ */
+ public jalview.schemabinding.version2.CalcIdParam getCalcIdParam(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._calcIdParamList.size())
+ {
+ throw new IndexOutOfBoundsException("getCalcIdParam: Index value '"
+ + index + "' not in range [0.."
+ + (this._calcIdParamList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.CalcIdParam) _calcIdParamList
+ .get(index);
+ }
+
+ /**
+ * Method getCalcIdParam.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.CalcIdParam[] getCalcIdParam()
+ {
+ jalview.schemabinding.version2.CalcIdParam[] array = new jalview.schemabinding.version2.CalcIdParam[0];
+ return (jalview.schemabinding.version2.CalcIdParam[]) this._calcIdParamList
+ .toArray(array);
+ }
+
+ /**
+ * Method getCalcIdParamCount.
+ *
+ * @return the size of this collection
+ */
+ public int getCalcIdParamCount()
+ {
+ return this._calcIdParamList.size();
+ }
+
+ /**
+ * Returns the value of field 'centreColumnLabels'.
+ *
+ * @return the value of field 'CentreColumnLabels'.
+ */
+ public boolean getCentreColumnLabels()
+ {
+ return this._centreColumnLabels;
+ }
+
+ /**
+ * Returns the value of field 'complementId'. The field 'complementId' has the
+ * following description: The viewport id of this viewport's (cdna/protein)
+ * coding complement, if any
+ *
+ *
+ * @return the value of field 'ComplementId'.
+ */
+ public java.lang.String getComplementId()
+ {
+ return this._complementId;
+ }
+
+ /**
+ * Returns the value of field 'consThreshold'.
+ *
+ * @return the value of field 'ConsThreshold'.
+ */
+ public int getConsThreshold()
+ {
+ return this._consThreshold;
+ }
+
+ /**
+ * Returns the value of field 'conservationSelected'.
+ *
+ * @return the value of field 'ConservationSelected'.
+ */
+ public boolean getConservationSelected()
+ {
+ return this._conservationSelected;
+ }
+
+ /**
+ * Returns the value of field 'followHighlight'.
+ *
+ * @return the value of field 'FollowHighlight'.
+ */
+ public boolean getFollowHighlight()
+ {
+ return this._followHighlight;
+ }
+
+ /**
+ * Returns the value of field 'followSelection'.
+ *
+ * @return the value of field 'FollowSelection'.
+ */
+ public boolean getFollowSelection()
+ {
+ return this._followSelection;
+ }
+
+ /**
+ * Returns the value of field 'fontName'.
+ *
+ * @return the value of field 'FontName'.
+ */
+ public java.lang.String getFontName()
+ {
+ return this._fontName;
+ }
+
+ /**
+ * Returns the value of field 'fontSize'.
+ *
+ * @return the value of field 'FontSize'.
+ */
+ public int getFontSize()
+ {
+ return this._fontSize;
+ }
+
+ /**
+ * Returns the value of field 'fontStyle'.
+ *
+ * @return the value of field 'FontStyle'.
+ */
+ public int getFontStyle()
+ {
+ return this._fontStyle;
+ }
+
+ /**
+ * Returns the value of field 'gatheredViews'.
+ *
+ * @return the value of field 'GatheredViews'.
+ */
+ public boolean getGatheredViews()
+ {
+ return this._gatheredViews;
+ }
+
+ /**
+ * Returns the value of field 'height'.
+ *
+ * @return the value of field 'Height'.
+ */
+ public int getHeight()
+ {
+ return this._height;
+ }
+
+ /**
+ * Method getHiddenColumns.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.HiddenColumns at
+ * the given index
+ */
+ public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._hiddenColumnsList.size())
+ {
+ throw new IndexOutOfBoundsException("getHiddenColumns: Index value '"
+ + index + "' not in range [0.."
+ + (this._hiddenColumnsList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList
+ .get(index);
+ }
+
+ /**
+ * Method getHiddenColumns.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()
+ {
+ jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
+ return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList
+ .toArray(array);
+ }
+
+ /**
+ * Method getHiddenColumnsCount.
+ *
+ * @return the size of this collection
+ */
+ public int getHiddenColumnsCount()
+ {
+ return this._hiddenColumnsList.size();
+ }
+
+ /**
+ * Returns the value of field 'id'. The field 'id' has the following
+ * description: unique id used by jalview to synchronize between stored and
+ * instantiated views
+ *
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ }
+
+ /**
+ * Returns the value of field 'ignoreGapsinConsensus'.
+ *
+ * @return the value of field 'IgnoreGapsinConsensus'.
+ */
+ public boolean getIgnoreGapsinConsensus()
+ {
+ return this._ignoreGapsinConsensus;
+ }
+
+ /**
+ * Returns the value of field 'normaliseSequenceLogo'.
+ *
+ * @return the value of field 'NormaliseSequenceLogo'.
+ */
+ public boolean getNormaliseSequenceLogo()
+ {
+ return this._normaliseSequenceLogo;
+ }
+
+ /**
+ * Returns the value of field 'pidSelected'.
+ *
+ * @return the value of field 'PidSelected'.
+ */
+ public boolean getPidSelected()
+ {
+ return this._pidSelected;
+ }
+
+ /**
+ * Returns the value of field 'pidThreshold'.
+ *
+ * @return the value of field 'PidThreshold'.
+ */
+ public int getPidThreshold()
+ {
+ return this._pidThreshold;
+ }
+
+ /**
+ * Returns the value of field 'renderGaps'.
