X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FViewport.java;h=948d7d0da5aeaa4dd1caae7fcbdda928600f9fd9;hb=7243db3d99cc1760c2d4802f3005b4f86d1b4bd6;hp=978ab5cb229be080d8544e466a6d8514f0808a23;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git
diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java
old mode 100755
new mode 100644
index 978ab5c..948d7d0
--- a/src/jalview/schemabinding/version2/Viewport.java
+++ b/src/jalview/schemabinding/version2/Viewport.java
@@ -1,1773 +1,2451 @@
-/*
- * This class was automatically generated with
- * Castor 0.9.6, using an XML
- * Schema.
- * $Id$
- */
-
-package jalview.schemabinding.version2;
-
-//---------------------------------/
-//- Imported classes and packages -/
-//---------------------------------/
-
-import java.util.*;
-
-import org.exolab.castor.xml.*;
-
-/**
- * Class Viewport.
- *
- * @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 _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 _showAnnotation
- */
- private boolean _showAnnotation;
-
- /**
- * keeps track of state for field: _showAnnotation
- */
- private boolean _has_showAnnotation;
-
- /**
- * 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 _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 _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 _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;
-
- /**
- * Field _annotationColours
- */
- private jalview.schemabinding.version2.AnnotationColours _annotationColours;
-
- /**
- * Field _hiddenColumnsList
- */
- private java.util.Vector _hiddenColumnsList;
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Viewport()
- {
- super();
- _hiddenColumnsList = new Vector();
- } //-- jalview.schemabinding.version2.Viewport()
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addHiddenColumns
- *
- *
- *
- * @param vHiddenColumns
- */
- public void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns
- vHiddenColumns)
- throws java.lang.IndexOutOfBoundsException
- {
- _hiddenColumnsList.addElement(vHiddenColumns);
- } //-- void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns)
-
- /**
- * Method addHiddenColumns
- *
- *
- *
- * @param index
- * @param vHiddenColumns
- */
- public void addHiddenColumns(int index,
- jalview.schemabinding.version2.HiddenColumns
- vHiddenColumns)
- throws java.lang.IndexOutOfBoundsException
- {
- _hiddenColumnsList.insertElementAt(vHiddenColumns, index);
- } //-- void addHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns)
-
- /**
- * Method deleteConsThreshold
- *
- */
- public void deleteConsThreshold()
- {
- this._has_consThreshold = false;
- } //-- void deleteConsThreshold()
-
- /**
- * Method deleteConservationSelected
- *
- */
- public void deleteConservationSelected()
- {
- this._has_conservationSelected = false;
- } //-- void deleteConservationSelected()
-
- /**
- * Method deleteFontSize
- *
- */
- public void deleteFontSize()
- {
- this._has_fontSize = false;
- } //-- void deleteFontSize()
-
- /**
- * Method deleteFontStyle
- *
- */
- public void deleteFontStyle()
- {
- this._has_fontStyle = false;
- } //-- void deleteFontStyle()
-
- /**
- * Method deleteGatheredViews
- *
- */
- public void deleteGatheredViews()
- {
- this._has_gatheredViews = false;
- } //-- void deleteGatheredViews()
-
- /**
- * Method deleteHeight
- *
- */
- public void deleteHeight()
- {
- this._has_height = false;
- } //-- void deleteHeight()
-
- /**
- * Method deletePidSelected
- *
- */
- public void deletePidSelected()
- {
- this._has_pidSelected = false;
- } //-- void deletePidSelected()
-
- /**
- * Method deletePidThreshold
- *
- */
- public void deletePidThreshold()
- {
- this._has_pidThreshold = false;
- } //-- void deletePidThreshold()
-
- /**
- * Method deleteRenderGaps
- *
- */
- public void deleteRenderGaps()
- {
- this._has_renderGaps = false;
- } //-- void deleteRenderGaps()
-
- /**
- * Method deleteRightAlignIds
