--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
+\r
+/**\r
+ * Class Viewport.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class Viewport implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _conservationSelected\r
+ */\r
+ private boolean _conservationSelected;\r
+\r
+ /**\r
+ * keeps track of state for field: _conservationSelected\r
+ */\r
+ private boolean _has_conservationSelected;\r
+\r
+ /**\r
+ * Field _pidSelected\r
+ */\r
+ private boolean _pidSelected;\r
+\r
+ /**\r
+ * keeps track of state for field: _pidSelected\r
+ */\r
+ private boolean _has_pidSelected;\r
+\r
+ /**\r
+ * Field _bgColour\r
+ */\r
+ private java.lang.String _bgColour;\r
+\r
+ /**\r
+ * Field _consThreshold\r
+ */\r
+ private int _consThreshold;\r
+\r
+ /**\r
+ * keeps track of state for field: _consThreshold\r
+ */\r
+ private boolean _has_consThreshold;\r
+\r
+ /**\r
+ * Field _pidThreshold\r
+ */\r
+ private int _pidThreshold;\r
+\r
+ /**\r
+ * keeps track of state for field: _pidThreshold\r
+ */\r
+ private boolean _has_pidThreshold;\r
+\r
+ /**\r
+ * Field _title\r
+ */\r
+ private java.lang.String _title;\r
+\r
+ /**\r
+ * Field _showFullId\r
+ */\r
+ private boolean _showFullId;\r
+\r
+ /**\r
+ * keeps track of state for field: _showFullId\r
+ */\r
+ private boolean _has_showFullId;\r
+\r
+ /**\r
+ * Field _showText\r
+ */\r
+ private boolean _showText;\r
+\r
+ /**\r
+ * keeps track of state for field: _showText\r
+ */\r
+ private boolean _has_showText;\r
+\r
+ /**\r
+ * Field _showColourText\r
+ */\r
+ private boolean _showColourText;\r
+\r
+ /**\r
+ * keeps track of state for field: _showColourText\r
+ */\r
+ private boolean _has_showColourText;\r
+\r
+ /**\r
+ * Field _showBoxes\r
+ */\r
+ private boolean _showBoxes;\r
+\r
+ /**\r
+ * keeps track of state for field: _showBoxes\r
+ */\r
+ private boolean _has_showBoxes;\r
+\r
+ /**\r
+ * Field _wrapAlignment\r
+ */\r
+ private boolean _wrapAlignment;\r
+\r
+ /**\r
+ * keeps track of state for field: _wrapAlignment\r
+ */\r
+ private boolean _has_wrapAlignment;\r
+\r
+ /**\r
+ * Field _renderGaps\r
+ */\r
+ private boolean _renderGaps;\r
+\r
+ /**\r
+ * keeps track of state for field: _renderGaps\r
+ */\r
+ private boolean _has_renderGaps;\r
+\r
+ /**\r
+ * Field _showSequenceFeatures\r
+ */\r
+ private boolean _showSequenceFeatures;\r
+\r
+ /**\r
+ * keeps track of state for field: _showSequenceFeatures\r
+ */\r
+ private boolean _has_showSequenceFeatures;\r
+\r
+ /**\r
+ * Field _showAnnotation\r
+ */\r
+ private boolean _showAnnotation;\r
+\r
+ /**\r
+ * keeps track of state for field: _showAnnotation\r
+ */\r
+ private boolean _has_showAnnotation;\r
+\r
+ /**\r
+ * Field _showConservation\r
+ */\r
+ private boolean _showConservation;\r
+\r
+ /**\r
+ * keeps track of state for field: _showConservation\r
+ */\r
+ private boolean _has_showConservation;\r
+\r
+ /**\r
+ * Field _showQuality\r
+ */\r
+ private boolean _showQuality;\r
+\r
+ /**\r
+ * keeps track of state for field: _showQuality\r
+ */\r
+ private boolean _has_showQuality;\r
+\r
+ /**\r
+ * Field _showIdentity\r
+ */\r
+ private boolean _showIdentity;\r
+\r
+ /**\r
+ * keeps track of state for field: _showIdentity\r
+ */\r
+ private boolean _has_showIdentity;\r
+\r
+ /**\r
+ * Field _xpos\r
+ */\r
+ private int _xpos;\r
+\r
+ /**\r
+ * keeps track of state for field: _xpos\r
+ */\r
+ private boolean _has_xpos;\r
+\r
+ /**\r
+ * Field _ypos\r
+ */\r
+ private int _ypos;\r
+\r
+ /**\r
+ * keeps track of state for field: _ypos\r
+ */\r
+ private boolean _has_ypos;\r
+\r
+ /**\r
+ * Field _width\r
+ */\r
+ private int _width;\r
+\r
+ /**\r
+ * keeps track of state for field: _width\r
+ */\r
+ private boolean _has_width;\r
+\r
+ /**\r
+ * Field _height\r
+ */\r
+ private int _height;\r
+\r
+ /**\r
+ * keeps track of state for field: _height\r
+ */\r
+ private boolean _has_height;\r
+\r
+ /**\r
+ * Field _startRes\r
+ */\r
+ private int _startRes;\r
+\r
+ /**\r
+ * keeps track of state for field: _startRes\r
+ */\r
+ private boolean _has_startRes;\r
+\r
+ /**\r