+ *
+ * @return the value of field 'RenderGaps'.
+ */
+ public boolean getRenderGaps()
+ {
+ return this._renderGaps;
+ }
+
+ /**
+ * Returns the value of field 'rightAlignIds'.
+ *
+ * @return the value of field 'RightAlignIds'.
+ */
+ public boolean getRightAlignIds()
+ {
+ return this._rightAlignIds;
+ }
+
+ /**
+ * Returns the value of field 'scaleProteinAsCdna'.
+ *
+ * @return the value of field 'ScaleProteinAsCdna'.
+ */
+ public boolean getScaleProteinAsCdna()
+ {
+ return this._scaleProteinAsCdna;
+ }
+
+ /**
+ * Returns the value of field 'sequenceSetId'.
+ *
+ * @return the value of field 'SequenceSetId'.
+ */
+ public java.lang.String getSequenceSetId()
+ {
+ return this._sequenceSetId;
+ }
+
+ /**
+ * Returns the value of field 'showAnnotation'.
+ *
+ * @return the value of field 'ShowAnnotation'.
+ */
+ public boolean getShowAnnotation()
+ {
+ return this._showAnnotation;
+ }
+
+ /**
+ * Returns the value of field 'showBoxes'.
+ *
+ * @return the value of field 'ShowBoxes'.
+ */
+ public boolean getShowBoxes()
+ {
+ return this._showBoxes;
+ }
+
+ /**
+ * Returns the value of field 'showColourText'.
+ *
+ * @return the value of field 'ShowColourText'.
+ */
+ public boolean getShowColourText()
+ {
+ return this._showColourText;
+ }
+
+ /**
+ * Returns the value of field 'showConsensusHistogram'.
+ *
+ * @return the value of field 'ShowConsensusHistogram'.
+ */
+ public boolean getShowConsensusHistogram()
+ {
+ return this._showConsensusHistogram;
+ }
+
+ /**
+ * Returns the value of field 'showDbRefTooltip'.
+ *
+ * @return the value of field 'ShowDbRefTooltip'.
+ */
+ public boolean getShowDbRefTooltip()
+ {
+ return this._showDbRefTooltip;
+ }
+
+ /**
+ * Returns the value of field 'showFullId'.
+ *
+ * @return the value of field 'ShowFullId'.
+ */
+ public boolean getShowFullId()
+ {
+ return this._showFullId;
+ }
+
+ /**
+ * Returns the value of field 'showGroupConsensus'.
+ *
+ * @return the value of field 'ShowGroupConsensus'.
+ */
+ public boolean getShowGroupConsensus()
+ {
+ return this._showGroupConsensus;
+ }
+
+ /**
+ * Returns the value of field 'showGroupConservation'.
+ *
+ * @return the value of field 'ShowGroupConservation'.
+ */
+ public boolean getShowGroupConservation()
+ {
+ return this._showGroupConservation;
+ }
+
+ /**
+ * Returns the value of field 'showNPfeatureTooltip'.
+ *
+ * @return the value of field 'ShowNPfeatureTooltip'.
+ */
+ public boolean getShowNPfeatureTooltip()
+ {
+ return this._showNPfeatureTooltip;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceFeatures'.
+ *
+ * @return the value of field 'ShowSequenceFeatures'.
+ */
+ public boolean getShowSequenceFeatures()
+ {
+ return this._showSequenceFeatures;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceLogo'.
+ *
+ * @return the value of field 'ShowSequenceLogo'.
+ */
+ public boolean getShowSequenceLogo()
+ {
+ return this._showSequenceLogo;
+ }
+
+ /**
+ * Returns the value of field 'showText'.
+ *
+ * @return the value of field 'ShowText'.
+ */
+ public boolean getShowText()
+ {
+ return this._showText;
+ }
+
+ /**
+ * Returns the value of field 'showUnconserved'.
+ *
+ * @return the value of field 'ShowUnconserved'.
+ */
+ public boolean getShowUnconserved()
+ {
+ return this._showUnconserved;
+ }
+
+ /**
+ * Returns the value of field 'startRes'.
+ *
+ * @return the value of field 'StartRes'.
+ */
+ public int getStartRes()
+ {
+ return this._startRes;
+ }
+
+ /**
+ * Returns the value of field 'startSeq'.
+ *
+ * @return the value of field 'StartSeq'.
+ */
+ public int getStartSeq()
+ {
+ return this._startSeq;
+ }
+
+ /**
+ * Returns the value of field 'textCol1'.
+ *
+ * @return the value of field 'TextCol1'.
+ */
+ public int getTextCol1()
+ {
+ return this._textCol1;
+ }
+
+ /**
+ * Returns the value of field 'textCol2'.
+ *
+ * @return the value of field 'TextCol2'.
+ */
+ public int getTextCol2()
+ {
+ return this._textCol2;
+ }
+
+ /**
+ * Returns the value of field 'textColThreshold'.
+ *
+ * @return the value of field 'TextColThreshold'.
+ */
+ public int getTextColThreshold()
+ {
+ return this._textColThreshold;
+ }
+
+ /**
+ * Returns the value of field 'title'.
+ *
+ * @return the value of field 'Title'.
+ */
+ public java.lang.String getTitle()
+ {
+ return this._title;
+ }
+
+ /**
+ * Returns the value of field 'viewName'.
+ *
+ * @return the value of field 'ViewName'.
+ */
+ public java.lang.String getViewName()
+ {
+ return this._viewName;
+ }
+
+ /**
+ * Returns the value of field 'width'.