- *
- */
- public void deleteRightAlignIds()
- {
- this._has_rightAlignIds = false;
- } //-- void deleteRightAlignIds()
-
- /**
- * Method deleteShowAnnotation
- *
- */
- public void deleteShowAnnotation()
- {
- this._has_showAnnotation = false;
- } //-- void deleteShowAnnotation()
-
- /**
- * Method deleteShowBoxes
- *
- */
- public void deleteShowBoxes()
- {
- this._has_showBoxes = false;
- } //-- void deleteShowBoxes()
-
- /**
- * Method deleteShowColourText
- *
- */
- public void deleteShowColourText()
- {
- this._has_showColourText = false;
- } //-- void deleteShowColourText()
-
- /**
- * Method deleteShowFullId
- *
- */
- public void deleteShowFullId()
- {
- this._has_showFullId = false;
- } //-- void deleteShowFullId()
-
- /**
- * Method deleteShowSequenceFeatures
- *
- */
- public void deleteShowSequenceFeatures()
- {
- this._has_showSequenceFeatures = false;
- } //-- void deleteShowSequenceFeatures()
-
- /**
- * Method deleteShowText
- *
- */
- public void deleteShowText()
- {
- this._has_showText = false;
- } //-- void deleteShowText()
-
- /**
- * Method deleteStartRes
- *
- */
- public void deleteStartRes()
- {
- this._has_startRes = false;
- } //-- void deleteStartRes()
-
- /**
- * Method deleteStartSeq
- *
- */
- public void deleteStartSeq()
- {
- this._has_startSeq = false;
- } //-- void deleteStartSeq()
-
- /**
- * Method deleteTextCol1
- *
- */
- public void deleteTextCol1()
- {
- this._has_textCol1 = false;
- } //-- void deleteTextCol1()
-
- /**
- * Method deleteTextCol2
- *
- */
- public void deleteTextCol2()
- {
- this._has_textCol2 = false;
- } //-- void deleteTextCol2()
-
- /**
- * Method deleteTextColThreshold
- *
- */
- public void deleteTextColThreshold()
- {
- this._has_textColThreshold = false;
- } //-- void deleteTextColThreshold()
-
- /**
- * Method deleteWidth
- *
- */
- public void deleteWidth()
- {
- this._has_width = false;
- } //-- void deleteWidth()
-
- /**
- * Method deleteWrapAlignment
- *
- */
- public void deleteWrapAlignment()
- {
- this._has_wrapAlignment = false;
- } //-- void deleteWrapAlignment()
-
- /**
- * Method deleteXpos
- *
- */
- public void deleteXpos()
- {
- this._has_xpos = false;
- } //-- void deleteXpos()
-
- /**
- * Method deleteYpos
- *
- */
- public void deleteYpos()
- {
- this._has_ypos = false;
- } //-- void deleteYpos()
-
- /**
- * Method enumerateHiddenColumns
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateHiddenColumns()
- {
- return _hiddenColumnsList.elements();
- } //-- java.util.Enumeration enumerateHiddenColumns()
-
- /**
- * Returns the value of field 'annotationColours'.
- *
- * @return AnnotationColours
- * @return the value of field 'annotationColours'.
- */
- public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()
- {
- return this._annotationColours;
- } //-- jalview.schemabinding.version2.AnnotationColours getAnnotationColours()
-
- /**
- * Returns the value of field 'bgColour'.
- *
- * @return String
- * @return the value of field 'bgColour'.
- */
- public java.lang.String getBgColour()
- {
- return this._bgColour;
- } //-- java.lang.String getBgColour()
-
- /**
- * Returns the value of field 'consThreshold'.
- *
- * @return int
- * @return the value of field 'consThreshold'.
- */
- public int getConsThreshold()
- {
- return this._consThreshold;
- } //-- int getConsThreshold()
-
- /**
- * Returns the value of field 'conservationSelected'.
- *
- * @return boolean
- * @return the value of field 'conservationSelected'.
- */
- public boolean getConservationSelected()
- {
- return this._conservationSelected;
- } //-- boolean getConservationSelected()
-
- /**
- * Returns the value of field 'fontName'.
- *
- * @return String
- * @return the value of field 'fontName'.
- */
- public java.lang.String getFontName()
- {
- return this._fontName;
- } //-- java.lang.String getFontName()
-
- /**
- * Returns the value of field 'fontSize'.