+ * Field _startSeq\r
+ */\r
+ private int _startSeq;\r
+\r
+ /**\r
+ * keeps track of state for field: _startSeq\r
+ */\r
+ private boolean _has_startSeq;\r
+\r
+ /**\r
+ * Field _fontName\r
+ */\r
+ private java.lang.String _fontName;\r
+\r
+ /**\r
+ * Field _fontSize\r
+ */\r
+ private int _fontSize;\r
+\r
+ /**\r
+ * keeps track of state for field: _fontSize\r
+ */\r
+ private boolean _has_fontSize;\r
+\r
+ /**\r
+ * Field _fontStyle\r
+ */\r
+ private int _fontStyle;\r
+\r
+ /**\r
+ * keeps track of state for field: _fontStyle\r
+ */\r
+ private boolean _has_fontStyle;\r
+\r
+ /**\r
+ * Field _annotationColours\r
+ */\r
+ private jalview.schemabinding.version2.AnnotationColours _annotationColours;\r
+\r
+ /**\r
+ * Field _hiddenColumnsList\r
+ */\r
+ private java.util.Vector _hiddenColumnsList;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Viewport() {\r
+ super();\r
+ _hiddenColumnsList = new Vector();\r
+ } //-- jalview.schemabinding.version2.Viewport()\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method addHiddenColumns\r
+ * \r
+ * \r
+ * \r
+ * @param vHiddenColumns\r
+ */\r
+ public void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _hiddenColumnsList.addElement(vHiddenColumns);\r
+ } //-- void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns) \r
+\r
+ /**\r
+ * Method addHiddenColumns\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vHiddenColumns\r
+ */\r
+ public void addHiddenColumns(int index, jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _hiddenColumnsList.insertElementAt(vHiddenColumns, index);\r
+ } //-- void addHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns) \r
+\r
+ /**\r
+ * Method deleteConsThreshold\r
+ * \r
+ */\r
+ public void deleteConsThreshold()\r
+ {\r
+ this._has_consThreshold= false;\r
+ } //-- void deleteConsThreshold() \r
+\r
+ /**\r
+ * Method deleteConservationSelected\r
+ * \r
+ */\r
+ public void deleteConservationSelected()\r
+ {\r
+ this._has_conservationSelected= false;\r
+ } //-- void deleteConservationSelected() \r
+\r
+ /**\r
+ * Method deleteFontSize\r
+ * \r
+ */\r
+ public void deleteFontSize()\r
+ {\r
+ this._has_fontSize= false;\r
+ } //-- void deleteFontSize() \r
+\r
+ /**\r
+ * Method deleteFontStyle\r
+ * \r
+ */\r
+ public void deleteFontStyle()\r
+ {\r
+ this._has_fontStyle= false;\r
+ } //-- void deleteFontStyle() \r
+\r
+ /**\r
+ * Method deleteHeight\r
+ * \r
+ */\r
+ public void deleteHeight()\r
+ {\r
+ this._has_height= false;\r
+ } //-- void deleteHeight() \r
+\r
+ /**\r
+ * Method deletePidSelected\r
+ * \r
+ */\r
+ public void deletePidSelected()\r
+ {\r
+ this._has_pidSelected= false;\r
+ } //-- void deletePidSelected() \r
+\r
+ /**\r
+ * Method deletePidThreshold\r
+ * \r
+ */\r
+ public void deletePidThreshold()\r
+ {\r
+ this._has_pidThreshold= false;\r
+ } //-- void deletePidThreshold() \r
+\r
+ /**\r
+ * Method deleteRenderGaps\r
+ * \r
+ */\r
+ public void deleteRenderGaps()\r
+ {\r
+ this._has_renderGaps= false;\r
+ } //-- void deleteRenderGaps() \r
+\r
+ /**\r
+ * Method deleteShowAnnotation\r
+ * \r
+ */\r
+ public void deleteShowAnnotation()\r
+ {\r
+ this._has_showAnnotation= false;\r
+ } //-- void deleteShowAnnotation() \r
+\r
+ /**\r
+ * Method deleteShowBoxes\r
+ * \r
+ */\r
+ public void deleteShowBoxes()\r
+ {\r
+ this._has_showBoxes= false;\r
+ } //-- void deleteShowBoxes() \r
+\r
+ /**\r
+ * Method deleteShowColourText\r
+ * \r
+ */\r
+ public void deleteShowColourText()\r
+ {\r
+ this._has_showColourText= false;\r
+ } //-- void deleteShowColourText() \r
+\r
+ /**\r
+ * Method deleteShowConservation\r
+ * \r
+ */\r
+ public void deleteShowConservation()\r
+ {\r
+ this._has_showConservation= false;\r
+ } //-- void deleteShowConservation() \r
+\r
+ /**\r
+ * Method deleteShowFullId\r
+ * \r
+ */\r
+ public void deleteShowFullId()\r
+ {\r
+ this._has_showFullId= false;\r
+ } //-- void deleteShowFullId() \r
+\r
+ /**\r
+ * Method deleteShowIdentity\r
+ * \r
+ */\r
+ public void deleteShowIdentity()\r
+ {\r
+ this._has_showIdentity= false;\r