+ *
+ * @return the value of field 'Width'.
+ */
+ public int getWidth()
+ {
+ return this._width;
+ }
+
+ /**
+ * Returns the value of field 'wrapAlignment'.
+ *
+ * @return the value of field 'WrapAlignment'.
+ */
+ public boolean getWrapAlignment()
+ {
+ return this._wrapAlignment;
+ }
+
+ /**
+ * Returns the value of field 'xpos'.
+ *
+ * @return the value of field 'Xpos'.
+ */
+ public int getXpos()
+ {
+ return this._xpos;
+ }
+
+ /**
+ * Returns the value of field 'ypos'.
+ *
+ * @return the value of field 'Ypos'.
+ */
+ public int getYpos()
+ {
+ return this._ypos;
+ }
+
+ /**
+ * Method hasCentreColumnLabels.
+ *
+ * @return true if at least one CentreColumnLabels has been adde
+ */
+ public boolean hasCentreColumnLabels()
+ {
+ return this._has_centreColumnLabels;
+ }
+
+ /**
+ * Method hasConsThreshold.
+ *
+ * @return true if at least one ConsThreshold has been added
+ */
+ public boolean hasConsThreshold()
+ {
+ return this._has_consThreshold;
+ }
+
+ /**
+ * Method hasConservationSelected.
+ *
+ * @return true if at least one ConservationSelected has been added
+ */
+ public boolean hasConservationSelected()
+ {
+ return this._has_conservationSelected;
+ }
+
+ /**
+ * Method hasFollowHighlight.
+ *
+ * @return true if at least one FollowHighlight has been added
+ */
+ public boolean hasFollowHighlight()
+ {
+ return this._has_followHighlight;
+ }
+
+ /**
+ * Method hasFollowSelection.
+ *
+ * @return true if at least one FollowSelection has been added
+ */
+ public boolean hasFollowSelection()
+ {
+ return this._has_followSelection;
+ }
+
+ /**
+ * Method hasFontSize.
+ *
+ * @return true if at least one FontSize has been added
+ */
+ public boolean hasFontSize()
+ {
+ return this._has_fontSize;
+ }
+
+ /**
+ * Method hasFontStyle.
+ *
+ * @return true if at least one FontStyle has been added
+ */
+ public boolean hasFontStyle()
+ {
+ return this._has_fontStyle;
+ }
+
+ /**
+ * Method hasGatheredViews.
+ *
+ * @return true if at least one GatheredViews has been added
+ */
+ public boolean hasGatheredViews()
+ {
+ return this._has_gatheredViews;
+ }
+
+ /**
+ * Method hasHeight.
+ *
+ * @return true if at least one Height has been added
+ */
+ public boolean hasHeight()
+ {
+ return this._has_height;
+ }
+
+ /**
+ * Method hasIgnoreGapsinConsensus.
+ *
+ * @return true if at least one IgnoreGapsinConsensus has been added
+ */
+ public boolean hasIgnoreGapsinConsensus()
+ {
+ return this._has_ignoreGapsinConsensus;
+ }
+
+ /**
+ * Method hasNormaliseSequenceLogo.
+ *
+ * @return true if at least one NormaliseSequenceLogo has been added
+ */
+ public boolean hasNormaliseSequenceLogo()
+ {
+ return this._has_normaliseSequenceLogo;
+ }
+
+ /**
+ * Method hasPidSelected.
+ *
+ * @return true if at least one PidSelected has been added
+ */
+ public boolean hasPidSelected()
+ {
+ return this._has_pidSelected;
+ }
+
+ /**
+ * Method hasPidThreshold.
+ *
+ * @return true if at least one PidThreshold has been added
+ */
+ public boolean hasPidThreshold()
+ {
+ return this._has_pidThreshold;
+ }
+
+ /**
+ * Method hasRenderGaps.
+ *
+ * @return true if at least one RenderGaps has been added
+ */
+ public boolean hasRenderGaps()
+ {
+ return this._has_renderGaps;
+ }
+
+ /**
+ * Method hasRightAlignIds.
+ *
+ * @return true if at least one RightAlignIds has been added
+ */
+ public boolean hasRightAlignIds()
+ {
+ return this._has_rightAlignIds;
+ }
+
+ /**
+ * Method hasScaleProteinAsCdna.
+ *
+ * @return true if at least one ScaleProteinAsCdna has been adde
+ */
+ public boolean hasScaleProteinAsCdna()
+ {
+ return this._has_scaleProteinAsCdna;
+ }
+
+ /**
+ * Method hasShowAnnotation.
+ *
+ * @return true if at least one ShowAnnotation has been added
+ */
+ public boolean hasShowAnnotation()
+ {
+ return this._has_showAnnotation;
+ }
+
+ /**
+ * Method hasShowBoxes.
+ *
+ * @return true if at least one ShowBoxes has been added
+ */
+ public boolean hasShowBoxes()
+ {
+ return this._has_showBoxes;
+ }
+
+ /**
+ * Method hasShowColourText.
+ *
+ * @return true if at least one ShowColourText has been added
+ */
+ public boolean hasShowColourText()
+ {
+ return this._has_showColourText;
+ }
+
+ /**
+ * Method hasShowConsensusHistogram.
+ *
+ * @return true if at least one ShowConsensusHistogram has been added
+ */
+ public boolean hasShowConsensusHistogram()
+ {
+ return this._has_showConsensusHistogram;
+ }
+
+ /**
+ * Method hasShowDbRefTooltip.
