/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
- * Schema.\r
- * $Id$\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
-\r
package jalview.schemabinding.version2;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import java.util.Enumeration;\r
-import java.util.Vector;\r
-import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class Viewport.\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class Viewport implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _conservationSelected\r
- */\r
- private boolean _conservationSelected;\r
-\r
- /**\r
- * keeps track of state for field: _conservationSelected\r
- */\r
- private boolean _has_conservationSelected;\r
-\r
- /**\r
- * Field _pidSelected\r
- */\r
- private boolean _pidSelected;\r
-\r
- /**\r
- * keeps track of state for field: _pidSelected\r
- */\r
- private boolean _has_pidSelected;\r
-\r
- /**\r
- * Field _bgColour\r
- */\r
- private java.lang.String _bgColour;\r
-\r
- /**\r
- * Field _consThreshold\r
- */\r
- private int _consThreshold;\r
-\r
- /**\r
- * keeps track of state for field: _consThreshold\r
- */\r
- private boolean _has_consThreshold;\r
-\r
- /**\r
- * Field _pidThreshold\r
- */\r
- private int _pidThreshold;\r
-\r
- /**\r
- * keeps track of state for field: _pidThreshold\r
- */\r
- private boolean _has_pidThreshold;\r
-\r
- /**\r
- * Field _title\r
- */\r
- private java.lang.String _title;\r
-\r
- /**\r
- * Field _showFullId\r
- */\r
- private boolean _showFullId;\r
-\r
- /**\r
- * keeps track of state for field: _showFullId\r
- */\r
- private boolean _has_showFullId;\r
-\r
- /**\r
- * Field _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 _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
+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 = false;\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 _showNPfeatureTooltip.\r
+ */\r
+ private boolean _showNPfeatureTooltip;\r
+\r
+ /**\r
+ * keeps track of state for field: _showNPfeatureTooltip\r
+ */\r
+ private boolean _has_showNPfeatureTooltip;\r
+\r
+ /**\r
+ * Field _showDbRefTooltip.\r
+ */\r
+ private boolean _showDbRefTooltip;\r
+\r
+ /**\r
+ * keeps track of state for field: _showDbRefTooltip\r
+ */\r
+ private boolean _has_showDbRefTooltip;\r
+\r
+ /**\r
+ * Field _followHighlight.\r
+ */\r
+ private boolean _followHighlight = true;\r
+\r
+ /**\r
+ * keeps track of state for field: _followHighlight\r
+ */\r
+ private boolean _has_followHighlight;\r
+\r
+ /**\r
+ * Field _followSelection.\r
+ */\r
+ private boolean _followSelection = true;\r
+\r
+ /**\r
+ * keeps track of state for field: _followSelection\r
+ */\r
+ private boolean _has_followSelection;\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 _centreColumnLabels.\r
+ */\r
+ private boolean _centreColumnLabels = false;\r
+\r
+ /**\r
+ * keeps track of state for field: _centreColumnLabels\r
+ */\r
+ private boolean _has_centreColumnLabels;\r
+\r
+ /**\r
+ * Field _showGroupConservation.\r
+ */\r
+ private boolean _showGroupConservation = false;\r
+\r
+ /**\r
+ * keeps track of state for field: _showGroupConservation\r
+ */\r
+ private boolean _has_showGroupConservation;\r
+\r
+ /**\r
+ * Field _showGroupConsensus.\r
+ */\r
+ private boolean _showGroupConsensus = false;\r
+\r
+ /**\r
+ * keeps track of state for field: _showGroupConsensus\r
+ */\r
+ private boolean _has_showGroupConsensus;\r
+\r
+ /**\r
+ * Field _showConsensusHistogram.\r
+ */\r
+ private boolean _showConsensusHistogram = true;\r
+\r
+ /**\r
+ * keeps track of state for field: _showConsensusHistogram\r
+ */\r
+ private boolean _has_showConsensusHistogram;\r
+\r
+ /**\r
+ * Field _showSequenceLogo.\r
+ */\r
+ private boolean _showSequenceLogo = false;\r
+\r
+ /**\r
+ * keeps track of state for field: _showSequenceLogo\r
+ */\r
+ private boolean _has_showSequenceLogo;\r
+\r
+ /**\r
+ * Field _ignoreGapsinConsensus.\r
+ */\r
+ private boolean _ignoreGapsinConsensus = true;\r
+\r
+ /**\r
+ * keeps track of state for field: _ignoreGapsinConsensus\r
+ */\r
+ private boolean _has_ignoreGapsinConsensus;\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 instantiated\r
+ * 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
+ // - Constructors -/\r
+ // ----------------/\r
+\r
+ public Viewport()\r
+ {\r
+ super();\r
+ this._hiddenColumnsList = new java.util.Vector();\r
+ }\r
+\r
+ // -----------/\r
+ // - Methods -/\r
+ // -----------/\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vHiddenColumns\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index 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
+ {\r
+ this._hiddenColumnsList.addElement(vHiddenColumns);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vHiddenColumns\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addHiddenColumns(final int index,\r
+ final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._hiddenColumnsList.add(index, vHiddenColumns);\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteCentreColumnLabels()\r
+ {\r
+ this._has_centreColumnLabels = false;\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 deleteFollowHighlight()\r
+ {\r
+ this._has_followHighlight = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteFollowSelection()\r
+ {\r
+ this._has_followSelection = 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
- * Field _ypos\r
+ /**\r
*/\r
- private int _ypos;\r
+ public void deleteGatheredViews()\r
+ {\r
+ this._has_gatheredViews = false;\r
+ }\r
\r
- /**\r
- * keeps track of state for field: _ypos\r
+ /**\r
*/\r
- private boolean _has_ypos;\r
+ public void deleteHeight()\r
+ {\r
+ this._has_height = false;\r
+ }\r
\r
- /**\r
- * Field _width\r
+ /**\r
*/\r
- private int _width;\r
+ public void deleteIgnoreGapsinConsensus()\r
+ {\r
+ this._has_ignoreGapsinConsensus = false;\r
+ }\r
\r
- /**\r
- * keeps track of state for field: _width\r
+ /**\r
*/\r
- private boolean _has_width;\r
+ public void deletePidSelected()\r
+ {\r
+ this._has_pidSelected = false;\r
+ }\r
\r
- /**\r
- * Field _height\r
+ /**\r
*/\r
- private int _height;\r
+ public void deletePidThreshold()\r
+ {\r
+ this._has_pidThreshold = false;\r
+ }\r
\r
- /**\r
- * keeps track of state for field: _height\r
+ /**\r
*/\r
- private boolean _has_height;\r
+ public void deleteRenderGaps()\r
+ {\r
+ this._has_renderGaps = false;\r
+ }\r
\r
- /**\r
- * Field _startRes\r
+ /**\r
*/\r
- private int _startRes;\r
+ public void deleteRightAlignIds()\r
+ {\r
+ this._has_rightAlignIds = false;\r
+ }\r
\r
- /**\r
- * keeps track of state for field: _startRes\r
+ /**\r
*/\r
- private boolean _has_startRes;\r
+ public void deleteShowAnnotation()\r
+ {\r
+ this._has_showAnnotation = false;\r
+ }\r
\r
- /**\r
- * Field _startSeq\r
+ /**\r
*/\r
- private int _startSeq;\r
+ public void deleteShowBoxes()\r
+ {\r
+ this._has_showBoxes = false;\r
+ }\r
\r
- /**\r
- * keeps track of state for field: _startSeq\r
+ /**\r
*/\r
- private boolean _has_startSeq;\r
+ public void deleteShowColourText()\r
+ {\r
+ this._has_showColourText = false;\r
+ }\r
\r
- /**\r
- * Field _fontName\r
+ /**\r
*/\r
- private java.lang.String _fontName;\r
+ public void deleteShowConsensusHistogram()\r
+ {\r
+ this._has_showConsensusHistogram = false;\r
+ }\r
\r
- /**\r
- * Field _fontSize\r
+ /**\r
*/\r
- private int _fontSize;\r
+ public void deleteShowDbRefTooltip()\r
+ {\r
+ this._has_showDbRefTooltip = false;\r
+ }\r
\r
- /**\r
- * keeps track of state for field: _fontSize\r
+ /**\r
*/\r
- private boolean _has_fontSize;\r
+ public void deleteShowFullId()\r
+ {\r
+ this._has_showFullId = false;\r
+ }\r
\r
- /**\r
- * Field _fontStyle\r
+ /**\r
*/\r