+ } //-- void deleteShowIdentity() \r
+\r
+ /**\r
+ * Method deleteShowQuality\r
+ * \r
+ */\r
+ public void deleteShowQuality()\r
+ {\r
+ this._has_showQuality= false;\r
+ } //-- void deleteShowQuality() \r
+\r
+ /**\r
+ * Method deleteShowSequenceFeatures\r
+ * \r
+ */\r
+ public void deleteShowSequenceFeatures()\r
+ {\r
+ this._has_showSequenceFeatures= false;\r
+ } //-- void deleteShowSequenceFeatures() \r
+\r
+ /**\r
+ * Method deleteShowText\r
+ * \r
+ */\r
+ public void deleteShowText()\r
+ {\r
+ this._has_showText= false;\r
+ } //-- void deleteShowText() \r
+\r
+ /**\r
+ * Method deleteStartRes\r
+ * \r
+ */\r
+ public void deleteStartRes()\r
+ {\r
+ this._has_startRes= false;\r
+ } //-- void deleteStartRes() \r
+\r
+ /**\r
+ * Method deleteStartSeq\r
+ * \r
+ */\r
+ public void deleteStartSeq()\r
+ {\r
+ this._has_startSeq= false;\r
+ } //-- void deleteStartSeq() \r
+\r
+ /**\r
+ * Method deleteWidth\r
+ * \r
+ */\r
+ public void deleteWidth()\r
+ {\r
+ this._has_width= false;\r
+ } //-- void deleteWidth() \r
+\r
+ /**\r
+ * Method deleteWrapAlignment\r
+ * \r
+ */\r
+ public void deleteWrapAlignment()\r
+ {\r
+ this._has_wrapAlignment= false;\r
+ } //-- void deleteWrapAlignment() \r
+\r
+ /**\r
+ * Method deleteXpos\r
+ * \r
+ */\r
+ public void deleteXpos()\r
+ {\r
+ this._has_xpos= false;\r
+ } //-- void deleteXpos() \r
+\r
+ /**\r
+ * Method deleteYpos\r
+ * \r
+ */\r
+ public void deleteYpos()\r
+ {\r
+ this._has_ypos= false;\r
+ } //-- void deleteYpos() \r
+\r
+ /**\r
+ * Method enumerateHiddenColumns\r
+ * \r
+ * \r
+ * \r
+ * @return Enumeration\r
+ */\r
+ public java.util.Enumeration enumerateHiddenColumns()\r
+ {\r
+ return _hiddenColumnsList.elements();\r
+ } //-- java.util.Enumeration enumerateHiddenColumns() \r
+\r
+ /**\r
+ * Returns the value of field 'annotationColours'.\r
+ * \r
+ * @return AnnotationColours\r
+ * @return the value of field 'annotationColours'.\r
+ */\r
+ public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()\r
+ {\r
+ return this._annotationColours;\r
+ } //-- jalview.schemabinding.version2.AnnotationColours getAnnotationColours() \r
+\r
+ /**\r
+ * Returns the value of field 'bgColour'.\r
+ * \r
+ * @return String\r
+ * @return the value of field 'bgColour'.\r
+ */\r
+ public java.lang.String getBgColour()\r
+ {\r
+ return this._bgColour;\r
+ } //-- java.lang.String getBgColour() \r
+\r
+ /**\r
+ * Returns the value of field 'consThreshold'.\r
+ * \r
+ * @return int\r
+ * @return the value of field 'consThreshold'.\r
+ */\r
+ public int getConsThreshold()\r
+ {\r
+ return this._consThreshold;\r
+ } //-- int getConsThreshold() \r
+\r
+ /**\r
+ * Returns the value of field 'conservationSelected'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'conservationSelected'.\r
+ */\r
+ public boolean getConservationSelected()\r
+ {\r
+ return this._conservationSelected;\r
+ } //-- boolean getConservationSelected() \r
+\r
+ /**\r
+ * Returns the value of field 'fontName'.\r
+ * \r
+ * @return String\r
+ * @return the value of field 'fontName'.\r
+ */\r
+ public java.lang.String getFontName()\r
+ {\r
+ return this._fontName;\r
+ } //-- java.lang.String getFontName() \r
+\r
+ /**\r
+ * Returns the value of field 'fontSize'.\r
+ * \r
+ * @return int\r
+ * @return the value of field 'fontSize'.\r
+ */\r
+ public int getFontSize()\r
+ {\r
+ return this._fontSize;\r
+ } //-- int getFontSize() \r
+\r
+ /**\r
+ * Returns the value of field 'fontStyle'.\r
+ * \r
+ * @return int\r
+ * @return the value of field 'fontStyle'.\r
+ */\r
+ public int getFontStyle()\r
+ {\r
+ return this._fontStyle;\r
+ } //-- int getFontStyle() \r
+\r
+ /**\r
+ * Returns the value of field 'height'.\r
+ * \r
+ * @return int\r
+ * @return the value of field 'height'.\r
+ */\r
+ public int getHeight()\r
+ {\r
+ return this._height;\r
+ } //-- int getHeight() \r
+\r
+ /**\r
+ * Method getHiddenColumns\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return HiddenColumns\r
+ */\r
+ public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _hiddenColumnsList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.elementAt(index);\r
