-/*\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
-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 = 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
- */\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 deleteIgnoreGapsinConsensus()\r
- {\r
- this._has_ignoreGapsinConsensus = 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 deleteShowConsensusHistogram()\r
- {\r
- this._has_showConsensusHistogram = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteShowDbRefTooltip()\r
- {\r
- this._has_showDbRefTooltip = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteShowFullId()\r
- {\r
- this._has_showFullId = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteShowGroupConsensus()\r
- {\r
- this._has_showGroupConsensus = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteShowGroupConservation()\r
- {\r
- this._has_showGroupConservation = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteShowNPfeatureTooltip()\r
- {\r
- this._has_showNPfeatureTooltip = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteShowSequenceFeatures()\r
- {\r
- this._has_showSequenceFeatures = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteShowSequenceLogo()\r
- {\r
- this._has_showSequenceLogo = 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 '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
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview.
+ * If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ ******************************************************************************/
+/*
+ * 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 _normaliseSequenceLogo.
+ */
+ private boolean _normaliseSequenceLogo = false;
+
+ /**
+ * keeps track of state for field: _normaliseSequenceLogo
+ */
+ private boolean _has_normaliseSequenceLogo;
+
+ /**
+ * 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;
+
+ /**
+ * Field _calcIdParamList.
+ */
+ private java.util.Vector _calcIdParamList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Viewport()
+ {
+ super();
+ this._hiddenColumnsList = new java.util.Vector();
+ this._calcIdParamList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vCalcIdParam
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addCalcIdParam(
+ final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._calcIdParamList.addElement(vCalcIdParam);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vCalcIdParam
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addCalcIdParam(final int index,
+ final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._calcIdParamList.add(index, vCalcIdParam);
+ }
+
+ /**
+ *
+ *
+ * @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 deleteNormaliseSequenceLogo()
+ {
+ this._has_normaliseSequenceLogo = 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 enumerateCalcIdParam.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.CalcIdParam
+ * elements
+ */
+ public java.util.Enumeration enumerateCalcIdParam()
+ {
+ return this._calcIdParamList.elements();
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * Method getCalcIdParam.
+ *
+ * @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.CalcIdParam at the
+ * given index
+ */
+ public jalview.schemabinding.version2.CalcIdParam getCalcIdParam(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._calcIdParamList.size())
+ {
+ throw new IndexOutOfBoundsException("getCalcIdParam: Index value '"
+ + index + "' not in range [0.."
+ + (this._calcIdParamList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.CalcIdParam) _calcIdParamList
+ .get(index);
+ }
+
+ /**
+ * Method getCalcIdParam.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.CalcIdParam[] getCalcIdParam()
+ {
+ jalview.schemabinding.version2.CalcIdParam[] array = new jalview.schemabinding.version2.CalcIdParam[0];
+ return (jalview.schemabinding.version2.CalcIdParam[]) this._calcIdParamList
+ .toArray(array);
+ }
+
+ /**
+ * Method getCalcIdParamCount.
+ *
+ * @return the size of this collection
+ */
+ public int getCalcIdParamCount()
+ {
+ return this._calcIdParamList.size();
+ }
+
+ /**
+ * Returns the value of field 'centreColumnLabels'.
+ *
+ * @return the value of field 'CentreColumnLabels'.
+ */
+ public boolean getCentreColumnLabels()
+ {
+ return this._centreColumnLabels;
+ }
+
+ /**
+ * Returns the value of field 'consThreshold'.
+ *
+ * @return the value of field 'ConsThreshold'.
+ */
+ public int getConsThreshold()
+ {
+ return this._consThreshold;
+ }
+
+ /**
+ * Returns the value of field 'conservationSelected'.
+ *
+ * @return the value of field 'ConservationSelected'.
+ */
+ public boolean getConservationSelected()
+ {
+ return this._conservationSelected;
+ }
+
+ /**
+ * Returns the value of field 'followHighlight'.
+ *
+ * @return the value of field 'FollowHighlight'.
+ */
+ public boolean getFollowHighlight()
+ {
+ return this._followHighlight;
+ }
+
+ /**
+ * Returns the value of field 'followSelection'.
+ *
+ * @return the value of field 'FollowSelection'.
+ */
+ public boolean getFollowSelection()
+ {
+ return this._followSelection;
+ }
+
+ /**
+ * Returns the value of field 'fontName'.
+ *
+ * @return the value of field 'FontName'.
+ */
+ public java.lang.String getFontName()
+ {
+ return this._fontName;
+ }
+
+ /**
+ * Returns the value of field 'fontSize'.
+ *
+ * @return the value of field 'FontSize'.
+ */
+ public int getFontSize()
+ {
+ return this._fontSize;
+ }
+
+ /**
+ * Returns the value of field 'fontStyle'.
+ *
+ * @return the value of field 'FontStyle'.
+ */
+ public int getFontStyle()
+ {
+ return this._fontStyle;
+ }
+
+ /**
+ * Returns the value of field 'gatheredViews'.
+ *
+ * @return the value of field 'GatheredViews'.
+ */
+ public boolean getGatheredViews()
+ {
+ return this._gatheredViews;
+ }
+
+ /**
+ * Returns the value of field 'height'.
