-/*\r
- * This class was automatically generated with\r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package jalview.schemabinding.version2;\r
-\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.xml.*;\r
-\r
-/**\r
- * Class Tree.\r
- *\r
- * @version $Revision$ $Date$\r
- */\r
-public class Tree\r
- implements java.io.Serializable\r
-{\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\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 _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 _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 _threshold\r
- */\r
- private float _threshold;\r
-\r
- /**\r
- * keeps track of state for field: _threshold\r
- */\r
- private boolean _has_threshold;\r
-\r
- /**\r
- * Field _showBootstrap\r
- */\r
- private boolean _showBootstrap;\r
-\r
- /**\r
- * keeps track of state for field: _showBootstrap\r
- */\r
- private boolean _has_showBootstrap;\r
-\r
- /**\r
- * Field _showDistances\r
- */\r
- private boolean _showDistances;\r
-\r
- /**\r
- * keeps track of state for field: _showDistances\r
- */\r
- private boolean _has_showDistances;\r
-\r
- /**\r
- * Field _markUnlinked\r
- */\r
- private boolean _markUnlinked;\r
-\r
- /**\r
- * keeps track of state for field: _markUnlinked\r
- */\r
- private boolean _has_markUnlinked;\r
-\r
- /**\r
- * Field _fitToWindow\r
- */\r
- private boolean _fitToWindow;\r
-\r
- /**\r
- * keeps track of state for field: _fitToWindow\r
- */\r
- private boolean _has_fitToWindow;\r
-\r
- /**\r
- * Field _currentTree\r
- */\r
- private boolean _currentTree;\r
-\r
- /**\r
- * keeps track of state for field: _currentTree\r
- */\r
- private boolean _has_currentTree;\r
-\r
- /**\r
- * Field _title\r
- */\r
- private java.lang.String _title;\r
-\r
- /**\r
- * Field _newick\r
- */\r
- private java.lang.String _newick;\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Tree()\r
- {\r
- super();\r
- } //-- jalview.schemabinding.version2.Tree()\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method deleteCurrentTree\r
- *\r
- */\r
- public void deleteCurrentTree()\r
- {\r
- this._has_currentTree = false;\r
- } //-- void deleteCurrentTree()\r
-\r
- /**\r
- * Method deleteFitToWindow\r
- *\r
- */\r
- public void deleteFitToWindow()\r
- {\r
- this._has_fitToWindow = false;\r
- } //-- void deleteFitToWindow()\r
-\r
- /**\r
- * Method deleteFontSize\r
- *\r
- */\r
- public void deleteFontSize()\r
- {\r
- this._has_fontSize = false;\r
- } //-- void deleteFontSize()\r
-\r
- /**\r
- * Method deleteFontStyle\r
- *\r
- */\r
- public void deleteFontStyle()\r
- {\r
- this._has_fontStyle = false;\r
- } //-- void deleteFontStyle()\r
-\r
- /**\r
- * Method deleteHeight\r
- *\r
- */\r
- public void deleteHeight()\r
- {\r
- this._has_height = false;\r
- } //-- void deleteHeight()\r
-\r
- /**\r
- * Method deleteMarkUnlinked\r
- *\r
- */\r
- public void deleteMarkUnlinked()\r
- {\r
- this._has_markUnlinked = false;\r
- } //-- void deleteMarkUnlinked()\r
-\r
- /**\r
- * Method deleteShowBootstrap\r
- *\r
- */\r
- public void deleteShowBootstrap()\r
- {\r
- this._has_showBootstrap = false;\r
- } //-- void deleteShowBootstrap()\r
-\r
- /**\r
- * Method deleteShowDistances\r
- *\r
- */\r
- public void deleteShowDistances()\r
- {\r
- this._has_showDistances = false;\r
- } //-- void deleteShowDistances()\r
-\r
- /**\r
- * Method deleteThreshold\r
- *\r
- */\r
- public void deleteThreshold()\r
- {\r
- this._has_threshold = false;\r
- } //-- void deleteThreshold()\r
-\r
- /**\r
- * Method deleteWidth\r
- *\r
- */\r
- public void deleteWidth()\r
- {\r
- this._has_width = false;\r
- } //-- void deleteWidth()\r
-\r
- /**\r
- * Method deleteXpos\r
- *\r
- */\r
- public void deleteXpos()\r
- {\r
- this._has_xpos = false;\r
