-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package jalview.schemabinding.version2;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-\r
-/**\r
- * Class Viewport.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Viewport implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _conservationSelected.\r
- */\r
- private boolean _conservationSelected;\r
-\r
- /**\r
- * keeps track of state for field: _conservationSelected\r
- */\r
- private boolean _has_conservationSelected;\r
-\r
- /**\r
- * Field _pidSelected.\r
- */\r
- private boolean _pidSelected;\r
-\r
- /**\r
- * keeps track of state for field: _pidSelected\r
- */\r
- private boolean _has_pidSelected;\r
-\r
- /**\r
- * Field _bgColour.\r
- */\r
- private java.lang.String _bgColour;\r
-\r
- /**\r
- * Field _consThreshold.\r
- */\r
- private int _consThreshold;\r
-\r
- /**\r
- * keeps track of state for field: _consThreshold\r
- */\r
- private boolean _has_consThreshold;\r
-\r
- /**\r
- * Field _pidThreshold.\r
- */\r
- private int _pidThreshold;\r
-\r
- /**\r
- * keeps track of state for field: _pidThreshold\r
- */\r
- private boolean _has_pidThreshold;\r
-\r
- /**\r
- * Field _title.\r
- */\r
- private java.lang.String _title;\r
-\r
- /**\r
- * Field _showFullId.\r
- */\r
- private boolean _showFullId;\r
-\r
- /**\r
- * keeps track of state for field: _showFullId\r
- */\r
- private boolean _has_showFullId;\r
-\r
- /**\r
- * Field _rightAlignIds.\r
- */\r
- private boolean _rightAlignIds;\r
-\r
- /**\r
- * keeps track of state for field: _rightAlignIds\r
- */\r
- private boolean _has_rightAlignIds;\r
-\r
- /**\r
- * Field _showText.\r
- */\r
- private boolean _showText;\r
-\r
- /**\r
- * keeps track of state for field: _showText\r
- */\r
- private boolean _has_showText;\r
-\r
- /**\r
- * Field _showColourText.\r
- */\r
- private boolean _showColourText;\r
-\r
- /**\r
- * keeps track of state for field: _showColourText\r
- */\r
- private boolean _has_showColourText;\r
-\r
- /**\r
- * Field _showUnconserved.\r
- */\r
- private boolean _showUnconserved;\r
-\r
- /**\r
- * keeps track of state for field: _showUnconserved\r
- */\r
- private boolean _has_showUnconserved;\r
-\r
- /**\r
- * Field _showBoxes.\r
- */\r
- private boolean _showBoxes;\r
-\r
- /**\r
- * keeps track of state for field: _showBoxes\r
- */\r
- private boolean _has_showBoxes;\r
-\r
- /**\r
- * Field _wrapAlignment.\r
- */\r
- private boolean _wrapAlignment;\r
-\r
- /**\r
- * keeps track of state for field: _wrapAlignment\r
- */\r
- private boolean _has_wrapAlignment;\r
-\r
- /**\r
- * Field _renderGaps.\r
- */\r
- private boolean _renderGaps;\r
-\r
- /**\r
- * keeps track of state for field: _renderGaps\r
- */\r
- private boolean _has_renderGaps;\r
-\r
- /**\r
- * Field _showSequenceFeatures.\r
- */\r
- private boolean _showSequenceFeatures;\r
-\r
- /**\r
- * keeps track of state for field: _showSequenceFeatures\r
- */\r
- private boolean _has_showSequenceFeatures;\r
-\r
- /**\r
- * Field _showAnnotation.\r
- */\r
- private boolean _showAnnotation;\r
-\r
- /**\r
- * keeps track of state for field: _showAnnotation\r
- */\r
- private boolean _has_showAnnotation;\r
-\r
- /**\r
- * Field _xpos.\r
- */\r
- private int _xpos;\r
-\r
- /**\r
- * keeps track of state for field: _xpos\r
- */\r
- private boolean _has_xpos;\r
-\r
- /**\r
- * Field _ypos.\r
- */\r
- private int _ypos;\r
-\r
- /**\r
- * keeps track of state for field: _ypos\r
- */\r
- private boolean _has_ypos;\r
-\r
- /**\r
- * Field _width.\r
- */\r
- private int _width;\r
-\r
- /**\r
- * keeps track of state for field: _width\r
- */\r
- private boolean _has_width;\r
-\r
- /**\r
- * Field _height.\r
- */\r
- private int _height;\r
-\r
- /**\r
- * keeps track of state for field: _height\r
- */\r
- private boolean _has_height;\r
-\r
- /**\r
- * Field _startRes.\r
- */\r
- private int _startRes;\r
-\r
- /**\r
- * keeps track of state for field: _startRes\r
- */\r
- private boolean _has_startRes;\r
-\r
- /**\r
- * Field _startSeq.\r
- */\r
- private int _startSeq;\r
-\r
- /**\r
- * keeps track of state for field: _startSeq\r
- */\r
- private boolean _has_startSeq;\r
-\r
- /**\r
- * Field _fontName.\r
- */\r
- private java.lang.String _fontName;\r
-\r
- /**\r
- * Field _fontSize.\r
- */\r
- private int _fontSize;\r
-\r
- /**\r
- * keeps track of state for field: _fontSize\r
- */\r
- private boolean _has_fontSize;\r
-\r
- /**\r
- * Field _fontStyle.\r
- */\r
- private int _fontStyle;\r
-\r
- /**\r
- * keeps track of state for field: _fontStyle\r
- */\r
- private boolean _has_fontStyle;\r
-\r
- /**\r
- * Field _viewName.\r
- */\r
- private java.lang.String _viewName;\r
-\r
- /**\r
- * Field _sequenceSetId.\r
- */\r
- private java.lang.String _sequenceSetId;\r
-\r
- /**\r
- * Field _gatheredViews.\r
- */\r
- private boolean _gatheredViews;\r
-\r
- /**\r
- * keeps track of state for field: _gatheredViews\r
- */\r
- private boolean _has_gatheredViews;\r
-\r
- /**\r
- * Field _textCol1.\r
- */\r
- private int _textCol1;\r
-\r
- /**\r
- * keeps track of state for field: _textCol1\r
- */\r
- private boolean _has_textCol1;\r
-\r
- /**\r
- * Field _textCol2.\r
- */\r
- private int _textCol2;\r
-\r
- /**\r
- * keeps track of state for field: _textCol2\r
- */\r
- private boolean _has_textCol2;\r
-\r
- /**\r
- * Field _textColThreshold.\r
- */\r
- private int _textColThreshold;\r
-\r
- /**\r
- * keeps track of state for field: _textColThreshold\r
- */\r
- private boolean _has_textColThreshold;\r
-\r
- /**\r
- * unique id used by jalview to synchronize between stored and\r
- * instantiated views\r
- * \r
- */\r
- private java.lang.String _id;\r
-\r
- /**\r
- * Field _annotationColours.\r
- */\r
- private jalview.schemabinding.version2.AnnotationColours _annotationColours;\r
-\r
- /**\r
- * Field _hiddenColumnsList.\r
- */\r
- private java.util.Vector _hiddenColumnsList;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Viewport() {\r
- super();\r
- this._hiddenColumnsList = new java.util.Vector();\r
- }\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vHiddenColumns\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addHiddenColumns(\r
- final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._hiddenColumnsList.addElement(vHiddenColumns);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vHiddenColumns\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addHiddenColumns(\r
- final int index,\r
- final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._hiddenColumnsList.add(index, vHiddenColumns);\r
- }\r
-\r
- /**\r
- */\r
- public void deleteConsThreshold(\r
- ) {\r
- this._has_consThreshold= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteConservationSelected(\r
- ) {\r
- this._has_conservationSelected= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteFontSize(\r
- ) {\r
- this._has_fontSize= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteFontStyle(\r
- ) {\r
- this._has_fontStyle= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteGatheredViews(\r
- ) {\r
- this._has_gatheredViews= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteHeight(\r
- ) {\r
- this._has_height= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deletePidSelected(\r
- ) {\r
- this._has_pidSelected= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deletePidThreshold(\r
- ) {\r
- this._has_pidThreshold= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteRenderGaps(\r
- ) {\r
- this._has_renderGaps= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteRightAlignIds(\r
- ) {\r
- this._has_rightAlignIds= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteShowAnnotation(\r
- ) {\r
- this._has_showAnnotation= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteShowBoxes(\r
- ) {\r
- this._has_showBoxes= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteShowColourText(\r
- ) {\r
- this._has_showColourText= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteShowFullId(\r
- ) {\r
- this._has_showFullId= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteShowSequenceFeatures(\r
- ) {\r
- this._has_showSequenceFeatures= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteShowText(\r
- ) {\r
- this._has_showText= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteShowUnconserved(\r
- ) {\r
- this._has_showUnconserved= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteStartRes(\r
- ) {\r
- this._has_startRes= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteStartSeq(\r
- ) {\r
- this._has_startSeq= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteTextCol1(\r
- ) {\r
- this._has_textCol1= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteTextCol2(\r
- ) {\r
- this._has_textCol2= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteTextColThreshold(\r
- ) {\r
- this._has_textColThreshold= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteWidth(\r
- ) {\r
- this._has_width= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteWrapAlignment(\r
- ) {\r
- this._has_wrapAlignment= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteXpos(\r
- ) {\r
- this._has_xpos= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteYpos(\r
- ) {\r
- this._has_ypos= false;\r
- }\r
-\r
- /**\r
- * Method enumerateHiddenColumns.\r
- * \r
- * @return an Enumeration over all\r
- * jalview.schemabinding.version2.HiddenColumns elements\r
- */\r
- public java.util.Enumeration enumerateHiddenColumns(\r
- ) {\r
- return this._hiddenColumnsList.elements();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'annotationColours'.\r
- * \r
- * @return the value of field 'AnnotationColours'.\r
- */\r
- public jalview.schemabinding.version2.AnnotationColours getAnnotationColours(\r
- ) {\r
- return this._annotationColours;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'bgColour'.\r
- * \r
- * @return the value of field 'BgColour'.\r
- */\r
- public java.lang.String getBgColour(\r
- ) {\r
- return this._bgColour;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'consThreshold'.\r
- * \r
- * @return the value of field 'ConsThreshold'.\r
- */\r
- public int getConsThreshold(\r
- ) {\r
- return this._consThreshold;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'conservationSelected'.\r
- * \r
- * @return the value of field 'ConservationSelected'.\r
- */\r
- public boolean getConservationSelected(\r
- ) {\r
- return this._conservationSelected;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'fontName'.\r
- * \r
- * @return the value of field 'FontName'.\r
- */\r
- public java.lang.String getFontName(\r
- ) {\r
- return this._fontName;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'fontSize'.\r
- * \r