+ *
+ * @return the value of field 'Height'.
+ */
+ public int getHeight()
+ {
+ return this._height;
+ }
+
+ /**
+ * Method getHiddenColumns.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.HiddenColumns at
+ * the given index
+ */
+ public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._hiddenColumnsList.size())
+ {
+ throw new IndexOutOfBoundsException("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 'normaliseSequenceLogo'.
+ *
+ * @return the value of field 'NormaliseSequenceLogo'.
+ */
+ public boolean getNormaliseSequenceLogo()
+ {
+ return this._normaliseSequenceLogo;
+ }
+
+ /**
+ * Returns the value of field 'pidSelected'.
+ *
+ * @return the value of field 'PidSelected'.
+ */
+ public boolean getPidSelected()
+ {
+ return this._pidSelected;
+ }
+
+ /**
+ * Returns the value of field 'pidThreshold'.
+ *
+ * @return the value of field 'PidThreshold'.
+ */
+ public int getPidThreshold()
+ {
+ return this._pidThreshold;
+ }
+
+ /**
+ * Returns the value of field 'renderGaps'.
+ *
+ * @return the value of field 'RenderGaps'.
+ */
+ public boolean getRenderGaps()
+ {
+ return this._renderGaps;
+ }
+
+ /**
+ * Returns the value of field 'rightAlignIds'.
+ *
+ * @return the value of field 'RightAlignIds'.
+ */
+ public boolean getRightAlignIds()
+ {
+ return this._rightAlignIds;
+ }
+
+ /**
+ * Returns the value of field 'sequenceSetId'.
+ *
+ * @return the value of field 'SequenceSetId'.
+ */
+ public java.lang.String getSequenceSetId()
+ {
+ return this._sequenceSetId;
+ }
+
+ /**
+ * Returns the value of field 'showAnnotation'.
+ *
+ * @return the value of field 'ShowAnnotation'.
+ */
+ public boolean getShowAnnotation()
+ {
+ return this._showAnnotation;
+ }
+
+ /**
+ * Returns the value of field 'showBoxes'.
+ *
+ * @return the value of field 'ShowBoxes'.
+ */
+ public boolean getShowBoxes()
+ {
+ return this._showBoxes;
+ }
+
+ /**
+ * Returns the value of field 'showColourText'.
+ *
+ * @return the value of field 'ShowColourText'.
+ */
+ public boolean getShowColourText()
+ {
+ return this._showColourText;
+ }
+
+ /**
+ * Returns the value of field 'showConsensusHistogram'.
+ *
+ * @return the value of field 'ShowConsensusHistogram'.
+ */
+ public boolean getShowConsensusHistogram()
+ {
+ return this._showConsensusHistogram;
+ }
+
+ /**
+ * Returns the value of field 'showDbRefTooltip'.
+ *
+ * @return the value of field 'ShowDbRefTooltip'.
+ */
+ public boolean getShowDbRefTooltip()
+ {
+ return this._showDbRefTooltip;
+ }
+
+ /**
+ * Returns the value of field 'showFullId'.
+ *
+ * @return the value of field 'ShowFullId'.
+ */
+ public boolean getShowFullId()
+ {
+ return this._showFullId;
+ }
+
+ /**
+ * Returns the value of field 'showGroupConsensus'.
+ *
+ * @return the value of field 'ShowGroupConsensus'.
+ */
+ public boolean getShowGroupConsensus()
+ {
+ return this._showGroupConsensus;
+ }
+
+ /**
+ * Returns the value of field 'showGroupConservation'.
+ *
+ * @return the value of field 'ShowGroupConservation'.
+ */
+ public boolean getShowGroupConservation()
+ {
+ return this._showGroupConservation;
+ }
+
+ /**
+ * Returns the value of field 'showNPfeatureTooltip'.
+ *
+ * @return the value of field 'ShowNPfeatureTooltip'.
+ */
+ public boolean getShowNPfeatureTooltip()
+ {
+ return this._showNPfeatureTooltip;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceFeatures'.
+ *
+ * @return the value of field 'ShowSequenceFeatures'.
+ */
+ public boolean getShowSequenceFeatures()
+ {
+ return this._showSequenceFeatures;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceLogo'.
+ *
+ * @return the value of field 'ShowSequenceLogo'.
+ */
+ public boolean getShowSequenceLogo()
+ {
+ return this._showSequenceLogo;
+ }
+
+ /**
+ * Returns the value of field 'showText'.
+ *
+ * @return the value of field 'ShowText'.
+ */
+ public boolean getShowText()
+ {
+ return this._showText;
+ }
+
+ /**
+ * Returns the value of field 'showUnconserved'.
+ *
+ * @return the value of field 'ShowUnconserved'.
+ */
+ public boolean getShowUnconserved()
+ {
+ return this._showUnconserved;
+ }
+
+ /**
+ * Returns the value of field 'startRes'.
+ *
+ * @return the value of field 'StartRes'.
+ */
+ public int getStartRes()
+ {
+ return this._startRes;
+ }
+
+ /**
+ * Returns the value of field 'startSeq'.
+ *
+ * @return the value of field 'StartSeq'.
+ */
+ public int getStartSeq()
+ {
+ return this._startSeq;
+ }
+
+ /**
+ * Returns the value of field 'textCol1'.