+ *
+ * @return true if at least one ShowDbRefTooltip has been added
+ */
+ public boolean hasShowDbRefTooltip()
+ {
+ return this._has_showDbRefTooltip;
+ }
+
+ /**
+ * Method hasShowFullId.
+ *
+ * @return true if at least one ShowFullId has been added
+ */
+ public boolean hasShowFullId()
+ {
+ return this._has_showFullId;
+ }
+
+ /**
+ * Method hasShowGroupConsensus.
+ *
+ * @return true if at least one ShowGroupConsensus has been adde
+ */
+ public boolean hasShowGroupConsensus()
+ {
+ return this._has_showGroupConsensus;
+ }
+
+ /**
+ * Method hasShowGroupConservation.
+ *
+ * @return true if at least one ShowGroupConservation has been added
+ */
+ public boolean hasShowGroupConservation()
+ {
+ return this._has_showGroupConservation;
+ }
+
+ /**
+ * Method hasShowNPfeatureTooltip.
+ *
+ * @return true if at least one ShowNPfeatureTooltip has been added
+ */
+ public boolean hasShowNPfeatureTooltip()
+ {
+ return this._has_showNPfeatureTooltip;
+ }
+
+ /**
+ * Method hasShowSequenceFeatures.
+ *
+ * @return true if at least one ShowSequenceFeatures has been added
+ */
+ public boolean hasShowSequenceFeatures()
+ {
+ return this._has_showSequenceFeatures;
+ }
+
+ /**
+ * Method hasShowSequenceLogo.
+ *
+ * @return true if at least one ShowSequenceLogo has been added
+ */
+ public boolean hasShowSequenceLogo()
+ {
+ return this._has_showSequenceLogo;
+ }
+
+ /**
+ * Method hasShowText.
+ *
+ * @return true if at least one ShowText has been added
+ */
+ public boolean hasShowText()
+ {
+ return this._has_showText;
+ }
+
+ /**
+ * Method hasShowUnconserved.
+ *
+ * @return true if at least one ShowUnconserved has been added
+ */
+ public boolean hasShowUnconserved()
+ {
+ return this._has_showUnconserved;
+ }
+
+ /**
+ * Method hasStartRes.
+ *
+ * @return true if at least one StartRes has been added
+ */
+ public boolean hasStartRes()
+ {
+ return this._has_startRes;
+ }
+
+ /**
+ * Method hasStartSeq.
+ *
+ * @return true if at least one StartSeq has been added
+ */
+ public boolean hasStartSeq()
+ {
+ return this._has_startSeq;
+ }
+
+ /**
+ * Method hasTextCol1.
+ *
+ * @return true if at least one TextCol1 has been added
+ */
+ public boolean hasTextCol1()
+ {
+ return this._has_textCol1;
+ }
+
+ /**
+ * Method hasTextCol2.
+ *
+ * @return true if at least one TextCol2 has been added
+ */
+ public boolean hasTextCol2()
+ {
+ return this._has_textCol2;
+ }
+
+ /**
+ * Method hasTextColThreshold.
+ *
+ * @return true if at least one TextColThreshold has been added
+ */
+ public boolean hasTextColThreshold()
+ {
+ return this._has_textColThreshold;
+ }
+
+ /**
+ * Method hasWidth.
+ *
+ * @return true if at least one Width has been added
+ */
+ public boolean hasWidth()
+ {
+ return this._has_width;
+ }
+
+ /**
+ * Method hasWrapAlignment.
+ *
+ * @return true if at least one WrapAlignment has been added
+ */
+ public boolean hasWrapAlignment()
+ {
+ return this._has_wrapAlignment;
+ }
+
+ /**
+ * Method hasXpos.
+ *
+ * @return true if at least one Xpos has been added
+ */
+ public boolean hasXpos()
+ {
+ return this._has_xpos;
+ }
+
+ /**
+ * Method hasYpos.
+ *
+ * @return true if at least one Ypos has been added
+ */
+ public boolean hasYpos()
+ {
+ return this._has_ypos;
+ }
+
+ /**
+ * Returns the value of field 'centreColumnLabels'.
+ *
+ * @return the value of field 'CentreColumnLabels'.
+ */
+ public boolean isCentreColumnLabels()
+ {
+ return this._centreColumnLabels;
+ }
+
+ /**
+ * Returns the value of field 'conservationSelected'.
+ *
+ * @return the value of field 'ConservationSelected'.
+ */
+ public boolean isConservationSelected()
+ {
+ return this._conservationSelected;
+ }
+
+ /**
+ * Returns the value of field 'followHighlight'.
+ *
+ * @return the value of field 'FollowHighlight'.
+ */
+ public boolean isFollowHighlight()
+ {
+ return this._followHighlight;
+ }
+
+ /**
+ * Returns the value of field 'followSelection'.
+ *
+ * @return the value of field 'FollowSelection'.
+ */
+ public boolean isFollowSelection()
+ {
+ return this._followSelection;
+ }
+
+ /**
+ * Returns the value of field 'gatheredViews'.
+ *
+ * @return the value of field 'GatheredViews'.
+ */
+ public boolean isGatheredViews()
+ {
+ return this._gatheredViews;
+ }
+
+ /**
+ * Returns the value of field 'ignoreGapsinConsensus'.
+ *
+ * @return the value of field 'IgnoreGapsinConsensus'.
+ */
+ public boolean isIgnoreGapsinConsensus()
+ {
+ return this._ignoreGapsinConsensus;
+ }
+
+ /**
+ * Returns the value of field 'normaliseSequenceLogo'.