- * @return the value of field 'FontSize'.\r
- */\r
- public int getFontSize(\r
- ) {\r
- return this._fontSize;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'fontStyle'.\r
- * \r
- * @return the value of field 'FontStyle'.\r
- */\r
- public int getFontStyle(\r
- ) {\r
- return this._fontStyle;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'gatheredViews'.\r
- * \r
- * @return the value of field 'GatheredViews'.\r
- */\r
- public boolean getGatheredViews(\r
- ) {\r
- return this._gatheredViews;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'height'.\r
- * \r
- * @return the value of field 'Height'.\r
- */\r
- public int getHeight(\r
- ) {\r
- return this._height;\r
- }\r
-\r
- /**\r
- * Method getHiddenColumns.\r
- * \r
- * @param index\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- * @return the value of the\r
- * jalview.schemabinding.version2.HiddenColumns at the given\r
- * index\r
- */\r
- public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(\r
- final int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._hiddenColumnsList.size()) {\r
- throw new IndexOutOfBoundsException("getHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");\r
- }\r
- \r
- return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.get(index);\r
- }\r
-\r
- /**\r
- * Method getHiddenColumns.Returns the contents of the\r
- * collection in an Array. <p>Note: Just in case the\r
- * collection contents are changing in another thread, we pass\r
- * a 0-length Array of the correct type into the API call. \r
- * This way we <i>know</i> that the Array returned is of\r
- * exactly the correct length.\r
- * \r
- * @return this collection as an Array\r
- */\r
- public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns(\r
- ) {\r
- jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];\r
- return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList.toArray(array);\r
- }\r
-\r
- /**\r
- * Method getHiddenColumnsCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getHiddenColumnsCount(\r
- ) {\r
- return this._hiddenColumnsList.size();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'id'. The field 'id' has the\r
- * following description: unique id used by jalview to\r
- * synchronize between stored and instantiated views\r
- * \r
- * \r
- * @return the value of field 'Id'.\r
- */\r
- public java.lang.String getId(\r
- ) {\r
- return this._id;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'pidSelected'.\r
- * \r
- * @return the value of field 'PidSelected'.\r
- */\r
- public boolean getPidSelected(\r
- ) {\r
- return this._pidSelected;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'pidThreshold'.\r
- * \r
- * @return the value of field 'PidThreshold'.\r
- */\r
- public int getPidThreshold(\r
- ) {\r
- return this._pidThreshold;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'renderGaps'.\r
- * \r
- * @return the value of field 'RenderGaps'.\r
- */\r
- public boolean getRenderGaps(\r
- ) {\r
- return this._renderGaps;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'rightAlignIds'.\r
- * \r
- * @return the value of field 'RightAlignIds'.\r
- */\r
- public boolean getRightAlignIds(\r
- ) {\r
- return this._rightAlignIds;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'sequenceSetId'.\r
- * \r
- * @return the value of field 'SequenceSetId'.\r
- */\r
- public java.lang.String getSequenceSetId(\r
- ) {\r
- return this._sequenceSetId;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showAnnotation'.\r
- * \r
- * @return the value of field 'ShowAnnotation'.\r
- */\r
- public boolean getShowAnnotation(\r
- ) {\r
- return this._showAnnotation;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showBoxes'.\r
- * \r
- * @return the value of field 'ShowBoxes'.\r
- */\r
- public boolean getShowBoxes(\r
- ) {\r
- return this._showBoxes;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showColourText'.\r
- * \r
- * @return the value of field 'ShowColourText'.\r
- */\r
- public boolean getShowColourText(\r
- ) {\r
- return this._showColourText;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showFullId'.\r
- * \r
- * @return the value of field 'ShowFullId'.\r
- */\r
- public boolean getShowFullId(\r
- ) {\r
- return this._showFullId;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showSequenceFeatures'.\r
- * \r
- * @return the value of field 'ShowSequenceFeatures'.\r
- */\r
- public boolean getShowSequenceFeatures(\r
- ) {\r
- return this._showSequenceFeatures;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showText'.\r
- * \r
- * @return the value of field 'ShowText'.\r
- */\r
- public boolean getShowText(\r
- ) {\r
- return this._showText;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showUnconserved'.\r
- * \r
- * @return the value of field 'ShowUnconserved'.\r
- */\r
- public boolean getShowUnconserved(\r
- ) {\r
- return this._showUnconserved;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'startRes'.\r
- * \r
- * @return the value of field 'StartRes'.\r
- */\r
- public int getStartRes(\r
- ) {\r
- return this._startRes;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'startSeq'.\r
- * \r
- * @return the value of field 'StartSeq'.\r
- */\r
- public int getStartSeq(\r
- ) {\r
- return this._startSeq;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'textCol1'.\r
- * \r
- * @return the value of field 'TextCol1'.\r
- */\r
- public int getTextCol1(\r
- ) {\r
- return this._textCol1;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'textCol2'.\r
- * \r
- * @return the value of field 'TextCol2'.\r
- */\r
- public int getTextCol2(\r
- ) {\r
- return this._textCol2;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'textColThreshold'.\r
- * \r
- * @return the value of field 'TextColThreshold'.\r
- */\r
- public int getTextColThreshold(\r
- ) {\r
- return this._textColThreshold;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'title'.\r
- * \r
- * @return the value of field 'Title'.\r
- */\r
- public java.lang.String getTitle(\r
- ) {\r
- return this._title;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'viewName'.\r
- * \r
- * @return the value of field 'ViewName'.\r
- */\r
- public java.lang.String getViewName(\r
- ) {\r
- return this._viewName;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'width'.\r
- * \r
- * @return the value of field 'Width'.\r
- */\r
- public int getWidth(\r
- ) {\r
- return this._width;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'wrapAlignment'.\r
- * \r
- * @return the value of field 'WrapAlignment'.\r
- */\r
- public boolean getWrapAlignment(\r
- ) {\r
- return this._wrapAlignment;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'xpos'.\r
- * \r
- * @return the value of field 'Xpos'.\r
- */\r
- public int getXpos(\r
- ) {\r
- return this._xpos;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'ypos'.\r
- * \r
- * @return the value of field 'Ypos'.\r
- */\r
- public int getYpos(\r
- ) {\r
- return this._ypos;\r
- }\r
-\r
- /**\r
- * Method hasConsThreshold.\r
- * \r
- * @return true if at least one ConsThreshold has been added\r
- */\r
- public boolean hasConsThreshold(\r
- ) {\r
- return this._has_consThreshold;\r
- }\r
-\r
- /**\r
- * Method hasConservationSelected.\r
- * \r
- * @return true if at least one ConservationSelected has been\r
- * added\r
- */\r
- public boolean hasConservationSelected(\r
- ) {\r
- return this._has_conservationSelected;\r
- }\r
-\r
- /**\r
- * Method hasFontSize.\r
- * \r
- * @return true if at least one FontSize has been added\r
- */\r
- public boolean hasFontSize(\r
- ) {\r
- return this._has_fontSize;\r
- }\r
-\r
- /**\r
- * Method hasFontStyle.\r
- * \r
- * @return true if at least one FontStyle has been added\r
- */\r
- public boolean hasFontStyle(\r
- ) {\r
- return this._has_fontStyle;\r
- }\r
-\r
- /**\r
- * Method hasGatheredViews.\r
- * \r
- * @return true if at least one GatheredViews has been added\r
- */\r
- public boolean hasGatheredViews(\r
- ) {\r
- return this._has_gatheredViews;\r
- }\r
-\r
- /**\r
- * Method hasHeight.\r
- * \r
- * @return true if at least one Height has been added\r
- */\r
- public boolean hasHeight(\r
- ) {\r
- return this._has_height;\r
- }\r
-\r
- /**\r
- * Method hasPidSelected.\r
- * \r
- * @return true if at least one PidSelected has been added\r
- */\r
- public boolean hasPidSelected(\r
- ) {\r
- return this._has_pidSelected;\r
- }\r
-\r
- /**\r
- * Method hasPidThreshold.\r
- * \r
- * @return true if at least one PidThreshold has been added\r
- */\r
- public boolean hasPidThreshold(\r
- ) {\r
- return this._has_pidThreshold;\r
- }\r
-\r
- /**\r
- * Method hasRenderGaps.\r
- * \r
- * @return true if at least one RenderGaps has been added\r
- */\r
- public boolean hasRenderGaps(\r
- ) {\r
- return this._has_renderGaps;\r
- }\r
-\r
- /**\r
- * Method hasRightAlignIds.\r
- * \r
- * @return true if at least one RightAlignIds has been added\r
- */\r
- public boolean hasRightAlignIds(\r
- ) {\r
- return this._has_rightAlignIds;\r
- }\r
-\r
- /**\r
- * Method hasShowAnnotation.\r
- * \r
- * @return true if at least one ShowAnnotation has been added\r
- */\r
- public boolean hasShowAnnotation(\r
- ) {\r
- return this._has_showAnnotation;\r
- }\r
-\r
- /**\r
- * Method hasShowBoxes.\r
- * \r
- * @return true if at least one ShowBoxes has been added\r
- */\r
- public boolean hasShowBoxes(\r
- ) {\r
- return this._has_showBoxes;\r
- }\r
-\r
- /**\r
- * Method hasShowColourText.\r
- * \r
- * @return true if at least one ShowColourText has been added\r
- */\r
- public boolean hasShowColourText(\r
- ) {\r
- return this._has_showColourText;\r
- }\r
-\r
- /**\r
- * Method hasShowFullId.\r
- * \r
- * @return true if at least one ShowFullId has been added\r
- */\r
- public boolean hasShowFullId(\r
- ) {\r
- return this._has_showFullId;\r
- }\r
-\r
- /**\r
- * Method hasShowSequenceFeatures.\r
- * \r
- * @return true if at least one ShowSequenceFeatures has been\r
- * added\r
- */\r
- public boolean hasShowSequenceFeatures(\r
- ) {\r
- return this._has_showSequenceFeatures;\r
- }\r
-\r
- /**\r
- * Method hasShowText.\r
- * \r
- * @return true if at least one ShowText has been added\r
- */\r
- public boolean hasShowText(\r
- ) {\r
- return this._has_showText;\r
- }\r
-\r
- /**\r
- * Method hasShowUnconserved.\r
- * \r
- * @return true if at least one ShowUnconserved has been added\r
- */\r
- public boolean hasShowUnconserved(\r
- ) {\r
- return this._has_showUnconserved;\r
- }\r
-\r
- /**\r
- * Method hasStartRes.\r
- * \r
- * @return true if at least one StartRes has been added\r
- */\r
- public boolean hasStartRes(\r
- ) {\r
- return this._has_startRes;\r