+ } //-- jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int) \r
+\r
+ /**\r
+ * Method getHiddenColumns\r
+ * \r
+ * \r
+ * \r
+ * @return HiddenColumns\r
+ */\r
+ public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()\r
+ {\r
+ int size = _hiddenColumnsList.size();\r
+ jalview.schemabinding.version2.HiddenColumns[] mArray = new jalview.schemabinding.version2.HiddenColumns[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns() \r
+\r
+ /**\r
+ * Method getHiddenColumnsCount\r
+ * \r
+ * \r
+ * \r
+ * @return int\r
+ */\r
+ public int getHiddenColumnsCount()\r
+ {\r
+ return _hiddenColumnsList.size();\r
+ } //-- int getHiddenColumnsCount() \r
+\r
+ /**\r
+ * Returns the value of field 'pidSelected'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'pidSelected'.\r
+ */\r
+ public boolean getPidSelected()\r
+ {\r
+ return this._pidSelected;\r
+ } //-- boolean getPidSelected() \r
+\r
+ /**\r
+ * Returns the value of field 'pidThreshold'.\r
+ * \r
+ * @return int\r
+ * @return the value of field 'pidThreshold'.\r
+ */\r
+ public int getPidThreshold()\r
+ {\r
+ return this._pidThreshold;\r
+ } //-- int getPidThreshold() \r
+\r
+ /**\r
+ * Returns the value of field 'renderGaps'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'renderGaps'.\r
+ */\r
+ public boolean getRenderGaps()\r
+ {\r
+ return this._renderGaps;\r
+ } //-- boolean getRenderGaps() \r
+\r
+ /**\r
+ * Returns the value of field 'showAnnotation'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'showAnnotation'.\r
+ */\r
+ public boolean getShowAnnotation()\r
+ {\r
+ return this._showAnnotation;\r
+ } //-- boolean getShowAnnotation() \r
+\r
+ /**\r
+ * Returns the value of field 'showBoxes'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'showBoxes'.\r
+ */\r
+ public boolean getShowBoxes()\r
+ {\r
+ return this._showBoxes;\r
+ } //-- boolean getShowBoxes() \r
+\r
+ /**\r
+ * Returns the value of field 'showColourText'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'showColourText'.\r
+ */\r
+ public boolean getShowColourText()\r
+ {\r
+ return this._showColourText;\r
+ } //-- boolean getShowColourText() \r
+\r
+ /**\r
+ * Returns the value of field 'showConservation'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'showConservation'.\r
+ */\r
+ public boolean getShowConservation()\r
+ {\r
+ return this._showConservation;\r
+ } //-- boolean getShowConservation() \r
+\r
+ /**\r
+ * Returns the value of field 'showFullId'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'showFullId'.\r
+ */\r
+ public boolean getShowFullId()\r
+ {\r
+ return this._showFullId;\r
+ } //-- boolean getShowFullId() \r
+\r
+ /**\r
+ * Returns the value of field 'showIdentity'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'showIdentity'.\r
+ */\r
+ public boolean getShowIdentity()\r
+ {\r
+ return this._showIdentity;\r
+ } //-- boolean getShowIdentity() \r
+\r
+ /**\r
+ * Returns the value of field 'showQuality'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'showQuality'.\r
+ */\r
+ public boolean getShowQuality()\r
+ {\r
+ return this._showQuality;\r
+ } //-- boolean getShowQuality() \r
+\r
+ /**\r
+ * Returns the value of field 'showSequenceFeatures'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'showSequenceFeatures'.\r
+ */\r
+ public boolean getShowSequenceFeatures()\r
+ {\r
+ return this._showSequenceFeatures;\r
+ } //-- boolean getShowSequenceFeatures() \r
+\r
+ /**\r
+ * Returns the value of field 'showText'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'showText'.\r
+ */\r
+ public boolean getShowText()\r
+ {\r
+ return this._showText;\r
+ } //-- boolean getShowText() \r
+\r
+ /**\r
+ * Returns the value of field 'startRes'.\r
+ * \r
+ * @return int\r
+ * @return the value of field 'startRes'.\r
+ */\r
+ public int getStartRes()\r
+ {\r
+ return this._startRes;\r
+ } //-- int getStartRes() \r
+\r
+ /**\r
+ * Returns the value of field 'startSeq'.\r
+ * \r
+ * @return int\r
+ * @return the value of field 'startSeq'.\r