- *
- * @return int
- * @return the value of field 'fontSize'.
- */
- public int getFontSize()
- {
- return this._fontSize;
- } //-- int getFontSize()
-
- /**
- * Returns the value of field 'fontStyle'.
- *
- * @return int
- * @return the value of field 'fontStyle'.
- */
- public int getFontStyle()
- {
- return this._fontStyle;
- } //-- int getFontStyle()
-
- /**
- * Returns the value of field 'gatheredViews'.
- *
- * @return boolean
- * @return the value of field 'gatheredViews'.
- */
- public boolean getGatheredViews()
- {
- return this._gatheredViews;
- } //-- boolean getGatheredViews()
-
- /**
- * Returns the value of field 'height'.
- *
- * @return int
- * @return the value of field 'height'.
- */
- public int getHeight()
- {
- return this._height;
- } //-- int getHeight()
-
- /**
- * Method getHiddenColumns
- *
- *
- *
- * @param index
- * @return HiddenColumns
- */
- public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int
- index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ( (index < 0) || (index > _hiddenColumnsList.size()))
- {
- throw new IndexOutOfBoundsException();
- }
-
- return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.
- elementAt(index);
- } //-- jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int)
-
- /**
- * Method getHiddenColumns
- *
- *
- *
- * @return HiddenColumns
- */
- public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()
- {
- int size = _hiddenColumnsList.size();
- jalview.schemabinding.version2.HiddenColumns[] mArray = new jalview.
- schemabinding.version2.HiddenColumns[size];
- for (int index = 0; index < size; index++)
- {
- mArray[index] = (jalview.schemabinding.version2.HiddenColumns)
- _hiddenColumnsList.elementAt(index);
- }
- return mArray;
- } //-- jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()
-
- /**
- * Method getHiddenColumnsCount
- *
- *
- *
- * @return int
- */
- public int getHiddenColumnsCount()
- {
- return _hiddenColumnsList.size();
- } //-- int getHiddenColumnsCount()
-
- /**
- * Returns the value of field 'pidSelected'.
- *
- * @return boolean
- * @return the value of field 'pidSelected'.
- */
- public boolean getPidSelected()
- {
- return this._pidSelected;
- } //-- boolean getPidSelected()
-
- /**
- * Returns the value of field 'pidThreshold'.
- *
- * @return int
- * @return the value of field 'pidThreshold'.
- */
- public int getPidThreshold()
- {
- return this._pidThreshold;
- } //-- int getPidThreshold()
-
- /**
- * Returns the value of field 'renderGaps'.
- *
- * @return boolean
- * @return the value of field 'renderGaps'.
- */
- public boolean getRenderGaps()
- {
- return this._renderGaps;
- } //-- boolean getRenderGaps()
-
- /**
- * Returns the value of field 'rightAlignIds'.
- *
- * @return boolean
- * @return the value of field 'rightAlignIds'.
- */
- public boolean getRightAlignIds()
- {
- return this._rightAlignIds;
- } //-- boolean getRightAlignIds()
-
- /**
- * Returns the value of field 'sequenceSetId'.
- *
- * @return String
- * @return the value of field 'sequenceSetId'.
- */
- public java.lang.String getSequenceSetId()
- {
- return this._sequenceSetId;
- } //-- java.lang.String getSequenceSetId()
-
- /**
- * Returns the value of field 'showAnnotation'.
- *
- * @return boolean
- * @return the value of field 'showAnnotation'.
- */
- public boolean getShowAnnotation()
- {
- return this._showAnnotation;
- } //-- boolean getShowAnnotation()
-
- /**
- * Returns the value of field 'showBoxes'.
- *
- * @return boolean
- * @return the value of field 'showBoxes'.
- */
- public boolean getShowBoxes()
- {
- return this._showBoxes;
- } //-- boolean getShowBoxes()
-
- /**
- * Returns the value of field 'showColourText'.
- *
- * @return boolean
- * @return the value of field 'showColourText'.
- */
- public boolean getShowColourText()
- {
- return this._showColourText;
- } //-- boolean getShowColourText()
-
- /**
- * Returns the value of field 'showFullId'.