- }\r
-\r
- /**\r
- * Method hasStartSeq.\r
- * \r
- * @return true if at least one StartSeq has been added\r
- */\r
- public boolean hasStartSeq(\r
- ) {\r
- return this._has_startSeq;\r
- }\r
-\r
- /**\r
- * Method hasTextCol1.\r
- * \r
- * @return true if at least one TextCol1 has been added\r
- */\r
- public boolean hasTextCol1(\r
- ) {\r
- return this._has_textCol1;\r
- }\r
-\r
- /**\r
- * Method hasTextCol2.\r
- * \r
- * @return true if at least one TextCol2 has been added\r
- */\r
- public boolean hasTextCol2(\r
- ) {\r
- return this._has_textCol2;\r
- }\r
-\r
- /**\r
- * Method hasTextColThreshold.\r
- * \r
- * @return true if at least one TextColThreshold has been added\r
- */\r
- public boolean hasTextColThreshold(\r
- ) {\r
- return this._has_textColThreshold;\r
- }\r
-\r
- /**\r
- * Method hasWidth.\r
- * \r
- * @return true if at least one Width has been added\r
- */\r
- public boolean hasWidth(\r
- ) {\r
- return this._has_width;\r
- }\r
-\r
- /**\r
- * Method hasWrapAlignment.\r
- * \r
- * @return true if at least one WrapAlignment has been added\r
- */\r
- public boolean hasWrapAlignment(\r
- ) {\r
- return this._has_wrapAlignment;\r
- }\r
-\r
- /**\r
- * Method hasXpos.\r
- * \r
- * @return true if at least one Xpos has been added\r
- */\r
- public boolean hasXpos(\r
- ) {\r
- return this._has_xpos;\r
- }\r
-\r
- /**\r
- * Method hasYpos.\r
- * \r
- * @return true if at least one Ypos has been added\r
- */\r
- public boolean hasYpos(\r
- ) {\r
- return this._has_ypos;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'conservationSelected'.\r
- * \r
- * @return the value of field 'ConservationSelected'.\r
- */\r
- public boolean isConservationSelected(\r
- ) {\r
- return this._conservationSelected;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'gatheredViews'.\r
- * \r
- * @return the value of field 'GatheredViews'.\r
- */\r
- public boolean isGatheredViews(\r
- ) {\r
- return this._gatheredViews;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'pidSelected'.\r
- * \r
- * @return the value of field 'PidSelected'.\r
- */\r
- public boolean isPidSelected(\r
- ) {\r
- return this._pidSelected;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'renderGaps'.\r
- * \r
- * @return the value of field 'RenderGaps'.\r
- */\r
- public boolean isRenderGaps(\r
- ) {\r
- return this._renderGaps;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'rightAlignIds'.\r
- * \r
- * @return the value of field 'RightAlignIds'.\r
- */\r
- public boolean isRightAlignIds(\r
- ) {\r
- return this._rightAlignIds;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showAnnotation'.\r
- * \r
- * @return the value of field 'ShowAnnotation'.\r
- */\r
- public boolean isShowAnnotation(\r
- ) {\r
- return this._showAnnotation;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showBoxes'.\r
- * \r
- * @return the value of field 'ShowBoxes'.\r
- */\r
- public boolean isShowBoxes(\r
- ) {\r
- return this._showBoxes;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showColourText'.\r
- * \r
- * @return the value of field 'ShowColourText'.\r
- */\r
- public boolean isShowColourText(\r
- ) {\r
- return this._showColourText;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showFullId'.\r
- * \r
- * @return the value of field 'ShowFullId'.\r
- */\r
- public boolean isShowFullId(\r
- ) {\r
- return this._showFullId;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showSequenceFeatures'.\r
- * \r
- * @return the value of field 'ShowSequenceFeatures'.\r
- */\r
- public boolean isShowSequenceFeatures(\r
- ) {\r
- return this._showSequenceFeatures;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showText'.\r
- * \r
- * @return the value of field 'ShowText'.\r
- */\r
- public boolean isShowText(\r
- ) {\r
- return this._showText;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showUnconserved'.\r
- * \r
- * @return the value of field 'ShowUnconserved'.\r
- */\r
- public boolean isShowUnconserved(\r
- ) {\r
- return this._showUnconserved;\r
- }\r
-\r
- /**\r
- * Method isValid.\r
- * \r
- * @return true if this object is valid according to the schema\r
- */\r
- public boolean isValid(\r
- ) {\r
- try {\r
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'wrapAlignment'.\r
- * \r
- * @return the value of field 'WrapAlignment'.\r
- */\r
- public boolean isWrapAlignment(\r
- ) {\r
- return this._wrapAlignment;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param out\r
- * @throws org.exolab.castor.xml.MarshalException if object is\r
- * null or if any SAXException is thrown during marshaling\r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- */\r
- public void marshal(\r
- final java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
- Marshaller.marshal(this, out);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param handler\r
- * @throws java.io.IOException if an IOException occurs during\r
- * marshaling\r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- * @throws org.exolab.castor.xml.MarshalException if object is\r
- * null or if any SAXException is thrown during marshaling\r
- */\r
- public void marshal(\r
- final org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
- Marshaller.marshal(this, handler);\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllHiddenColumns(\r
- ) {\r
- this._hiddenColumnsList.clear();\r
- }\r
-\r
- /**\r
- * Method removeHiddenColumns.\r
- * \r
- * @param vHiddenColumns\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeHiddenColumns(\r
- final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) {\r
- boolean removed = _hiddenColumnsList.remove(vHiddenColumns);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeHiddenColumnsAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(\r
- final int index) {\r
- java.lang.Object obj = this._hiddenColumnsList.remove(index);\r
- return (jalview.schemabinding.version2.HiddenColumns) obj;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'annotationColours'.\r
- * \r
- * @param annotationColours the value of field\r
- * 'annotationColours'.\r
- */\r
- public void setAnnotationColours(\r
- final jalview.schemabinding.version2.AnnotationColours annotationColours) {\r
- this._annotationColours = annotationColours;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'bgColour'.\r
- * \r
- * @param bgColour the value of field 'bgColour'.\r
- */\r
- public void setBgColour(\r
- final java.lang.String bgColour) {\r
- this._bgColour = bgColour;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'consThreshold'.\r
- * \r
- * @param consThreshold the value of field 'consThreshold'.\r
- */\r
- public void setConsThreshold(\r
- final int consThreshold) {\r
- this._consThreshold = consThreshold;\r
- this._has_consThreshold = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'conservationSelected'.\r
- * \r
- * @param conservationSelected the value of field\r
- * 'conservationSelected'.\r
- */\r
- public void setConservationSelected(\r
- final boolean conservationSelected) {\r
- this._conservationSelected = conservationSelected;\r
- this._has_conservationSelected = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'fontName'.\r
- * \r
- * @param fontName the value of field 'fontName'.\r
- */\r
- public void setFontName(\r
- final java.lang.String fontName) {\r
- this._fontName = fontName;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'fontSize'.\r
- * \r
- * @param fontSize the value of field 'fontSize'.\r
- */\r
- public void setFontSize(\r
- final int fontSize) {\r
- this._fontSize = fontSize;\r
- this._has_fontSize = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'fontStyle'.\r
- * \r
- * @param fontStyle the value of field 'fontStyle'.\r
- */\r
- public void setFontStyle(\r
- final int fontStyle) {\r
- this._fontStyle = fontStyle;\r
- this._has_fontStyle = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'gatheredViews'.\r
- * \r
- * @param gatheredViews the value of field 'gatheredViews'.\r
- */\r
- public void setGatheredViews(\r
- final boolean gatheredViews) {\r
- this._gatheredViews = gatheredViews;\r
- this._has_gatheredViews = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'height'.\r
- * \r
- * @param height the value of field 'height'.\r
- */\r
- public void setHeight(\r
- final int height) {\r
- this._height = height;\r
- this._has_height = true;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vHiddenColumns\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void setHiddenColumns(\r
- final int index,\r
- final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._hiddenColumnsList.size()) {\r
- throw new IndexOutOfBoundsException("setHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");\r
- }\r
- \r
- this._hiddenColumnsList.set(index, vHiddenColumns);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vHiddenColumnsArray\r
- */\r
- public void setHiddenColumns(\r
- final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray) {\r
- //-- copy array\r
- _hiddenColumnsList.clear();\r
- \r
- for (int i = 0; i < vHiddenColumnsArray.length; i++) {\r
- this._hiddenColumnsList.add(vHiddenColumnsArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * Sets the value of field 'id'. The field 'id' has the\r
- * following description: unique id used by jalview to\r
- * synchronize between stored and instantiated views\r
- * \r
- * \r
- * @param id the value of field 'id'.\r
- */\r
- public void setId(\r
- final java.lang.String id) {\r
- this._id = id;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'pidSelected'.\r
- * \r
- * @param pidSelected the value of field 'pidSelected'.\r
- */\r
- public void setPidSelected(\r
- final boolean pidSelected) {\r
- this._pidSelected = pidSelected;\r
- this._has_pidSelected = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'pidThreshold'.\r
- * \r
- * @param pidThreshold the value of field 'pidThreshold'.\r
- */\r
- public void setPidThreshold(\r
- final int pidThreshold) {\r
- this._pidThreshold = pidThreshold;\r
- this._has_pidThreshold = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'renderGaps'.\r
- * \r
- * @param renderGaps the value of field 'renderGaps'.\r
- */\r
- public void setRenderGaps(\r
- final boolean renderGaps) {\r
- this._renderGaps = renderGaps;\r
- this._has_renderGaps = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'rightAlignIds'.\r
- * \r
- * @param rightAlignIds the value of field 'rightAlignIds'.\r
- */\r
- public void setRightAlignIds(\r
- final boolean rightAlignIds) {\r
- this._rightAlignIds = rightAlignIds;\r
- this._has_rightAlignIds = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'sequenceSetId'.\r