+ *
+ * @return the value of field 'NormaliseSequenceLogo'.
+ */
+ public boolean isNormaliseSequenceLogo()
+ {
+ return this._normaliseSequenceLogo;
+ }
+
+ /**
+ * Returns the value of field 'pidSelected'.
+ *
+ * @return the value of field 'PidSelected'.
+ */
+ public boolean isPidSelected()
+ {
+ return this._pidSelected;
+ }
+
+ /**
+ * Returns the value of field 'renderGaps'.
+ *
+ * @return the value of field 'RenderGaps'.
+ */
+ public boolean isRenderGaps()
+ {
+ return this._renderGaps;
+ }
+
+ /**
+ * Returns the value of field 'rightAlignIds'.
+ *
+ * @return the value of field 'RightAlignIds'.
+ */
+ public boolean isRightAlignIds()
+ {
+ return this._rightAlignIds;
+ }
+
+ /**
+ * Returns the value of field 'scaleProteinAsCdna'.
+ *
+ * @return the value of field 'ScaleProteinAsCdna'.
+ */
+ public boolean isScaleProteinAsCdna()
+ {
+ return this._scaleProteinAsCdna;
+ }
+
+ /**
+ * Returns the value of field 'showAnnotation'.
+ *
+ * @return the value of field 'ShowAnnotation'.
+ */
+ public boolean isShowAnnotation()
+ {
+ return this._showAnnotation;
+ }
+
+ /**
+ * Returns the value of field 'showBoxes'.
+ *
+ * @return the value of field 'ShowBoxes'.
+ */
+ public boolean isShowBoxes()
+ {
+ return this._showBoxes;
+ }
+
+ /**
+ * Returns the value of field 'showColourText'.
+ *
+ * @return the value of field 'ShowColourText'.
+ */
+ public boolean isShowColourText()
+ {
+ return this._showColourText;
+ }
+
+ /**
+ * Returns the value of field 'showConsensusHistogram'.
+ *
+ * @return the value of field 'ShowConsensusHistogram'.
+ */
+ public boolean isShowConsensusHistogram()
+ {
+ return this._showConsensusHistogram;
+ }
+
+ /**
+ * Returns the value of field 'showDbRefTooltip'.
+ *
+ * @return the value of field 'ShowDbRefTooltip'.
+ */
+ public boolean isShowDbRefTooltip()
+ {
+ return this._showDbRefTooltip;
+ }
+
+ /**
+ * Returns the value of field 'showFullId'.
+ *
+ * @return the value of field 'ShowFullId'.
+ */
+ public boolean isShowFullId()
+ {
+ return this._showFullId;
+ }
+
+ /**
+ * Returns the value of field 'showGroupConsensus'.
+ *
+ * @return the value of field 'ShowGroupConsensus'.
+ */
+ public boolean isShowGroupConsensus()
+ {
+ return this._showGroupConsensus;
+ }
+
+ /**
+ * Returns the value of field 'showGroupConservation'.
+ *
+ * @return the value of field 'ShowGroupConservation'.
+ */
+ public boolean isShowGroupConservation()
+ {
+ return this._showGroupConservation;
+ }
+
+ /**
+ * Returns the value of field 'showNPfeatureTooltip'.
+ *
+ * @return the value of field 'ShowNPfeatureTooltip'.
+ */
+ public boolean isShowNPfeatureTooltip()
+ {
+ return this._showNPfeatureTooltip;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceFeatures'.
+ *
+ * @return the value of field 'ShowSequenceFeatures'.
+ */
+ public boolean isShowSequenceFeatures()
+ {
+ return this._showSequenceFeatures;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceLogo'.
+ *
+ * @return the value of field 'ShowSequenceLogo'.
+ */
+ public boolean isShowSequenceLogo()
+ {
+ return this._showSequenceLogo;
+ }
+
+ /**
+ * Returns the value of field 'showText'.
+ *
+ * @return the value of field 'ShowText'.
+ */
+ public boolean isShowText()
+ {
+ return this._showText;
+ }
+
+ /**
+ * Returns the value of field 'showUnconserved'.
+ *
+ * @return the value of field 'ShowUnconserved'.
+ */
+ public boolean isShowUnconserved()
+ {
+ return this._showUnconserved;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * Returns the value of field 'wrapAlignment'.
+ *
+ * @return the value of field 'WrapAlignment'.
+ */
+ public boolean isWrapAlignment()
+ {
+ return this._wrapAlignment;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllCalcIdParam()
+ {
+ this._calcIdParamList.clear();
+ }
+
+ /**
+ */
+ public void removeAllHiddenColumns()
+ {
+ this._hiddenColumnsList.clear();
+ }
+
+ /**
+ * Method removeCalcIdParam.
+ *
+ * @param vCalcIdParam
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeCalcIdParam(
+ final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
+ {
+ boolean removed = _calcIdParamList.remove(vCalcIdParam);
+ return removed;
+ }
+
+ /**
+ * Method removeCalcIdParamAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.CalcIdParam removeCalcIdParamAt(
+ final int index)
+ {
+ java.lang.Object obj = this._calcIdParamList.remove(index);
+ return (jalview.schemabinding.version2.CalcIdParam) obj;
+ }
+
+ /**
+ * Method removeHiddenColumns.