- *
- * @return boolean
- * @return the value of field 'showFullId'.
- */
- public boolean getShowFullId()
- {
- return this._showFullId;
- } //-- boolean getShowFullId()
-
- /**
- * Returns the value of field 'showSequenceFeatures'.
- *
- * @return boolean
- * @return the value of field 'showSequenceFeatures'.
- */
- public boolean getShowSequenceFeatures()
- {
- return this._showSequenceFeatures;
- } //-- boolean getShowSequenceFeatures()
-
- /**
- * Returns the value of field 'showText'.
- *
- * @return boolean
- * @return the value of field 'showText'.
- */
- public boolean getShowText()
- {
- return this._showText;
- } //-- boolean getShowText()
-
- /**
- * Returns the value of field 'startRes'.
- *
- * @return int
- * @return the value of field 'startRes'.
- */
- public int getStartRes()
- {
- return this._startRes;
- } //-- int getStartRes()
-
- /**
- * Returns the value of field 'startSeq'.
- *
- * @return int
- * @return the value of field 'startSeq'.
- */
- public int getStartSeq()
- {
- return this._startSeq;
- } //-- int getStartSeq()
-
- /**
- * Returns the value of field 'textCol1'.
- *
- * @return int
- * @return the value of field 'textCol1'.
- */
- public int getTextCol1()
- {
- return this._textCol1;
- } //-- int getTextCol1()
-
- /**
- * Returns the value of field 'textCol2'.
- *
- * @return int
- * @return the value of field 'textCol2'.
- */
- public int getTextCol2()
- {
- return this._textCol2;
- } //-- int getTextCol2()
-
- /**
- * Returns the value of field 'textColThreshold'.
- *
- * @return int
- * @return the value of field 'textColThreshold'.
- */
- public int getTextColThreshold()
- {
- return this._textColThreshold;
- } //-- int getTextColThreshold()
-
- /**
- * Returns the value of field 'title'.
- *
- * @return String
- * @return the value of field 'title'.
- */
- public java.lang.String getTitle()
- {
- return this._title;
- } //-- java.lang.String getTitle()
-
- /**
- * Returns the value of field 'viewName'.
- *
- * @return String
- * @return the value of field 'viewName'.
- */
- public java.lang.String getViewName()
- {
- return this._viewName;
- } //-- java.lang.String getViewName()
-
- /**
- * Returns the value of field 'width'.
- *
- * @return int
- * @return the value of field 'width'.
- */
- public int getWidth()
- {
- return this._width;
- } //-- int getWidth()
-
- /**
- * Returns the value of field 'wrapAlignment'.
- *
- * @return boolean
- * @return the value of field 'wrapAlignment'.
- */
- public boolean getWrapAlignment()
- {
- return this._wrapAlignment;
- } //-- boolean getWrapAlignment()
-
- /**
- * Returns the value of field 'xpos'.
- *
- * @return int
- * @return the value of field 'xpos'.
- */
- public int getXpos()
- {
- return this._xpos;
- } //-- int getXpos()
-
- /**
- * Returns the value of field 'ypos'.
- *
- * @return int
- * @return the value of field 'ypos'.