+ */\r
+ public int getStartSeq()\r
+ {\r
+ return this._startSeq;\r
+ } //-- int getStartSeq() \r
+\r
+ /**\r
+ * Returns the value of field 'title'.\r
+ * \r
+ * @return String\r
+ * @return the value of field 'title'.\r
+ */\r
+ public java.lang.String getTitle()\r
+ {\r
+ return this._title;\r
+ } //-- java.lang.String getTitle() \r
+\r
+ /**\r
+ * Returns the value of field 'width'.\r
+ * \r
+ * @return int\r
+ * @return the value of field 'width'.\r
+ */\r
+ public int getWidth()\r
+ {\r
+ return this._width;\r
+ } //-- int getWidth() \r
+\r
+ /**\r
+ * Returns the value of field 'wrapAlignment'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'wrapAlignment'.\r
+ */\r
+ public boolean getWrapAlignment()\r
+ {\r
+ return this._wrapAlignment;\r
+ } //-- boolean getWrapAlignment() \r
+\r
+ /**\r
+ * Returns the value of field 'xpos'.\r
+ * \r
+ * @return int\r
+ * @return the value of field 'xpos'.\r
+ */\r
+ public int getXpos()\r
+ {\r
+ return this._xpos;\r
+ } //-- int getXpos() \r
+\r
+ /**\r
+ * Returns the value of field 'ypos'.\r
+ * \r
+ * @return int\r
+ * @return the value of field 'ypos'.\r
+ */\r
+ public int getYpos()\r
+ {\r
+ return this._ypos;\r
+ } //-- int getYpos() \r
+\r
+ /**\r
+ * Method hasConsThreshold\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasConsThreshold()\r
+ {\r
+ return this._has_consThreshold;\r
+ } //-- boolean hasConsThreshold() \r
+\r
+ /**\r
+ * Method hasConservationSelected\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasConservationSelected()\r
+ {\r
+ return this._has_conservationSelected;\r
+ } //-- boolean hasConservationSelected() \r
+\r
+ /**\r
+ * Method hasFontSize\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasFontSize()\r
+ {\r
+ return this._has_fontSize;\r
+ } //-- boolean hasFontSize() \r
+\r
+ /**\r
+ * Method hasFontStyle\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasFontStyle()\r
+ {\r
+ return this._has_fontStyle;\r
+ } //-- boolean hasFontStyle() \r
+\r
+ /**\r
+ * Method hasHeight\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasHeight()\r
+ {\r
+ return this._has_height;\r
+ } //-- boolean hasHeight() \r
+\r
+ /**\r
+ * Method hasPidSelected\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasPidSelected()\r
+ {\r
+ return this._has_pidSelected;\r
+ } //-- boolean hasPidSelected() \r
+\r
+ /**\r
+ * Method hasPidThreshold\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasPidThreshold()\r
+ {\r
+ return this._has_pidThreshold;\r
+ } //-- boolean hasPidThreshold() \r
+\r
+ /**\r
+ * Method hasRenderGaps\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasRenderGaps()\r
+ {\r
+ return this._has_renderGaps;\r
+ } //-- boolean hasRenderGaps() \r
+\r
+ /**\r
+ * Method hasShowAnnotation\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasShowAnnotation()\r
+ {\r
+ return this._has_showAnnotation;\r
+ } //-- boolean hasShowAnnotation() \r
+\r
+ /**\r
+ * Method hasShowBoxes\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasShowBoxes()\r
+ {\r
+ return this._has_showBoxes;\r
+ } //-- boolean hasShowBoxes() \r
+\r
+ /**\r
+ * Method hasShowColourText\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasShowColourText()\r
+ {\r
+ return this._has_showColourText;\r
+ } //-- boolean hasShowColourText() \r
+\r
+ /**\r
+ * Method hasShowConservation\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasShowConservation()\r
+ {\r
+ return this._has_showConservation;\r
+ } //-- boolean hasShowConservation() \r
+\r
+ /**\r
+ * Method hasShowFullId\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasShowFullId()\r
+ {\r
+ return this._has_showFullId;\r
+ } //-- boolean hasShowFullId() \r
+\r
+ /**\r
+ * Method hasShowIdentity\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasShowIdentity()\r
+ {\r
+ return this._has_showIdentity;\r
+ } //-- boolean hasShowIdentity() \r
+\r
+ /**\r
+ * Method hasShowQuality\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasShowQuality()\r
+ {\r
+ return this._has_showQuality;\r
+ } //-- boolean hasShowQuality() \r