+ *
+ * @param vHiddenColumns
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeHiddenColumns(
+ final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+ {
+ boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
+ return removed;
+ }
+
+ /**
+ * Method removeHiddenColumnsAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
+ final int index)
+ {
+ java.lang.Object obj = this._hiddenColumnsList.remove(index);
+ return (jalview.schemabinding.version2.HiddenColumns) obj;
+ }
+
+ /**
+ * Sets the value of field 'annotationColours'.
+ *
+ * @param annotationColours
+ * the value of field 'annotationColours'.
+ */
+ public void setAnnotationColours(
+ final jalview.schemabinding.version2.AnnotationColours annotationColours)
+ {
+ this._annotationColours = annotationColours;
+ }
+
+ /**
+ * Sets the value of field 'bgColour'.
+ *
+ * @param bgColour
+ * the value of field 'bgColour'.
+ */
+ public void setBgColour(final java.lang.String bgColour)
+ {
+ this._bgColour = bgColour;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vCalcIdParam
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setCalcIdParam(final int index,
+ final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._calcIdParamList.size())
+ {
+ throw new IndexOutOfBoundsException("setCalcIdParam: Index value '"
+ + index + "' not in range [0.."
+ + (this._calcIdParamList.size() - 1) + "]");
+ }
+
+ this._calcIdParamList.set(index, vCalcIdParam);
+ }
+
+ /**
+ *
+ *
+ * @param vCalcIdParamArray
+ */
+ public void setCalcIdParam(
+ final jalview.schemabinding.version2.CalcIdParam[] vCalcIdParamArray)
+ {
+ // -- copy array
+ _calcIdParamList.clear();
+
+ for (int i = 0; i < vCalcIdParamArray.length; i++)
+ {
+ this._calcIdParamList.add(vCalcIdParamArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'centreColumnLabels'.
+ *
+ * @param centreColumnLabels
+ * the value of field 'centreColumnLabels'.
+ */
+ public void setCentreColumnLabels(final boolean centreColumnLabels)
+ {
+ this._centreColumnLabels = centreColumnLabels;
+ this._has_centreColumnLabels = true;
+ }
+
+ /**
+ * Sets the value of field 'complementId'. The field 'complementId' has the
+ * following description: The viewport id of this viewport's (cdna/protein)
+ * coding complement, if any
+ *
+ *
+ * @param complementId
+ * the value of field 'complementId'.
+ */
+ public void setComplementId(final java.lang.String complementId)
+ {
+ this._complementId = complementId;
+ }
+
+ /**
+ * Sets the value of field 'consThreshold'.
+ *
+ * @param consThreshold
+ * the value of field 'consThreshold'.
+ */
+ public void setConsThreshold(final int consThreshold)
+ {
+ this._consThreshold = consThreshold;
+ this._has_consThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'conservationSelected'.
+ *
+ * @param conservationSelected
+ * the value of field 'conservationSelected'.
+ */
+ public void setConservationSelected(final boolean conservationSelected)
+ {
+ this._conservationSelected = conservationSelected;
+ this._has_conservationSelected = true;
+ }
+
+ /**
+ * Sets the value of field 'followHighlight'.
+ *
+ * @param followHighlight
+ * the value of field 'followHighlight'.
+ */
+ public void setFollowHighlight(final boolean followHighlight)
+ {
+ this._followHighlight = followHighlight;
+ this._has_followHighlight = true;
+ }
+
+ /**
+ * Sets the value of field 'followSelection'.
+ *
+ * @param followSelection
+ * the value of field 'followSelection'.
+ */
+ public void setFollowSelection(final boolean followSelection)
+ {
+ this._followSelection = followSelection;
+ this._has_followSelection = true;
+ }
+
+ /**
+ * Sets the value of field 'fontName'.
+ *
+ * @param fontName
+ * the value of field 'fontName'.
+ */
+ public void setFontName(final java.lang.String fontName)
+ {
+ this._fontName = fontName;
+ }
+
+ /**
+ * Sets the value of field 'fontSize'.
+ *
+ * @param fontSize
+ * the value of field 'fontSize'.
+ */
+ public void setFontSize(final int fontSize)
+ {
+ this._fontSize = fontSize;
+ this._has_fontSize = true;
+ }
+
+ /**
+ * Sets the value of field 'fontStyle'.
+ *
+ * @param fontStyle
+ * the value of field 'fontStyle'.
+ */
+ public void setFontStyle(final int fontStyle)
+ {
+ this._fontStyle = fontStyle;
+ this._has_fontStyle = true;
+ }
+
+ /**
+ * Sets the value of field 'gatheredViews'.
+ *
+ * @param gatheredViews
+ * the value of field 'gatheredViews'.
+ */
+ public void setGatheredViews(final boolean gatheredViews)
+ {
+ this._gatheredViews = gatheredViews;
+ this._has_gatheredViews = true;
+ }
+
+ /**
+ * Sets the value of field 'height'.
+ *
+ * @param height
+ * the value of field 'height'.
+ */
+ public void setHeight(final int height)
+ {
+ this._height = height;
+ this._has_height = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vHiddenColumns
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setHiddenColumns(final int index,
+ final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._hiddenColumnsList.size())
+ {
+ throw new IndexOutOfBoundsException("setHiddenColumns: Index value '"
+ + index + "' not in range [0.."