- */
- public int getYpos()
- {
- return this._ypos;
- } //-- int getYpos()
-
- /**
- * Method hasConsThreshold
- *
- *
- *
- * @return boolean
- */
- public boolean hasConsThreshold()
- {
- return this._has_consThreshold;
- } //-- boolean hasConsThreshold()
-
- /**
- * Method hasConservationSelected
- *
- *
- *
- * @return boolean
- */
- public boolean hasConservationSelected()
- {
- return this._has_conservationSelected;
- } //-- boolean hasConservationSelected()
-
- /**
- * Method hasFontSize
- *
- *
- *
- * @return boolean
- */
- public boolean hasFontSize()
- {
- return this._has_fontSize;
- } //-- boolean hasFontSize()
-
- /**
- * Method hasFontStyle
- *
- *
- *
- * @return boolean
- */
- public boolean hasFontStyle()
- {
- return this._has_fontStyle;
- } //-- boolean hasFontStyle()
-
- /**
- * Method hasGatheredViews
- *
- *
- *
- * @return boolean
- */
- public boolean hasGatheredViews()
- {
- return this._has_gatheredViews;
- } //-- boolean hasGatheredViews()
-
- /**
- * Method hasHeight
- *
- *
- *
- * @return boolean
- */
- public boolean hasHeight()
- {
- return this._has_height;
- } //-- boolean hasHeight()
-
- /**
- * Method hasPidSelected
- *
- *
- *
- * @return boolean
- */
- public boolean hasPidSelected()
- {
- return this._has_pidSelected;
- } //-- boolean hasPidSelected()
-
- /**
- * Method hasPidThreshold
- *
- *
- *
- * @return boolean
- */
- public boolean hasPidThreshold()
- {
- return this._has_pidThreshold;
- } //-- boolean hasPidThreshold()
-
- /**
- * Method hasRenderGaps
- *
- *
- *
- * @return boolean
- */
- public boolean hasRenderGaps()
- {
- return this._has_renderGaps;
- } //-- boolean hasRenderGaps()
-
- /**
- * Method hasRightAlignIds
- *
- *
- *
- * @return boolean
- */
- public boolean hasRightAlignIds()
- {
- return this._has_rightAlignIds;
- } //-- boolean hasRightAlignIds()
-
- /**
- * Method hasShowAnnotation
- *
- *
- *
- * @return boolean
- */
- public boolean hasShowAnnotation()
- {
- return this._has_showAnnotation;
- } //-- boolean hasShowAnnotation()
-
- /**
- * Method hasShowBoxes
- *
- *
- *
- * @return boolean
- */
- public boolean hasShowBoxes()
- {
- return this._has_showBoxes;
- } //-- boolean hasShowBoxes()
-
- /**
- * Method hasShowColourText
- *
- *
- *
- * @return boolean
- */
- public boolean hasShowColourText()
- {
- return this._has_showColourText;
- } //-- boolean hasShowColourText()
-
- /**
- * Method hasShowFullId
- *
- *
- *
- * @return boolean
- */
- public boolean hasShowFullId()
- {
- return this._has_showFullId;
- } //-- boolean hasShowFullId()
-
- /**
- * Method hasShowSequenceFeatures
- *
- *
- *
- * @return boolean
- */
- public boolean hasShowSequenceFeatures()
- {
- return this._has_showSequenceFeatures;
- } //-- boolean hasShowSequenceFeatures()
-
- /**
- * Method hasShowText
- *
- *
- *
- * @return boolean
- */
- public boolean hasShowText()
- {
- return this._has_showText;
- } //-- boolean hasShowText()
-
- /**
- * Method hasStartRes
- *
- *
- *
- * @return boolean
- */
- public boolean hasStartRes()
- {
- return this._has_startRes;
- } //-- boolean hasStartRes()
-
- /**
- * Method hasStartSeq
- *
- *
- *
- * @return boolean
- */
- public boolean hasStartSeq()
- {
- return this._has_startSeq;
- } //-- boolean hasStartSeq()
-
- /**
- * Method hasTextCol1
- *
- *
- *
- * @return boolean
- */
- public boolean hasTextCol1()
- {
- return this._has_textCol1;
- } //-- boolean hasTextCol1()
-
- /**
- * Method hasTextCol2
- *
- *
- *
- * @return boolean
- */
- public boolean hasTextCol2()
- {
- return this._has_textCol2;
- } //-- boolean hasTextCol2()
-
- /**
- * Method hasTextColThreshold
- *
- *
- *
- * @return boolean
- */
- public boolean hasTextColThreshold()
- {
- return this._has_textColThreshold;
- } //-- boolean hasTextColThreshold()
-
- /**
- * Method hasWidth
- *
- *
- *
- * @return boolean
- */
- public boolean hasWidth()
- {
- return this._has_width;
- } //-- boolean hasWidth()
-
- /**
- * Method hasWrapAlignment
- *
- *
- *
- * @return boolean
- */