- } //-- void deleteXpos()\r
-\r
- /**\r
- * Method deleteYpos\r
- *\r
- */\r
- public void deleteYpos()\r
- {\r
- this._has_ypos = false;\r
- } //-- void deleteYpos()\r
-\r
- /**\r
- * Returns the value of field 'currentTree'.\r
- *\r
- * @return boolean\r
- * @return the value of field 'currentTree'.\r
- */\r
- public boolean getCurrentTree()\r
- {\r
- return this._currentTree;\r
- } //-- boolean getCurrentTree()\r
-\r
- /**\r
- * Returns the value of field 'fitToWindow'.\r
- *\r
- * @return boolean\r
- * @return the value of field 'fitToWindow'.\r
- */\r
- public boolean getFitToWindow()\r
- {\r
- return this._fitToWindow;\r
- } //-- boolean getFitToWindow()\r
-\r
- /**\r
- * Returns the value of field 'fontName'.\r
- *\r
- * @return String\r
- * @return the value of field 'fontName'.\r
- */\r
- public java.lang.String getFontName()\r
- {\r
- return this._fontName;\r
- } //-- java.lang.String getFontName()\r
-\r
- /**\r
- * Returns the value of field 'fontSize'.\r
- *\r
- * @return int\r
- * @return the value of field 'fontSize'.\r
- */\r
- public int getFontSize()\r
- {\r
- return this._fontSize;\r
- } //-- int getFontSize()\r
-\r
- /**\r
- * Returns the value of field 'fontStyle'.\r
- *\r
- * @return int\r
- * @return the value of field 'fontStyle'.\r
- */\r
- public int getFontStyle()\r
- {\r
- return this._fontStyle;\r
- } //-- int getFontStyle()\r
-\r
- /**\r
- * Returns the value of field 'height'.\r
- *\r
- * @return int\r
- * @return the value of field 'height'.\r
- */\r
- public int getHeight()\r
- {\r
- return this._height;\r
- } //-- int getHeight()\r
-\r
- /**\r
- * Returns the value of field 'markUnlinked'.\r
- *\r
- * @return boolean\r
- * @return the value of field 'markUnlinked'.\r
- */\r
- public boolean getMarkUnlinked()\r
- {\r
- return this._markUnlinked;\r
- } //-- boolean getMarkUnlinked()\r
-\r
- /**\r
- * Returns the value of field 'newick'.\r
- *\r
- * @return String\r
- * @return the value of field 'newick'.\r
- */\r
- public java.lang.String getNewick()\r
- {\r
- return this._newick;\r
- } //-- java.lang.String getNewick()\r
-\r
- /**\r
- * Returns the value of field 'showBootstrap'.\r
- *\r
- * @return boolean\r
- * @return the value of field 'showBootstrap'.\r
- */\r
- public boolean getShowBootstrap()\r
- {\r
- return this._showBootstrap;\r
- } //-- boolean getShowBootstrap()\r
-\r
- /**\r
- * Returns the value of field 'showDistances'.\r
- *\r
- * @return boolean\r
- * @return the value of field 'showDistances'.\r
- */\r
- public boolean getShowDistances()\r
- {\r
- return this._showDistances;\r
- } //-- boolean getShowDistances()\r
-\r
- /**\r
- * Returns the value of field 'threshold'.\r
- *\r
- * @return float\r
- * @return the value of field 'threshold'.\r
- */\r
- public float getThreshold()\r
- {\r
- return this._threshold;\r
- } //-- float getThreshold()\r
-\r
- /**\r
- * Returns the value of field 'title'.\r
- *\r
- * @return String\r
- * @return the value of field 'title'.\r
- */\r
- public java.lang.String getTitle()\r
- {\r
- return this._title;\r
- } //-- java.lang.String getTitle()\r
-\r
- /**\r
- * Returns the value of field 'width'.\r
- *\r
- * @return int\r
- * @return the value of field 'width'.\r
- */\r
- public int getWidth()\r
- {\r
- return this._width;\r
- } //-- int getWidth()\r
-\r
- /**\r
- * Returns the value of field 'xpos'.\r
- *\r
- * @return int\r
- * @return the value of field 'xpos'.\r
- */\r
- public int getXpos()\r
- {\r
- return this._xpos;\r
- } //-- int getXpos()\r
-\r
- /**\r
- * Returns the value of field 'ypos'.\r
- *\r
- * @return int\r
- * @return the value of field 'ypos'.\r
- */\r
- public int getYpos()\r
- {\r
- return this._ypos;\r
- } //-- int getYpos()\r
-\r
- /**\r