+ + (this._hiddenColumnsList.size() - 1) + "]");
+ }
+
+ this._hiddenColumnsList.set(index, vHiddenColumns);
+ }
+
+ /**
+ *
+ *
+ * @param vHiddenColumnsArray
+ */
+ public void setHiddenColumns(
+ final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray)
+ {
+ // -- copy array
+ _hiddenColumnsList.clear();
+
+ for (int i = 0; i < vHiddenColumnsArray.length; i++)
+ {
+ this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'id'. The field 'id' has the following description:
+ * unique id used by jalview to synchronize between stored and instantiated
+ * views
+ *
+ *
+ * @param id
+ * the value of field 'id'.
+ */
+ public void setId(final java.lang.String id)
+ {
+ this._id = id;
+ }
+
+ /**
+ * Sets the value of field 'ignoreGapsinConsensus'.
+ *
+ * @param ignoreGapsinConsensus
+ * the value of field 'ignoreGapsinConsensus'.
+ */
+ public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus)
+ {
+ this._ignoreGapsinConsensus = ignoreGapsinConsensus;
+ this._has_ignoreGapsinConsensus = true;
+ }
+
+ /**
+ * Sets the value of field 'normaliseSequenceLogo'.
+ *
+ * @param normaliseSequenceLogo
+ * the value of field 'normaliseSequenceLogo'.
+ */
+ public void setNormaliseSequenceLogo(final boolean normaliseSequenceLogo)
+ {
+ this._normaliseSequenceLogo = normaliseSequenceLogo;
+ this._has_normaliseSequenceLogo = true;
+ }
+
+ /**
+ * Sets the value of field 'pidSelected'.
+ *
+ * @param pidSelected
+ * the value of field 'pidSelected'.
+ */
+ public void setPidSelected(final boolean pidSelected)
+ {
+ this._pidSelected = pidSelected;
+ this._has_pidSelected = true;
+ }
+
+ /**
+ * Sets the value of field 'pidThreshold'.
+ *
+ * @param pidThreshold
+ * the value of field 'pidThreshold'.
+ */
+ public void setPidThreshold(final int pidThreshold)
+ {
+ this._pidThreshold = pidThreshold;
+ this._has_pidThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'renderGaps'.
+ *
+ * @param renderGaps
+ * the value of field 'renderGaps'.
+ */
+ public void setRenderGaps(final boolean renderGaps)
+ {
+ this._renderGaps = renderGaps;
+ this._has_renderGaps = true;
+ }
+
+ /**
+ * Sets the value of field 'rightAlignIds'.
+ *
+ * @param rightAlignIds
+ * the value of field 'rightAlignIds'.
+ */
+ public void setRightAlignIds(final boolean rightAlignIds)
+ {
+ this._rightAlignIds = rightAlignIds;
+ this._has_rightAlignIds = true;
+ }
+
+ /**
+ * Sets the value of field 'scaleProteinAsCdna'.
+ *
+ * @param scaleProteinAsCdna
+ * the value of field 'scaleProteinAsCdna'.
+ */
+ public void setScaleProteinAsCdna(final boolean scaleProteinAsCdna)
+ {
+ this._scaleProteinAsCdna = scaleProteinAsCdna;
+ this._has_scaleProteinAsCdna = true;
+ }
+
+ /**
+ * Sets the value of field 'sequenceSetId'.
+ *
+ * @param sequenceSetId
+ * the value of field 'sequenceSetId'.
+ */
+ public void setSequenceSetId(final java.lang.String sequenceSetId)
+ {
+ this._sequenceSetId = sequenceSetId;
+ }
+
+ /**
+ * Sets the value of field 'showAnnotation'.
+ *
+ * @param showAnnotation
+ * the value of field 'showAnnotation'.
+ */
+ public void setShowAnnotation(final boolean showAnnotation)
+ {
+ this._showAnnotation = showAnnotation;
+ this._has_showAnnotation = true;
+ }
+
+ /**
+ * Sets the value of field 'showBoxes'.
+ *
+ * @param showBoxes
+ * the value of field 'showBoxes'.
+ */
+ public void setShowBoxes(final boolean showBoxes)
+ {
+ this._showBoxes = showBoxes;
+ this._has_showBoxes = true;
+ }
+
+ /**
+ * Sets the value of field 'showColourText'.
+ *
+ * @param showColourText
+ * the value of field 'showColourText'.
+ */
+ public void setShowColourText(final boolean showColourText)
+ {
+ this._showColourText = showColourText;
+ this._has_showColourText = true;
+ }
+
+ /**
+ * Sets the value of field 'showConsensusHistogram'.
+ *
+ * @param showConsensusHistogram
+ * the value of field 'showConsensusHistogram'.
+ */
+ public void setShowConsensusHistogram(final boolean showConsensusHistogram)
+ {
+ this._showConsensusHistogram = showConsensusHistogram;
+ this._has_showConsensusHistogram = true;
+ }
+
+ /**
+ * Sets the value of field 'showDbRefTooltip'.
+ *
+ * @param showDbRefTooltip
+ * the value of field 'showDbRefTooltip'
+ */
+ public void setShowDbRefTooltip(final boolean showDbRefTooltip)
+ {
+ this._showDbRefTooltip = showDbRefTooltip;
+ this._has_showDbRefTooltip = true;
+ }
+
+ /**
+ * Sets the value of field 'showFullId'.
+ *
+ * @param showFullId
+ * the value of field 'showFullId'.
+ */
+ public void setShowFullId(final boolean showFullId)
+ {
+ this._showFullId = showFullId;
+ this._has_showFullId = true;
+ }
+
+ /**
+ * Sets the value of field 'showGroupConsensus'.
+ *
+ * @param showGroupConsensus
+ * the value of field 'showGroupConsensus'.