- private int _fontStyle;\r
+ public void deleteShowGroupConsensus()\r
+ {\r
+ this._has_showGroupConsensus = false;\r
+ }\r
\r
- /**\r
- * keeps track of state for field: _fontStyle\r
+ /**\r
*/\r
- private boolean _has_fontStyle;\r
+ public void deleteShowGroupConservation()\r
+ {\r
+ this._has_showGroupConservation = false;\r
+ }\r
\r
- /**\r
- * Field _viewName\r
+ /**\r
*/\r
- private java.lang.String _viewName;\r
+ public void deleteShowNPfeatureTooltip()\r
+ {\r
+ this._has_showNPfeatureTooltip = false;\r
+ }\r
\r
- /**\r
- * Field _sequenceSetId\r
+ /**\r
*/\r
- private java.lang.String _sequenceSetId;\r
+ public void deleteShowSequenceFeatures()\r
+ {\r
+ this._has_showSequenceFeatures = false;\r
+ }\r
\r
- /**\r
- * Field _gatheredViews\r
+ /**\r
*/\r
- private boolean _gatheredViews;\r
+ public void deleteShowSequenceLogo()\r
+ {\r
+ this._has_showSequenceLogo = false;\r
+ }\r
\r
- /**\r
- * keeps track of state for field: _gatheredViews\r
+ /**\r
*/\r
- private boolean _has_gatheredViews;\r
+ public void deleteShowText()\r
+ {\r
+ this._has_showText = false;\r
+ }\r
\r
- /**\r
- * Field _textCol1\r
+ /**\r
*/\r
- private int _textCol1;\r
+ public void deleteShowUnconserved()\r
+ {\r
+ this._has_showUnconserved = false;\r
+ }\r
\r
- /**\r
- * keeps track of state for field: _textCol1\r
+ /**\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
- * Field _annotationColours\r
- */\r
- private jalview.schemabinding.version2.AnnotationColours _annotationColours;\r
-\r
- /**\r
- * Field _hiddenColumnsList\r
- */\r
- private java.util.Vector _hiddenColumnsList;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Viewport() {\r
- super();\r
- _hiddenColumnsList = new Vector();\r
- } //-- jalview.schemabinding.version2.Viewport()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addHiddenColumns\r
- * \r
- * \r
- * \r
- * @param vHiddenColumns\r
- */\r
- public void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _hiddenColumnsList.addElement(vHiddenColumns);\r
- } //-- void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns) \r
-\r
- /**\r
- * Method addHiddenColumns\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vHiddenColumns\r
- */\r
- public void addHiddenColumns(int index, jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _hiddenColumnsList.insertElementAt(vHiddenColumns, index);\r
- } //-- void addHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns) \r
-\r
- /**\r
- * Method deleteConsThreshold\r
- * \r
- */\r
- public void deleteConsThreshold()\r
- {\r
- this._has_consThreshold= false;\r
- } //-- void deleteConsThreshold() \r
-\r
- /**\r
- * Method deleteConservationSelected\r
- * \r
- */\r
- public void deleteConservationSelected()\r
- {\r
- this._has_conservationSelected= false;\r
- } //-- void deleteConservationSelected() \r
-\r
- /**\r
- * Method deleteFontSize\r
- * \r
- */\r
- public void deleteFontSize()\r
- {\r
- this._has_fontSize= false;\r
- } //-- void deleteFontSize() \r
-\r
- /**\r
- * Method deleteFontStyle\r
- * \r
- */\r
- public void deleteFontStyle()\r
- {\r
- this._has_fontStyle= false;\r
- } //-- void deleteFontStyle() \r
-\r
- /**\r
- * Method deleteGatheredViews\r
- * \r
- */\r
- public void deleteGatheredViews()\r
- {\r
- this._has_gatheredViews= false;\r
- } //-- void deleteGatheredViews() \r
-\r
- /**\r
- * Method deleteHeight\r
- * \r
- */\r
- public void deleteHeight()\r
- {\r
- this._has_height= false;\r
- } //-- void deleteHeight() \r
-\r
- /**\r
- * Method deletePidSelected\r
- * \r
- */\r
- public void deletePidSelected()\r
- {\r
- this._has_pidSelected= false;\r
- } //-- void deletePidSelected() \r
-\r
- /**\r
- * Method deletePidThreshold\r
- * \r
- */\r
- public void deletePidThreshold()\r
- {\r
- this._has_pidThreshold= false;\r
- } //-- void deletePidThreshold() \r
-\r
- /**\r
- * Method deleteRenderGaps\r
- * \r
- */\r
- public void deleteRenderGaps()\r
- {\r
- this._has_renderGaps= false;\r
- } //-- void deleteRenderGaps() \r
-\r
- /**\r
- * Method deleteRightAlignIds\r
- * \r
- */\r
- public void deleteRightAlignIds()\r
- {\r
- this._has_rightAlignIds= false;\r
- } //-- void deleteRightAlignIds() \r
-\r
- /**\r
- * Method deleteShowAnnotation\r
- * \r
- */\r
- public void deleteShowAnnotation()\r
- {\r
- this._has_showAnnotation= false;\r
- } //-- void deleteShowAnnotation() \r
-\r
- /**\r
- * Method deleteShowBoxes\r
- * \r
- */\r
- public void deleteShowBoxes()\r
- {\r
- this._has_showBoxes= false;\r
- } //-- void deleteShowBoxes() \r
-\r
- /**\r
- * Method deleteShowColourText\r
- * \r
- */\r
- public void deleteShowColourText()\r
- {\r
- this._has_showColourText= false;\r
- } //-- void deleteShowColourText() \r
-\r
- /**\r
- * Method deleteShowFullId\r
- * \r
- */\r
- public void deleteShowFullId()\r
- {\r
- this._has_showFullId= false;\r
- } //-- void deleteShowFullId() \r
-\r
- /**\r
- * Method deleteShowSequenceFeatures\r
- * \r
- */\r
- public void deleteShowSequenceFeatures()\r
- {\r
- this._has_showSequenceFeatures= false;\r
- } //-- void deleteShowSequenceFeatures() \r
-\r
- /**\r
- * Method deleteShowText\r
- * \r
- */\r
- public void deleteShowText()\r
- {\r
- this._has_showText= false;\r
- } //-- void deleteShowText() \r
-\r
- /**\r
- * Method deleteStartRes\r
- * \r
- */\r
- public void deleteStartRes()\r
- {\r
- this._has_startRes= false;\r
- } //-- void deleteStartRes() \r
-\r
- /**\r
- * Method deleteStartSeq\r
- * \r
- */\r
- public void deleteStartSeq()\r
- {\r
- this._has_startSeq= false;\r
- } //-- void deleteStartSeq() \r
-\r
- /**\r
- * Method deleteTextCol1\r
- * \r
- */\r
- public void deleteTextCol1()\r
- {\r
- this._has_textCol1= false;\r
- } //-- void deleteTextCol1() \r
-\r
- /**\r
- * Method deleteTextCol2\r
- * \r
- */\r
- public void deleteTextCol2()\r
- {\r
- this._has_textCol2= false;\r
- } //-- void deleteTextCol2() \r
-\r
- /**\r
- * Method deleteTextColThreshold\r
- * \r
- */\r
- public void deleteTextColThreshold()\r
- {\r
- this._has_textColThreshold= false;\r
- } //-- void deleteTextColThreshold() \r
-\r
- /**\r
- * Method deleteWidth\r
- * \r
- */\r
- public void deleteWidth()\r
- {\r
- this._has_width= false;\r
- } //-- void deleteWidth() \r
-\r
- /**\r
- * Method deleteWrapAlignment\r
- * \r
- */\r
- public void deleteWrapAlignment()\r
- {\r
- this._has_wrapAlignment= false;\r
- } //-- void deleteWrapAlignment() \r
-\r
- /**\r
- * Method deleteXpos\r
- * \r
- */\r
- public void deleteXpos()\r
- {\r
- this._has_xpos= false;\r
- } //-- void deleteXpos() \r
-\r
- /**\r
- * Method deleteYpos\r
- * \r
- */\r
- public void deleteYpos()\r
- {\r
- this._has_ypos= false;\r
- } //-- void deleteYpos() \r
-\r
- /**\r
- * Method enumerateHiddenColumns\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateHiddenColumns()\r
- {\r
- return _hiddenColumnsList.elements();\r
- } //-- java.util.Enumeration enumerateHiddenColumns() \r
-\r
- /**\r
- * Returns the value of field 'annotationColours'.\r
- * \r
- * @return AnnotationColours\r
- * @return the value of field 'annotationColours'.\r
- */\r
- public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()\r
- {\r
- return this._annotationColours;\r
- } //-- jalview.schemabinding.version2.AnnotationColours getAnnotationColours() \r
-\r
- /**\r
- * Returns the value of field 'bgColour'.\r
- * \r
- * @return String\r
- * @return the value of field 'bgColour'.\r
- */\r
- public java.lang.String getBgColour()\r
- {\r
- return this._bgColour;\r
- } //-- java.lang.String getBgColour() \r
-\r
- /**\r
- * Returns the value of field 'consThreshold'.\r
- * \r
- * @return int\r
- * @return the value of field 'consThreshold'.\r
- */\r
- public int getConsThreshold()\r