- * Method hasCurrentTree\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasCurrentTree()\r
- {\r
- return this._has_currentTree;\r
- } //-- boolean hasCurrentTree()\r
-\r
- /**\r
- * Method hasFitToWindow\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasFitToWindow()\r
- {\r
- return this._has_fitToWindow;\r
- } //-- boolean hasFitToWindow()\r
-\r
- /**\r
- * Method hasFontSize\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasFontSize()\r
- {\r
- return this._has_fontSize;\r
- } //-- boolean hasFontSize()\r
-\r
- /**\r
- * Method hasFontStyle\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasFontStyle()\r
- {\r
- return this._has_fontStyle;\r
- } //-- boolean hasFontStyle()\r
-\r
- /**\r
- * Method hasHeight\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasHeight()\r
- {\r
- return this._has_height;\r
- } //-- boolean hasHeight()\r
-\r
- /**\r
- * Method hasMarkUnlinked\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasMarkUnlinked()\r
- {\r
- return this._has_markUnlinked;\r
- } //-- boolean hasMarkUnlinked()\r
-\r
- /**\r
- * Method hasShowBootstrap\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasShowBootstrap()\r
- {\r
- return this._has_showBootstrap;\r
- } //-- boolean hasShowBootstrap()\r
-\r
- /**\r
- * Method hasShowDistances\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasShowDistances()\r
- {\r
- return this._has_showDistances;\r
- } //-- boolean hasShowDistances()\r
-\r
- /**\r
- * Method hasThreshold\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasThreshold()\r
- {\r
- return this._has_threshold;\r
- } //-- boolean hasThreshold()\r
-\r
- /**\r
- * Method hasWidth\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasWidth()\r
- {\r
- return this._has_width;\r
- } //-- boolean hasWidth()\r
-\r
- /**\r
- * Method hasXpos\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasXpos()\r
- {\r
- return this._has_xpos;\r
- } //-- boolean hasXpos()\r
-\r
- /**\r
- * Method hasYpos\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasYpos()\r
- {\r
- return this._has_ypos;\r
- } //-- boolean hasYpos()\r
-\r
- /**\r
- * Method isValid\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try\r
- {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid()\r
-\r
- /**\r
- * Method marshal\r
- *\r
- *\r
- *\r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException,\r
- org.exolab.castor.xml.ValidationException\r
- {\r
-\r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
-\r
- /**\r
- * Method marshal\r
- *\r
- *\r
- *\r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
- org.exolab.castor.xml.ValidationException\r
- {\r
-\r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
- /**\r
- * Sets the value of field 'currentTree'.\r
- *\r
- * @param currentTree the value of field 'currentTree'.\r
- */\r
- public void setCurrentTree(boolean currentTree)\r
- {\r
- this._currentTree = currentTree;\r
- this._has_currentTree = true;\r
- } //-- void setCurrentTree(boolean)\r
-\r
- /**\r
- * Sets the value of field 'fitToWindow'.\r
- *\r
- * @param fitToWindow the value of field 'fitToWindow'.\r
- */\r
- public void setFitToWindow(boolean fitToWindow)\r
- {\r
- this._fitToWindow = fitToWindow;\r
- this._has_fitToWindow = true;\r
- } //-- void setFitToWindow(boolean)\r
-\r
- /**\r
- * Sets the value of field 'fontName'.\r
- *\r
- * @param fontName the value of field 'fontName'.\r
- */\r
- public void setFontName(java.lang.String fontName)\r
- {\r
- this._fontName = fontName;\r
- } //-- void setFontName(java.lang.String)\r
-\r
- /**\r
- * Sets the value of field 'fontSize'.\r
- *\r
- * @param fontSize the value of field 'fontSize'.\r
- */\r
- public void setFontSize(int fontSize)\r
- {\r
- this._fontSize = fontSize;\r
- this._has_fontSize = true;\r