+ */
+ public void setShowGroupConsensus(final boolean showGroupConsensus)
+ {
+ this._showGroupConsensus = showGroupConsensus;
+ this._has_showGroupConsensus = true;
+ }
+
+ /**
+ * Sets the value of field 'showGroupConservation'.
+ *
+ * @param showGroupConservation
+ * the value of field 'showGroupConservation'.
+ */
+ public void setShowGroupConservation(final boolean showGroupConservation)
+ {
+ this._showGroupConservation = showGroupConservation;
+ this._has_showGroupConservation = true;
+ }
+
+ /**
+ * Sets the value of field 'showNPfeatureTooltip'.
+ *
+ * @param showNPfeatureTooltip
+ * the value of field 'showNPfeatureTooltip'.
+ */
+ public void setShowNPfeatureTooltip(final boolean showNPfeatureTooltip)
+ {
+ this._showNPfeatureTooltip = showNPfeatureTooltip;
+ this._has_showNPfeatureTooltip = true;
+ }
+
+ /**
+ * Sets the value of field 'showSequenceFeatures'.
+ *
+ * @param showSequenceFeatures
+ * the value of field 'showSequenceFeatures'.
+ */
+ public void setShowSequenceFeatures(final boolean showSequenceFeatures)
+ {
+ this._showSequenceFeatures = showSequenceFeatures;
+ this._has_showSequenceFeatures = true;
+ }
+
+ /**
+ * Sets the value of field 'showSequenceLogo'.
+ *
+ * @param showSequenceLogo
+ * the value of field 'showSequenceLogo'
+ */
+ public void setShowSequenceLogo(final boolean showSequenceLogo)
+ {
+ this._showSequenceLogo = showSequenceLogo;
+ this._has_showSequenceLogo = true;
+ }
+
+ /**
+ * Sets the value of field 'showText'.
+ *
+ * @param showText
+ * the value of field 'showText'.
+ */
+ public void setShowText(final boolean showText)
+ {
+ this._showText = showText;
+ this._has_showText = true;
+ }
+
+ /**
+ * Sets the value of field 'showUnconserved'.
+ *
+ * @param showUnconserved
+ * the value of field 'showUnconserved'.
+ */
+ public void setShowUnconserved(final boolean showUnconserved)
+ {
+ this._showUnconserved = showUnconserved;
+ this._has_showUnconserved = true;
+ }
+
+ /**
+ * Sets the value of field 'startRes'.
+ *
+ * @param startRes
+ * the value of field 'startRes'.
+ */
+ public void setStartRes(final int startRes)
+ {
+ this._startRes = startRes;
+ this._has_startRes = true;
+ }
+
+ /**
+ * Sets the value of field 'startSeq'.
+ *
+ * @param startSeq
+ * the value of field 'startSeq'.
+ */
+ public void setStartSeq(final int startSeq)
+ {
+ this._startSeq = startSeq;
+ this._has_startSeq = true;
+ }
+
+ /**
+ * Sets the value of field 'textCol1'.
+ *
+ * @param textCol1
+ * the value of field 'textCol1'.
+ */
+ public void setTextCol1(final int textCol1)
+ {
+ this._textCol1 = textCol1;
+ this._has_textCol1 = true;
+ }
+
+ /**
+ * Sets the value of field 'textCol2'.
+ *
+ * @param textCol2
+ * the value of field 'textCol2'.
+ */
+ public void setTextCol2(final int textCol2)
+ {
+ this._textCol2 = textCol2;
+ this._has_textCol2 = true;
+ }
+
+ /**
+ * Sets the value of field 'textColThreshold'.
+ *
+ * @param textColThreshold
+ * the value of field 'textColThreshold'
+ */
+ public void setTextColThreshold(final int textColThreshold)
+ {
+ this._textColThreshold = textColThreshold;
+ this._has_textColThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'title'.
+ *
+ * @param title
+ * the value of field 'title'.
+ */
+ public void setTitle(final java.lang.String title)
+ {
+ this._title = title;
+ }
+
+ /**
+ * Sets the value of field 'viewName'.
+ *
+ * @param viewName
+ * the value of field 'viewName'.
+ */
+ public void setViewName(final java.lang.String viewName)
+ {
+ this._viewName = viewName;
+ }
+
+ /**
+ * Sets the value of field 'width'.
+ *
+ * @param width
+ * the value of field 'width'.
+ */
+ public void setWidth(final int width)
+ {
+ this._width = width;
+ this._has_width = true;
+ }
+
+ /**
+ * Sets the value of field 'wrapAlignment'.
+ *
+ * @param wrapAlignment
+ * the value of field 'wrapAlignment'.
+ */
+ public void setWrapAlignment(final boolean wrapAlignment)
+ {
+ this._wrapAlignment = wrapAlignment;
+ this._has_wrapAlignment = true;
+ }
+
+ /**
+ * Sets the value of field 'xpos'.
+ *
+ * @param xpos
+ * the value of field 'xpos'.
+ */
+ public void setXpos(final int xpos)
+ {
+ this._xpos = xpos;
+ this._has_xpos = true;
+ }
+
+ /**
+ * Sets the value of field 'ypos'.
+ *
+ * @param ypos
+ * the value of field 'ypos'.
+ */
+ public void setYpos(final int ypos)
+ {
+ this._ypos = ypos;
+ this._has_ypos = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.Viewport
+ */
+ public static jalview.schemabinding.version2.Viewport unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.Viewport) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.Viewport.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
git://source.jalview.org / jalview.git / blobdiff