- {\r
- return this._consThreshold;\r
- } //-- int getConsThreshold() \r
-\r
- /**\r
- * Returns the value of field 'conservationSelected'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'conservationSelected'.\r
- */\r
- public boolean getConservationSelected()\r
- {\r
- return this._conservationSelected;\r
- } //-- boolean getConservationSelected() \r
-\r
- /**\r
- * Returns the value of field 'fontName'.\r
- * \r
- * @return String\r
- * @return the value of field 'fontName'.\r
- */\r
- public java.lang.String getFontName()\r
- {\r
- return this._fontName;\r
- } //-- java.lang.String getFontName() \r
-\r
- /**\r
- * Returns the value of field 'fontSize'.\r
- * \r
- * @return int\r
- * @return the value of field 'fontSize'.\r
- */\r
- public int getFontSize()\r
- {\r
- return this._fontSize;\r
- } //-- int getFontSize() \r
-\r
- /**\r
- * Returns the value of field 'fontStyle'.\r
- * \r
- * @return int\r
- * @return the value of field 'fontStyle'.\r
- */\r
- public int getFontStyle()\r
- {\r
- return this._fontStyle;\r
- } //-- int getFontStyle() \r
-\r
- /**\r
- * Returns the value of field 'gatheredViews'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'gatheredViews'.\r
- */\r
- public boolean getGatheredViews()\r
- {\r
- return this._gatheredViews;\r
- } //-- boolean getGatheredViews() \r
-\r
- /**\r
- * Returns the value of field 'height'.\r
- * \r
- * @return int\r
- * @return the value of field 'height'.\r
- */\r
- public int getHeight()\r
- {\r
- return this._height;\r
- } //-- int getHeight() \r
-\r
- /**\r
- * Method getHiddenColumns\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return HiddenColumns\r
- */\r
- public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _hiddenColumnsList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- \r
- return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int) \r
-\r
- /**\r
- * Method getHiddenColumns\r
- * \r
- * \r
- * \r
- * @return HiddenColumns\r
- */\r
- public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()\r
- {\r
- int size = _hiddenColumnsList.size();\r
- jalview.schemabinding.version2.HiddenColumns[] mArray = new jalview.schemabinding.version2.HiddenColumns[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns() \r
-\r
- /**\r
- * Method getHiddenColumnsCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getHiddenColumnsCount()\r
- {\r
- return _hiddenColumnsList.size();\r
- } //-- int getHiddenColumnsCount() \r
-\r
- /**\r
- * Returns the value of field 'pidSelected'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'pidSelected'.\r
- */\r
- public boolean getPidSelected()\r
- {\r
- return this._pidSelected;\r
- } //-- boolean getPidSelected() \r
-\r
- /**\r
- * Returns the value of field 'pidThreshold'.\r
- * \r
- * @return int\r
- * @return the value of field 'pidThreshold'.\r
- */\r
- public int getPidThreshold()\r
- {\r
- return this._pidThreshold;\r
- } //-- int getPidThreshold() \r
-\r
- /**\r
- * Returns the value of field 'renderGaps'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'renderGaps'.\r
- */\r
- public boolean getRenderGaps()\r
- {\r
- return this._renderGaps;\r
- } //-- boolean getRenderGaps() \r
-\r
- /**\r
- * Returns the value of field 'rightAlignIds'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'rightAlignIds'.\r
- */\r
- public boolean getRightAlignIds()\r
- {\r
- return this._rightAlignIds;\r
- } //-- boolean getRightAlignIds() \r
-\r
- /**\r
- * Returns the value of field 'sequenceSetId'.\r
- * \r
- * @return String\r
- * @return the value of field 'sequenceSetId'.\r
- */\r
- public java.lang.String getSequenceSetId()\r
- {\r
- return this._sequenceSetId;\r
- } //-- java.lang.String getSequenceSetId() \r
-\r
- /**\r
- * Returns the value of field 'showAnnotation'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'showAnnotation'.\r
- */\r
- public boolean getShowAnnotation()\r
- {\r
- return this._showAnnotation;\r
- } //-- boolean getShowAnnotation() \r
-\r
- /**\r
- * Returns the value of field 'showBoxes'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'showBoxes'.\r
- */\r
- public boolean getShowBoxes()\r
- {\r
- return this._showBoxes;\r
- } //-- boolean getShowBoxes() \r
-\r
- /**\r
- * Returns the value of field 'showColourText'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'showColourText'.\r
- */\r
- public boolean getShowColourText()\r
- {\r
- return this._showColourText;\r
- } //-- boolean getShowColourText() \r
-\r
- /**\r
- * Returns the value of field 'showFullId'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'showFullId'.\r
- */\r
- public boolean getShowFullId()\r
- {\r
- return this._showFullId;\r
- } //-- boolean getShowFullId() \r
-\r
- /**\r
- * Returns the value of field 'showSequenceFeatures'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'showSequenceFeatures'.\r
- */\r
- public boolean getShowSequenceFeatures()\r
- {\r
- return this._showSequenceFeatures;\r
- } //-- boolean getShowSequenceFeatures() \r
-\r
- /**\r
- * Returns the value of field 'showText'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'showText'.\r
- */\r
- public boolean getShowText()\r
- {\r
- return this._showText;\r
- } //-- boolean getShowText() \r
-\r
- /**\r
- * Returns the value of field 'startRes'.\r
- * \r
- * @return int\r
- * @return the value of field 'startRes'.\r
- */\r
- public int getStartRes()\r
- {\r
- return this._startRes;\r
- } //-- int getStartRes() \r
-\r
- /**\r
- * Returns the value of field 'startSeq'.\r
- * \r
- * @return int\r
- * @return the value of field 'startSeq'.\r
- */\r
- public int getStartSeq()\r
- {\r
- return this._startSeq;\r
- } //-- int getStartSeq() \r
-\r
- /**\r
- * Returns the value of field 'textCol1'.\r
- * \r
- * @return int\r
- * @return the value of field 'textCol1'.\r
- */\r
- public int getTextCol1()\r
- {\r
- return this._textCol1;\r
- } //-- int getTextCol1() \r
-\r
- /**\r
- * Returns the value of field 'textCol2'.\r
- * \r
- * @return int\r
- * @return the value of field 'textCol2'.\r
- */\r
- public int getTextCol2()\r
- {\r
- return this._textCol2;\r
- } //-- int getTextCol2() \r
-\r
- /**\r
- * Returns the value of field 'textColThreshold'.\r
- * \r
- * @return int\r
- * @return the value of field 'textColThreshold'.\r
- */\r
- public int getTextColThreshold()\r
- {\r
- return this._textColThreshold;\r
- } //-- int getTextColThreshold() \r
-\r
- /**\r
- * Returns the value of field 'title'.\r
- * \r
- * @return String\r
- * @return the value of field 'title'.\r
- */\r
- public java.lang.String getTitle()\r
- {\r
- return this._title;\r
- } //-- java.lang.String getTitle() \r
-\r
- /**\r
- * Returns the value of field 'viewName'.\r
- * \r
- * @return String\r
- * @return the value of field 'viewName'.\r
- */\r
- public java.lang.String getViewName()\r
- {\r
- return this._viewName;\r
- } //-- java.lang.String getViewName() \r
-\r
- /**\r
- * Returns the value of field 'width'.\r
- * \r
- * @return int\r
- * @return the value of field 'width'.\r
- */\r
- public int getWidth()\r
- {\r
- return this._width;\r
- } //-- int getWidth() \r
-\r
- /**\r
- * Returns the value of field 'wrapAlignment'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'wrapAlignment'.\r
- */\r
- public boolean getWrapAlignment()\r
- {\r
- return this._wrapAlignment;\r
- } //-- boolean getWrapAlignment() \r
-\r
- /**\r
- * Returns the value of field 'xpos'.\r
- * \r
- * @return int\r
- * @return the value of field 'xpos'.\r
- */\r
- public int getXpos()\r
- {\r
- return this._xpos;\r
- } //-- int getXpos() \r
-\r
- /**\r
- * Returns the value of field 'ypos'.\r
- * \r
- * @return int\r
