X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FViewport.java;h=022dca71b4d6074cf57e4f256a8df3d4414c2340;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=4e6747ee25a7b3e1716f256f70e0c0d63951c89d;hpb=65df62f4b048a1615d32ea2c3576082ad2b63af8;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 4e6747e..022dca7
--- a/src/jalview/schemabinding/version2/Viewport.java
+++ b/src/jalview/schemabinding/version2/Viewport.java
@@ -1,1420 +1,2734 @@
-/*
- * 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.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
-
-/**
- * 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 _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 _showConservation
- */
- private boolean _showConservation;
-
- /**
- * keeps track of state for field: _showConservation
- */
- private boolean _has_showConservation;
-
- /**
- * Field _showQuality
- */
- private boolean _showQuality;
-
- /**
- * keeps track of state for field: _showQuality
- */
- private boolean _has_showQuality;
-
- /**
- * Field _showIdentity
- */
- private boolean _showIdentity;
-
- /**
- * keeps track of state for field: _showIdentity
- */
- private boolean _has_showIdentity;
-
- /**
- * 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;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Viewport() {
- super();
- } //-- jalview.schemabinding.version2.Viewport()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * 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 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 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 deleteShowConservation
- *
- */
- public void deleteShowConservation()
- {
- this._has_showConservation= false;
- } //-- void deleteShowConservation()
-
- /**
- * Method deleteShowFullId
- *
- */
- public void deleteShowFullId()
- {
- this._has_showFullId= false;
- } //-- void deleteShowFullId()
-
- /**
- * Method deleteShowIdentity
- *
- */
- public void deleteShowIdentity()
- {
- this._has_showIdentity= false;
- } //-- void deleteShowIdentity()
-
- /**
- * Method deleteShowQuality
- *
- */
- public void deleteShowQuality()
- {
- this._has_showQuality= false;
- } //-- void deleteShowQuality()
-
- /**
- * 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 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()
-
- /**
- * 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 'height'.
- *
- * @return int
- * @return the value of field 'height'.
- */
- public int getHeight()
- {
- return this._height;
- } //-- int getHeight()
-
- /**
- * 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 '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 'showConservation'.
- *
- * @return boolean
- * @return the value of field 'showConservation'.
- */
- public boolean getShowConservation()
- {
- return this._showConservation;
- } //-- boolean getShowConservation()
-
- /**
- * 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 'showIdentity'.
- *
- * @return boolean
- * @return the value of field 'showIdentity'.
- */
- public boolean getShowIdentity()
- {
- return this._showIdentity;
- } //-- boolean getShowIdentity()
-
- /**
- * Returns the value of field 'showQuality'.
- *
- * @return boolean
- * @return the value of field 'showQuality'.
- */
- public boolean getShowQuality()
- {
- return this._showQuality;
- } //-- boolean getShowQuality()
-
- /**
- * 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 '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 '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 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 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 hasShowConservation
- *
- *
- *
- * @return boolean
- */
- public boolean hasShowConservation()
- {
- return this._has_showConservation;
- } //-- boolean hasShowConservation()
-
- /**
- * Method hasShowFullId
- *
- *
- *
- * @return boolean
- */
- public boolean hasShowFullId()
- {
- return this._has_showFullId;
- } //-- boolean hasShowFullId()
-
- /**
- * Method hasShowIdentity
- *
- *
- *
- * @return boolean
- */
- public boolean hasShowIdentity()
- {
- return this._has_showIdentity;
- } //-- boolean hasShowIdentity()
-
- /**
- * Method hasShowQuality
- *
- *
- *
- * @return boolean
- */
- public boolean hasShowQuality()
- {
- return this._has_showQuality;
- } //-- boolean hasShowQuality()
-
- /**
- * 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 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)
-
- /**
- * 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 'height'.
- *
- * @param height the value of field 'height'.
- */
- public void setHeight(int height)
- {
- this._height = height;
- this._has_height = true;
- } //-- void setHeight(int)
-
- /**
- * 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 '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 'showConservation'.
- *
- * @param showConservation the value of field 'showConservation'
- */
- public void setShowConservation(boolean showConservation)
- {
- this._showConservation = showConservation;
- this._has_showConservation = true;
- } //-- void setShowConservation(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 'showIdentity'.
- *
- * @param showIdentity the value of field 'showIdentity'.
- */
- public void setShowIdentity(boolean showIdentity)
- {
- this._showIdentity = showIdentity;
- this._has_showIdentity = true;
- } //-- void setShowIdentity(boolean)
-
- /**
- * Sets the value of field 'showQuality'.
- *
- * @param showQuality the value of field 'showQuality'.
- */
- public void setShowQuality(boolean showQuality)
- {
- this._showQuality = showQuality;
- this._has_showQuality = true;
- } //-- void setShowQuality(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 '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 '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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * 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.CalcIdParam[] getCalcIdParam() + { + jalview.schemabinding.version2.CalcIdParam[] array = new jalview.schemabinding.version2.CalcIdParam[0]; + return (jalview.schemabinding.version2.CalcIdParam[]) this._calcIdParamList + .toArray(array); + } + + /** + * Method getCalcIdParamCount. + * + * @return the size of this collection + */ + public int getCalcIdParamCount() + { + return this._calcIdParamList.size(); + } + + /** + * Returns the value of field 'centreColumnLabels'. + * + * @return the value of field 'CentreColumnLabels'. + */ + public boolean getCentreColumnLabels() + { + return this._centreColumnLabels; + } + + /** + * Returns the value of field 'consThreshold'. + * + * @return the value of field 'ConsThreshold'. + */ + public int getConsThreshold() + { + return this._consThreshold; + } + + /** + * Returns the value of field 'conservationSelected'. + * + * @return the value of field 'ConservationSelected'. + */ + public boolean getConservationSelected() + { + return this._conservationSelected; + } + + /** + * Returns the value of field 'followHighlight'. + * + * @return the value of field 'FollowHighlight'. + */ + public boolean getFollowHighlight() + { + return this._followHighlight; + } + + /** + * Returns the value of field 'followSelection'. + * + * @return the value of field 'FollowSelection'. + */ + public boolean getFollowSelection() + { + return this._followSelection; + } + + /** + * Returns the value of field 'fontName'. + * + * @return the value of field 'FontName'. + */ + public java.lang.String getFontName() + { + return this._fontName; + } + + /** + * Returns the value of field 'fontSize'. + * + * @return the value of field 'FontSize'. + */ + public int getFontSize() + { + return this._fontSize; + } + + /** + * Returns the value of field 'fontStyle'. + * + * @return the value of field 'FontStyle'. + */ + public int getFontStyle() + { + return this._fontStyle; + } + + /** + * Returns the value of field 'gatheredViews'. + * + * @return the value of field 'GatheredViews'. + */ + public boolean getGatheredViews() + { + return this._gatheredViews; + } + + /** + * Returns the value of field 'height'. + * + * @return the value of field 'Height'. + */ + public int getHeight() + { + return this._height; + } + + /** + * Method getHiddenColumns. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + * @return the value of the jalview.schemabinding.version2.HiddenColumns at + * the given index + */ + public jalview.schemabinding.version2.HiddenColumns getHiddenColumns( + final int index) throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._hiddenColumnsList.size()) + { + throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ + "getHiddenColumns", + Integer.valueOf(index).toString(), + Integer.valueOf((this._hiddenColumnsList.size() - 1)).toString() + })); + } + + return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList + .get(index); + } + + /** + * Method getHiddenColumns.Returns the contents of the collection in an Array. + *
+ * 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 'normaliseSequenceLogo'. + * + * @return the value of field 'NormaliseSequenceLogo'. + */ + public boolean getNormaliseSequenceLogo() + { + return this._normaliseSequenceLogo; + } + + /** + * Returns the value of field 'pidSelected'. + * + * @return the value of field 'PidSelected'. + */ + public boolean getPidSelected() + { + return this._pidSelected; + } + + /** + * Returns the value of field 'pidThreshold'. + * + * @return the value of field 'PidThreshold'. + */ + public int getPidThreshold() + { + return this._pidThreshold; + } + + /** + * Returns the value of field 'renderGaps'. + * + * @return the value of field 'RenderGaps'. + */ + public boolean getRenderGaps() + { + return this._renderGaps; + } + + /** + * Returns the value of field 'rightAlignIds'. + * + * @return the value of field 'RightAlignIds'. + */ + public boolean getRightAlignIds() + { + return this._rightAlignIds; + } + + /** + * Returns the value of field 'sequenceSetId'. + * + * @return the value of field 'SequenceSetId'. + */ + public java.lang.String getSequenceSetId() + { + return this._sequenceSetId; + } + + /** + * Returns the value of field 'showAnnotation'. + * + * @return the value of field 'ShowAnnotation'. + */ + public boolean getShowAnnotation() + { + return this._showAnnotation; + } + + /** + * Returns the value of field 'showBoxes'. + * + * @return the value of field 'ShowBoxes'. + */ + public boolean getShowBoxes() + { + return this._showBoxes; + } + + /** + * Returns the value of field 'showColourText'. + * + * @return the value of field 'ShowColourText'. + */ + public boolean getShowColourText() + { + return this._showColourText; + } + + /** + * Returns the value of field 'showConsensusHistogram'. + * + * @return the value of field 'ShowConsensusHistogram'. + */ + public boolean getShowConsensusHistogram() + { + return this._showConsensusHistogram; + } + + /** + * Returns the value of field 'showDbRefTooltip'. + * + * @return the value of field 'ShowDbRefTooltip'. + */ + public boolean getShowDbRefTooltip() + { + return this._showDbRefTooltip; + } + + /** + * Returns the value of field 'showFullId'. + * + * @return the value of field 'ShowFullId'. + */ + public boolean getShowFullId() + { + return this._showFullId; + } + + /** + * Returns the value of field 'showGroupConsensus'. + * + * @return the value of field 'ShowGroupConsensus'. + */ + public boolean getShowGroupConsensus() + { + return this._showGroupConsensus; + } + + /** + * Returns the value of field 'showGroupConservation'. + * + * @return the value of field 'ShowGroupConservation'. + */ + public boolean getShowGroupConservation() + { + return this._showGroupConservation; + } + + /** + * Returns the value of field 'showNPfeatureTooltip'. + * + * @return the value of field 'ShowNPfeatureTooltip'. + */ + public boolean getShowNPfeatureTooltip() + { + return this._showNPfeatureTooltip; + } + + /** + * Returns the value of field 'showSequenceFeatures'. + * + * @return the value of field 'ShowSequenceFeatures'. + */ + public boolean getShowSequenceFeatures() + { + return this._showSequenceFeatures; + } + + /** + * Returns the value of field 'showSequenceLogo'. + * + * @return the value of field 'ShowSequenceLogo'. + */ + public boolean getShowSequenceLogo() + { + return this._showSequenceLogo; + } + + /** + * Returns the value of field 'showText'. + * + * @return the value of field 'ShowText'. + */ + public boolean getShowText() + { + return this._showText; + } + + /** + * Returns the value of field 'showUnconserved'. + * + * @return the value of field 'ShowUnconserved'. + */ + public boolean getShowUnconserved() + { + return this._showUnconserved; + } + + /** + * Returns the value of field 'startRes'. + * + * @return the value of field 'StartRes'. + */ + public int getStartRes() + { + return this._startRes; + } + + /** + * Returns the value of field 'startSeq'. + * + * @return the value of field 'StartSeq'. + */ + public int getStartSeq() + { + return this._startSeq; + } + + /** + * Returns the value of field 'textCol1'. + * + * @return the value of field 'TextCol1'. + */ + public int getTextCol1() + { + return this._textCol1; + } + + /** + * Returns the value of field 'textCol2'. + * + * @return the value of field 'TextCol2'. + */ + public int getTextCol2() + { + return this._textCol2; + } + + /** + * Returns the value of field 'textColThreshold'. + * + * @return the value of field 'TextColThreshold'. + */ + public int getTextColThreshold() + { + return this._textColThreshold; + } + + /** + * Returns the value of field 'title'. + * + * @return the value of field 'Title'. + */ + public java.lang.String getTitle() + { + return this._title; + } + + /** + * Returns the value of field 'viewName'. + * + * @return the value of field 'ViewName'. + */ + public java.lang.String getViewName() + { + return this._viewName; + } + + /** + * Returns the value of field 'width'. + * + * @return the value of field 'Width'. + */ + public int getWidth() + { + return this._width; + } + + /** + * Returns the value of field 'wrapAlignment'. + * + * @return the value of field 'WrapAlignment'. + */ + public boolean getWrapAlignment() + { + return this._wrapAlignment; + } + + /** + * Returns the value of field 'xpos'. + * + * @return the value of field 'Xpos'. + */ + public int getXpos() + { + return this._xpos; + } + + /** + * Returns the value of field 'ypos'. + * + * @return the value of field 'Ypos'. + */ + public int getYpos() + { + return this._ypos; + } + + /** + * Method hasCentreColumnLabels. + * + * @return true if at least one CentreColumnLabels has been adde + */ + public boolean hasCentreColumnLabels() + { + return this._has_centreColumnLabels; + } + + /** + * Method hasConsThreshold. + * + * @return true if at least one ConsThreshold has been added + */ + public boolean hasConsThreshold() + { + return this._has_consThreshold; + } + + /** + * Method hasConservationSelected. + * + * @return true if at least one ConservationSelected has been added + */ + public boolean hasConservationSelected() + { + return this._has_conservationSelected; + } + + /** + * Method hasFollowHighlight. + * + * @return true if at least one FollowHighlight has been added + */ + public boolean hasFollowHighlight() + { + return this._has_followHighlight; + } + + /** + * Method hasFollowSelection. + * + * @return true if at least one FollowSelection has been added + */ + public boolean hasFollowSelection() + { + return this._has_followSelection; + } + + /** + * Method hasFontSize. + * + * @return true if at least one FontSize has been added + */ + public boolean hasFontSize() + { + return this._has_fontSize; + } + + /** + * Method hasFontStyle. + * + * @return true if at least one FontStyle has been added + */ + public boolean hasFontStyle() + { + return this._has_fontStyle; + } + + /** + * Method hasGatheredViews. + * + * @return true if at least one GatheredViews has been added + */ + public boolean hasGatheredViews() + { + return this._has_gatheredViews; + } + + /** + * Method hasHeight. + * + * @return true if at least one Height has been added + */ + public boolean hasHeight() + { + return this._has_height; + } + + /** + * Method hasIgnoreGapsinConsensus. + * + * @return true if at least one IgnoreGapsinConsensus has been added + */ + public boolean hasIgnoreGapsinConsensus() + { + return this._has_ignoreGapsinConsensus; + } + + /** + * Method hasNormaliseSequenceLogo. + * + * @return true if at least one NormaliseSequenceLogo has been added + */ + public boolean hasNormaliseSequenceLogo() + { + return this._has_normaliseSequenceLogo; + } + + /** + * Method hasPidSelected. + * + * @return true if at least one PidSelected has been added + */ + public boolean hasPidSelected() + { + return this._has_pidSelected; + } + + /** + * Method hasPidThreshold. + * + * @return true if at least one PidThreshold has been added + */ + public boolean hasPidThreshold() + { + return this._has_pidThreshold; + } + + /** + * Method hasRenderGaps. + * + * @return true if at least one RenderGaps has been added + */ + public boolean hasRenderGaps() + { + return this._has_renderGaps; + } + + /** + * Method hasRightAlignIds. + * + * @return true if at least one RightAlignIds has been added + */ + public boolean hasRightAlignIds() + { + return this._has_rightAlignIds; + } + + /** + * Method hasShowAnnotation. + * + * @return true if at least one ShowAnnotation has been added + */ + public boolean hasShowAnnotation() + { + return this._has_showAnnotation; + } + + /** + * Method hasShowBoxes. + * + * @return true if at least one ShowBoxes has been added + */ + public boolean hasShowBoxes() + { + return this._has_showBoxes; + } + + /** + * Method hasShowColourText. + * + * @return true if at least one ShowColourText has been added + */ + public boolean hasShowColourText() + { + return this._has_showColourText; + } + + /** + * Method hasShowConsensusHistogram. + * + * @return true if at least one ShowConsensusHistogram has been added + */ + public boolean hasShowConsensusHistogram() + { + return this._has_showConsensusHistogram; + } + + /** + * Method hasShowDbRefTooltip. + * + * @return true if at least one ShowDbRefTooltip has been added + */ + public boolean hasShowDbRefTooltip() + { + return this._has_showDbRefTooltip; + } + + /** + * Method hasShowFullId. + * + * @return true if at least one ShowFullId has been added + */ + public boolean hasShowFullId() + { + return this._has_showFullId; + } + + /** + * Method hasShowGroupConsensus. + * + * @return true if at least one ShowGroupConsensus has been adde + */ + public boolean hasShowGroupConsensus() + { + return this._has_showGroupConsensus; + } + + /** + * Method hasShowGroupConservation. + * + * @return true if at least one ShowGroupConservation has been added + */ + public boolean hasShowGroupConservation() + { + return this._has_showGroupConservation; + } + + /** + * Method hasShowNPfeatureTooltip. + * + * @return true if at least one ShowNPfeatureTooltip has been added + */ + public boolean hasShowNPfeatureTooltip() + { + return this._has_showNPfeatureTooltip; + } + + /** + * Method hasShowSequenceFeatures. + * + * @return true if at least one ShowSequenceFeatures has been added + */ + public boolean hasShowSequenceFeatures() + { + return this._has_showSequenceFeatures; + } + + /** + * Method hasShowSequenceLogo. + * + * @return true if at least one ShowSequenceLogo has been added + */ + public boolean hasShowSequenceLogo() + { + return this._has_showSequenceLogo; + } + + /** + * Method hasShowText. + * + * @return true if at least one ShowText has been added + */ + public boolean hasShowText() + { + return this._has_showText; + } + + /** + * Method hasShowUnconserved. + * + * @return true if at least one ShowUnconserved has been added + */ + public boolean hasShowUnconserved() + { + return this._has_showUnconserved; + } + + /** + * Method hasStartRes. + * + * @return true if at least one StartRes has been added + */ + public boolean hasStartRes() + { + return this._has_startRes; + } + + /** + * Method hasStartSeq. + * + * @return true if at least one StartSeq has been added + */ + public boolean hasStartSeq() + { + return this._has_startSeq; + } + + /** + * Method hasTextCol1. + * + * @return true if at least one TextCol1 has been added + */ + public boolean hasTextCol1() + { + return this._has_textCol1; + } + + /** + * Method hasTextCol2. + * + * @return true if at least one TextCol2 has been added + */ + public boolean hasTextCol2() + { + return this._has_textCol2; + } + + /** + * Method hasTextColThreshold. + * + * @return true if at least one TextColThreshold has been added + */ + public boolean hasTextColThreshold() + { + return this._has_textColThreshold; + } + + /** + * Method hasWidth. + * + * @return true if at least one Width has been added + */ + public boolean hasWidth() + { + return this._has_width; + } + + /** + * Method hasWrapAlignment. + * + * @return true if at least one WrapAlignment has been added + */ + public boolean hasWrapAlignment() + { + return this._has_wrapAlignment; + } + + /** + * Method hasXpos. + * + * @return true if at least one Xpos has been added + */ + public boolean hasXpos() + { + return this._has_xpos; + } + + /** + * Method hasYpos. + * + * @return true if at least one Ypos has been added + */ + public boolean hasYpos() + { + return this._has_ypos; + } + + /** + * Returns the value of field 'centreColumnLabels'. + * + * @return the value of field 'CentreColumnLabels'. + */ + public boolean isCentreColumnLabels() + { + return this._centreColumnLabels; + } + + /** + * Returns the value of field 'conservationSelected'. + * + * @return the value of field 'ConservationSelected'. + */ + public boolean isConservationSelected() + { + return this._conservationSelected; + } + + /** + * Returns the value of field 'followHighlight'. + * + * @return the value of field 'FollowHighlight'. + */ + public boolean isFollowHighlight() + { + return this._followHighlight; + } + + /** + * Returns the value of field 'followSelection'. + * + * @return the value of field 'FollowSelection'. + */ + public boolean isFollowSelection() + { + return this._followSelection; + } + + /** + * Returns the value of field 'gatheredViews'. + * + * @return the value of field 'GatheredViews'. + */ + public boolean isGatheredViews() + { + return this._gatheredViews; + } + + /** + * Returns the value of field 'ignoreGapsinConsensus'. + * + * @return the value of field 'IgnoreGapsinConsensus'. + */ + public boolean isIgnoreGapsinConsensus() + { + return this._ignoreGapsinConsensus; + } + + /** + * Returns the value of field 'normaliseSequenceLogo'. + * + * @return the value of field 'NormaliseSequenceLogo'. + */ + public boolean isNormaliseSequenceLogo() + { + return this._normaliseSequenceLogo; + } + + /** + * Returns the value of field 'pidSelected'. + * + * @return the value of field 'PidSelected'. + */ + public boolean isPidSelected() + { + return this._pidSelected; + } + + /** + * Returns the value of field 'renderGaps'. + * + * @return the value of field 'RenderGaps'. + */ + public boolean isRenderGaps() + { + return this._renderGaps; + } + + /** + * Returns the value of field 'rightAlignIds'. + * + * @return the value of field 'RightAlignIds'. + */ + public boolean isRightAlignIds() + { + return this._rightAlignIds; + } + + /** + * Returns the value of field 'showAnnotation'. + * + * @return the value of field 'ShowAnnotation'. + */ + public boolean isShowAnnotation() + { + return this._showAnnotation; + } + + /** + * Returns the value of field 'showBoxes'. + * + * @return the value of field 'ShowBoxes'. + */ + public boolean isShowBoxes() + { + return this._showBoxes; + } + + /** + * Returns the value of field 'showColourText'. + * + * @return the value of field 'ShowColourText'. + */ + public boolean isShowColourText() + { + return this._showColourText; + } + + /** + * Returns the value of field 'showConsensusHistogram'. + * + * @return the value of field 'ShowConsensusHistogram'. + */ + public boolean isShowConsensusHistogram() + { + return this._showConsensusHistogram; + } + + /** + * Returns the value of field 'showDbRefTooltip'. + * + * @return the value of field 'ShowDbRefTooltip'. + */ + public boolean isShowDbRefTooltip() + { + return this._showDbRefTooltip; + } + + /** + * Returns the value of field 'showFullId'. + * + * @return the value of field 'ShowFullId'. + */ + public boolean isShowFullId() + { + return this._showFullId; + } + + /** + * Returns the value of field 'showGroupConsensus'. + * + * @return the value of field 'ShowGroupConsensus'. + */ + public boolean isShowGroupConsensus() + { + return this._showGroupConsensus; + } + + /** + * Returns the value of field 'showGroupConservation'. + * + * @return the value of field 'ShowGroupConservation'. + */ + public boolean isShowGroupConservation() + { + return this._showGroupConservation; + } + + /** + * Returns the value of field 'showNPfeatureTooltip'. + * + * @return the value of field 'ShowNPfeatureTooltip'. + */ + public boolean isShowNPfeatureTooltip() + { + return this._showNPfeatureTooltip; + } + + /** + * Returns the value of field 'showSequenceFeatures'. + * + * @return the value of field 'ShowSequenceFeatures'. + */ + public boolean isShowSequenceFeatures() + { + return this._showSequenceFeatures; + } + + /** + * Returns the value of field 'showSequenceLogo'. + * + * @return the value of field 'ShowSequenceLogo'. + */ + public boolean isShowSequenceLogo() + { + return this._showSequenceLogo; + } + + /** + * Returns the value of field 'showText'. + * + * @return the value of field 'ShowText'. + */ + public boolean isShowText() + { + return this._showText; + } + + /** + * Returns the value of field 'showUnconserved'. + * + * @return the value of field 'ShowUnconserved'. + */ + public boolean isShowUnconserved() + { + return this._showUnconserved; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid() + { + try + { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) + { + return false; + } + return true; + } + + /** + * Returns the value of field 'wrapAlignment'. + * + * @return the value of field 'WrapAlignment'. + */ + public boolean isWrapAlignment() + { + return this._wrapAlignment; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException + * if object is null or if any SAXException is thrown during + * marshaling + * @throws org.exolab.castor.xml.ValidationException + * if this object is an invalid instance according to the schema + */ + public void marshal(final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException + { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException + * if an IOException occurs during marshaling + * @throws org.exolab.castor.xml.ValidationException + * if this object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException + * if object is null or if any SAXException is thrown during + * marshaling + */ + public void marshal(final org.xml.sax.ContentHandler handler) + throws java.io.IOException, + org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException + { + Marshaller.marshal(this, handler); + } + + /** + */ + public void removeAllCalcIdParam() + { + this._calcIdParamList.clear(); + } + + /** + */ + public void removeAllHiddenColumns() + { + this._hiddenColumnsList.clear(); + } + + /** + * Method removeCalcIdParam. + * + * @param vCalcIdParam + * @return true if the object was removed from the collection. + */ + public boolean removeCalcIdParam( + final jalview.schemabinding.version2.CalcIdParam vCalcIdParam) + { + boolean removed = _calcIdParamList.remove(vCalcIdParam); + return removed; + } + + /** + * Method removeCalcIdParamAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.CalcIdParam removeCalcIdParamAt( + final int index) + { + java.lang.Object obj = this._calcIdParamList.remove(index); + return (jalview.schemabinding.version2.CalcIdParam) obj; + } + + /** + * Method removeHiddenColumns. + * + * @param vHiddenColumns + * @return true if the object was removed from the collection. + */ + public boolean removeHiddenColumns( + final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) + { + boolean removed = _hiddenColumnsList.remove(vHiddenColumns); + return removed; + } + + /** + * Method removeHiddenColumnsAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt( + final int index) + { + java.lang.Object obj = this._hiddenColumnsList.remove(index); + return (jalview.schemabinding.version2.HiddenColumns) obj; + } + + /** + * Sets the value of field 'annotationColours'. + * + * @param annotationColours + * the value of field 'annotationColours'. + */ + public void setAnnotationColours( + final jalview.schemabinding.version2.AnnotationColours annotationColours) + { + this._annotationColours = annotationColours; + } + + /** + * Sets the value of field 'bgColour'. + * + * @param bgColour + * the value of field 'bgColour'. + */ + public void setBgColour(final java.lang.String bgColour) + { + this._bgColour = bgColour; + } + + /** + * + * + * @param index + * @param vCalcIdParam + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setCalcIdParam(final int index, + final jalview.schemabinding.version2.CalcIdParam vCalcIdParam) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._calcIdParamList.size()) + { + throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ + "setCalcIdParam", + Integer.valueOf(index).toString(), + Integer.valueOf((this._calcIdParamList.size() - 1)).toString() + })); + } + + this._calcIdParamList.set(index, vCalcIdParam); + } + + /** + * + * + * @param vCalcIdParamArray + */ + public void setCalcIdParam( + final jalview.schemabinding.version2.CalcIdParam[] vCalcIdParamArray) + { + // -- copy array + _calcIdParamList.clear(); + + for (int i = 0; i < vCalcIdParamArray.length; i++) + { + this._calcIdParamList.add(vCalcIdParamArray[i]); + } + } + + /** + * Sets the value of field 'centreColumnLabels'. + * + * @param centreColumnLabels + * the value of field 'centreColumnLabels'. + */ + public void setCentreColumnLabels(final boolean centreColumnLabels) + { + this._centreColumnLabels = centreColumnLabels; + this._has_centreColumnLabels = true; + } + + /** + * Sets the value of field '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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ + "setHiddenColumns", + Integer.valueOf(index).toString(), + Integer.valueOf((this._hiddenColumnsList.size() - 1)).toString() + })); + } + + this._hiddenColumnsList.set(index, vHiddenColumns); + } + + /** + * + * + * @param vHiddenColumnsArray + */ + public void setHiddenColumns( + final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray) + { + // -- copy array + _hiddenColumnsList.clear(); + + for (int i = 0; i < vHiddenColumnsArray.length; i++) + { + this._hiddenColumnsList.add(vHiddenColumnsArray[i]); + } + } + + /** + * Sets the value of field 'id'. The field 'id' has the following description: + * unique id used by jalview to synchronize between stored and instantiated + * views + * + * + * @param id + * the value of field 'id'. + */ + public void setId(final java.lang.String id) + { + this._id = id; + } + + /** + * Sets the value of field 'ignoreGapsinConsensus'. + * + * @param ignoreGapsinConsensus + * the value of field 'ignoreGapsinConsensus'. + */ + public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus) + { + this._ignoreGapsinConsensus = ignoreGapsinConsensus; + this._has_ignoreGapsinConsensus = true; + } + + /** + * Sets the value of field 'normaliseSequenceLogo'. + * + * @param normaliseSequenceLogo + * the value of field 'normaliseSequenceLogo'. + */ + public void setNormaliseSequenceLogo(final boolean normaliseSequenceLogo) + { + this._normaliseSequenceLogo = normaliseSequenceLogo; + this._has_normaliseSequenceLogo = true; + } + + /** + * Sets the value of field 'pidSelected'. + * + * @param pidSelected + * the value of field 'pidSelected'. + */ + public void setPidSelected(final boolean pidSelected) + { + this._pidSelected = pidSelected; + this._has_pidSelected = true; + } + + /** + * Sets the value of field 'pidThreshold'. + * + * @param pidThreshold + * the value of field 'pidThreshold'. + */ + public void setPidThreshold(final int pidThreshold) + { + this._pidThreshold = pidThreshold; + this._has_pidThreshold = true; + } + + /** + * Sets the value of field 'renderGaps'. + * + * @param renderGaps + * the value of field 'renderGaps'. + */ + public void setRenderGaps(final boolean renderGaps) + { + this._renderGaps = renderGaps; + this._has_renderGaps = true; + } + + /** + * Sets the value of field 'rightAlignIds'. + * + * @param rightAlignIds + * the value of field 'rightAlignIds'. + */ + public void setRightAlignIds(final boolean rightAlignIds) + { + this._rightAlignIds = rightAlignIds; + this._has_rightAlignIds = true; + } + + /** + * Sets the value of field '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); + } + +}