- public boolean hasWrapAlignment()
- {
- return this._has_wrapAlignment;
- } //-- boolean hasWrapAlignment()
-
- /**
- * Method hasXpos
- *
- *
- *
- * @return boolean
- */
- public boolean hasXpos()
- {
- return this._has_xpos;
- } //-- boolean hasXpos()
-
- /**
- * Method hasYpos
- *
- *
- *
- * @return boolean
- */
- public boolean hasYpos()
- {
- return this._has_ypos;
- } //-- boolean hasYpos()
-
- /**
- * Method isValid
- *
- *
- *
- * @return boolean
- */
- public boolean isValid()
- {
- try
- {
- validate();
- }
- catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
- }
- return true;
- } //-- boolean isValid()
-
- /**
- * Method marshal
- *
- *
- *
- * @param out
- */
- public void marshal(java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
-
- Marshaller.marshal(this, out);
- } //-- void marshal(java.io.Writer)
-
- /**
- * Method marshal
- *
- *
- *
- * @param handler
- */
- public void marshal(org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
-
- Marshaller.marshal(this, handler);
- } //-- void marshal(org.xml.sax.ContentHandler)
-
- /**
- * Method removeAllHiddenColumns
- *
- */
- public void removeAllHiddenColumns()
- {
- _hiddenColumnsList.removeAllElements();
- } //-- void removeAllHiddenColumns()
-
- /**
- * Method removeHiddenColumns
- *
- *
- *
- * @param index
- * @return HiddenColumns
- */
- public jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int
- index)
- {
- java.lang.Object obj = _hiddenColumnsList.elementAt(index);
- _hiddenColumnsList.removeElementAt(index);
- return (jalview.schemabinding.version2.HiddenColumns) obj;
- } //-- jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int)
-
- /**
- * Sets the value of field 'annotationColours'.
- *
- * @param annotationColours the value of field
- * 'annotationColours'.
- */
- public void setAnnotationColours(jalview.schemabinding.version2.
- AnnotationColours annotationColours)
- {
- this._annotationColours = annotationColours;
- } //-- void setAnnotationColours(jalview.schemabinding.version2.AnnotationColours)
-
- /**
- * Sets the value of field 'bgColour'.
- *
- * @param bgColour the value of field 'bgColour'.
- */
- public void setBgColour(java.lang.String bgColour)
- {
- this._bgColour = bgColour;
- } //-- void setBgColour(java.lang.String)
-
- /**
- * Sets the value of field 'consThreshold'.
- *
- * @param consThreshold the value of field 'consThreshold'.
- */
- public void setConsThreshold(int consThreshold)
- {
- this._consThreshold = consThreshold;
- this._has_consThreshold = true;
- } //-- void setConsThreshold(int)
-
- /**
- * Sets the value of field 'conservationSelected'.
- *
- * @param conservationSelected the value of field
- * 'conservationSelected'.
- */
- public void setConservationSelected(boolean conservationSelected)
- {
- this._conservationSelected = conservationSelected;
- this._has_conservationSelected = true;
- } //-- void setConservationSelected(boolean)
-
- /**
- * Sets the value of field 'fontName'.
- *
- * @param fontName the value of field 'fontName'.
- */
- public void setFontName(java.lang.String fontName)
- {
- this._fontName = fontName;
- } //-- void setFontName(java.lang.String)
-
- /**
- * Sets the value of field 'fontSize'.
- *
- * @param fontSize the value of field 'fontSize'.
- */
- public void setFontSize(int fontSize)
- {
- this._fontSize = fontSize;
- this._has_fontSize = true;
- } //-- void setFontSize(int)
-
- /**
- * Sets the value of field 'fontStyle'.
- *
- * @param fontStyle the value of field 'fontStyle'.
- */
- public void setFontStyle(int fontStyle)
- {
- this._fontStyle = fontStyle;
- this._has_fontStyle = true;
- } //-- void setFontStyle(int)
-
- /**
- * Sets the value of field 'gatheredViews'.
- *
- * @param gatheredViews the value of field 'gatheredViews'.
- */
- public void setGatheredViews(boolean gatheredViews)
- {
- this._gatheredViews = gatheredViews;
- this._has_gatheredViews = true;
- } //-- void setGatheredViews(boolean)
-
- /**
- * Sets the value of field 'height'.