- * @return the value of field 'ypos'.\r
- */\r
- public int getYpos()\r
- {\r
- return this._ypos;\r
- } //-- int getYpos() \r
-\r
- /**\r
- * Method hasConsThreshold\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasConsThreshold()\r
- {\r
- return this._has_consThreshold;\r
- } //-- boolean hasConsThreshold() \r
-\r
- /**\r
- * Method hasConservationSelected\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasConservationSelected()\r
- {\r
- return this._has_conservationSelected;\r
- } //-- boolean hasConservationSelected() \r
-\r
- /**\r
- * Method hasFontSize\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasFontSize()\r
- {\r
- return this._has_fontSize;\r
- } //-- boolean hasFontSize() \r
-\r
- /**\r
- * Method hasFontStyle\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasFontStyle()\r
- {\r
- return this._has_fontStyle;\r
- } //-- boolean hasFontStyle() \r
-\r
- /**\r
- * Method hasGatheredViews\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasGatheredViews()\r
- {\r
- return this._has_gatheredViews;\r
- } //-- boolean hasGatheredViews() \r
-\r
- /**\r
- * Method hasHeight\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasHeight()\r
- {\r
- return this._has_height;\r
- } //-- boolean hasHeight() \r
-\r
- /**\r
- * Method hasPidSelected\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasPidSelected()\r
- {\r
- return this._has_pidSelected;\r
- } //-- boolean hasPidSelected() \r
-\r
- /**\r
- * Method hasPidThreshold\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasPidThreshold()\r
- {\r
- return this._has_pidThreshold;\r
- } //-- boolean hasPidThreshold() \r
-\r
- /**\r
- * Method hasRenderGaps\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasRenderGaps()\r
- {\r
- return this._has_renderGaps;\r
- } //-- boolean hasRenderGaps() \r
-\r
- /**\r
- * Method hasRightAlignIds\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasRightAlignIds()\r
- {\r
- return this._has_rightAlignIds;\r
- } //-- boolean hasRightAlignIds() \r
-\r
- /**\r
- * Method hasShowAnnotation\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasShowAnnotation()\r
- {\r
- return this._has_showAnnotation;\r
- } //-- boolean hasShowAnnotation() \r
-\r
- /**\r
- * Method hasShowBoxes\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasShowBoxes()\r
- {\r
- return this._has_showBoxes;\r
- } //-- boolean hasShowBoxes() \r
-\r
- /**\r
- * Method hasShowColourText\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasShowColourText()\r
- {\r
- return this._has_showColourText;\r
- } //-- boolean hasShowColourText() \r
-\r
- /**\r
- * Method hasShowFullId\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasShowFullId()\r
- {\r
- return this._has_showFullId;\r
- } //-- boolean hasShowFullId() \r
-\r
- /**\r
- * Method hasShowSequenceFeatures\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasShowSequenceFeatures()\r
- {\r
- return this._has_showSequenceFeatures;\r
- } //-- boolean hasShowSequenceFeatures() \r
-\r
- /**\r
- * Method hasShowText\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasShowText()\r
- {\r
- return this._has_showText;\r
- } //-- boolean hasShowText() \r
-\r
- /**\r
- * Method hasStartRes\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasStartRes()\r
- {\r
- return this._has_startRes;\r
- } //-- boolean hasStartRes() \r
-\r
- /**\r
- * Method hasStartSeq\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasStartSeq()\r
- {\r
- return this._has_startSeq;\r
- } //-- boolean hasStartSeq() \r
-\r
- /**\r
- * Method hasTextCol1\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasTextCol1()\r
- {\r
- return this._has_textCol1;\r
- } //-- boolean hasTextCol1() \r
-\r
- /**\r
- * Method hasTextCol2\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasTextCol2()\r
- {\r
- return this._has_textCol2;\r
- } //-- boolean hasTextCol2() \r
-\r
- /**\r
- * Method hasTextColThreshold\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasTextColThreshold()\r
- {\r
- return this._has_textColThreshold;\r
- } //-- boolean hasTextColThreshold() \r
-\r
- /**\r
- * Method hasWidth\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasWidth()\r
- {\r
- return this._has_width;\r
- } //-- boolean hasWidth() \r
-\r
- /**\r
- * Method hasWrapAlignment\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasWrapAlignment()\r
- {\r
- return this._has_wrapAlignment;\r
- } //-- boolean hasWrapAlignment() \r
-\r
- /**\r
- * Method hasXpos\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasXpos()\r
- {\r
- return this._has_xpos;\r
- } //-- boolean hasXpos() \r
-\r
- /**\r
- * Method hasYpos\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasYpos()\r
- {\r
- return this._has_ypos;\r
- } //-- boolean hasYpos() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Method removeAllHiddenColumns\r
- * \r
- */\r
- public void removeAllHiddenColumns()\r
- {\r
- _hiddenColumnsList.removeAllElements();\r
- } //-- void removeAllHiddenColumns() \r
-\r
- /**\r
- * Method removeHiddenColumns\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return HiddenColumns\r
- */\r
- public jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int index)\r
- {\r
- java.lang.Object obj = _hiddenColumnsList.elementAt(index);\r
- _hiddenColumnsList.removeElementAt(index);\r
- return (jalview.schemabinding.version2.HiddenColumns) obj;\r
- } //-- jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int) \r
-\r
- /**\r
- * Sets the value of field 'annotationColours'.\r
- * \r
- * @param annotationColours the value of field\r
- * 'annotationColours'.\r
- */\r
- public void setAnnotationColours(jalview.schemabinding.version2.AnnotationColours annotationColours)\r
- {\r
- this._annotationColours = annotationColours;\r
- } //-- void setAnnotationColours(jalview.schemabinding.version2.AnnotationColours) \r
-\r
- /**\r
- * Sets the value of field 'bgColour'.\r
- * \r
- * @param bgColour the value of field 'bgColour'.\r
- */\r
- public void setBgColour(java.lang.String bgColour)\r
- {\r
- this._bgColour = bgColour;\r
- } //-- void setBgColour(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'consThreshold'.\r
- * \r
- * @param consThreshold the value of field 'consThreshold'.\r
- */\r
- public void setConsThreshold(int consThreshold)\r
- {\r
- this._consThreshold = consThreshold;\r
- this._has_consThreshold = true;\r
- } //-- void setConsThreshold(int) \r
-\r
- /**\r
- * Sets the value of field 'conservationSelected'.\r
- * \r
- * @param conservationSelected the value of field\r
- * 'conservationSelected'.\r
- */\r
- public void setConservationSelected(boolean conservationSelected)\r
- {\r
- this._conservationSelected = conservationSelected;\r
- this._has_conservationSelected = true;\r
- } //-- void setConservationSelected(boolean) \r
-\r
- /**\r
- * Sets the value of field 'fontName'.\r
- * \r
- * @param fontName the value of field 'fontName'.\r
- */\r
- public void setFontName(java.lang.String fontName)\r
- {\r
- this._fontName = fontName;\r
- } //-- void setFontName(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'fontSize'.\r
- * \r
- * @param fontSize the value of field 'fontSize'.\r
- */\r
- public void setFontSize(int fontSize)\r
- {\r
- this._fontSize = fontSize;\r
- this._has_fontSize = true;\r
- } //-- void setFontSize(int) \r
-\r
- /**\r
- * Sets the value of field 'fontStyle'.\r
- * \r
- * @param fontStyle the value of field 'fontStyle'.\r
- */\r
- public void setFontStyle(int fontStyle)\r
- {\r
- this._fontStyle = fontStyle;\r
- this._has_fontStyle = true;\r
- } //-- void setFontStyle(int) \r
-\r
- /**\r
- * Sets the value of field 'gatheredViews'.\r
- * \r