+\r
+ /**\r
+ * Method hasShowSequenceFeatures\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasShowSequenceFeatures()\r
+ {\r
+ return this._has_showSequenceFeatures;\r
+ } //-- boolean hasShowSequenceFeatures() \r
+\r
+ /**\r
+ * Method hasShowText\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasShowText()\r
+ {\r
+ return this._has_showText;\r
+ } //-- boolean hasShowText() \r
+\r
+ /**\r
+ * Method hasStartRes\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasStartRes()\r
+ {\r
+ return this._has_startRes;\r
+ } //-- boolean hasStartRes() \r
+\r
+ /**\r
+ * Method hasStartSeq\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasStartSeq()\r
+ {\r
+ return this._has_startSeq;\r
+ } //-- boolean hasStartSeq() \r
+\r
+ /**\r
+ * Method hasWidth\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasWidth()\r
+ {\r
+ return this._has_width;\r
+ } //-- boolean hasWidth() \r
+\r
+ /**\r
+ * Method hasWrapAlignment\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasWrapAlignment()\r
+ {\r
+ return this._has_wrapAlignment;\r
+ } //-- boolean hasWrapAlignment() \r
+\r
+ /**\r
+ * Method hasXpos\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasXpos()\r
+ {\r
+ return this._has_xpos;\r
+ } //-- boolean hasXpos() \r
+\r
+ /**\r
+ * Method hasYpos\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasYpos()\r
+ {\r
+ return this._has_ypos;\r
+ } //-- boolean hasYpos() \r
+\r
+ /**\r
+ * Method isValid\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean isValid()\r
+ {\r
+ try {\r
+ validate();\r
+ }\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\r
+ }\r
+ return true;\r
+ } //-- boolean isValid() \r
+\r
+ /**\r
+ * Method marshal\r
+ * \r
+ * \r
+ * \r
+ * @param out\r
+ */\r
+ public void marshal(java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, out);\r
+ } //-- void marshal(java.io.Writer) \r
+\r
+ /**\r
+ * Method marshal\r
+ * \r
+ * \r
+ * \r
+ * @param handler\r
+ */\r
+ public void marshal(org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, handler);\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+ /**\r
+ * Method removeAllHiddenColumns\r
+ * \r
+ */\r
+ public void removeAllHiddenColumns()\r
+ {\r
+ _hiddenColumnsList.removeAllElements();\r
+ } //-- void removeAllHiddenColumns() \r
+\r
+ /**\r
+ * Method removeHiddenColumns\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return HiddenColumns\r
+ */\r
+ public jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int index)\r
+ {\r
+ java.lang.Object obj = _hiddenColumnsList.elementAt(index);\r
+ _hiddenColumnsList.removeElementAt(index);\r
+ return (jalview.schemabinding.version2.HiddenColumns) obj;\r
+ } //-- jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int) \r
+\r
+ /**\r
+ * Sets the value of field 'annotationColours'.\r
+ * \r
+ * @param annotationColours the value of field\r
+ * 'annotationColours'.\r
+ */\r
+ public void setAnnotationColours(jalview.schemabinding.version2.AnnotationColours annotationColours)\r
+ {\r
+ this._annotationColours = annotationColours;\r
+ } //-- void setAnnotationColours(jalview.schemabinding.version2.AnnotationColours) \r
+\r
+ /**\r
+ * Sets the value of field 'bgColour'.\r
+ * \r
+ * @param bgColour the value of field 'bgColour'.\r
+ */\r
+ public void setBgColour(java.lang.String bgColour)\r
+ {\r
+ this._bgColour = bgColour;\r
+ } //-- void setBgColour(java.lang.String) \r
+\r
+ /**\r
+ * Sets the value of field 'consThreshold'.\r
+ * \r
+ * @param consThreshold the value of field 'consThreshold'.\r
+ */\r
+ public void setConsThreshold(int consThreshold)\r
+ {\r
+ this._consThreshold = consThreshold;\r
+ this._has_consThreshold = true;\r
+ } //-- void setConsThreshold(int) \r
+\r
+ /**\r
+ * Sets the value of field 'conservationSelected'.\r
+ * \r
+ * @param conservationSelected the value of field\r
+ * 'conservationSelected'.\r
+ */\r
+ public void setConservationSelected(boolean conservationSelected)\r
+ {\r
+ this._conservationSelected = conservationSelected;\r
+ this._has_conservationSelected = true;\r