- } //-- void setFontSize(int)\r
-\r
- /**\r
- * Sets the value of field 'fontStyle'.\r
- *\r
- * @param fontStyle the value of field 'fontStyle'.\r
- */\r
- public void setFontStyle(int fontStyle)\r
- {\r
- this._fontStyle = fontStyle;\r
- this._has_fontStyle = true;\r
- } //-- void setFontStyle(int)\r
-\r
- /**\r
- * Sets the value of field 'height'.\r
- *\r
- * @param height the value of field 'height'.\r
- */\r
- public void setHeight(int height)\r
- {\r
- this._height = height;\r
- this._has_height = true;\r
- } //-- void setHeight(int)\r
-\r
- /**\r
- * Sets the value of field 'markUnlinked'.\r
- *\r
- * @param markUnlinked the value of field 'markUnlinked'.\r
- */\r
- public void setMarkUnlinked(boolean markUnlinked)\r
- {\r
- this._markUnlinked = markUnlinked;\r
- this._has_markUnlinked = true;\r
- } //-- void setMarkUnlinked(boolean)\r
-\r
- /**\r
- * Sets the value of field 'newick'.\r
- *\r
- * @param newick the value of field 'newick'.\r
- */\r
- public void setNewick(java.lang.String newick)\r
- {\r
- this._newick = newick;\r
- } //-- void setNewick(java.lang.String)\r
-\r
- /**\r
- * Sets the value of field 'showBootstrap'.\r
- *\r
- * @param showBootstrap the value of field 'showBootstrap'.\r
- */\r
- public void setShowBootstrap(boolean showBootstrap)\r
- {\r
- this._showBootstrap = showBootstrap;\r
- this._has_showBootstrap = true;\r
- } //-- void setShowBootstrap(boolean)\r
-\r
- /**\r
- * Sets the value of field 'showDistances'.\r
- *\r
- * @param showDistances the value of field 'showDistances'.\r
- */\r
- public void setShowDistances(boolean showDistances)\r
- {\r
- this._showDistances = showDistances;\r
- this._has_showDistances = true;\r
- } //-- void setShowDistances(boolean)\r
-\r
- /**\r
- * Sets the value of field 'threshold'.\r
- *\r
- * @param threshold the value of field 'threshold'.\r
- */\r
- public void setThreshold(float threshold)\r
- {\r
- this._threshold = threshold;\r
- this._has_threshold = true;\r
- } //-- void setThreshold(float)\r
-\r
- /**\r
- * Sets the value of field 'title'.\r
- *\r
- * @param title the value of field 'title'.\r
- */\r
- public void setTitle(java.lang.String title)\r
- {\r
- this._title = title;\r
- } //-- void setTitle(java.lang.String)\r
-\r
- /**\r
- * Sets the value of field 'width'.\r
- *\r
- * @param width the value of field 'width'.\r
- */\r
- public void setWidth(int width)\r
- {\r
- this._width = width;\r
- this._has_width = true;\r
- } //-- void setWidth(int)\r
-\r
- /**\r
- * Sets the value of field 'xpos'.\r
- *\r
- * @param xpos the value of field 'xpos'.\r
- */\r
- public void setXpos(int xpos)\r
- {\r
- this._xpos = xpos;\r
- this._has_xpos = true;\r
- } //-- void setXpos(int)\r
-\r
- /**\r
- * Sets the value of field 'ypos'.\r
- *\r
- * @param ypos the value of field 'ypos'.\r
- */\r
- public void setYpos(int ypos)\r
- {\r
- this._ypos = ypos;\r
- this._has_ypos = true;\r
- } //-- void setYpos(int)\r
-\r
- /**\r
- * Method unmarshal\r
- *\r
- *\r
- *\r
- * @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException,\r
- org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.schemabinding.version2.Tree) Unmarshaller.unmarshal(jalview.\r
- schemabinding.version2.Tree.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
- /**\r
- * Method validate\r
- *\r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
- Validator();\r
- validator.validate(this);\r
- } //-- void validate()\r
-\r
-}\r
+/*
+ * 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 Tree.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Tree implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * 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 _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 _threshold.
+ */
+ private float _threshold;
+
+ /**
+ * keeps track of state for field: _threshold
+ */
+ private boolean _has_threshold;
+
+ /**
+ * Field _showBootstrap.
+ */
+ private boolean _showBootstrap;
+
+ /**
+ * keeps track of state for field: _showBootstrap
+ */
+ private boolean _has_showBootstrap;
+
+ /**
+ * Field _showDistances.
+ */
+ private boolean _showDistances;
+
+ /**
+ * keeps track of state for field: _showDistances
+ */
+ private boolean _has_showDistances;
+
+ /**
+ * Field _markUnlinked.
+ */
+ private boolean _markUnlinked;
+
+ /**
+ * keeps track of state for field: _markUnlinked
+ */
+ private boolean _has_markUnlinked;
+
+ /**
+ * Field _fitToWindow.
+ */
+ private boolean _fitToWindow;
+
+ /**
+ * keeps track of state for field: _fitToWindow
+ */
+ private boolean _has_fitToWindow;
+
+ /**
+ * Field _currentTree.
+ */
+ private boolean _currentTree;
+
+ /**
+ * keeps track of state for field: _currentTree
+ */
+ private boolean _has_currentTree;
+
+ /**
+ * Tree ID added for binding tree visualization settings to
+ * vamsas document trees in jalview 2.4.1
+ */
+ private java.lang.String _id;
+
+ /**
+ * Field _title.
+ */
+ private java.lang.String _title;
+
+ /**
+ * Field _newick.
+ */
+ private java.lang.String _newick;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Tree() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ */
+ public void deleteCurrentTree(
+ ) {
+ this._has_currentTree= false;
+ }
+
+ /**
+ */
+ public void deleteFitToWindow(
+ ) {
+ this._has_fitToWindow= false;
+ }
+
+ /**
+ */
+ public void deleteFontSize(
+ ) {
+ this._has_fontSize= false;
+ }
+
+ /**
+ */
+ public void deleteFontStyle(
+ ) {
+ this._has_fontStyle= false;
+ }
+
+ /**
+ */
+ public void deleteHeight(
+ ) {
+ this._has_height= false;
+ }
+
+ /**
+ */
+ public void deleteMarkUnlinked(
+ ) {
+ this._has_markUnlinked= false;
+ }
+
+ /**
+ */
+ public void deleteShowBootstrap(
+ ) {
+ this._has_showBootstrap= false;
+ }
+
+ /**
+ */
+ public void deleteShowDistances(
+ ) {
+ this._has_showDistances= false;
+ }
+
+ /**
+ */
+ public void deleteThreshold(
+ ) {
+ this._has_threshold= false;
+ }
+
+ /**
+ */
+ public void deleteWidth(
+ ) {
+ this._has_width= false;
+ }
+
+ /**
+ */
+ public void deleteXpos(
+ ) {
+ this._has_xpos= false;
+ }
+
+ /**
+ */
+ public void deleteYpos(
+ ) {
+ this._has_ypos= false;
+ }
+
+ /**
+ * Returns the value of field 'currentTree'.
+ *
+ * @return the value of field 'CurrentTree'.
+ */
+ public boolean getCurrentTree(
+ ) {
+ return this._currentTree;
+ }
+
+ /**
+ * Returns the value of field 'fitToWindow'.
+ *
+ * @return the value of field 'FitToWindow'.
+ */
+ public boolean getFitToWindow(
+ ) {
+ return this._fitToWindow;
+ }
+
+ /**
+ * 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 'height'.
+ *
+ * @return the value of field 'Height'.
+ */
+ public int getHeight(
+ ) {
+ return this._height;
+ }
+
+ /**
+ * Returns the value of field 'id'. The field 'id' has the
+ * following description: Tree ID added for binding tree
+ * visualization settings to vamsas document trees in jalview
+ * 2.4.1
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId(
+ ) {
+ return this._id;
+ }
+
+ /**
+ * Returns the value of field 'markUnlinked'.
+ *
+ * @return the value of field 'MarkUnlinked'.
+ */
+ public boolean getMarkUnlinked(
+ ) {
+ return this._markUnlinked;
+ }
+
+ /**
+ * Returns the value of field 'newick'.
+ *
+ * @return the value of field 'Newick'.
+ */
+ public java.lang.String getNewick(
+ ) {
+ return this._newick;
+ }
+
+ /**
+ * Returns the value of field 'showBootstrap'.
+ *
+ * @return the value of field 'ShowBootstrap'.
+ */
+ public boolean getShowBootstrap(
+ ) {
+ return this._showBootstrap;
+ }
+
+ /**
+ * Returns the value of field 'showDistances'.
+ *
+ * @return the value of field 'ShowDistances'.
+ */
+ public boolean getShowDistances(
+ ) {
+ return this._showDistances;
+ }
+
+ /**
+ * Returns the value of field 'threshold'.
+ *
+ * @return the value of field 'Threshold'.
+ */
+ public float getThreshold(
+ ) {
+ return this._threshold;
+ }
+
+ /**
+ * 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 'width'.
+ *
+ * @return the value of field 'Width'.
+ */
+ public int getWidth(
+ ) {
+ return this._width;
+ }
+
+ /**
+ * 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 hasCurrentTree.
+ *
+ * @return true if at least one CurrentTree has been added
+ */
+ public boolean hasCurrentTree(
+ ) {
+ return this._has_currentTree;
+ }
+
+ /**
+ * Method hasFitToWindow.
+ *
+ * @return true if at least one FitToWindow has been added
+ */
+ public boolean hasFitToWindow(
+ ) {
+ return this._has_fitToWindow;
+ }
+
+ /**
+ * 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 hasHeight.
+ *
+ * @return true if at least one Height has been added
+ */
+ public boolean hasHeight(
+ ) {
+ return this._has_height;
+ }
+
+ /**
+ * Method hasMarkUnlinked.
+ *
+ * @return true if at least one MarkUnlinked has been added
+ */
+ public boolean hasMarkUnlinked(
+ ) {
+ return this._has_markUnlinked;
+ }
+
+ /**
+ * Method hasShowBootstrap.
+ *
+ * @return true if at least one ShowBootstrap has been added
+ */
+ public boolean hasShowBootstrap(
+ ) {
+ return this._has_showBootstrap;
+ }
+
+ /**
+ * Method hasShowDistances.
+ *
+ * @return true if at least one ShowDistances has been added
+ */
+ public boolean hasShowDistances(
+ ) {
+ return this._has_showDistances;
+ }
+
+ /**
+ * Method hasThreshold.
+ *
+ * @return true if at least one Threshold has been added
+ */
+ public boolean hasThreshold(
+ ) {
+ return this._has_threshold;
+ }
+
+ /**
+ * Method hasWidth.
+ *
+ * @return true if at least one Width has been added
+ */
+ public boolean hasWidth(
+ ) {
+ return this._has_width;
+ }
+
+ /**
+ * 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 'currentTree'.
+ *
+ * @return the value of field 'CurrentTree'.
+ */
+ public boolean isCurrentTree(
+ ) {
+ return this._currentTree;
+ }
+
+ /**
+ * Returns the value of field 'fitToWindow'.
+ *
+ * @return the value of field 'FitToWindow'.
+ */
+ public boolean isFitToWindow(
+ ) {
+ return this._fitToWindow;
+ }
+
+ /**
+ * Returns the value of field 'markUnlinked'.
+ *
+ * @return the value of field 'MarkUnlinked'.
+ */
+ public boolean isMarkUnlinked(
+ ) {
+ return this._markUnlinked;
+ }
+
+ /**
+ * Returns the value of field 'showBootstrap'.
+ *
+ * @return the value of field 'ShowBootstrap'.
+ */
+ public boolean isShowBootstrap(
+ ) {
+ return this._showBootstrap;
+ }
+
+ /**
+ * Returns the value of field 'showDistances'.
+ *
+ * @return the value of field 'ShowDistances'.
+ */
+ public boolean isShowDistances(
+ ) {
+ return this._showDistances;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ *
+ *
+ * @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);
+ }
+
+ /**
+ * Sets the value of field 'currentTree'.
+ *
+ * @param currentTree the value of field 'currentTree'.
+ */
+ public void setCurrentTree(
+ final boolean currentTree) {
+ this._currentTree = currentTree;
+ this._has_currentTree = true;
+ }
+
+ /**
+ * Sets the value of field 'fitToWindow'.
+ *
+ * @param fitToWindow the value of field 'fitToWindow'.
+ */
+ public void setFitToWindow(
+ final boolean fitToWindow) {
+ this._fitToWindow = fitToWindow;
+ this._has_fitToWindow = 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 'height'.
+ *
+ * @param height the value of field 'height'.
+ */
+ public void setHeight(
+ final int height) {
+ this._height = height;
+ this._has_height = true;
+ }
+
+ /**
+ * Sets the value of field 'id'. The field 'id' has the
+ * following description: Tree ID added for binding tree
+ * visualization settings to vamsas document trees in jalview
+ * 2.4.1
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(
+ final java.lang.String id) {
+ this._id = id;
+ }
+
+ /**
+ * Sets the value of field 'markUnlinked'.
+ *
+ * @param markUnlinked the value of field 'markUnlinked'.
+ */
+ public void setMarkUnlinked(
+ final boolean markUnlinked) {
+ this._markUnlinked = markUnlinked;
+ this._has_markUnlinked = true;
+ }
+
+ /**
+ * Sets the value of field 'newick'.
+ *
+ * @param newick the value of field 'newick'.
+ */
+ public void setNewick(
+ final java.lang.String newick) {
+ this._newick = newick;
+ }
+
+ /**
+ * Sets the value of field 'showBootstrap'.
+ *
+ * @param showBootstrap the value of field 'showBootstrap'.
+ */
+ public void setShowBootstrap(
+ final boolean showBootstrap) {
+ this._showBootstrap = showBootstrap;
+ this._has_showBootstrap = true;
+ }
+
+ /**
+ * Sets the value of field 'showDistances'.
+ *
+ * @param showDistances the value of field 'showDistances'.
+ */
+ public void setShowDistances(
+ final boolean showDistances) {
+ this._showDistances = showDistances;
+ this._has_showDistances = true;
+ }
+
+ /**
+ * Sets the value of field 'threshold'.
+ *
+ * @param threshold the value of field 'threshold'.
+ */
+ public void setThreshold(
+ final float threshold) {
+ this._threshold = threshold;
+ this._has_threshold = 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 '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 '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.Tree
+ */
+ public static jalview.schemabinding.version2.Tree unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.schemabinding.version2.Tree) Unmarshaller.unmarshal(jalview.schemabinding.version2.Tree.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