- * @param gatheredViews the value of field 'gatheredViews'.\r
- */\r
- public void setGatheredViews(boolean gatheredViews)\r
- {\r
- this._gatheredViews = gatheredViews;\r
- this._has_gatheredViews = true;\r
- } //-- void setGatheredViews(boolean) \r
-\r
- /**\r
- * Sets the value of field 'height'.\r
- * \r
- * @param height the value of field 'height'.\r
- */\r
- public void setHeight(int height)\r
- {\r
- this._height = height;\r
- this._has_height = true;\r
- } //-- void setHeight(int) \r
-\r
- /**\r
- * Method setHiddenColumns\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vHiddenColumns\r
- */\r
- public void setHiddenColumns(int index, jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _hiddenColumnsList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _hiddenColumnsList.setElementAt(vHiddenColumns, index);\r
- } //-- void setHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns) \r
-\r
- /**\r
- * Method setHiddenColumns\r
- * \r
- * \r
- * \r
- * @param hiddenColumnsArray\r
- */\r
- public void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns[] hiddenColumnsArray)\r
- {\r
- //-- copy array\r
- _hiddenColumnsList.removeAllElements();\r
- for (int i = 0; i < hiddenColumnsArray.length; i++) {\r
- _hiddenColumnsList.addElement(hiddenColumnsArray[i]);\r
- }\r
- } //-- void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns) \r
-\r
- /**\r
- * Sets the value of field 'pidSelected'.\r
- * \r
- * @param pidSelected the value of field 'pidSelected'.\r
- */\r
- public void setPidSelected(boolean pidSelected)\r
- {\r
- this._pidSelected = pidSelected;\r
- this._has_pidSelected = true;\r
- } //-- void setPidSelected(boolean) \r
-\r
- /**\r
- * Sets the value of field 'pidThreshold'.\r
- * \r
- * @param pidThreshold the value of field 'pidThreshold'.\r
- */\r
- public void setPidThreshold(int pidThreshold)\r
- {\r
- this._pidThreshold = pidThreshold;\r
- this._has_pidThreshold = true;\r
- } //-- void setPidThreshold(int) \r
-\r
- /**\r
- * Sets the value of field 'renderGaps'.\r
- * \r
- * @param renderGaps the value of field 'renderGaps'.\r
- */\r
- public void setRenderGaps(boolean renderGaps)\r
- {\r
- this._renderGaps = renderGaps;\r
- this._has_renderGaps = true;\r
- } //-- void setRenderGaps(boolean) \r
-\r
- /**\r
- * Sets the value of field 'rightAlignIds'.\r
- * \r
- * @param rightAlignIds the value of field 'rightAlignIds'.\r
- */\r
- public void setRightAlignIds(boolean rightAlignIds)\r
- {\r
- this._rightAlignIds = rightAlignIds;\r
- this._has_rightAlignIds = true;\r
- } //-- void setRightAlignIds(boolean) \r
-\r
- /**\r
- * Sets the value of field 'sequenceSetId'.\r
- * \r
- * @param sequenceSetId the value of field 'sequenceSetId'.\r
- */\r
- public void setSequenceSetId(java.lang.String sequenceSetId)\r
- {\r
- this._sequenceSetId = sequenceSetId;\r
- } //-- void setSequenceSetId(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'showAnnotation'.\r
- * \r
- * @param showAnnotation the value of field 'showAnnotation'.\r
- */\r
- public void setShowAnnotation(boolean showAnnotation)\r
- {\r
- this._showAnnotation = showAnnotation;\r
- this._has_showAnnotation = true;\r
- } //-- void setShowAnnotation(boolean) \r
-\r
- /**\r
- * Sets the value of field 'showBoxes'.\r
- * \r
- * @param showBoxes the value of field 'showBoxes'.\r
- */\r
- public void setShowBoxes(boolean showBoxes)\r
- {\r
- this._showBoxes = showBoxes;\r
- this._has_showBoxes = true;\r
- } //-- void setShowBoxes(boolean) \r
-\r
- /**\r
- * Sets the value of field 'showColourText'.\r
- * \r
- * @param showColourText the value of field 'showColourText'.\r
- */\r
- public void setShowColourText(boolean showColourText)\r
- {\r
- this._showColourText = showColourText;\r
- this._has_showColourText = true;\r
- } //-- void setShowColourText(boolean) \r
-\r
- /**\r
- * Sets the value of field 'showFullId'.\r
- * \r
- * @param showFullId the value of field 'showFullId'.\r
- */\r
- public void setShowFullId(boolean showFullId)\r
- {\r
- this._showFullId = showFullId;\r
- this._has_showFullId = true;\r
- } //-- void setShowFullId(boolean) \r
-\r
- /**\r
- * Sets the value of field 'showSequenceFeatures'.\r
- * \r
- * @param showSequenceFeatures the value of field\r
- * 'showSequenceFeatures'.\r
- */\r
- public void setShowSequenceFeatures(boolean showSequenceFeatures)\r
- {\r
- this._showSequenceFeatures = showSequenceFeatures;\r
- this._has_showSequenceFeatures = true;\r
- } //-- void setShowSequenceFeatures(boolean) \r
-\r
- /**\r
- * Sets the value of field 'showText'.\r
- * \r
- * @param showText the value of field 'showText'.\r
- */\r
- public void setShowText(boolean showText)\r
- {\r
- this._showText = showText;\r
- this._has_showText = true;\r
- } //-- void setShowText(boolean) \r
-\r
- /**\r
- * Sets the value of field 'startRes'.\r
- * \r
- * @param startRes the value of field 'startRes'.\r
- */\r
- public void setStartRes(int startRes)\r
- {\r
- this._startRes = startRes;\r
- this._has_startRes = true;\r
- } //-- void setStartRes(int) \r
-\r
- /**\r
- * Sets the value of field 'startSeq'.\r
- * \r
- * @param startSeq the value of field 'startSeq'.\r
- */\r
- public void setStartSeq(int startSeq)\r
- {\r
- this._startSeq = startSeq;\r
- this._has_startSeq = true;\r
- } //-- void setStartSeq(int) \r
-\r
- /**\r
- * Sets the value of field 'textCol1'.\r
- * \r
- * @param textCol1 the value of field 'textCol1'.\r
- */\r
- public void setTextCol1(int textCol1)\r
- {\r
- this._textCol1 = textCol1;\r
- this._has_textCol1 = true;\r
- } //-- void setTextCol1(int) \r
-\r
- /**\r
- * Sets the value of field 'textCol2'.\r
- * \r
- * @param textCol2 the value of field 'textCol2'.\r
- */\r
- public void setTextCol2(int textCol2)\r
- {\r
- this._textCol2 = textCol2;\r
- this._has_textCol2 = true;\r
- } //-- void setTextCol2(int) \r
-\r
- /**\r
- * Sets the value of field 'textColThreshold'.\r
- * \r
- * @param textColThreshold the value of field 'textColThreshold'\r
- */\r
- public void setTextColThreshold(int textColThreshold)\r
- {\r
- this._textColThreshold = textColThreshold;\r
- this._has_textColThreshold = true;\r
- } //-- void setTextColThreshold(int) \r
-\r
- /**\r
- * Sets the value of field 'title'.\r
- * \r
- * @param title the value of field 'title'.\r
- */\r
- public void setTitle(java.lang.String title)\r
- {\r
- this._title = title;\r
- } //-- void setTitle(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'viewName'.\r
- * \r
- * @param viewName the value of field 'viewName'.\r
- */\r
- public void setViewName(java.lang.String viewName)\r
- {\r
- this._viewName = viewName;\r
- } //-- void setViewName(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'width'.\r
- * \r
- * @param width the value of field 'width'.\r
- */\r
- public void setWidth(int width)\r
- {\r
- this._width = width;\r
- this._has_width = true;\r
- } //-- void setWidth(int) \r
-\r
- /**\r
- * Sets the value of field 'wrapAlignment'.\r
- * \r
- * @param wrapAlignment the value of field 'wrapAlignment'.\r
- */\r
- public void setWrapAlignment(boolean wrapAlignment)\r
- {\r
- this._wrapAlignment = wrapAlignment;\r
- this._has_wrapAlignment = true;\r
- } //-- void setWrapAlignment(boolean) \r
-\r
- /**\r
- * Sets the value of field 'xpos'.\r
- * \r
- * @param xpos the value of field 'xpos'.\r
- */\r
- public void setXpos(int xpos)\r
- {\r
- this._xpos = xpos;\r
- this._has_xpos = true;\r
- } //-- void setXpos(int) \r
-\r
- /**\r
- * Sets the value of field 'ypos'.\r
- * \r
- * @param ypos the value of field 'ypos'.\r
- */\r
- public void setYpos(int ypos)\r
- {\r
- this._ypos = ypos;\r
- this._has_ypos = true;\r