- *
- * @param height the value of field 'height'.
- */
- public void setHeight(int height)
- {
- this._height = height;
- this._has_height = true;
- } //-- void setHeight(int)
-
- /**
- * Method setHiddenColumns
- *
- *
- *
- * @param index
- * @param vHiddenColumns
- */
- public void setHiddenColumns(int index,
- jalview.schemabinding.version2.HiddenColumns
- vHiddenColumns)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ( (index < 0) || (index > _hiddenColumnsList.size()))
- {
- throw new IndexOutOfBoundsException();
- }
- _hiddenColumnsList.setElementAt(vHiddenColumns, index);
- } //-- void setHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns)
-
- /**
- * Method setHiddenColumns
- *
- *
- *
- * @param hiddenColumnsArray
- */
- public void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns[]
- hiddenColumnsArray)
- {
- //-- copy array
- _hiddenColumnsList.removeAllElements();
- for (int i = 0; i < hiddenColumnsArray.length; i++)
- {
- _hiddenColumnsList.addElement(hiddenColumnsArray[i]);
- }
- } //-- void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns)
-
- /**
- * Sets the value of field 'pidSelected'.
- *
- * @param pidSelected the value of field 'pidSelected'.
- */
- public void setPidSelected(boolean pidSelected)
- {
- this._pidSelected = pidSelected;
- this._has_pidSelected = true;
- } //-- void setPidSelected(boolean)
-
- /**
- * Sets the value of field 'pidThreshold'.
- *
- * @param pidThreshold the value of field 'pidThreshold'.
- */
- public void setPidThreshold(int pidThreshold)
- {
- this._pidThreshold = pidThreshold;
- this._has_pidThreshold = true;
- } //-- void setPidThreshold(int)
-
- /**
- * Sets the value of field 'renderGaps'.
- *
- * @param renderGaps the value of field 'renderGaps'.
- */
- public void setRenderGaps(boolean renderGaps)
- {
- this._renderGaps = renderGaps;
- this._has_renderGaps = true;
- } //-- void setRenderGaps(boolean)
-
- /**
- * Sets the value of field 'rightAlignIds'.
- *
- * @param rightAlignIds the value of field 'rightAlignIds'.
- */
- public void setRightAlignIds(boolean rightAlignIds)
- {
- this._rightAlignIds = rightAlignIds;
- this._has_rightAlignIds = true;
- } //-- void setRightAlignIds(boolean)
-
- /**
- * Sets the value of field 'sequenceSetId'.
- *
- * @param sequenceSetId the value of field 'sequenceSetId'.
- */
- public void setSequenceSetId(java.lang.String sequenceSetId)
- {
- this._sequenceSetId = sequenceSetId;
- } //-- void setSequenceSetId(java.lang.String)
-
- /**
- * Sets the value of field 'showAnnotation'.
- *
- * @param showAnnotation the value of field 'showAnnotation'.
- */
- public void setShowAnnotation(boolean showAnnotation)
- {
- this._showAnnotation = showAnnotation;
- this._has_showAnnotation = true;
- } //-- void setShowAnnotation(boolean)
-
- /**
- * Sets the value of field 'showBoxes'.
- *
- * @param showBoxes the value of field 'showBoxes'.
- */
- public void setShowBoxes(boolean showBoxes)
- {
- this._showBoxes = showBoxes;
- this._has_showBoxes = true;
- } //-- void setShowBoxes(boolean)
-
- /**
- * Sets the value of field 'showColourText'.
- *
- * @param showColourText the value of field 'showColourText'.
- */
- public void setShowColourText(boolean showColourText)
- {
- this._showColourText = showColourText;
- this._has_showColourText = true;
- } //-- void setShowColourText(boolean)
-
- /**
- * Sets the value of field 'showFullId'.
- *
- * @param showFullId the value of field 'showFullId'.
- */
- public void setShowFullId(boolean showFullId)
- {
- this._showFullId = showFullId;
- this._has_showFullId = true;
- } //-- void setShowFullId(boolean)
-
- /**
- * Sets the value of field 'showSequenceFeatures'.