+ } //-- void setConservationSelected(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'fontName'.\r
+ * \r
+ * @param fontName the value of field 'fontName'.\r
+ */\r
+ public void setFontName(java.lang.String fontName)\r
+ {\r
+ this._fontName = fontName;\r
+ } //-- void setFontName(java.lang.String) \r
+\r
+ /**\r
+ * Sets the value of field 'fontSize'.\r
+ * \r
+ * @param fontSize the value of field 'fontSize'.\r
+ */\r
+ public void setFontSize(int fontSize)\r
+ {\r
+ this._fontSize = fontSize;\r
+ this._has_fontSize = true;\r
+ } //-- void setFontSize(int) \r
+\r
+ /**\r
+ * Sets the value of field 'fontStyle'.\r
+ * \r
+ * @param fontStyle the value of field 'fontStyle'.\r
+ */\r
+ public void setFontStyle(int fontStyle)\r
+ {\r
+ this._fontStyle = fontStyle;\r
+ this._has_fontStyle = true;\r
+ } //-- void setFontStyle(int) \r
+\r
+ /**\r
+ * Sets the value of field 'height'.\r
+ * \r
+ * @param height the value of field 'height'.\r
+ */\r
+ public void setHeight(int height)\r
+ {\r
+ this._height = height;\r
+ this._has_height = true;\r
+ } //-- void setHeight(int) \r
+\r
+ /**\r
+ * Method setHiddenColumns\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vHiddenColumns\r
+ */\r
+ public void setHiddenColumns(int index, jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _hiddenColumnsList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ _hiddenColumnsList.setElementAt(vHiddenColumns, index);\r
+ } //-- void setHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns) \r
+\r
+ /**\r
+ * Method setHiddenColumns\r
+ * \r
+ * \r
+ * \r
+ * @param hiddenColumnsArray\r
+ */\r
+ public void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns[] hiddenColumnsArray)\r
+ {\r
+ //-- copy array\r
+ _hiddenColumnsList.removeAllElements();\r
+ for (int i = 0; i < hiddenColumnsArray.length; i++) {\r
+ _hiddenColumnsList.addElement(hiddenColumnsArray[i]);\r
+ }\r
+ } //-- void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns) \r
+\r
+ /**\r
+ * Sets the value of field 'pidSelected'.\r
+ * \r
+ * @param pidSelected the value of field 'pidSelected'.\r
+ */\r
+ public void setPidSelected(boolean pidSelected)\r
+ {\r
+ this._pidSelected = pidSelected;\r
+ this._has_pidSelected = true;\r
+ } //-- void setPidSelected(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'pidThreshold'.\r
+ * \r
+ * @param pidThreshold the value of field 'pidThreshold'.\r
+ */\r
+ public void setPidThreshold(int pidThreshold)\r
+ {\r
+ this._pidThreshold = pidThreshold;\r
+ this._has_pidThreshold = true;\r
+ } //-- void setPidThreshold(int) \r
+\r
+ /**\r
+ * Sets the value of field 'renderGaps'.\r
+ * \r
+ * @param renderGaps the value of field 'renderGaps'.\r
+ */\r
+ public void setRenderGaps(boolean renderGaps)\r
+ {\r
+ this._renderGaps = renderGaps;\r
+ this._has_renderGaps = true;\r
+ } //-- void setRenderGaps(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'showAnnotation'.\r
+ * \r
+ * @param showAnnotation the value of field 'showAnnotation'.\r
+ */\r
+ public void setShowAnnotation(boolean showAnnotation)\r
+ {\r
+ this._showAnnotation = showAnnotation;\r
+ this._has_showAnnotation = true;\r
+ } //-- void setShowAnnotation(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'showBoxes'.\r
+ * \r
+ * @param showBoxes the value of field 'showBoxes'.\r
+ */\r
+ public void setShowBoxes(boolean showBoxes)\r
+ {\r
+ this._showBoxes = showBoxes;\r
+ this._has_showBoxes = true;\r
+ } //-- void setShowBoxes(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'showColourText'.\r
+ * \r
+ * @param showColourText the value of field 'showColourText'.\r
+ */\r
+ public void setShowColourText(boolean showColourText)\r
+ {\r
+ this._showColourText = showColourText;\r
+ this._has_showColourText = true;\r
+ } //-- void setShowColourText(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'showConservation'.\r
+ * \r
+ * @param showConservation the value of field 'showConservation'\r
+ */\r
+ public void setShowConservation(boolean showConservation)\r
+ {\r