- * \r
- * @param sequenceSetId the value of field 'sequenceSetId'.\r
- */\r
- public void setSequenceSetId(\r
- final java.lang.String sequenceSetId) {\r
- this._sequenceSetId = sequenceSetId;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showAnnotation'.\r
- * \r
- * @param showAnnotation the value of field 'showAnnotation'.\r
- */\r
- public void setShowAnnotation(\r
- final boolean showAnnotation) {\r
- this._showAnnotation = showAnnotation;\r
- this._has_showAnnotation = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showBoxes'.\r
- * \r
- * @param showBoxes the value of field 'showBoxes'.\r
- */\r
- public void setShowBoxes(\r
- final boolean showBoxes) {\r
- this._showBoxes = showBoxes;\r
- this._has_showBoxes = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showColourText'.\r
- * \r
- * @param showColourText the value of field 'showColourText'.\r
- */\r
- public void setShowColourText(\r
- final boolean showColourText) {\r
- this._showColourText = showColourText;\r
- this._has_showColourText = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showFullId'.\r
- * \r
- * @param showFullId the value of field 'showFullId'.\r
- */\r
- public void setShowFullId(\r
- final boolean showFullId) {\r
- this._showFullId = showFullId;\r
- this._has_showFullId = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showSequenceFeatures'.\r
- * \r
- * @param showSequenceFeatures the value of field\r
- * 'showSequenceFeatures'.\r
- */\r
- public void setShowSequenceFeatures(\r
- final boolean showSequenceFeatures) {\r
- this._showSequenceFeatures = showSequenceFeatures;\r
- this._has_showSequenceFeatures = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showText'.\r
- * \r
- * @param showText the value of field 'showText'.\r
- */\r
- public void setShowText(\r
- final boolean showText) {\r
- this._showText = showText;\r
- this._has_showText = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showUnconserved'.\r
- * \r
- * @param showUnconserved the value of field 'showUnconserved'.\r
- */\r
- public void setShowUnconserved(\r
- final boolean showUnconserved) {\r
- this._showUnconserved = showUnconserved;\r
- this._has_showUnconserved = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'startRes'.\r
- * \r
- * @param startRes the value of field 'startRes'.\r
- */\r
- public void setStartRes(\r
- final int startRes) {\r
- this._startRes = startRes;\r
- this._has_startRes = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'startSeq'.\r
- * \r
- * @param startSeq the value of field 'startSeq'.\r
- */\r
- public void setStartSeq(\r
- final int startSeq) {\r
- this._startSeq = startSeq;\r
- this._has_startSeq = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'textCol1'.\r
- * \r
- * @param textCol1 the value of field 'textCol1'.\r
- */\r
- public void setTextCol1(\r
- final int textCol1) {\r
- this._textCol1 = textCol1;\r
- this._has_textCol1 = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'textCol2'.\r
- * \r
- * @param textCol2 the value of field 'textCol2'.\r
- */\r
- public void setTextCol2(\r
- final int textCol2) {\r
- this._textCol2 = textCol2;\r
- this._has_textCol2 = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'textColThreshold'.\r
- * \r
- * @param textColThreshold the value of field 'textColThreshold'\r
- */\r
- public void setTextColThreshold(\r
- final int textColThreshold) {\r
- this._textColThreshold = textColThreshold;\r
- this._has_textColThreshold = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'title'.\r
- * \r
- * @param title the value of field 'title'.\r
- */\r
- public void setTitle(\r
- final java.lang.String title) {\r
- this._title = title;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'viewName'.\r
- * \r
- * @param viewName the value of field 'viewName'.\r
- */\r
- public void setViewName(\r
- final java.lang.String viewName) {\r
- this._viewName = viewName;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'width'.\r
- * \r
- * @param width the value of field 'width'.\r
- */\r
- public void setWidth(\r
- final int width) {\r
- this._width = width;\r
- this._has_width = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'wrapAlignment'.\r
- * \r
- * @param wrapAlignment the value of field 'wrapAlignment'.\r
- */\r
- public void setWrapAlignment(\r
- final boolean wrapAlignment) {\r
- this._wrapAlignment = wrapAlignment;\r
- this._has_wrapAlignment = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'xpos'.\r
- * \r
- * @param xpos the value of field 'xpos'.\r
- */\r
- public void setXpos(\r
- final int xpos) {\r
- this._xpos = xpos;\r
- this._has_xpos = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'ypos'.\r
- * \r
- * @param ypos the value of field 'ypos'.\r
- */\r
- public void setYpos(\r
- final int ypos) {\r
- this._ypos = ypos;\r
- this._has_ypos = true;\r
- }\r
-\r
- /**\r
- * Method unmarshal.\r
- * \r
- * @param reader\r
- * @throws org.exolab.castor.xml.MarshalException if object is\r
- * null or if any SAXException is thrown during marshaling\r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- * @return the unmarshaled\r
- * jalview.schemabinding.version2.Viewport\r
- */\r
- public static jalview.schemabinding.version2.Viewport unmarshal(\r
- final java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
- return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(jalview.schemabinding.version2.Viewport.class, reader);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- */\r
- public void validate(\r
- )\r
- throws org.exolab.castor.xml.ValidationException {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- }\r
-\r
-}\r
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ *******************************************************************************/
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * 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 _showUnconserved.
+ */
+ private boolean _showUnconserved = false;
+
+ /**
+ * keeps track of state for field: _showUnconserved
+ */
+ private boolean _has_showUnconserved;
+
+ /**
+ * Field _showBoxes.
+ */
+ private boolean _showBoxes;
+
+ /**
+ * keeps track of state for field: _showBoxes
+ */
+ private boolean _has_showBoxes;
+
+ /**
+ * Field _wrapAlignment.
+ */
+ private boolean _wrapAlignment;
+
+ /**
+ * keeps track of state for field: _wrapAlignment
+ */
+ private boolean _has_wrapAlignment;
+
+ /**
+ * Field _renderGaps.
+ */
+ private boolean _renderGaps;
+
+ /**
+ * keeps track of state for field: _renderGaps
+ */
+ private boolean _has_renderGaps;
+
+ /**
+ * Field _showSequenceFeatures.
+ */
+ private boolean _showSequenceFeatures;
+
+ /**
+ * keeps track of state for field: _showSequenceFeatures
+ */
+ private boolean _has_showSequenceFeatures;
+
+ /**
+ * Field _showNPfeatureTooltip.
+ */
+ private boolean _showNPfeatureTooltip;
+
+ /**
+ * keeps track of state for field: _showNPfeatureTooltip
+ */
+ private boolean _has_showNPfeatureTooltip;
+
+ /**
+ * Field _showDbRefTooltip.
+ */
+ private boolean _showDbRefTooltip;
+
+ /**
+ * keeps track of state for field: _showDbRefTooltip
+ */
+ private boolean _has_showDbRefTooltip;
+
+ /**
+ * Field _followHighlight.
+ */
+ private boolean _followHighlight = true;
+
+ /**
+ * keeps track of state for field: _followHighlight
+ */
+ private boolean _has_followHighlight;
+
+ /**
+ * Field _followSelection.
+ */
+ private boolean _followSelection = true;
+
+ /**
+ * keeps track of state for field: _followSelection
+ */
+ private boolean _has_followSelection;
+
+ /**
+ * Field _showAnnotation.
+ */
+ private boolean _showAnnotation;
+
+ /**
+ * keeps track of state for field: _showAnnotation
+ */
+ private boolean _has_showAnnotation;
+
+ /**
+ * Field _centreColumnLabels.
+ */
+ private boolean _centreColumnLabels = false;
+
+ /**
+ * keeps track of state for field: _centreColumnLabels
+ */
+ private boolean _has_centreColumnLabels;
+
+ /**
+ * Field _showGroupConservation.
+ */
+ private boolean _showGroupConservation = false;
+
+ /**
+ * keeps track of state for field: _showGroupConservation
+ */
+ private boolean _has_showGroupConservation;
+
+ /**
+ * Field _showGroupConsensus.
+ */
+ private boolean _showGroupConsensus = false;
+
+ /**
+ * keeps track of state for field: _showGroupConsensus
+ */
+ private boolean _has_showGroupConsensus;
+
+ /**
+ * Field _showConsensusHistogram.
+ */
+ private boolean _showConsensusHistogram = true;
+
+ /**
+ * keeps track of state for field: _showConsensusHistogram
+ */
+ private boolean _has_showConsensusHistogram;
+
+ /**
+ * Field _showSequenceLogo.
+ */
+ private boolean _showSequenceLogo = false;
+
+ /**
+ * keeps track of state for field: _showSequenceLogo
+ */
+ private boolean _has_showSequenceLogo;
+
+ /**
+ * Field _ignoreGapsinConsensus.
+ */
+ private boolean _ignoreGapsinConsensus = true;
+
+ /**
+ * keeps track of state for field: _ignoreGapsinConsensus
+ */
+ private boolean _has_ignoreGapsinConsensus;
+
+ /**
+ * Field _startRes.
+ */
+ private int _startRes;
+
+ /**
+ * keeps track of state for field: _startRes
+ */
+ private boolean _has_startRes;
+
+ /**
+ * Field _startSeq.
+ */
+ private int _startSeq;
+
+ /**
+ * keeps track of state for field: _startSeq
+ */
+ private boolean _has_startSeq;
+
+ /**
+ * Field _fontName.
+ */
+ private java.lang.String _fontName;
+
+ /**
+ * Field _fontSize.
+ */
+ private int _fontSize;
+
+ /**
+ * keeps track of state for field: _fontSize
+ */
+ private boolean _has_fontSize;
+
+ /**
+ * Field _fontStyle.
+ */
+ private int _fontStyle;
+
+ /**
+ * keeps track of state for field: _fontStyle
+ */
+ private boolean _has_fontStyle;
+
+ /**
+ * Field _viewName.
+ */
+ private java.lang.String _viewName;
+
+ /**
+ * Field _sequenceSetId.
+ */
+ private java.lang.String _sequenceSetId;
+
+ /**
+ * Field _gatheredViews.
+ */
+ private boolean _gatheredViews;
+
+ /**
+ * keeps track of state for field: _gatheredViews
+ */
+ private boolean _has_gatheredViews;
+
+ /**
+ * Field _textCol1.
+ */
+ private int _textCol1;
+
+ /**
+ * keeps track of state for field: _textCol1
+ */
+ private boolean _has_textCol1;
+
+ /**
+ * Field _textCol2.
+ */
+ private int _textCol2;
+
+ /**
+ * keeps track of state for field: _textCol2
+ */
+ private boolean _has_textCol2;
+
+ /**
+ * Field _textColThreshold.
+ */
+ private int _textColThreshold;
+
+ /**
+ * keeps track of state for field: _textColThreshold
+ */
+ private boolean _has_textColThreshold;
+
+ /**
+ * unique id used by jalview to synchronize between stored and
+ * instantiated views
+ *
+ */
+ private java.lang.String _id;
+
+ /**
+ * Field _width.