- *
- * @param showSequenceFeatures the value of field
- * 'showSequenceFeatures'.
- */
- public void setShowSequenceFeatures(boolean showSequenceFeatures)
- {
- this._showSequenceFeatures = showSequenceFeatures;
- this._has_showSequenceFeatures = true;
- } //-- void setShowSequenceFeatures(boolean)
-
- /**
- * Sets the value of field 'showText'.
- *
- * @param showText the value of field 'showText'.
- */
- public void setShowText(boolean showText)
- {
- this._showText = showText;
- this._has_showText = true;
- } //-- void setShowText(boolean)
-
- /**
- * Sets the value of field 'startRes'.
- *
- * @param startRes the value of field 'startRes'.
- */
- public void setStartRes(int startRes)
- {
- this._startRes = startRes;
- this._has_startRes = true;
- } //-- void setStartRes(int)
-
- /**
- * Sets the value of field 'startSeq'.
- *
- * @param startSeq the value of field 'startSeq'.
- */
- public void setStartSeq(int startSeq)
- {
- this._startSeq = startSeq;
- this._has_startSeq = true;
- } //-- void setStartSeq(int)
-
- /**
- * Sets the value of field 'textCol1'.
- *
- * @param textCol1 the value of field 'textCol1'.
- */
- public void setTextCol1(int textCol1)
- {
- this._textCol1 = textCol1;
- this._has_textCol1 = true;
- } //-- void setTextCol1(int)
-
- /**
- * Sets the value of field 'textCol2'.
- *
- * @param textCol2 the value of field 'textCol2'.
- */
- public void setTextCol2(int textCol2)
- {
- this._textCol2 = textCol2;
- this._has_textCol2 = true;
- } //-- void setTextCol2(int)
-
- /**
- * Sets the value of field 'textColThreshold'.
- *
- * @param textColThreshold the value of field 'textColThreshold'
- */
- public void setTextColThreshold(int textColThreshold)
- {
- this._textColThreshold = textColThreshold;
- this._has_textColThreshold = true;
- } //-- void setTextColThreshold(int)
-
- /**
- * Sets the value of field 'title'.
- *
- * @param title the value of field 'title'.
- */
- public void setTitle(java.lang.String title)
- {
- this._title = title;
- } //-- void setTitle(java.lang.String)
-
- /**
- * Sets the value of field 'viewName'.
- *
- * @param viewName the value of field 'viewName'.
- */
- public void setViewName(java.lang.String viewName)
- {
- this._viewName = viewName;
- } //-- void setViewName(java.lang.String)
-
- /**
- * Sets the value of field 'width'.
- *
- * @param width the value of field 'width'.
- */
- public void setWidth(int width)
- {
- this._width = width;
- this._has_width = true;
- } //-- void setWidth(int)
-
- /**
- * Sets the value of field 'wrapAlignment'.
- *
- * @param wrapAlignment the value of field 'wrapAlignment'.
- */
- public void setWrapAlignment(boolean wrapAlignment)
- {
- this._wrapAlignment = wrapAlignment;
- this._has_wrapAlignment = true;
- } //-- void setWrapAlignment(boolean)
-
- /**
- * Sets the value of field 'xpos'.
- *
- * @param xpos the value of field 'xpos'.
- */
- public void setXpos(int xpos)
- {
- this._xpos = xpos;
- this._has_xpos = true;
- } //-- void setXpos(int)
-
- /**
- * Sets the value of field 'ypos'.
- *
- * @param ypos the value of field 'ypos'.
- */
- public void setYpos(int ypos)
- {
- this._ypos = ypos;
- this._has_ypos = true;
- } //-- void setYpos(int)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return Object
- */
- public static java.lang.Object unmarshal(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);
- } //-- java.lang.Object unmarshal(java.io.Reader)
-
- /**
- * Method validate
- *
- */
- public void validate()
- throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
- Validator();
- validator.validate(this);
- } //-- void validate()
-
-}
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see
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 know 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 '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 '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 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 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 '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 '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 removeAllHiddenColumns( + ) { + this._hiddenColumnsList.clear(); + } + + /** + * 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; + } + + /** + * 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 '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 '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 '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); + } + +}