+ this._showConservation = showConservation;\r
+ this._has_showConservation = true;\r
+ } //-- void setShowConservation(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'showFullId'.\r
+ * \r
+ * @param showFullId the value of field 'showFullId'.\r
+ */\r
+ public void setShowFullId(boolean showFullId)\r
+ {\r
+ this._showFullId = showFullId;\r
+ this._has_showFullId = true;\r
+ } //-- void setShowFullId(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'showIdentity'.\r
+ * \r
+ * @param showIdentity the value of field 'showIdentity'.\r
+ */\r
+ public void setShowIdentity(boolean showIdentity)\r
+ {\r
+ this._showIdentity = showIdentity;\r
+ this._has_showIdentity = true;\r
+ } //-- void setShowIdentity(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'showQuality'.\r
+ * \r
+ * @param showQuality the value of field 'showQuality'.\r
+ */\r
+ public void setShowQuality(boolean showQuality)\r
+ {\r
+ this._showQuality = showQuality;\r
+ this._has_showQuality = true;\r
+ } //-- void setShowQuality(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'showSequenceFeatures'.\r
+ * \r
+ * @param showSequenceFeatures the value of field\r
+ * 'showSequenceFeatures'.\r
+ */\r
+ public void setShowSequenceFeatures(boolean showSequenceFeatures)\r
+ {\r
+ this._showSequenceFeatures = showSequenceFeatures;\r
+ this._has_showSequenceFeatures = true;\r
+ } //-- void setShowSequenceFeatures(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'showText'.\r
+ * \r
+ * @param showText the value of field 'showText'.\r
+ */\r
+ public void setShowText(boolean showText)\r
+ {\r
+ this._showText = showText;\r
+ this._has_showText = true;\r
+ } //-- void setShowText(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'startRes'.\r
+ * \r
+ * @param startRes the value of field 'startRes'.\r
+ */\r
+ public void setStartRes(int startRes)\r
+ {\r
+ this._startRes = startRes;\r
+ this._has_startRes = true;\r
+ } //-- void setStartRes(int) \r
+\r
+ /**\r
+ * Sets the value of field 'startSeq'.\r
+ * \r
+ * @param startSeq the value of field 'startSeq'.\r
+ */\r
+ public void setStartSeq(int startSeq)\r
+ {\r
+ this._startSeq = startSeq;\r
+ this._has_startSeq = true;\r
+ } //-- void setStartSeq(int) \r
+\r
+ /**\r
+ * Sets the value of field 'title'.\r
+ * \r
+ * @param title the value of field 'title'.\r
+ */\r
+ public void setTitle(java.lang.String title)\r
+ {\r
+ this._title = title;\r
+ } //-- void setTitle(java.lang.String) \r
+\r
+ /**\r
+ * Sets the value of field 'width'.\r
+ * \r
+ * @param width the value of field 'width'.\r
+ */\r
+ public void setWidth(int width)\r
+ {\r
+ this._width = width;\r
+ this._has_width = true;\r
+ } //-- void setWidth(int) \r
+\r
+ /**\r
+ * Sets the value of field 'wrapAlignment'.\r
+ * \r
+ * @param wrapAlignment the value of field 'wrapAlignment'.\r
+ */\r
+ public void setWrapAlignment(boolean wrapAlignment)\r
+ {\r
+ this._wrapAlignment = wrapAlignment;\r
+ this._has_wrapAlignment = true;\r
+ } //-- void setWrapAlignment(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'xpos'.\r
+ * \r
+ * @param xpos the value of field 'xpos'.\r
+ */\r
+ public void setXpos(int xpos)\r
+ {\r
+ this._xpos = xpos;\r
+ this._has_xpos = true;\r
+ } //-- void setXpos(int) \r
+\r
+ /**\r
+ * Sets the value of field 'ypos'.\r
+ * \r
+ * @param ypos the value of field 'ypos'.\r
+ */\r
+ public void setYpos(int ypos)\r
+ {\r
+ this._ypos = ypos;\r
+ this._has_ypos = true;\r
+ } //-- void setYpos(int) \r
+\r
+ /**\r
+ * Method unmarshal\r
+ * \r
+ * \r
+ * \r
+ * @param reader\r
+ * @return Object\r
+ */\r
+ public static java.lang.Object unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(jalview.schemabinding.version2.Viewport.class, reader);\r
+ } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+ /**\r
+ * Method validate\r
+ * \r
+ */\r
+ public void validate()\r
+ throws org.exolab.castor.xml.ValidationException\r
+ {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ } //-- void validate() \r
+\r
+}\r
git://source.jalview.org / jalview.git / blobdiff