+ */
+ private int _width;
+
+ /**
+ * keeps track of state for field: _width
+ */
+ private boolean _has_width;
+
+ /**
+ * Field _height.
+ */
+ private int _height;
+
+ /**
+ * keeps track of state for field: _height
+ */
+ private boolean _has_height;
+
+ /**
+ * Field _xpos.
+ */
+ private int _xpos;
+
+ /**
+ * keeps track of state for field: _xpos
+ */
+ private boolean _has_xpos;
+
+ /**
+ * Field _ypos.
+ */
+ private int _ypos;
+
+ /**
+ * keeps track of state for field: _ypos
+ */
+ private boolean _has_ypos;
+
+ /**
+ * Field _annotationColours.
+ */
+ private jalview.schemabinding.version2.AnnotationColours _annotationColours;
+
+ /**
+ * Field _hiddenColumnsList.
+ */
+ private java.util.Vector _hiddenColumnsList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Viewport() {
+ super();
+ this._hiddenColumnsList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vHiddenColumns
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addHiddenColumns(
+ final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+ throws java.lang.IndexOutOfBoundsException {
+ this._hiddenColumnsList.addElement(vHiddenColumns);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vHiddenColumns
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addHiddenColumns(
+ final int index,
+ final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+ throws java.lang.IndexOutOfBoundsException {
+ this._hiddenColumnsList.add(index, vHiddenColumns);
+ }
+
+ /**
+ */
+ public void deleteCentreColumnLabels(
+ ) {
+ this._has_centreColumnLabels= false;
+ }
+
+ /**
+ */
+ public void deleteConsThreshold(
+ ) {
+ this._has_consThreshold= false;
+ }
+
+ /**
+ */
+ public void deleteConservationSelected(
+ ) {
+ this._has_conservationSelected= false;
+ }
+
+ /**
+ */
+ public void deleteFollowHighlight(
+ ) {
+ this._has_followHighlight= false;
+ }
+
+ /**
+ */
+ public void deleteFollowSelection(
+ ) {
+ this._has_followSelection= false;
+ }
+
+ /**
+ */
+ public void deleteFontSize(
+ ) {
+ this._has_fontSize= false;
+ }
+
+ /**
+ */
+ public void deleteFontStyle(
+ ) {
+ this._has_fontStyle= false;
+ }
+
+ /**
+ */
+ public void deleteGatheredViews(
+ ) {
+ this._has_gatheredViews= false;
+ }
+
+ /**
+ */
+ public void deleteHeight(
+ ) {
+ this._has_height= false;
+ }
+
+ /**
+ */
+ public void deleteIgnoreGapsinConsensus(
+ ) {
+ this._has_ignoreGapsinConsensus= false;
+ }
+
+ /**
+ */
+ public void deletePidSelected(
+ ) {
+ this._has_pidSelected= false;
+ }
+
+ /**
+ */
+ public void deletePidThreshold(
+ ) {
+ this._has_pidThreshold= false;
+ }
+
+ /**
+ */
+ public void deleteRenderGaps(
+ ) {
+ this._has_renderGaps= false;
+ }
+
+ /**
+ */
+ public void deleteRightAlignIds(
+ ) {
+ this._has_rightAlignIds= false;
+ }
+
+ /**
+ */
+ public void deleteShowAnnotation(
+ ) {
+ this._has_showAnnotation= false;
+ }
+
+ /**
+ */
+ public void deleteShowBoxes(
+ ) {
+ this._has_showBoxes= false;
+ }
+
+ /**
+ */
+ public void deleteShowColourText(
+ ) {
+ this._has_showColourText= false;
+ }
+
+ /**
+ */
+ public void deleteShowConsensusHistogram(
+ ) {
+ this._has_showConsensusHistogram= false;
+ }
+
+ /**
+ */
+ public void deleteShowDbRefTooltip(
+ ) {
+ this._has_showDbRefTooltip= false;
+ }
+
+ /**
+ */
+ public void deleteShowFullId(
+ ) {
+ this._has_showFullId= false;
+ }
+
+ /**
+ */
+ public void deleteShowGroupConsensus(
+ ) {
+ this._has_showGroupConsensus= false;
+ }
+
+ /**
+ */
+ public void deleteShowGroupConservation(
+ ) {
+ this._has_showGroupConservation= false;
+ }
+
+ /**
+ */
+ public void deleteShowNPfeatureTooltip(
+ ) {
+ this._has_showNPfeatureTooltip= false;
+ }
+
+ /**
+ */
+ public void deleteShowSequenceFeatures(
+ ) {
+ this._has_showSequenceFeatures= false;
+ }
+
+ /**
+ */
+ public void deleteShowSequenceLogo(
+ ) {
+ this._has_showSequenceLogo= false;
+ }
+
+ /**
+ */
+ public void deleteShowText(
+ ) {
+ this._has_showText= false;
+ }
+
+ /**
+ */
+ public void deleteShowUnconserved(
+ ) {
+ this._has_showUnconserved= false;
+ }
+
+ /**
+ */
+ public void deleteStartRes(
+ ) {
+ this._has_startRes= false;
+ }
+
+ /**
+ */
+ public void deleteStartSeq(
+ ) {
+ this._has_startSeq= false;
+ }
+
+ /**
+ */
+ public void deleteTextCol1(
+ ) {
+ this._has_textCol1= false;
+ }
+
+ /**
+ */
+ public void deleteTextCol2(
+ ) {
+ this._has_textCol2= false;
+ }
+
+ /**
+ */
+ public void deleteTextColThreshold(
+ ) {
+ this._has_textColThreshold= false;
+ }
+
+ /**
+ */
+ public void deleteWidth(
+ ) {
+ this._has_width= false;
+ }
+
+ /**
+ */
+ public void deleteWrapAlignment(
+ ) {
+ this._has_wrapAlignment= false;
+ }
+
+ /**
+ */
+ public void deleteXpos(
+ ) {
+ this._has_xpos= false;
+ }
+
+ /**
+ */
+ public void deleteYpos(
+ ) {
+ this._has_ypos= false;
+ }
+
+ /**
+ * Method enumerateHiddenColumns.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.HiddenColumns elements
+ */
+ public java.util.Enumeration enumerateHiddenColumns(
+ ) {
+ return this._hiddenColumnsList.elements();
+ }
+
+ /**
+ * Returns the value of field 'annotationColours'.
+ *
+ * @return the value of field 'AnnotationColours'.
+ */
+ public jalview.schemabinding.version2.AnnotationColours getAnnotationColours(
+ ) {
+ return this._annotationColours;
+ }
+
+ /**
+ * Returns the value of field 'bgColour'.
+ *
+ * @return the value of field 'BgColour'.
+ */
+ public java.lang.String getBgColour(
+ ) {
+ return this._bgColour;
+ }
+
+ /**
+ * 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("getHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.get(index);
+ }
+
+ /**
+ * Method getHiddenColumns.Returns the contents of the
+ * collection in an Array. <p>Note: Just in case the
+ * collection contents are changing in another thread, we pass
+ * a 0-length Array of the correct type into the API call.
+ * This way we <i>know</i> that the Array returned is of
+ * exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns(
+ ) {
+ jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
+ return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList.toArray(array);
+ }
+
+ /**
+ * Method getHiddenColumnsCount.
+ *
+ * @return the size of this collection
+ */
+ public int getHiddenColumnsCount(
+ ) {
+ return this._hiddenColumnsList.size();
+ }
+
+ /**
+ * Returns the value of field 'id'. The field 'id' has the
+ * following description: unique id used by jalview to
+ * synchronize between stored and instantiated views
+ *
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId(
+ ) {
+ return this._id;
+ }
+
+ /**
+ * Returns the value of field 'ignoreGapsinConsensus'.
+ *
+ * @return the value of field 'IgnoreGapsinConsensus'.
+ */
+ public boolean getIgnoreGapsinConsensus(
+ ) {
+ return this._ignoreGapsinConsensus;
+ }
+
+ /**
+ * Returns the value of field 'pidSelected'.
+ *
+ * @return the value of field 'PidSelected'.
+ */
+ public boolean getPidSelected(
+ ) {
+ return this._pidSelected;
+ }
+
+ /**
+ * Returns the value of field 'pidThreshold'.
+ *
+ * @return the value of field 'PidThreshold'.
+ */
+ public int getPidThreshold(
+ ) {
+ return this._pidThreshold;
+ }
+
+ /**
+ * Returns the value of field 'renderGaps'.
+ *
+ * @return the value of field 'RenderGaps'.
+ */
+ public boolean getRenderGaps(
+ ) {
+ return this._renderGaps;
+ }
+
+ /**
+ * Returns the value of field 'rightAlignIds'.
+ *
+ * @return the value of field 'RightAlignIds'.
+ */
+ public boolean getRightAlignIds(
+ ) {
+ return this._rightAlignIds;
+ }
+
+ /**
+ * Returns the value of field 'sequenceSetId'.
+ *
+ * @return the value of field 'SequenceSetId'.
+ */
+ public java.lang.String getSequenceSetId(
+ ) {
+ return this._sequenceSetId;
+ }
+
+ /**
+ * Returns the value of field 'showAnnotation'.
+ *
+ * @return the value of field 'ShowAnnotation'.
+ */
+ public boolean getShowAnnotation(
+ ) {
+ return this._showAnnotation;
+ }
+
+ /**
+ * Returns the value of field 'showBoxes'.
+ *
+ * @return the value of field 'ShowBoxes'.
+ */
+ public boolean getShowBoxes(
+ ) {
+ return this._showBoxes;
+ }
+
+ /**
+ * Returns the value of field 'showColourText'.
+ *
+ * @return the value of field 'ShowColourText'.
+ */
+ public boolean getShowColourText(
+ ) {
+ return this._showColourText;
+ }
+
+ /**
+ * Returns the value of field 'showConsensusHistogram'.
+ *
+ * @return the value of field 'ShowConsensusHistogram'.
+ */
+ public boolean getShowConsensusHistogram(
+ ) {
+ return this._showConsensusHistogram;
+ }
+
+ /**
+ * Returns the value of field 'showDbRefTooltip'.
+ *
+ * @return the value of field 'ShowDbRefTooltip'.
+ */
+ public boolean getShowDbRefTooltip(
+ ) {
+ return this._showDbRefTooltip;
+ }
+
+ /**
+ * Returns the value of field 'showFullId'.
+ *
+ * @return the value of field 'ShowFullId'.
+ */
+ public boolean getShowFullId(
+ ) {
+ return this._showFullId;
+ }
+
+ /**
+ * Returns the value of field 'showGroupConsensus'.
+ *
+ * @return the value of field 'ShowGroupConsensus'.
+ */
+ public boolean getShowGroupConsensus(
+ ) {
+ return this._showGroupConsensus;
+ }
+
+ /**
+ * Returns the value of field 'showGroupConservation'.
+ *
+ * @return the value of field 'ShowGroupConservation'.
+ */
+ public boolean getShowGroupConservation(
+ ) {
+ return this._showGroupConservation;
+ }
+
+ /**
+ * Returns the value of field 'showNPfeatureTooltip'.
+ *
+ * @return the value of field 'ShowNPfeatureTooltip'.
+ */
+ public boolean getShowNPfeatureTooltip(
+ ) {
+ return this._showNPfeatureTooltip;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceFeatures'.
+ *
+ * @return the value of field 'ShowSequenceFeatures'.
+ */
+ public boolean getShowSequenceFeatures(
+ ) {
+ return this._showSequenceFeatures;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceLogo'.
+ *
+ * @return the value of field 'ShowSequenceLogo'.
+ */
+ public boolean getShowSequenceLogo(
+ ) {
+ return this._showSequenceLogo;
+ }
+
+ /**
+ * Returns the value of field 'showText'.
+ *
+ * @return the value of field 'ShowText'.
+ */
+ public boolean getShowText(
+ ) {
+ return this._showText;
+ }
+
+ /**
+ * Returns the value of field 'showUnconserved'.
+ *
+ * @return the value of field 'ShowUnconserved'.
+ */
+ public boolean getShowUnconserved(
+ ) {
+ return this._showUnconserved;
+ }
+
+ /**
+ * Returns the value of field 'startRes'.
+ *
+ * @return the value of field 'StartRes'.
+ */
+ public int getStartRes(
+ ) {
+ return this._startRes;
+ }
+
+ /**
+ * Returns the value of field 'startSeq'.
+ *
+ * @return the value of field 'StartSeq'.
+ */
+ public int getStartSeq(
+ ) {
+ return this._startSeq;
+ }
+
+ /**
+ * Returns the value of field 'textCol1'.
+ *
+ * @return the value of field 'TextCol1'.
+ */
+ public int getTextCol1(
+ ) {
+ return this._textCol1;
+ }
+
+ /**
+ * Returns the value of field 'textCol2'.
+ *
+ * @return the value of field 'TextCol2'.
+ */
+ public int getTextCol2(
+ ) {
+ return this._textCol2;
+ }
+
+ /**
+ * Returns the value of field 'textColThreshold'.
+ *
+ * @return the value of field 'TextColThreshold'.
+ */
+ public int getTextColThreshold(
+ ) {
+ return this._textColThreshold;
+ }
+
+ /**
+ * Returns the value of field 'title'.
+ *
+ * @return the value of field 'Title'.
+ */
+ public java.lang.String getTitle(
+ ) {
+ return this._title;
+ }
+
+ /**
+ * Returns the value of field 'viewName'.
+ *
+ * @return the value of field 'ViewName'.
+ */
+ public java.lang.String getViewName(
+ ) {
+ return this._viewName;
+ }
+
+ /**
+ * Returns the value of field 'width'.
+ *
+ * @return the value of field 'Width'.
+ */
+ public int getWidth(
+ ) {
+ return this._width;
+ }
+
+ /**
+ * Returns the value of field 'wrapAlignment'.
+ *
+ * @return the value of field 'WrapAlignment'.
+ */
+ public boolean getWrapAlignment(
+ ) {
+ return this._wrapAlignment;
+ }
+
+ /**
+ * Returns the value of field 'xpos'.
+ *
+ * @return the value of field 'Xpos'.
+ */
+ public int getXpos(
+ ) {
+ return this._xpos;
+ }
+
+ /**
+ * Returns the value of field 'ypos'.
+ *
+ * @return the value of field 'Ypos'.
+ */
+ public int getYpos(
+ ) {
+ return this._ypos;
+ }
+
+ /**
+ * Method hasCentreColumnLabels.
+ *
+ * @return true if at least one CentreColumnLabels has been adde
+ */
+ public boolean hasCentreColumnLabels(
+ ) {
+ return this._has_centreColumnLabels;
+ }
+
+ /**
+ * Method hasConsThreshold.
+ *
+ * @return true if at least one ConsThreshold has been added
+ */
+ public boolean hasConsThreshold(
+ ) {
+ return this._has_consThreshold;
+ }
+
+ /**
+ * Method hasConservationSelected.
+ *
+ * @return true if at least one ConservationSelected has been
+ * added
+ */
+ public boolean hasConservationSelected(
+ ) {
+ return this._has_conservationSelected;
+ }
+
+ /**
+ * Method hasFollowHighlight.
+ *
+ * @return true if at least one FollowHighlight has been added
+ */
+ public boolean hasFollowHighlight(
+ ) {
+ return this._has_followHighlight;
+ }
+
+ /**
+ * Method hasFollowSelection.
+ *
+ * @return true if at least one FollowSelection has been added
+ */
+ public boolean hasFollowSelection(
+ ) {
+ return this._has_followSelection;
+ }
+
+ /**
+ * Method hasFontSize.
+ *
+ * @return true if at least one FontSize has been added
+ */
+ public boolean hasFontSize(
+ ) {
+ return this._has_fontSize;
+ }
+
+ /**
+ * Method hasFontStyle.
+ *
+ * @return true if at least one FontStyle has been added
+ */
+ public boolean hasFontStyle(
+ ) {
+ return this._has_fontStyle;
+ }
+
+ /**
+ * Method hasGatheredViews.
+ *
+ * @return true if at least one GatheredViews has been added
+ */
+ public boolean hasGatheredViews(
+ ) {
+ return this._has_gatheredViews;
+ }
+
+ /**
+ * Method hasHeight.
+ *
+ * @return true if at least one Height has been added
+ */
+ public boolean hasHeight(
+ ) {
+ return this._has_height;
+ }
+
+ /**
+ * Method hasIgnoreGapsinConsensus.
+ *
+ * @return true if at least one IgnoreGapsinConsensus has been
+ * added
+ */
+ public boolean hasIgnoreGapsinConsensus(
+ ) {
+ return this._has_ignoreGapsinConsensus;
+ }
+
+ /**
+ * Method hasPidSelected.
+ *
+ * @return true if at least one PidSelected has been added
+ */
+ public boolean hasPidSelected(
+ ) {
+ return this._has_pidSelected;
+ }
+
+ /**
+ * Method hasPidThreshold.
+ *
+ * @return true if at least one PidThreshold has been added
+ */
+ public boolean hasPidThreshold(
+ ) {
+ return this._has_pidThreshold;
+ }
+
+ /**
+ * Method hasRenderGaps.
+ *
+ * @return true if at least one RenderGaps has been added
+ */
+ public boolean hasRenderGaps(
+ ) {
+ return this._has_renderGaps;
+ }
+
+ /**
+ * Method hasRightAlignIds.
+ *
+ * @return true if at least one RightAlignIds has been added
+ */
+ public boolean hasRightAlignIds(
+ ) {
+ return this._has_rightAlignIds;
+ }
+
+ /**
+ * Method hasShowAnnotation.
+ *
+ * @return true if at least one ShowAnnotation has been added
+ */
+ public boolean hasShowAnnotation(
+ ) {
+ return this._has_showAnnotation;
+ }
+
+ /**
+ * Method hasShowBoxes.
+ *
+ * @return true if at least one ShowBoxes has been added
+ */
+ public boolean hasShowBoxes(
+ ) {
+ return this._has_showBoxes;
+ }
+
+ /**
+ * Method hasShowColourText.
+ *
+ * @return true if at least one ShowColourText has been added
+ */
+ public boolean hasShowColourText(
+ ) {
+ return this._has_showColourText;
+ }
+
+ /**
+ * Method hasShowConsensusHistogram.
+ *
+ * @return true if at least one ShowConsensusHistogram has been
+ * added
+ */
+ public boolean hasShowConsensusHistogram(
+ ) {
+ return this._has_showConsensusHistogram;
+ }
+
+ /**
+ * Method hasShowDbRefTooltip.
+ *
+ * @return true if at least one ShowDbRefTooltip has been added
+ */
+ public boolean hasShowDbRefTooltip(
+ ) {
+ return this._has_showDbRefTooltip;
+ }
+
+ /**
+ * Method hasShowFullId.
+ *
+ * @return true if at least one ShowFullId has been added
+ */
+ public boolean hasShowFullId(
+ ) {
+ return this._has_showFullId;
+ }
+
+ /**
+ * Method hasShowGroupConsensus.
+ *
+ * @return true if at least one ShowGroupConsensus has been adde
+ */
+ public boolean hasShowGroupConsensus(
+ ) {
+ return this._has_showGroupConsensus;
+ }
+
+ /**
+ * Method hasShowGroupConservation.
+ *
+ * @return true if at least one ShowGroupConservation has been
+ * added
+ */
+ public boolean hasShowGroupConservation(
+ ) {
+ return this._has_showGroupConservation;
+ }
+
+ /**
+ * Method hasShowNPfeatureTooltip.
+ *
+ * @return true if at least one ShowNPfeatureTooltip has been
+ * added
+ */
+ public boolean hasShowNPfeatureTooltip(
+ ) {
+ return this._has_showNPfeatureTooltip;
+ }
+
+ /**
+ * Method hasShowSequenceFeatures.
+ *
+ * @return true if at least one ShowSequenceFeatures has been
+ * added
+ */
+ public boolean hasShowSequenceFeatures(
+ ) {
+ return this._has_showSequenceFeatures;
+ }
+
+ /**
+ * Method hasShowSequenceLogo.
+ *
+ * @return true if at least one ShowSequenceLogo has been added
+ */
+ public boolean hasShowSequenceLogo(
+ ) {
+ return this._has_showSequenceLogo;
+ }
+
+ /**
+ * Method hasShowText.
+ *
+ * @return true if at least one ShowText has been added
+ */
+ public boolean hasShowText(
+ ) {
+ return this._has_showText;
+ }
+
+ /**
+ * Method hasShowUnconserved.
+ *
+ * @return true if at least one ShowUnconserved has been added
+ */
+ public boolean hasShowUnconserved(
+ ) {
+ return this._has_showUnconserved;
+ }
+
+ /**
+ * Method hasStartRes.
+ *
+ * @return true if at least one StartRes has been added
+ */
+ public boolean hasStartRes(
+ ) {
+ return this._has_startRes;
+ }
+
+ /**
+ * Method hasStartSeq.
+ *
+ * @return true if at least one StartSeq has been added
+ */
+ public boolean hasStartSeq(
+ ) {
+ return this._has_startSeq;
+ }
+
+ /**
+ * Method hasTextCol1.
+ *
+ * @return true if at least one TextCol1 has been added
+ */
+ public boolean hasTextCol1(
+ ) {
+ return this._has_textCol1;
+ }
+
+ /**
+ * Method hasTextCol2.
+ *
+ * @return true if at least one TextCol2 has been added
+ */
+ public boolean hasTextCol2(
+ ) {
+ return this._has_textCol2;
+ }
+
+ /**
+ * Method hasTextColThreshold.
+ *
+ * @return true if at least one TextColThreshold has been added
+ */
+ public boolean hasTextColThreshold(
+ ) {
+ return this._has_textColThreshold;
+ }
+
+ /**
+ * Method hasWidth.
+ *
+ * @return true if at least one Width has been added
+ */
+ public boolean hasWidth(
+ ) {
+ return this._has_width;
+ }
+
+ /**
+ * Method hasWrapAlignment.
+ *
+ * @return true if at least one WrapAlignment has been added
+ */
+ public boolean hasWrapAlignment(
+ ) {
+ return this._has_wrapAlignment;
+ }
+
+ /**
+ * Method hasXpos.
+ *
+ * @return true if at least one Xpos has been added
+ */
+ public boolean hasXpos(
+ ) {
+ return this._has_xpos;
+ }
+
+ /**
+ * Method hasYpos.
+ *
+ * @return true if at least one Ypos has been added
+ */
+ public boolean hasYpos(
+ ) {
+ return this._has_ypos;
+ }
+
+ /**
+ * Returns the value of field 'centreColumnLabels'.
+ *
+ * @return the value of field 'CentreColumnLabels'.
+ */
+ public boolean isCentreColumnLabels(
+ ) {
+ return this._centreColumnLabels;
+ }
+
+ /**
+ * Returns the value of field 'conservationSelected'.
+ *
+ * @return the value of field 'ConservationSelected'.
+ */
+ public boolean isConservationSelected(
+ ) {
+ return this._conservationSelected;
+ }
+
+ /**
+ * Returns the value of field 'followHighlight'.
+ *
+ * @return the value of field 'FollowHighlight'.
+ */
+ public boolean isFollowHighlight(
+ ) {
+ return this._followHighlight;
+ }
+
+ /**
+ * Returns the value of field 'followSelection'.
+ *
+ * @return the value of field 'FollowSelection'.
+ */
+ public boolean isFollowSelection(
+ ) {
+ return this._followSelection;
+ }
+
+ /**
+ * Returns the value of field 'gatheredViews'.
+ *
+ * @return the value of field 'GatheredViews'.
+ */
+ public boolean isGatheredViews(
+ ) {
+ return this._gatheredViews;
+ }
+
+ /**
+ * Returns the value of field 'ignoreGapsinConsensus'.
+ *
+ * @return the value of field 'IgnoreGapsinConsensus'.
+ */
+ public boolean isIgnoreGapsinConsensus(
+ ) {
+ return this._ignoreGapsinConsensus;
+ }
+
+ /**
+ * Returns the value of field 'pidSelected'.
+ *
+ * @return the value of field 'PidSelected'.
+ */
+ public boolean isPidSelected(
+ ) {
+ return this._pidSelected;
+ }
+
+ /**
+ * Returns the value of field 'renderGaps'.
+ *
+ * @return the value of field 'RenderGaps'.
+ */
+ public boolean isRenderGaps(
+ ) {
+ return this._renderGaps;
+ }
+
+ /**
+ * Returns the value of field 'rightAlignIds'.
+ *
+ * @return the value of field 'RightAlignIds'.
+ */
+ public boolean isRightAlignIds(
+ ) {
+ return this._rightAlignIds;
+ }
+
+ /**
+ * Returns the value of field 'showAnnotation'.
+ *
+ * @return the value of field 'ShowAnnotation'.
+ */
+ public boolean isShowAnnotation(
+ ) {
+ return this._showAnnotation;
+ }
+
+ /**
+ * Returns the value of field 'showBoxes'.
+ *
+ * @return the value of field 'ShowBoxes'.
+ */
+ public boolean isShowBoxes(
+ ) {
+ return this._showBoxes;
+ }
+
+ /**
+ * Returns the value of field 'showColourText'.
+ *
+ * @return the value of field 'ShowColourText'.
+ */
+ public boolean isShowColourText(
+ ) {
+ return this._showColourText;
+ }
+
+ /**
+ * Returns the value of field 'showConsensusHistogram'.
+ *
+ * @return the value of field 'ShowConsensusHistogram'.
+ */
+ public boolean isShowConsensusHistogram(
+ ) {
+ return this._showConsensusHistogram;
+ }
+
+ /**
+ * Returns the value of field 'showDbRefTooltip'.
+ *
+ * @return the value of field 'ShowDbRefTooltip'.
+ */
+ public boolean isShowDbRefTooltip(
+ ) {
+ return this._showDbRefTooltip;
+ }
+
+ /**
+ * Returns the value of field 'showFullId'.
+ *
+ * @return the value of field 'ShowFullId'.
+ */
+ public boolean isShowFullId(
+ ) {
+ return this._showFullId;
+ }
+
+ /**
+ * Returns the value of field 'showGroupConsensus'.
+ *
+ * @return the value of field 'ShowGroupConsensus'.
+ */
+ public boolean isShowGroupConsensus(
+ ) {
+ return this._showGroupConsensus;
+ }
+
+ /**
+ * Returns the value of field 'showGroupConservation'.
+ *
+ * @return the value of field 'ShowGroupConservation'.
+ */
+ public boolean isShowGroupConservation(
+ ) {
+ return this._showGroupConservation;
+ }
+
+ /**
+ * Returns the value of field 'showNPfeatureTooltip'.
+ *
+ * @return the value of field 'ShowNPfeatureTooltip'.
+ */
+ public boolean isShowNPfeatureTooltip(
+ ) {
+ return this._showNPfeatureTooltip;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceFeatures'.
+ *
+ * @return the value of field 'ShowSequenceFeatures'.
+ */
+ public boolean isShowSequenceFeatures(
+ ) {
+ return this._showSequenceFeatures;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceLogo'.
+ *
+ * @return the value of field 'ShowSequenceLogo'.
+ */
+ public boolean isShowSequenceLogo(
+ ) {
+ return this._showSequenceLogo;
+ }
+
+ /**
+ * Returns the value of field 'showText'.
+ *
+ * @return the value of field 'ShowText'.
+ */
+ public boolean isShowText(
+ ) {
+ return this._showText;
+ }
+
+ /**
+ * Returns the value of field 'showUnconserved'.
+ *
+ * @return the value of field 'ShowUnconserved'.
+ */
+ public boolean isShowUnconserved(
+ ) {
+ return this._showUnconserved;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * Returns the value of field 'wrapAlignment'.
+ *
+ * @return the value of field 'WrapAlignment'.
+ */
+ public boolean isWrapAlignment(
+ ) {
+ return this._wrapAlignment;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllHiddenColumns(
+ ) {
+ this._hiddenColumnsList.clear();
+ }
+
+ /**
+ * Method removeHiddenColumns.
+ *
+ * @param vHiddenColumns
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeHiddenColumns(
+ final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) {
+ boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
+ return removed;
+ }
+
+ /**
+ * Method removeHiddenColumnsAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
+ final int index) {
+ java.lang.Object obj = this._hiddenColumnsList.remove(index);
+ return (jalview.schemabinding.version2.HiddenColumns) obj;
+ }
+
+ /**
+ * Sets the value of field 'annotationColours'.
+ *
+ * @param annotationColours the value of field
+ * 'annotationColours'.
+ */
+ public void setAnnotationColours(
+ final jalview.schemabinding.version2.AnnotationColours annotationColours) {
+ this._annotationColours = annotationColours;
+ }
+
+ /**
+ * Sets the value of field 'bgColour'.
+ *
+ * @param bgColour the value of field 'bgColour'.
+ */
+ public void setBgColour(
+ final java.lang.String bgColour) {
+ this._bgColour = bgColour;
+ }
+
+ /**
+ * Sets the value of field 'centreColumnLabels'.
+ *
+ * @param centreColumnLabels the value of field
+ * 'centreColumnLabels'.
+ */
+ public void setCentreColumnLabels(
+ final boolean centreColumnLabels) {
+ this._centreColumnLabels = centreColumnLabels;
+ this._has_centreColumnLabels = true;
+ }
+
+ /**
+ * Sets the value of field 'consThreshold'.
+ *
+ * @param consThreshold the value of field 'consThreshold'.
+ */
+ public void setConsThreshold(
+ final int consThreshold) {
+ this._consThreshold = consThreshold;
+ this._has_consThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'conservationSelected'.
+ *
+ * @param conservationSelected the value of field
+ * 'conservationSelected'.
+ */
+ public void setConservationSelected(
+ final boolean conservationSelected) {
+ this._conservationSelected = conservationSelected;
+ this._has_conservationSelected = true;
+ }
+
+ /**
+ * Sets the value of field 'followHighlight'.
+ *
+ * @param followHighlight the value of field 'followHighlight'.
+ */
+ public void setFollowHighlight(
+ final boolean followHighlight) {
+ this._followHighlight = followHighlight;
+ this._has_followHighlight = true;
+ }
+
+ /**
+ * Sets the value of field 'followSelection'.
+ *
+ * @param followSelection the value of field 'followSelection'.
+ */
+ public void setFollowSelection(
+ final boolean followSelection) {
+ this._followSelection = followSelection;
+ this._has_followSelection = true;
+ }
+
+ /**
+ * Sets the value of field 'fontName'.
+ *
+ * @param fontName the value of field 'fontName'.
+ */
+ public void setFontName(
+ final java.lang.String fontName) {
+ this._fontName = fontName;
+ }
+
+ /**
+ * Sets the value of field 'fontSize'.
+ *
+ * @param fontSize the value of field 'fontSize'.
+ */
+ public void setFontSize(
+ final int fontSize) {
+ this._fontSize = fontSize;
+ this._has_fontSize = true;
+ }
+
+ /**
+ * Sets the value of field 'fontStyle'.
+ *
+ * @param fontStyle the value of field 'fontStyle'.
+ */
+ public void setFontStyle(
+ final int fontStyle) {
+ this._fontStyle = fontStyle;
+ this._has_fontStyle = true;
+ }
+
+ /**
+ * Sets the value of field 'gatheredViews'.
+ *
+ * @param gatheredViews the value of field 'gatheredViews'.
+ */
+ public void setGatheredViews(
+ final boolean gatheredViews) {
+ this._gatheredViews = gatheredViews;
+ this._has_gatheredViews = true;
+ }
+
+ /**
+ * Sets the value of field 'height'.
+ *
+ * @param height the value of field 'height'.
+ */
+ public void setHeight(
+ final int height) {
+ this._height = height;
+ this._has_height = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vHiddenColumns
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setHiddenColumns(
+ final int index,
+ final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._hiddenColumnsList.size()) {
+ throw new IndexOutOfBoundsException("setHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
+ }
+
+ this._hiddenColumnsList.set(index, vHiddenColumns);
+ }
+
+ /**
+ *
+ *
+ * @param vHiddenColumnsArray
+ */
+ public void setHiddenColumns(
+ final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray) {
+ //-- copy array
+ _hiddenColumnsList.clear();
+
+ for (int i = 0; i < vHiddenColumnsArray.length; i++) {
+ this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'id'. The field 'id' has the
+ * following description: unique id used by jalview to
+ * synchronize between stored and instantiated views
+ *
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(
+ final java.lang.String id) {
+ this._id = id;
+ }
+
+ /**
+ * Sets the value of field 'ignoreGapsinConsensus'.
+ *
+ * @param ignoreGapsinConsensus the value of field
+ * 'ignoreGapsinConsensus'.
+ */
+ public void setIgnoreGapsinConsensus(
+ final boolean ignoreGapsinConsensus) {
+ this._ignoreGapsinConsensus = ignoreGapsinConsensus;
+ this._has_ignoreGapsinConsensus = true;
+ }
+
+ /**
+ * Sets the value of field 'pidSelected'.
+ *
+ * @param pidSelected the value of field 'pidSelected'.
+ */
+ public void setPidSelected(
+ final boolean pidSelected) {
+ this._pidSelected = pidSelected;
+ this._has_pidSelected = true;
+ }
+
+ /**
+ * Sets the value of field 'pidThreshold'.
+ *
+ * @param pidThreshold the value of field 'pidThreshold'.
+ */
+ public void setPidThreshold(
+ final int pidThreshold) {
+ this._pidThreshold = pidThreshold;
+ this._has_pidThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'renderGaps'.
+ *
+ * @param renderGaps the value of field 'renderGaps'.
+ */
+ public void setRenderGaps(
+ final boolean renderGaps) {
+ this._renderGaps = renderGaps;
+ this._has_renderGaps = true;
+ }
+
+ /**
+ * Sets the value of field 'rightAlignIds'.
+ *
+ * @param rightAlignIds the value of field 'rightAlignIds'.
+ */
+ public void setRightAlignIds(
+ final boolean rightAlignIds) {
+ this._rightAlignIds = rightAlignIds;
+ this._has_rightAlignIds = true;
+ }
+
+ /**
+ * Sets the value of field 'sequenceSetId'.
+ *
+ * @param sequenceSetId the value of field 'sequenceSetId'.
+ */
+ public void setSequenceSetId(
+ final java.lang.String sequenceSetId) {
+ this._sequenceSetId = sequenceSetId;
+ }
+
+ /**
+ * Sets the value of field 'showAnnotation'.
+ *
+ * @param showAnnotation the value of field 'showAnnotation'.
+ */
+ public void setShowAnnotation(
+ final boolean showAnnotation) {
+ this._showAnnotation = showAnnotation;
+ this._has_showAnnotation = true;
+ }
+
+ /**
+ * Sets the value of field 'showBoxes'.
+ *
+ * @param showBoxes the value of field 'showBoxes'.
+ */
+ public void setShowBoxes(
+ final boolean showBoxes) {
+ this._showBoxes = showBoxes;
+ this._has_showBoxes = true;
+ }
+
+ /**
+ * Sets the value of field 'showColourText'.
+ *
+ * @param showColourText the value of field 'showColourText'.
+ */
+ public void setShowColourText(
+ final boolean showColourText) {
+ this._showColourText = showColourText;
+ this._has_showColourText = true;
+ }
+
+ /**
+ * Sets the value of field 'showConsensusHistogram'.
+ *
+ * @param showConsensusHistogram the value of field
+ * 'showConsensusHistogram'.
+ */
+ public void setShowConsensusHistogram(
+ final boolean showConsensusHistogram) {
+ this._showConsensusHistogram = showConsensusHistogram;
+ this._has_showConsensusHistogram = true;
+ }
+
+ /**
+ * Sets the value of field 'showDbRefTooltip'.
+ *
+ * @param showDbRefTooltip the value of field 'showDbRefTooltip'
+ */
+ public void setShowDbRefTooltip(
+ final boolean showDbRefTooltip) {
+ this._showDbRefTooltip = showDbRefTooltip;
+ this._has_showDbRefTooltip = true;
+ }
+
+ /**
+ * Sets the value of field 'showFullId'.
+ *
+ * @param showFullId the value of field 'showFullId'.
+ */
+ public void setShowFullId(
+ final boolean showFullId) {
+ this._showFullId = showFullId;
+ this._has_showFullId = true;
+ }
+
+ /**
+ * Sets the value of field 'showGroupConsensus'.
+ *
+ * @param showGroupConsensus the value of field
+ * 'showGroupConsensus'.
+ */
+ public void setShowGroupConsensus(
+ final boolean showGroupConsensus) {
+ this._showGroupConsensus = showGroupConsensus;
+ this._has_showGroupConsensus = true;
+ }
+
+ /**
+ * Sets the value of field 'showGroupConservation'.
+ *
+ * @param showGroupConservation the value of field
+ * 'showGroupConservation'.
+ */
+ public void setShowGroupConservation(
+ final boolean showGroupConservation) {
+ this._showGroupConservation = showGroupConservation;
+ this._has_showGroupConservation = true;
+ }
+
+ /**
+ * Sets the value of field 'showNPfeatureTooltip'.
+ *
+ * @param showNPfeatureTooltip the value of field
+ * 'showNPfeatureTooltip'.
+ */
+ public void setShowNPfeatureTooltip(
+ final boolean showNPfeatureTooltip) {
+ this._showNPfeatureTooltip = showNPfeatureTooltip;
+ this._has_showNPfeatureTooltip = true;
+ }
+
+ /**
+ * Sets the value of field 'showSequenceFeatures'.
+ *
+ * @param showSequenceFeatures the value of field
+ * 'showSequenceFeatures'.
+ */
+ public void setShowSequenceFeatures(
+ final boolean showSequenceFeatures) {
+ this._showSequenceFeatures = showSequenceFeatures;
+ this._has_showSequenceFeatures = true;
+ }
+
+ /**
+ * Sets the value of field 'showSequenceLogo'.
+ *
+ * @param showSequenceLogo the value of field 'showSequenceLogo'
+ */
+ public void setShowSequenceLogo(
+ final boolean showSequenceLogo) {
+ this._showSequenceLogo = showSequenceLogo;
+ this._has_showSequenceLogo = true;
+ }
+
+ /**
+ * Sets the value of field 'showText'.
+ *
+ * @param showText the value of field 'showText'.
+ */
+ public void setShowText(
+ final boolean showText) {
+ this._showText = showText;
+ this._has_showText = true;
+ }
+
+ /**
+ * Sets the value of field 'showUnconserved'.
+ *
+ * @param showUnconserved the value of field 'showUnconserved'.
+ */
+ public void setShowUnconserved(
+ final boolean showUnconserved) {
+ this._showUnconserved = showUnconserved;
+ this._has_showUnconserved = true;
+ }
+
+ /**
+ * Sets the value of field 'startRes'.
+ *
+ * @param startRes the value of field 'startRes'.
+ */
+ public void setStartRes(
+ final int startRes) {
+ this._startRes = startRes;
+ this._has_startRes = true;
+ }
+
+ /**
+ * Sets the value of field 'startSeq'.
+ *
+ * @param startSeq the value of field 'startSeq'.
+ */
+ public void setStartSeq(
+ final int startSeq) {
+ this._startSeq = startSeq;
+ this._has_startSeq = true;
+ }
+
+ /**
+ * Sets the value of field 'textCol1'.
+ *
+ * @param textCol1 the value of field 'textCol1'.
+ */
+ public void setTextCol1(
+ final int textCol1) {
+ this._textCol1 = textCol1;
+ this._has_textCol1 = true;
+ }
+
+ /**
+ * Sets the value of field 'textCol2'.
+ *
+ * @param textCol2 the value of field 'textCol2'.
+ */
+ public void setTextCol2(
+ final int textCol2) {
+ this._textCol2 = textCol2;
+ this._has_textCol2 = true;
+ }
+
+ /**
+ * Sets the value of field 'textColThreshold'.
+ *
+ * @param textColThreshold the value of field 'textColThreshold'
+ */
+ public void setTextColThreshold(
+ final int textColThreshold) {
+ this._textColThreshold = textColThreshold;
+ this._has_textColThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'title'.
+ *
+ * @param title the value of field 'title'.
+ */
+ public void setTitle(
+ final java.lang.String title) {
+ this._title = title;
+ }
+
+ /**
+ * Sets the value of field 'viewName'.
+ *
+ * @param viewName the value of field 'viewName'.
+ */
+ public void setViewName(
+ final java.lang.String viewName) {
+ this._viewName = viewName;
+ }
+
+ /**
+ * Sets the value of field 'width'.
+ *
+ * @param width the value of field 'width'.
+ */
+ public void setWidth(
+ final int width) {
+ this._width = width;
+ this._has_width = true;
+ }
+
+ /**
+ * Sets the value of field 'wrapAlignment'.
+ *
+ * @param wrapAlignment the value of field 'wrapAlignment'.
+ */
+ public void setWrapAlignment(
+ final boolean wrapAlignment) {
+ this._wrapAlignment = wrapAlignment;
+ this._has_wrapAlignment = true;
+ }
+
+ /**
+ * Sets the value of field 'xpos'.
+ *
+ * @param xpos the value of field 'xpos'.
+ */
+ public void setXpos(
+ final int xpos) {
+ this._xpos = xpos;
+ this._has_xpos = true;
+ }
+
+ /**
+ * Sets the value of field 'ypos'.
+ *
+ * @param ypos the value of field 'ypos'.
+ */
+ public void setYpos(
+ final int ypos) {
+ this._ypos = ypos;
+ this._has_ypos = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled
+ * jalview.schemabinding.version2.Viewport
+ */
+ public static jalview.schemabinding.version2.Viewport unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(jalview.schemabinding.version2.Viewport.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff