X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FViewport.java;h=978ab5cb229be080d8544e466a6d8514f0808a23;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=6dfb14fe72e32b8abffc2eea44308318ad127d70;hpb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;p=jalview.git diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java index 6dfb14f..978ab5c 100755 --- a/src/jalview/schemabinding/version2/Viewport.java +++ b/src/jalview/schemabinding/version2/Viewport.java @@ -1,5 +1,5 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ @@ -7,1752 +7,1767 @@ package jalview.schemabinding.version2; - //---------------------------------/ - //- Imported classes and packages -/ //---------------------------------/ +//- Imported classes and packages -/ +//---------------------------------/ + +import java.util.*; -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -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; +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() +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() }