+ *
+ * @return the value of field 'TextCol1'.
+ */
+ public int getTextCol1()
+ {
+ return this._textCol1;
+ }
+
+ /**
+ * Returns the value of field 'textCol2'.
+ *
+ * @return the value of field 'TextCol2'.
+ */
+ public int getTextCol2()
+ {
+ return this._textCol2;
+ }
+
+ /**
+ * Returns the value of field 'textColThreshold'.
+ *
+ * @return the value of field 'TextColThreshold'.
+ */
+ public int getTextColThreshold()
+ {
+ return this._textColThreshold;
+ }
+
+ /**
+ * Returns the value of field 'title'.
+ *
+ * @return the value of field 'Title'.
+ */
+ public java.lang.String getTitle()
+ {
+ return this._title;
+ }
+
+ /**
+ * Returns the value of field 'viewName'.
+ *
+ * @return the value of field 'ViewName'.
+ */
+ public java.lang.String getViewName()
+ {
+ return this._viewName;
+ }
+
+ /**
+ * Returns the value of field 'width'.
+ *
+ * @return the value of field 'Width'.
+ */
+ public int getWidth()
+ {
+ return this._width;
+ }
+
+ /**
+ * Returns the value of field 'wrapAlignment'.
+ *
+ * @return the value of field 'WrapAlignment'.
+ */
+ public boolean getWrapAlignment()
+ {
+ return this._wrapAlignment;
+ }
+
+ /**
+ * Returns the value of field 'xpos'.
+ *
+ * @return the value of field 'Xpos'.
+ */
+ public int getXpos()
+ {
+ return this._xpos;
+ }
+
+ /**
+ * Returns the value of field 'ypos'.
+ *
+ * @return the value of field 'Ypos'.
+ */
+ public int getYpos()
+ {
+ return this._ypos;
+ }
+
+ /**
+ * Method hasCentreColumnLabels.
+ *
+ * @return true if at least one CentreColumnLabels has been adde
+ */
+ public boolean hasCentreColumnLabels()
+ {
+ return this._has_centreColumnLabels;
+ }
+
+ /**
+ * Method hasConsThreshold.
+ *
+ * @return true if at least one ConsThreshold has been added
+ */
+ public boolean hasConsThreshold()
+ {
+ return this._has_consThreshold;
+ }
+
+ /**
+ * Method hasConservationSelected.
+ *
+ * @return true if at least one ConservationSelected has been added
+ */
+ public boolean hasConservationSelected()
+ {
+ return this._has_conservationSelected;
+ }
+
+ /**
+ * Method hasFollowHighlight.
+ *
+ * @return true if at least one FollowHighlight has been added
+ */
+ public boolean hasFollowHighlight()
+ {
+ return this._has_followHighlight;
+ }
+
+ /**
+ * Method hasFollowSelection.
+ *
+ * @return true if at least one FollowSelection has been added
+ */
+ public boolean hasFollowSelection()
+ {
+ return this._has_followSelection;
+ }
+
+ /**
+ * Method hasFontSize.
+ *
+ * @return true if at least one FontSize has been added
+ */
+ public boolean hasFontSize()
+ {
+ return this._has_fontSize;
+ }
+
+ /**
+ * Method hasFontStyle.
+ *
+ * @return true if at least one FontStyle has been added
+ */
+ public boolean hasFontStyle()
+ {
+ return this._has_fontStyle;
+ }
+
+ /**
+ * Method hasGatheredViews.
+ *
+ * @return true if at least one GatheredViews has been added
+ */
+ public boolean hasGatheredViews()
+ {
+ return this._has_gatheredViews;
+ }
+
+ /**
+ * Method hasHeight.
+ *
+ * @return true if at least one Height has been added
+ */
+ public boolean hasHeight()
+ {
+ return this._has_height;
+ }
+
+ /**
+ * Method hasIgnoreGapsinConsensus.
+ *
+ * @return true if at least one IgnoreGapsinConsensus has been added
+ */
+ public boolean hasIgnoreGapsinConsensus()
+ {
+ return this._has_ignoreGapsinConsensus;
+ }
+
+ /**
+ * Method hasNormaliseSequenceLogo.
+ *
+ * @return true if at least one NormaliseSequenceLogo has been added
+ */
+ public boolean hasNormaliseSequenceLogo()
+ {
+ return this._has_normaliseSequenceLogo;
+ }
+
+ /**
+ * Method hasPidSelected.
+ *
+ * @return true if at least one PidSelected has been added
+ */
+ public boolean hasPidSelected()
+ {
+ return this._has_pidSelected;
+ }
+
+ /**
+ * Method hasPidThreshold.
+ *
+ * @return true if at least one PidThreshold has been added
+ */
+ public boolean hasPidThreshold()
+ {
+ return this._has_pidThreshold;
+ }
+
+ /**
+ * Method hasRenderGaps.
+ *
+ * @return true if at least one RenderGaps has been added
+ */
+ public boolean hasRenderGaps()
+ {
+ return this._has_renderGaps;
+ }
+
+ /**
+ * Method hasRightAlignIds.
+ *
+ * @return true if at least one RightAlignIds has been added
+ */
+ public boolean hasRightAlignIds()
+ {
+ return this._has_rightAlignIds;
+ }
+
+ /**
+ * Method hasShowAnnotation.
+ *
+ * @return true if at least one ShowAnnotation has been added
+ */
+ public boolean hasShowAnnotation()
+ {
+ return this._has_showAnnotation;
+ }
+
+ /**
+ * Method hasShowBoxes.
+ *
+ * @return true if at least one ShowBoxes has been added
+ */
+ public boolean hasShowBoxes()
+ {
+ return this._has_showBoxes;
+ }
+
+ /**
+ * Method hasShowColourText.
+ *
+ * @return true if at least one ShowColourText has been added
+ */
+ public boolean hasShowColourText()
+ {
+ return this._has_showColourText;
+ }
+
+ /**
+ * Method hasShowConsensusHistogram.
+ *
+ * @return true if at least one ShowConsensusHistogram has been added
+ */
+ public boolean hasShowConsensusHistogram()
+ {
+ return this._has_showConsensusHistogram;
+ }
+
+ /**
+ * Method hasShowDbRefTooltip.
+ *
+ * @return true if at least one ShowDbRefTooltip has been added
+ */
+ public boolean hasShowDbRefTooltip()
+ {
+ return this._has_showDbRefTooltip;
+ }
+
+ /**
+ * Method hasShowFullId.
+ *
+ * @return true if at least one ShowFullId has been added
+ */
+ public boolean hasShowFullId()
+ {
+ return this._has_showFullId;
+ }
+
+ /**
+ * Method hasShowGroupConsensus.
+ *
+ * @return true if at least one ShowGroupConsensus has been adde
+ */
+ public boolean hasShowGroupConsensus()
+ {
+ return this._has_showGroupConsensus;
+ }
+
+ /**
+ * Method hasShowGroupConservation.
+ *
+ * @return true if at least one ShowGroupConservation has been added
+ */
+ public boolean hasShowGroupConservation()
+ {
+ return this._has_showGroupConservation;
+ }
+
+ /**
+ * Method hasShowNPfeatureTooltip.
+ *
+ * @return true if at least one ShowNPfeatureTooltip has been added
+ */
+ public boolean hasShowNPfeatureTooltip()
+ {
+ return this._has_showNPfeatureTooltip;
+ }
+
+ /**
+ * Method hasShowSequenceFeatures.
+ *
+ * @return true if at least one ShowSequenceFeatures has been added
+ */
+ public boolean hasShowSequenceFeatures()
+ {
+ return this._has_showSequenceFeatures;
+ }
+
+ /**
+ * Method hasShowSequenceLogo.
+ *
+ * @return true if at least one ShowSequenceLogo has been added
+ */
+ public boolean hasShowSequenceLogo()
+ {
+ return this._has_showSequenceLogo;
+ }
+
+ /**
+ * Method hasShowText.
+ *
+ * @return true if at least one ShowText has been added
+ */
+ public boolean hasShowText()
+ {
+ return this._has_showText;
+ }
+
+ /**
+ * Method hasShowUnconserved.
+ *
+ * @return true if at least one ShowUnconserved has been added
+ */
+ public boolean hasShowUnconserved()
+ {
+ return this._has_showUnconserved;
+ }
+
+ /**
+ * Method hasStartRes.
+ *
+ * @return true if at least one StartRes has been added
+ */
+ public boolean hasStartRes()
+ {
+ return this._has_startRes;
+ }
+
+ /**
+ * Method hasStartSeq.
+ *
+ * @return true if at least one StartSeq has been added
+ */
+ public boolean hasStartSeq()
+ {
+ return this._has_startSeq;
+ }
+
+ /**
+ * Method hasTextCol1.
+ *
+ * @return true if at least one TextCol1 has been added
+ */
+ public boolean hasTextCol1()
+ {
+ return this._has_textCol1;
+ }
+
+ /**
+ * Method hasTextCol2.
+ *
+ * @return true if at least one TextCol2 has been added
+ */
+ public boolean hasTextCol2()
+ {
+ return this._has_textCol2;
+ }
+
+ /**
+ * Method hasTextColThreshold.
+ *
+ * @return true if at least one TextColThreshold has been added
+ */
+ public boolean hasTextColThreshold()
+ {
+ return this._has_textColThreshold;
+ }
+
+ /**
+ * Method hasWidth.
+ *
+ * @return true if at least one Width has been added
+ */
+ public boolean hasWidth()
+ {
+ return this._has_width;
+ }
+
+ /**
+ * Method hasWrapAlignment.
+ *
+ * @return true if at least one WrapAlignment has been added
+ */
+ public boolean hasWrapAlignment()
+ {
+ return this._has_wrapAlignment;
+ }
+
+ /**
+ * Method hasXpos.
+ *
+ * @return true if at least one Xpos has been added
+ */
+ public boolean hasXpos()
+ {
+ return this._has_xpos;
+ }
+
+ /**
+ * Method hasYpos.
+ *
+ * @return true if at least one Ypos has been added
+ */
+ public boolean hasYpos()
+ {
+ return this._has_ypos;
+ }
+
+ /**
+ * Returns the value of field 'centreColumnLabels'.
+ *
+ * @return the value of field 'CentreColumnLabels'.
+ */
+ public boolean isCentreColumnLabels()
+ {
+ return this._centreColumnLabels;
+ }
+
+ /**
+ * Returns the value of field 'conservationSelected'.
+ *
+ * @return the value of field 'ConservationSelected'.
+ */
+ public boolean isConservationSelected()
+ {
+ return this._conservationSelected;
+ }
+
+ /**
+ * Returns the value of field 'followHighlight'.
+ *
+ * @return the value of field 'FollowHighlight'.
+ */
+ public boolean isFollowHighlight()
+ {
+ return this._followHighlight;
+ }
+
+ /**
+ * Returns the value of field 'followSelection'.
+ *
+ * @return the value of field 'FollowSelection'.
+ */
+ public boolean isFollowSelection()
+ {
+ return this._followSelection;
+ }
+
+ /**
+ * Returns the value of field 'gatheredViews'.
+ *
+ * @return the value of field 'GatheredViews'.
+ */
+ public boolean isGatheredViews()
+ {
+ return this._gatheredViews;
+ }
+
+ /**
+ * Returns the value of field 'ignoreGapsinConsensus'.
+ *
+ * @return the value of field 'IgnoreGapsinConsensus'.
+ */
+ public boolean isIgnoreGapsinConsensus()
+ {
+ return this._ignoreGapsinConsensus;
+ }
+
+ /**
+ * Returns the value of field 'normaliseSequenceLogo'.
+ *
+ * @return the value of field 'NormaliseSequenceLogo'.
+ */
+ public boolean isNormaliseSequenceLogo()
+ {
+ return this._normaliseSequenceLogo;
+ }
+
+ /**
+ * Returns the value of field 'pidSelected'.
+ *
+ * @return the value of field 'PidSelected'.
+ */
+ public boolean isPidSelected()
+ {
+ return this._pidSelected;
+ }
+
+ /**
+ * Returns the value of field 'renderGaps'.
+ *
+ * @return the value of field 'RenderGaps'.
+ */
+ public boolean isRenderGaps()
+ {
+ return this._renderGaps;
+ }
+
+ /**
+ * Returns the value of field 'rightAlignIds'.
+ *
+ * @return the value of field 'RightAlignIds'.
+ */
+ public boolean isRightAlignIds()
+ {
+ return this._rightAlignIds;
+ }
+
+ /**
+ * Returns the value of field 'showAnnotation'.
+ *
+ * @return the value of field 'ShowAnnotation'.
+ */
+ public boolean isShowAnnotation()
+ {
+ return this._showAnnotation;
+ }
+
+ /**
+ * Returns the value of field 'showBoxes'.
+ *
+ * @return the value of field 'ShowBoxes'.
+ */
+ public boolean isShowBoxes()
+ {
+ return this._showBoxes;
+ }
+
+ /**
+ * Returns the value of field 'showColourText'.
+ *
+ * @return the value of field 'ShowColourText'.
+ */
+ public boolean isShowColourText()
+ {
+ return this._showColourText;
+ }
+
+ /**
+ * Returns the value of field 'showConsensusHistogram'.
+ *
+ * @return the value of field 'ShowConsensusHistogram'.
+ */
+ public boolean isShowConsensusHistogram()
+ {
+ return this._showConsensusHistogram;
+ }
+
+ /**
+ * Returns the value of field 'showDbRefTooltip'.
+ *
+ * @return the value of field 'ShowDbRefTooltip'.
+ */
+ public boolean isShowDbRefTooltip()
+ {
+ return this._showDbRefTooltip;
+ }
+
+ /**
+ * Returns the value of field 'showFullId'.
+ *
+ * @return the value of field 'ShowFullId'.
+ */
+ public boolean isShowFullId()
+ {
+ return this._showFullId;
+ }
+
+ /**
+ * Returns the value of field 'showGroupConsensus'.
+ *
+ * @return the value of field 'ShowGroupConsensus'.
+ */
+ public boolean isShowGroupConsensus()
+ {
+ return this._showGroupConsensus;
+ }
+
+ /**
+ * Returns the value of field 'showGroupConservation'.
+ *
+ * @return the value of field 'ShowGroupConservation'.
+ */
+ public boolean isShowGroupConservation()
+ {
+ return this._showGroupConservation;
+ }
+
+ /**
+ * Returns the value of field 'showNPfeatureTooltip'.
+ *
+ * @return the value of field 'ShowNPfeatureTooltip'.
+ */
+ public boolean isShowNPfeatureTooltip()
+ {
+ return this._showNPfeatureTooltip;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceFeatures'.
+ *
+ * @return the value of field 'ShowSequenceFeatures'.
+ */
+ public boolean isShowSequenceFeatures()
+ {
+ return this._showSequenceFeatures;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceLogo'.
+ *
+ * @return the value of field 'ShowSequenceLogo'.
+ */
+ public boolean isShowSequenceLogo()
+ {
+ return this._showSequenceLogo;
+ }
+
+ /**
+ * Returns the value of field 'showText'.
+ *
+ * @return the value of field 'ShowText'.
+ */
+ public boolean isShowText()
+ {
+ return this._showText;
+ }
+
+ /**
+ * Returns the value of field 'showUnconserved'.
+ *
+ * @return the value of field 'ShowUnconserved'.
+ */
+ public boolean isShowUnconserved()
+ {
+ return this._showUnconserved;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * Returns the value of field 'wrapAlignment'.
+ *
+ * @return the value of field 'WrapAlignment'.
+ */
+ public boolean isWrapAlignment()
+ {
+ return this._wrapAlignment;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllCalcIdParam()
+ {
+ this._calcIdParamList.clear();
+ }
+
+ /**
+ */
+ public void removeAllHiddenColumns()
+ {
+ this._hiddenColumnsList.clear();
+ }
+
+ /**
+ * Method removeCalcIdParam.
+ *
+ * @param vCalcIdParam
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeCalcIdParam(
+ final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
+ {
+ boolean removed = _calcIdParamList.remove(vCalcIdParam);
+ return removed;
+ }
+
+ /**
+ * Method removeCalcIdParamAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.CalcIdParam removeCalcIdParamAt(
+ final int index)
+ {
+ java.lang.Object obj = this._calcIdParamList.remove(index);
+ return (jalview.schemabinding.version2.CalcIdParam) obj;
+ }
+
+ /**
+ * Method removeHiddenColumns.
+ *
+ * @param vHiddenColumns
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeHiddenColumns(
+ final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+ {
+ boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
+ return removed;
+ }
+
+ /**
+ * Method removeHiddenColumnsAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
+ final int index)
+ {
+ java.lang.Object obj = this._hiddenColumnsList.remove(index);
+ return (jalview.schemabinding.version2.HiddenColumns) obj;
+ }
+
+ /**
+ * Sets the value of field 'annotationColours'.
+ *
+ * @param annotationColours
+ * the value of field 'annotationColours'.
+ */
+ public void setAnnotationColours(
+ final jalview.schemabinding.version2.AnnotationColours annotationColours)
+ {
+ this._annotationColours = annotationColours;
+ }
+
+ /**
+ * Sets the value of field 'bgColour'.
+ *
+ * @param bgColour
+ * the value of field 'bgColour'.
+ */
+ public void setBgColour(final java.lang.String bgColour)
+ {
+ this._bgColour = bgColour;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vCalcIdParam
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setCalcIdParam(final int index,
+ final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._calcIdParamList.size())
+ {
+ throw new IndexOutOfBoundsException("setCalcIdParam: Index value '"
+ + index + "' not in range [0.."
+ + (this._calcIdParamList.size() - 1) + "]");
+ }
+
+ this._calcIdParamList.set(index, vCalcIdParam);
+ }
+
+ /**
+ *
+ *
+ * @param vCalcIdParamArray
+ */
+ public void setCalcIdParam(
+ final jalview.schemabinding.version2.CalcIdParam[] vCalcIdParamArray)
+ {
+ // -- copy array
+ _calcIdParamList.clear();
+
+ for (int i = 0; i < vCalcIdParamArray.length; i++)
+ {
+ this._calcIdParamList.add(vCalcIdParamArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'centreColumnLabels'.
+ *
+ * @param centreColumnLabels
+ * the value of field 'centreColumnLabels'.
+ */
+ public void setCentreColumnLabels(final boolean centreColumnLabels)
+ {
+ this._centreColumnLabels = centreColumnLabels;
+ this._has_centreColumnLabels = true;
+ }
+
+ /**
+ * Sets the value of field 'consThreshold'.
+ *
+ * @param consThreshold
+ * the value of field 'consThreshold'.
+ */
+ public void setConsThreshold(final int consThreshold)
+ {
+ this._consThreshold = consThreshold;
+ this._has_consThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'conservationSelected'.
+ *
+ * @param conservationSelected
+ * the value of field 'conservationSelected'.
+ */
+ public void setConservationSelected(final boolean conservationSelected)
+ {
+ this._conservationSelected = conservationSelected;
+ this._has_conservationSelected = true;
+ }
+
+ /**
+ * Sets the value of field 'followHighlight'.
+ *
+ * @param followHighlight
+ * the value of field 'followHighlight'.
+ */
+ public void setFollowHighlight(final boolean followHighlight)
+ {
+ this._followHighlight = followHighlight;
+ this._has_followHighlight = true;
+ }
+
+ /**
+ * Sets the value of field 'followSelection'.
+ *
+ * @param followSelection
+ * the value of field 'followSelection'.
+ */
+ public void setFollowSelection(final boolean followSelection)
+ {
+ this._followSelection = followSelection;
+ this._has_followSelection = true;
+ }
+
+ /**
+ * Sets the value of field 'fontName'.
+ *
+ * @param fontName
+ * the value of field 'fontName'.
+ */
+ public void setFontName(final java.lang.String fontName)
+ {
+ this._fontName = fontName;
+ }
+
+ /**
+ * Sets the value of field 'fontSize'.
+ *
+ * @param fontSize
+ * the value of field 'fontSize'.
+ */
+ public void setFontSize(final int fontSize)
+ {
+ this._fontSize = fontSize;
+ this._has_fontSize = true;
+ }
+
+ /**
+ * Sets the value of field 'fontStyle'.
+ *
+ * @param fontStyle
+ * the value of field 'fontStyle'.
+ */
+ public void setFontStyle(final int fontStyle)
+ {
+ this._fontStyle = fontStyle;
+ this._has_fontStyle = true;
+ }
+
+ /**
+ * Sets the value of field 'gatheredViews'.
+ *
+ * @param gatheredViews
+ * the value of field 'gatheredViews'.
+ */
+ public void setGatheredViews(final boolean gatheredViews)
+ {
+ this._gatheredViews = gatheredViews;
+ this._has_gatheredViews = true;
+ }
+
+ /**
+ * Sets the value of field 'height'.
+ *
+ * @param height
+ * the value of field 'height'.
+ */
+ public void setHeight(final int height)
+ {
+ this._height = height;
+ this._has_height = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vHiddenColumns
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setHiddenColumns(final int index,
+ final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._hiddenColumnsList.size())
+ {
+ throw new IndexOutOfBoundsException("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 'normaliseSequenceLogo'.
+ *
+ * @param normaliseSequenceLogo
+ * the value of field 'normaliseSequenceLogo'.
+ */
+ public void setNormaliseSequenceLogo(final boolean normaliseSequenceLogo)
+ {
+ this._normaliseSequenceLogo = normaliseSequenceLogo;
+ this._has_normaliseSequenceLogo = true;
+ }
+
+ /**
+ * Sets the value of field 'pidSelected'.
+ *
+ * @param pidSelected
+ * the value of field 'pidSelected'.
+ */
+ public void setPidSelected(final boolean pidSelected)
+ {
+ this._pidSelected = pidSelected;
+ this._has_pidSelected = true;
+ }
+
+ /**
+ * Sets the value of field 'pidThreshold'.
+ *
+ * @param pidThreshold
+ * the value of field 'pidThreshold'.
+ */
+ public void setPidThreshold(final int pidThreshold)
+ {
+ this._pidThreshold = pidThreshold;
+ this._has_pidThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'renderGaps'.
+ *
+ * @param renderGaps
+ * the value of field 'renderGaps'.
+ */
+ public void setRenderGaps(final boolean renderGaps)
+ {
+ this._renderGaps = renderGaps;
+ this._has_renderGaps = true;
+ }
+
+ /**
+ * Sets the value of field 'rightAlignIds'.
+ *
+ * @param rightAlignIds
+ * the value of field 'rightAlignIds'.
+ */
+ public void setRightAlignIds(final boolean rightAlignIds)
+ {
+ this._rightAlignIds = rightAlignIds;
+ this._has_rightAlignIds = true;
+ }
+
+ /**
+ * Sets the value of field 'sequenceSetId'.
+ *
+ * @param sequenceSetId
+ * the value of field 'sequenceSetId'.
+ */
+ public void setSequenceSetId(final java.lang.String sequenceSetId)
+ {
+ this._sequenceSetId = sequenceSetId;
+ }
+
+ /**
+ * Sets the value of field 'showAnnotation'.
+ *
+ * @param showAnnotation
+ * the value of field 'showAnnotation'.
+ */
+ public void setShowAnnotation(final boolean showAnnotation)
+ {
+ this._showAnnotation = showAnnotation;
+ this._has_showAnnotation = true;
+ }
+
+ /**
+ * Sets the value of field 'showBoxes'.
+ *
+ * @param showBoxes
+ * the value of field 'showBoxes'.
+ */
+ public void setShowBoxes(final boolean showBoxes)
+ {
+ this._showBoxes = showBoxes;
+ this._has_showBoxes = true;
+ }
+
+ /**
+ * Sets the value of field 'showColourText'.
+ *
+ * @param showColourText
+ * the value of field 'showColourText'.
+ */
+ public void setShowColourText(final boolean showColourText)
+ {
+ this._showColourText = showColourText;
+ this._has_showColourText = true;
+ }
+
+ /**
+ * Sets the value of field 'showConsensusHistogram'.
+ *
+ * @param showConsensusHistogram
+ * the value of field 'showConsensusHistogram'.
+ */
+ public void setShowConsensusHistogram(final boolean showConsensusHistogram)
+ {
+ this._showConsensusHistogram = showConsensusHistogram;
+ this._has_showConsensusHistogram = true;
+ }
+
+ /**
+ * Sets the value of field 'showDbRefTooltip'.
+ *
+ * @param showDbRefTooltip
+ * the value of field 'showDbRefTooltip'
+ */
+ public void setShowDbRefTooltip(final boolean showDbRefTooltip)
+ {
+ this._showDbRefTooltip = showDbRefTooltip;
+ this._has_showDbRefTooltip = true;
+ }
+
+ /**
+ * Sets the value of field 'showFullId'.
+ *
+ * @param showFullId
+ * the value of field 'showFullId'.
+ */
+ public void setShowFullId(final boolean showFullId)
+ {
+ this._showFullId = showFullId;
+ this._has_showFullId = true;
+ }
+
+ /**
+ * Sets the value of field 'showGroupConsensus'.
+ *
+ * @param showGroupConsensus
+ * the value of field 'showGroupConsensus'.
+ */
+ public void setShowGroupConsensus(final boolean showGroupConsensus)
+ {
+ this._showGroupConsensus = showGroupConsensus;
+ this._has_showGroupConsensus = true;
+ }
+
+ /**
+ * Sets the value of field 'showGroupConservation'.
+ *
+ * @param showGroupConservation
+ * the value of field 'showGroupConservation'.
+ */
+ public void setShowGroupConservation(final boolean showGroupConservation)
+ {
+ this._showGroupConservation = showGroupConservation;
+ this._has_showGroupConservation = true;
+ }
+
+ /**
+ * Sets the value of field 'showNPfeatureTooltip'.
+ *
+ * @param showNPfeatureTooltip
+ * the value of field 'showNPfeatureTooltip'.
+ */
+ public void setShowNPfeatureTooltip(final boolean showNPfeatureTooltip)
+ {
+ this._showNPfeatureTooltip = showNPfeatureTooltip;
+ this._has_showNPfeatureTooltip = true;
+ }
+
+ /**
+ * Sets the value of field 'showSequenceFeatures'.
+ *
+ * @param showSequenceFeatures
+ * the value of field 'showSequenceFeatures'.
+ */
+ public void setShowSequenceFeatures(final boolean showSequenceFeatures)
+ {
+ this._showSequenceFeatures = showSequenceFeatures;
+ this._has_showSequenceFeatures = true;
+ }
+
+ /**
+ * Sets the value of field 'showSequenceLogo'.
+ *
+ * @param showSequenceLogo
+ * the value of field 'showSequenceLogo'
+ */
+ public void setShowSequenceLogo(final boolean showSequenceLogo)
+ {
+ this._showSequenceLogo = showSequenceLogo;
+ this._has_showSequenceLogo = true;
+ }
+
+ /**
+ * Sets the value of field 'showText'.
+ *
+ * @param showText
+ * the value of field 'showText'.
+ */
+ public void setShowText(final boolean showText)
+ {
+ this._showText = showText;
+ this._has_showText = true;
+ }
+
+ /**
+ * Sets the value of field 'showUnconserved'.
+ *
+ * @param showUnconserved
+ * the value of field 'showUnconserved'.
+ */
+ public void setShowUnconserved(final boolean showUnconserved)
+ {
+ this._showUnconserved = showUnconserved;
+ this._has_showUnconserved = true;
+ }
+
+ /**
+ * Sets the value of field 'startRes'.
+ *
+ * @param startRes
+ * the value of field 'startRes'.
+ */
+ public void setStartRes(final int startRes)
+ {
+ this._startRes = startRes;
+ this._has_startRes = true;
+ }
+
+ /**
+ * Sets the value of field 'startSeq'.
+ *
+ * @param startSeq
+ * the value of field 'startSeq'.
+ */
+ public void setStartSeq(final int startSeq)
+ {
+ this._startSeq = startSeq;
+ this._has_startSeq = true;
+ }
+
+ /**
+ * Sets the value of field 'textCol1'.
+ *
+ * @param textCol1
+ * the value of field 'textCol1'.
+ */
+ public void setTextCol1(final int textCol1)
+ {
+ this._textCol1 = textCol1;
+ this._has_textCol1 = true;
+ }
+
+ /**
+ * Sets the value of field 'textCol2'.
+ *
+ * @param textCol2
+ * the value of field 'textCol2'.
+ */
+ public void setTextCol2(final int textCol2)
+ {
+ this._textCol2 = textCol2;
+ this._has_textCol2 = true;
+ }
+
+ /**
+ * Sets the value of field 'textColThreshold'.
+ *
+ * @param textColThreshold
+ * the value of field 'textColThreshold'
+ */
+ public void setTextColThreshold(final int textColThreshold)
+ {
+ this._textColThreshold = textColThreshold;
+ this._has_textColThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'title'.
+ *
+ * @param title
+ * the value of field 'title'.
+ */
+ public void setTitle(final java.lang.String title)
+ {
+ this._title = title;
+ }
+
+ /**
+ * Sets the value of field 'viewName'.
+ *
+ * @param viewName
+ * the value of field 'viewName'.
+ */
+ public void setViewName(final java.lang.String viewName)
+ {
+ this._viewName = viewName;
+ }
+
+ /**
+ * Sets the value of field 'width'.
+ *
+ * @param width
+ * the value of field 'width'.
+ */
+ public void setWidth(final int width)
+ {
+ this._width = width;
+ this._has_width = true;
+ }
+
+ /**
+ * Sets the value of field 'wrapAlignment'.
+ *
+ * @param wrapAlignment
+ * the value of field 'wrapAlignment'.
+ */
+ public void setWrapAlignment(final boolean wrapAlignment)
+ {
+ this._wrapAlignment = wrapAlignment;
+ this._has_wrapAlignment = true;
+ }
+
+ /**
+ * Sets the value of field 'xpos'.
+ *
+ * @param xpos
+ * the value of field 'xpos'.
+ */
+ public void setXpos(final int xpos)
+ {
+ this._xpos = xpos;
+ this._has_xpos = true;
+ }
+
+ /**
+ * Sets the value of field 'ypos'.
+ *
+ * @param ypos
+ * the value of field 'ypos'.
+ */
+ public void setYpos(final int ypos)
+ {
+ this._ypos = ypos;
+ this._has_ypos = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.Viewport
+ */
+ public static jalview.schemabinding.version2.Viewport unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.Viewport) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.Viewport.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff