X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FViewport.java;fp=src%2Fjalview%2Fschemabinding%2Fversion2%2FViewport.java;h=0000000000000000000000000000000000000000;hb=ca8504cf9d10874dce9f07cf7a9d933853fe0dd0;hp=159f7ae9ccb074ad5d38a3a72d57dc908a9d7560;hpb=775e7bc104584e88dddcea73fbf02c66f5200c16;p=jalview.git diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java deleted file mode 100644 index 159f7ae..0000000 --- a/src/jalview/schemabinding/version2/Viewport.java +++ /dev/null @@ -1,2803 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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 _scaleProteinAsCdna. - */ - private boolean _scaleProteinAsCdna = true; - - /** - * keeps track of state for field: _scaleProteinAsCdna - */ - private boolean _has_scaleProteinAsCdna; - - /** - * 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; - - /** - * The viewport id of this viewport's (cdna/protein) coding complement, if any - * - */ - private java.lang.String _complementId; - - /** - * 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 deleteScaleProteinAsCdna() - { - this._has_scaleProteinAsCdna = 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. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.CalcIdParam[] getCalcIdParam() - { - jalview.schemabinding.version2.CalcIdParam[] array = new jalview.schemabinding.version2.CalcIdParam[0]; - return (jalview.schemabinding.version2.CalcIdParam[]) this._calcIdParamList - .toArray(array); - } - - /** - * Method getCalcIdParamCount. - * - * @return the size of this collection - */ - public int getCalcIdParamCount() - { - return this._calcIdParamList.size(); - } - - /** - * Returns the value of field 'centreColumnLabels'. - * - * @return the value of field 'CentreColumnLabels'. - */ - public boolean getCentreColumnLabels() - { - return this._centreColumnLabels; - } - - /** - * Returns the value of field 'complementId'. The field 'complementId' has the - * following description: The viewport id of this viewport's (cdna/protein) - * coding complement, if any - * - * - * @return the value of field 'ComplementId'. - */ - public java.lang.String getComplementId() - { - return this._complementId; - } - - /** - * 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. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns() - { - jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0]; - return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList - .toArray(array); - } - - /** - * Method getHiddenColumnsCount. - * - * @return the size of this collection - */ - public int getHiddenColumnsCount() - { - return this._hiddenColumnsList.size(); - } - - /** - * Returns the value of field 'id'. The field 'id' has the following - * description: unique id used by jalview to synchronize between stored and - * instantiated views - * - * - * @return the value of field 'Id'. - */ - public java.lang.String getId() - { - return this._id; - } - - /** - * Returns the value of field 'ignoreGapsinConsensus'. - * - * @return the value of field 'IgnoreGapsinConsensus'. - */ - public boolean getIgnoreGapsinConsensus() - { - return this._ignoreGapsinConsensus; - } - - /** - * Returns the value of field 'normaliseSequenceLogo'. - * - * @return the value of field 'NormaliseSequenceLogo'. - */ - public boolean getNormaliseSequenceLogo() - { - return this._normaliseSequenceLogo; - } - - /** - * Returns the value of field 'pidSelected'. - * - * @return the value of field 'PidSelected'. - */ - public boolean getPidSelected() - { - return this._pidSelected; - } - - /** - * Returns the value of field 'pidThreshold'. - * - * @return the value of field 'PidThreshold'. - */ - public int getPidThreshold() - { - return this._pidThreshold; - } - - /** - * Returns the value of field 'renderGaps'. - * - * @return the value of field 'RenderGaps'. - */ - public boolean getRenderGaps() - { - return this._renderGaps; - } - - /** - * Returns the value of field 'rightAlignIds'. - * - * @return the value of field 'RightAlignIds'. - */ - public boolean getRightAlignIds() - { - return this._rightAlignIds; - } - - /** - * Returns the value of field 'scaleProteinAsCdna'. - * - * @return the value of field 'ScaleProteinAsCdna'. - */ - public boolean getScaleProteinAsCdna() - { - return this._scaleProteinAsCdna; - } - - /** - * 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 hasScaleProteinAsCdna. - * - * @return true if at least one ScaleProteinAsCdna has been adde - */ - public boolean hasScaleProteinAsCdna() - { - return this._has_scaleProteinAsCdna; - } - - /** - * 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 'scaleProteinAsCdna'. - * - * @return the value of field 'ScaleProteinAsCdna'. - */ - public boolean isScaleProteinAsCdna() - { - return this._scaleProteinAsCdna; - } - - /** - * 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 'complementId'. The field 'complementId' has the - * following description: The viewport id of this viewport's (cdna/protein) - * coding complement, if any - * - * - * @param complementId - * the value of field 'complementId'. - */ - public void setComplementId(final java.lang.String complementId) - { - this._complementId = complementId; - } - - /** - * 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 'scaleProteinAsCdna'. - * - * @param scaleProteinAsCdna - * the value of field 'scaleProteinAsCdna'. - */ - public void setScaleProteinAsCdna(final boolean scaleProteinAsCdna) - { - this._scaleProteinAsCdna = scaleProteinAsCdna; - this._has_scaleProteinAsCdna = 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); - } - -}