- } //-- void setYpos(int) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(jalview.schemabinding.version2.Viewport.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
+ 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 'centreColumnLabels'.\r
+ * \r
+ * @return the value of field 'CentreColumnLabels'.\r
+ */\r
+ public boolean getCentreColumnLabels()\r
+ {\r
+ return this._centreColumnLabels;\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 'followHighlight'.\r
+ * \r
+ * @return the value of field 'FollowHighlight'.\r
+ */\r
+ public boolean getFollowHighlight()\r
+ {\r
+ return this._followHighlight;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'followSelection'.\r
+ * \r
+ * @return the value of field 'FollowSelection'.\r
+ */\r
+ public boolean getFollowSelection()\r
+ {\r
+ return this._followSelection;\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\r
+ * if the index given is outside the bounds of the collection\r
+ * @return the value of the jalview.schemabinding.version2.HiddenColumns at\r
+ * the given index\r
+ */\r
+ public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(\r
+ final int index) throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._hiddenColumnsList.size())\r
+ {\r
+ throw new IndexOutOfBoundsException("getHiddenColumns: Index value '"\r
+ + index + "' not in range [0.."\r
+ + (this._hiddenColumnsList.size() - 1) + "]");\r
+ }\r
+\r
+ return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList\r
+ .get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getHiddenColumns.Returns the contents of the collection in an Array.\r
+ * <p>\r
+ * Note: Just in case the collection contents are changing in another thread,\r
+ * we pass a 0-length Array of the correct type into the API call. This way we\r
+ * <i>know</i> that the Array returned is of 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\r
+ .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 following\r
+ * description: unique id used by jalview to synchronize between stored and\r
+ * 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 'ignoreGapsinConsensus'.\r
+ * \r
+ * @return the value of field 'IgnoreGapsinConsensus'.\r
+ */\r
+ public boolean getIgnoreGapsinConsensus()\r
+ {\r
+ return this._ignoreGapsinConsensus;\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 'showConsensusHistogram'.\r
+ * \r
+ * @return the value of field 'ShowConsensusHistogram'.\r
+ */\r
+ public boolean getShowConsensusHistogram()\r
+ {\r
+ return this._showConsensusHistogram;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showDbRefTooltip'.\r
+ * \r
+ * @return the value of field 'ShowDbRefTooltip'.\r
+ */\r
+ public boolean getShowDbRefTooltip()\r
+ {\r
+ return this._showDbRefTooltip;\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 'showGroupConsensus'.\r
+ * \r
+ * @return the value of field 'ShowGroupConsensus'.\r
+ */\r
+ public boolean getShowGroupConsensus()\r
+ {\r
+ return this._showGroupConsensus;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showGroupConservation'.\r
+ * \r
+ * @return the value of field 'ShowGroupConservation'.\r
+ */\r
+ public boolean getShowGroupConservation()\r
+ {\r
+ return this._showGroupConservation;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showNPfeatureTooltip'.\r
+ * \r
+ * @return the value of field 'ShowNPfeatureTooltip'.\r
+ */\r
+ public boolean getShowNPfeatureTooltip()\r
+ {\r
+ return this._showNPfeatureTooltip;\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 'showSequenceLogo'.\r
+ * \r
+ * @return the value of field 'ShowSequenceLogo'.\r
+ */\r
+ public boolean getShowSequenceLogo()\r
+ {\r
+ return this._showSequenceLogo;\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 hasCentreColumnLabels.\r
+ * \r
+ * @return true if at least one CentreColumnLabels has been adde\r
+ */\r
+ public boolean hasCentreColumnLabels()\r
+ {\r
+ return this._has_centreColumnLabels;\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 added\r
+ */\r
+ public boolean hasConservationSelected()\r
+ {\r
+ return this._has_conservationSelected;\r
+ }\r
+\r
+ /**\r
+ * Method hasFollowHighlight.\r
+ * \r
+ * @return true if at least one FollowHighlight has been added\r
+ */\r
+ public boolean hasFollowHighlight()\r
+ {\r
+ return this._has_followHighlight;\r
+ }\r
+\r
+ /**\r
+ * Method hasFollowSelection.\r
+ * \r
+ * @return true if at least one FollowSelection has been added\r
+ */\r
+ public boolean hasFollowSelection()\r
+ {\r
+ return this._has_followSelection;\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 hasIgnoreGapsinConsensus.\r
+ * \r
+ * @return true if at least one IgnoreGapsinConsensus has been added\r
+ */\r
+ public boolean hasIgnoreGapsinConsensus()\r
+ {\r
+ return this._has_ignoreGapsinConsensus;\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 hasShowConsensusHistogram.\r
+ * \r
+ * @return true if at least one ShowConsensusHistogram has been added\r
+ */\r
+ public boolean hasShowConsensusHistogram()\r
+ {\r
+ return this._has_showConsensusHistogram;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowDbRefTooltip.\r
+ * \r
+ * @return true if at least one ShowDbRefTooltip has been added\r
+ */\r
+ public boolean hasShowDbRefTooltip()\r
+ {\r
+ return this._has_showDbRefTooltip;\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 hasShowGroupConsensus.\r
+ * \r
+ * @return true if at least one ShowGroupConsensus has been adde\r
+ */\r
+ public boolean hasShowGroupConsensus()\r
+ {\r
+ return this._has_showGroupConsensus;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowGroupConservation.\r
+ * \r
+ * @return true if at least one ShowGroupConservation has been added\r
+ */\r
+ public boolean hasShowGroupConservation()\r
+ {\r
+ return this._has_showGroupConservation;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowNPfeatureTooltip.\r
+ * \r
+ * @return true if at least one ShowNPfeatureTooltip has been added\r
+ */\r
+ public boolean hasShowNPfeatureTooltip()\r
+ {\r
+ return this._has_showNPfeatureTooltip;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowSequenceFeatures.\r
+ * \r
+ * @return true if at least one ShowSequenceFeatures has been added\r
+ */\r
+ public boolean hasShowSequenceFeatures()\r
+ {\r
+ return this._has_showSequenceFeatures;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowSequenceLogo.\r
+ * \r
+ * @return true if at least one ShowSequenceLogo has been added\r
+ */\r
+ public boolean hasShowSequenceLogo()\r
+ {\r
+ return this._has_showSequenceLogo;\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 'centreColumnLabels'.\r
+ * \r
+ * @return the value of field 'CentreColumnLabels'.\r
+ */\r
+ public boolean isCentreColumnLabels()\r
+ {\r
+ return this._centreColumnLabels;\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 'followHighlight'.\r
+ * \r
+ * @return the value of field 'FollowHighlight'.\r
+ */\r
+ public boolean isFollowHighlight()\r
+ {\r
+ return this._followHighlight;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'followSelection'.\r
+ * \r
+ * @return the value of field 'FollowSelection'.\r
+ */\r
+ public boolean isFollowSelection()\r
+ {\r
+ return this._followSelection;\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 'ignoreGapsinConsensus'.\r
+ * \r
+ * @return the value of field 'IgnoreGapsinConsensus'.\r
+ */\r
+ public boolean isIgnoreGapsinConsensus()\r
+ {\r
+ return this._ignoreGapsinConsensus;\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 'showConsensusHistogram'.\r
+ * \r
+ * @return the value of field 'ShowConsensusHistogram'.\r
+ */\r
+ public boolean isShowConsensusHistogram()\r
+ {\r
+ return this._showConsensusHistogram;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showDbRefTooltip'.\r
+ * \r
+ * @return the value of field 'ShowDbRefTooltip'.\r
+ */\r
+ public boolean isShowDbRefTooltip()\r
+ {\r
+ return this._showDbRefTooltip;\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 'showGroupConsensus'.\r
+ * \r
+ * @return the value of field 'ShowGroupConsensus'.\r
+ */\r
+ public boolean isShowGroupConsensus()\r
+ {\r
+ return this._showGroupConsensus;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showGroupConservation'.\r
+ * \r
+ * @return the value of field 'ShowGroupConservation'.\r
+ */\r
+ public boolean isShowGroupConservation()\r
+ {\r
+ return this._showGroupConservation;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showNPfeatureTooltip'.\r
+ * \r
+ * @return the value of field 'ShowNPfeatureTooltip'.\r
+ */\r
+ public boolean isShowNPfeatureTooltip()\r
+ {\r
+ return this._showNPfeatureTooltip;\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 'showSequenceLogo'.\r
+ * \r
+ * @return the value of field 'ShowSequenceLogo'.\r
+ */\r
+ public boolean isShowSequenceLogo()\r
+ {\r
+ return this._showSequenceLogo;\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
+ {\r
+ validate();\r
+ } catch (org.exolab.castor.xml.ValidationException vex)\r
+ {\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\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException\r
+ {\r
+ Marshaller.marshal(this, out);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param handler\r
+ * @throws java.io.IOException\r
+ * if an IOException occurs during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
+ */\r
+ public void marshal(final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException,\r
+ org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException\r
+ {\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
+ {\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
+ {\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\r
+ * the value of field 'annotationColours'.\r
+ */\r
+ public void setAnnotationColours(\r
+ final jalview.schemabinding.version2.AnnotationColours annotationColours)\r
+ {\r
+ this._annotationColours = annotationColours;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'bgColour'.\r
+ * \r
+ * @param bgColour\r
+ * the value of field 'bgColour'.\r
+ */\r
+ public void setBgColour(final java.lang.String bgColour)\r
+ {\r
+ this._bgColour = bgColour;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'centreColumnLabels'.\r
+ * \r
+ * @param centreColumnLabels\r
+ * the value of field 'centreColumnLabels'.\r
+ */\r
+ public void setCentreColumnLabels(final boolean centreColumnLabels)\r
+ {\r
+ this._centreColumnLabels = centreColumnLabels;\r
+ this._has_centreColumnLabels = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'consThreshold'.\r
+ * \r
+ * @param consThreshold\r
+ * the value of field 'consThreshold'.\r
+ */\r
+ public void setConsThreshold(final int consThreshold)\r
+ {\r
+ this._consThreshold = consThreshold;\r
+ this._has_consThreshold = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'conservationSelected'.\r
+ * \r
+ * @param conservationSelected\r
+ * the value of field 'conservationSelected'.\r
+ */\r
+ public void setConservationSelected(final boolean conservationSelected)\r
+ {\r
+ this._conservationSelected = conservationSelected;\r
+ this._has_conservationSelected = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'followHighlight'.\r
+ * \r
+ * @param followHighlight\r
+ * the value of field 'followHighlight'.\r
+ */\r
+ public void setFollowHighlight(final boolean followHighlight)\r
+ {\r
+ this._followHighlight = followHighlight;\r
+ this._has_followHighlight = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'followSelection'.\r
+ * \r
+ * @param followSelection\r
+ * the value of field 'followSelection'.\r
+ */\r
+ public void setFollowSelection(final boolean followSelection)\r
+ {\r
+ this._followSelection = followSelection;\r
+ this._has_followSelection = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'fontName'.\r
+ * \r
+ * @param fontName\r
+ * the value of field 'fontName'.\r
+ */\r
+ public void setFontName(final java.lang.String fontName)\r
+ {\r
+ this._fontName = fontName;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'fontSize'.\r
+ * \r
+ * @param fontSize\r
+ * the value of field 'fontSize'.\r
+ */\r
+ public void setFontSize(final int fontSize)\r
+ {\r
+ this._fontSize = fontSize;\r
+ this._has_fontSize = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'fontStyle'.\r
+ * \r
+ * @param fontStyle\r
+ * the value of field 'fontStyle'.\r
+ */\r
+ public void setFontStyle(final int fontStyle)\r
+ {\r
+ this._fontStyle = fontStyle;\r
+ this._has_fontStyle = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'gatheredViews'.\r
+ * \r
+ * @param gatheredViews\r
+ * the value of field 'gatheredViews'.\r
+ */\r
+ public void setGatheredViews(final boolean gatheredViews)\r
+ {\r
+ this._gatheredViews = gatheredViews;\r
+ this._has_gatheredViews = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'height'.\r
+ * \r
+ * @param height\r
+ * the value of field 'height'.\r
+ */\r
+ public void setHeight(final int height)\r
+ {\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\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void setHiddenColumns(final int index,\r
+ final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._hiddenColumnsList.size())\r
+ {\r
+ throw new IndexOutOfBoundsException("setHiddenColumns: Index value '"\r
+ + index + "' not in range [0.."\r
+ + (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
+ {\r
+ // -- copy array\r
+ _hiddenColumnsList.clear();\r
+\r
+ for (int i = 0; i < vHiddenColumnsArray.length; i++)\r
+ {\r
+ this._hiddenColumnsList.add(vHiddenColumnsArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'id'. The field 'id' has the following description:\r
+ * unique id used by jalview to synchronize between stored and instantiated\r
+ * views\r
+ * \r
+ * \r
+ * @param id\r
+ * the value of field 'id'.\r
+ */\r
+ public void setId(final java.lang.String id)\r
+ {\r
+ this._id = id;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'ignoreGapsinConsensus'.\r
+ * \r
+ * @param ignoreGapsinConsensus\r
+ * the value of field 'ignoreGapsinConsensus'.\r
+ */\r
+ public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus)\r
+ {\r
+ this._ignoreGapsinConsensus = ignoreGapsinConsensus;\r
+ this._has_ignoreGapsinConsensus = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'pidSelected'.\r
+ * \r
+ * @param pidSelected\r
+ * the value of field 'pidSelected'.\r
+ */\r
+ public void setPidSelected(final boolean pidSelected)\r
+ {\r
+ this._pidSelected = pidSelected;\r
+ this._has_pidSelected = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'pidThreshold'.\r
+ * \r
+ * @param pidThreshold\r
+ * the value of field 'pidThreshold'.\r
+ */\r
+ public void setPidThreshold(final int pidThreshold)\r
+ {\r
+ this._pidThreshold = pidThreshold;\r
+ this._has_pidThreshold = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'renderGaps'.\r
+ * \r
+ * @param renderGaps\r
+ * the value of field 'renderGaps'.\r
+ */\r
+ public void setRenderGaps(final boolean renderGaps)\r
+ {\r
+ this._renderGaps = renderGaps;\r
+ this._has_renderGaps = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'rightAlignIds'.\r
+ * \r
+ * @param rightAlignIds\r
+ * the value of field 'rightAlignIds'.\r
+ */\r
+ public void setRightAlignIds(final boolean rightAlignIds)\r
+ {\r
+ this._rightAlignIds = rightAlignIds;\r
+ this._has_rightAlignIds = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'sequenceSetId'.\r
+ * \r
+ * @param sequenceSetId\r
+ * the value of field 'sequenceSetId'.\r
+ */\r
+ public void setSequenceSetId(final java.lang.String sequenceSetId)\r
+ {\r
+ this._sequenceSetId = sequenceSetId;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showAnnotation'.\r
+ * \r
+ * @param showAnnotation\r
+ * the value of field 'showAnnotation'.\r
+ */\r
+ public void setShowAnnotation(final boolean showAnnotation)\r
+ {\r
+ this._showAnnotation = showAnnotation;\r
+ this._has_showAnnotation = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showBoxes'.\r
+ * \r
+ * @param showBoxes\r
+ * the value of field 'showBoxes'.\r
+ */\r
+ public void setShowBoxes(final boolean showBoxes)\r
+ {\r
+ this._showBoxes = showBoxes;\r
+ this._has_showBoxes = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showColourText'.\r
+ * \r
+ * @param showColourText\r
+ * the value of field 'showColourText'.\r
+ */\r
+ public void setShowColourText(final boolean showColourText)\r
+ {\r
+ this._showColourText = showColourText;\r
+ this._has_showColourText = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showConsensusHistogram'.\r
+ * \r
+ * @param showConsensusHistogram\r
+ * the value of field 'showConsensusHistogram'.\r
+ */\r
+ public void setShowConsensusHistogram(final boolean showConsensusHistogram)\r
+ {\r
+ this._showConsensusHistogram = showConsensusHistogram;\r
+ this._has_showConsensusHistogram = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showDbRefTooltip'.\r
+ * \r
+ * @param showDbRefTooltip\r
+ * the value of field 'showDbRefTooltip'\r
+ */\r
+ public void setShowDbRefTooltip(final boolean showDbRefTooltip)\r
+ {\r
+ this._showDbRefTooltip = showDbRefTooltip;\r
+ this._has_showDbRefTooltip = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showFullId'.\r
+ * \r
+ * @param showFullId\r
+ * the value of field 'showFullId'.\r
+ */\r
+ public void setShowFullId(final boolean showFullId)\r
+ {\r
+ this._showFullId = showFullId;\r
+ this._has_showFullId = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showGroupConsensus'.\r
+ * \r
+ * @param showGroupConsensus\r
+ * the value of field 'showGroupConsensus'.\r
+ */\r
+ public void setShowGroupConsensus(final boolean showGroupConsensus)\r
+ {\r
+ this._showGroupConsensus = showGroupConsensus;\r
+ this._has_showGroupConsensus = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showGroupConservation'.\r
+ * \r
+ * @param showGroupConservation\r
+ * the value of field 'showGroupConservation'.\r
+ */\r
+ public void setShowGroupConservation(final boolean showGroupConservation)\r
+ {\r
+ this._showGroupConservation = showGroupConservation;\r
+ this._has_showGroupConservation = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showNPfeatureTooltip'.\r
+ * \r
+ * @param showNPfeatureTooltip\r
+ * the value of field 'showNPfeatureTooltip'.\r
+ */\r
+ public void setShowNPfeatureTooltip(final boolean showNPfeatureTooltip)\r
+ {\r
+ this._showNPfeatureTooltip = showNPfeatureTooltip;\r
+ this._has_showNPfeatureTooltip = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showSequenceFeatures'.\r
+ * \r
+ * @param showSequenceFeatures\r
+ * the value of field 'showSequenceFeatures'.\r
+ */\r
+ public void setShowSequenceFeatures(final boolean showSequenceFeatures)\r
+ {\r
+ this._showSequenceFeatures = showSequenceFeatures;\r
+ this._has_showSequenceFeatures = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showSequenceLogo'.\r
+ * \r
+ * @param showSequenceLogo\r
+ * the value of field 'showSequenceLogo'\r
+ */\r
+ public void setShowSequenceLogo(final boolean showSequenceLogo)\r
+ {\r
+ this._showSequenceLogo = showSequenceLogo;\r
+ this._has_showSequenceLogo = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showText'.\r
+ * \r
+ * @param showText\r
+ * the value of field 'showText'.\r
+ */\r
+ public void setShowText(final boolean showText)\r
+ {\r
+ this._showText = showText;\r
+ this._has_showText = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showUnconserved'.\r
+ * \r
+ * @param showUnconserved\r
+ * the value of field 'showUnconserved'.\r
+ */\r
+ public void setShowUnconserved(final boolean showUnconserved)\r
+ {\r
+ this._showUnconserved = showUnconserved;\r
+ this._has_showUnconserved = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'startRes'.\r
+ * \r
+ * @param startRes\r
+ * the value of field 'startRes'.\r
+ */\r
+ public void setStartRes(final int startRes)\r
+ {\r
+ this._startRes = startRes;\r
+ this._has_startRes = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'startSeq'.\r
+ * \r
+ * @param startSeq\r
+ * the value of field 'startSeq'.\r
+ */\r
+ public void setStartSeq(final int startSeq)\r
+ {\r
+ this._startSeq = startSeq;\r
+ this._has_startSeq = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'textCol1'.\r
+ * \r
+ * @param textCol1\r
+ * the value of field 'textCol1'.\r
+ */\r
+ public void setTextCol1(final int textCol1)\r
+ {\r
+ this._textCol1 = textCol1;\r
+ this._has_textCol1 = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'textCol2'.\r
+ * \r
+ * @param textCol2\r
+ * the value of field 'textCol2'.\r
+ */\r
+ public void setTextCol2(final int textCol2)\r
+ {\r
+ this._textCol2 = textCol2;\r
+ this._has_textCol2 = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'textColThreshold'.\r
+ * \r
+ * @param textColThreshold\r
+ * the value of field 'textColThreshold'\r
+ */\r
+ public void setTextColThreshold(final int textColThreshold)\r
+ {\r
+ this._textColThreshold = textColThreshold;\r
+ this._has_textColThreshold = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'title'.\r
+ * \r
+ * @param title\r
+ * the value of field 'title'.\r
+ */\r
+ public void setTitle(final java.lang.String title)\r
+ {\r
+ this._title = title;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'viewName'.\r
+ * \r
+ * @param viewName\r
+ * the value of field 'viewName'.\r
+ */\r
+ public void setViewName(final java.lang.String viewName)\r
+ {\r
+ this._viewName = viewName;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'width'.\r
+ * \r
+ * @param width\r
+ * the value of field 'width'.\r
+ */\r
+ public void setWidth(final int width)\r
+ {\r
+ this._width = width;\r
+ this._has_width = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'wrapAlignment'.\r
+ * \r
+ * @param wrapAlignment\r
+ * the value of field 'wrapAlignment'.\r
+ */\r
+ public void setWrapAlignment(final boolean wrapAlignment)\r
+ {\r
+ this._wrapAlignment = wrapAlignment;\r
+ this._has_wrapAlignment = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'xpos'.\r
+ * \r
+ * @param xpos\r
+ * the value of field 'xpos'.\r
+ */\r
+ public void setXpos(final int xpos)\r
+ {\r
+ this._xpos = xpos;\r
+ this._has_xpos = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'ypos'.\r
+ * \r
+ * @param ypos\r
+ * the value of field 'ypos'.\r
+ */\r
+ public void setYpos(final int ypos)\r
+ {\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\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the schema\r
+ * @return the unmarshaled 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,\r
+ org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.schemabinding.version2.Viewport) Unmarshaller\r
+ .unmarshal(jalview.schemabinding.version2.Viewport.class,\r
+ reader);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the schema\r
+ */\r
+ public void validate() throws org.exolab.castor.xml.ValidationException\r
+ {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ }\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff