/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
* \r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
*/\r
package jalview.schemabinding.version2;\r
\r
-// ---------------------------------/\r
-// - Imported classes and packages -/\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
* @version $Revision$ $Date$\r
*/\r
-public class Tree 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
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- */\r
- public void deleteCurrentTree()\r
- {\r
- this._has_currentTree = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteFitToWindow()\r
- {\r
- this._has_fitToWindow = 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 deleteHeight()\r
- {\r
- this._has_height = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteMarkUnlinked()\r
- {\r
- this._has_markUnlinked = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteShowBootstrap()\r
- {\r
- this._has_showBootstrap = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteShowDistances()\r
- {\r
- this._has_showDistances = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteThreshold()\r
- {\r
- this._has_threshold = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteWidth()\r
- {\r
- this._has_width = 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
- * Returns the value of field 'currentTree'.\r
- * \r
- * @return the value of field 'CurrentTree'.\r
- */\r
- public boolean getCurrentTree()\r
- {\r
- return this._currentTree;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'fitToWindow'.\r
- * \r
- * @return the value of field 'FitToWindow'.\r
- */\r
- public boolean getFitToWindow()\r
- {\r
- return this._fitToWindow;\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 'height'.\r
- * \r
- * @return the value of field 'Height'.\r
- */\r
- public int getHeight()\r
- {\r
- return this._height;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'markUnlinked'.\r
- * \r
- * @return the value of field 'MarkUnlinked'.\r
- */\r
- public boolean getMarkUnlinked()\r
- {\r
- return this._markUnlinked;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'newick'.\r
- * \r
- * @return the value of field 'Newick'.\r
- */\r
- public java.lang.String getNewick()\r
- {\r
- return this._newick;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showBootstrap'.\r
- * \r
- * @return the value of field 'ShowBootstrap'.\r
- */\r
- public boolean getShowBootstrap()\r
- {\r
- return this._showBootstrap;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showDistances'.\r
- * \r
- * @return the value of field 'ShowDistances'.\r
- */\r
- public boolean getShowDistances()\r
- {\r
- return this._showDistances;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'threshold'.\r
- * \r
- * @return the value of field 'Threshold'.\r
- */\r
- public float getThreshold()\r
- {\r
- return this._threshold;\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 '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 '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 hasCurrentTree.\r
- * \r
- * @return true if at least one CurrentTree has been added\r
- */\r
- public boolean hasCurrentTree()\r
- {\r
- return this._has_currentTree;\r
- }\r
-\r
- /**\r
- * Method hasFitToWindow.\r
- * \r
- * @return true if at least one FitToWindow has been added\r
- */\r
- public boolean hasFitToWindow()\r
- {\r
- return this._has_fitToWindow;\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 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 hasMarkUnlinked.\r
- * \r
- * @return true if at least one MarkUnlinked has been added\r
- */\r
- public boolean hasMarkUnlinked()\r
- {\r
- return this._has_markUnlinked;\r
- }\r
-\r
- /**\r
- * Method hasShowBootstrap.\r
- * \r
- * @return true if at least one ShowBootstrap has been added\r
- */\r
- public boolean hasShowBootstrap()\r
- {\r
- return this._has_showBootstrap;\r
- }\r
-\r
- /**\r
- * Method hasShowDistances.\r
- * \r
- * @return true if at least one ShowDistances has been added\r
- */\r
- public boolean hasShowDistances()\r
- {\r
- return this._has_showDistances;\r
- }\r
-\r
- /**\r
- * Method hasThreshold.\r
- * \r
- * @return true if at least one Threshold has been added\r
- */\r
- public boolean hasThreshold()\r
- {\r
- return this._has_threshold;\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 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 'currentTree'.\r
- * \r
- * @return the value of field 'CurrentTree'.\r
- */\r
- public boolean isCurrentTree()\r
- {\r
- return this._currentTree;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'fitToWindow'.\r
- * \r
- * @return the value of field 'FitToWindow'.\r
- */\r
- public boolean isFitToWindow()\r
- {\r
- return this._fitToWindow;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'markUnlinked'.\r
- * \r
- * @return the value of field 'MarkUnlinked'.\r
- */\r
- public boolean isMarkUnlinked()\r
- {\r
- return this._markUnlinked;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showBootstrap'.\r
- * \r
- * @return the value of field 'ShowBootstrap'.\r
- */\r
- public boolean isShowBootstrap()\r
- {\r
- return this._showBootstrap;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showDistances'.\r
- * \r
- * @return the value of field 'ShowDistances'.\r
- */\r
- public boolean isShowDistances()\r
- {\r
- return this._showDistances;\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
- * \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\r
- * 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\r
- * 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
- * Sets the value of field 'currentTree'.\r
- * \r
- * @param currentTree\r
- * the value of field 'currentTree'.\r
- */\r
- public void setCurrentTree(final boolean currentTree)\r
- {\r
- this._currentTree = currentTree;\r
- this._has_currentTree = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'fitToWindow'.\r
- * \r
- * @param fitToWindow\r
- * the value of field 'fitToWindow'.\r
- */\r
- public void setFitToWindow(final boolean fitToWindow)\r
- {\r
- this._fitToWindow = fitToWindow;\r
- this._has_fitToWindow = 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 '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
- * Sets the value of field 'markUnlinked'.\r
- * \r
- * @param markUnlinked\r
- * the value of field 'markUnlinked'.\r
- */\r
- public void setMarkUnlinked(final boolean markUnlinked)\r
- {\r
- this._markUnlinked = markUnlinked;\r
- this._has_markUnlinked = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'newick'.\r
- * \r
- * @param newick\r
- * the value of field 'newick'.\r
- */\r
- public void setNewick(final java.lang.String newick)\r
- {\r
- this._newick = newick;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showBootstrap'.\r
- * \r
- * @param showBootstrap\r
- * the value of field 'showBootstrap'.\r
- */\r
- public void setShowBootstrap(final boolean showBootstrap)\r
- {\r
- this._showBootstrap = showBootstrap;\r
- this._has_showBootstrap = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showDistances'.\r
- * \r
- * @param showDistances\r
- * the value of field 'showDistances'.\r
- */\r
- public void setShowDistances(final boolean showDistances)\r
- {\r
- this._showDistances = showDistances;\r
- this._has_showDistances = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'threshold'.\r
- * \r
- * @param threshold\r
- * the value of field 'threshold'.\r
- */\r
- public void setThreshold(final float threshold)\r
- {\r
- this._threshold = threshold;\r
- this._has_threshold = 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 '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 '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\r
- * schema\r
- * @return the unmarshaled jalview.schemabinding.version2.Tree\r
- */\r
- public static jalview.schemabinding.version2.Tree 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.Tree) Unmarshaller.unmarshal(\r
- jalview.schemabinding.version2.Tree.class, reader);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the\r
- * 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
+public class Tree 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
+ * Tree ID added for binding tree visualization settings to\r
+ * vamsas document trees in jalview 2.4.1\r
+ */\r
+ private java.lang.String _id;\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
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Tree() {\r
+ super();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ */\r
+ public void deleteCurrentTree(\r
+ ) {\r
+ this._has_currentTree= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteFitToWindow(\r
+ ) {\r
+ this._has_fitToWindow= 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 deleteHeight(\r
+ ) {\r
+ this._has_height= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteMarkUnlinked(\r
+ ) {\r
+ this._has_markUnlinked= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowBootstrap(\r
+ ) {\r
+ this._has_showBootstrap= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowDistances(\r
+ ) {\r
+ this._has_showDistances= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteThreshold(\r
+ ) {\r
+ this._has_threshold= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteWidth(\r
+ ) {\r
+ this._has_width= 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
+ * Returns the value of field 'currentTree'.\r
+ * \r
+ * @return the value of field 'CurrentTree'.\r
+ */\r
+ public boolean getCurrentTree(\r
+ ) {\r
+ return this._currentTree;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'fitToWindow'.\r
+ * \r
+ * @return the value of field 'FitToWindow'.\r
+ */\r
+ public boolean getFitToWindow(\r
+ ) {\r
+ return this._fitToWindow;\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 'height'.\r
+ * \r
+ * @return the value of field 'Height'.\r
+ */\r
+ public int getHeight(\r
+ ) {\r
+ return this._height;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'id'. The field 'id' has the\r
+ * following description: Tree ID added for binding tree\r
+ * visualization settings to vamsas document trees in jalview\r
+ * 2.4.1\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 'markUnlinked'.\r
+ * \r
+ * @return the value of field 'MarkUnlinked'.\r
+ */\r
+ public boolean getMarkUnlinked(\r
+ ) {\r
+ return this._markUnlinked;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'newick'.\r
+ * \r
+ * @return the value of field 'Newick'.\r
+ */\r
+ public java.lang.String getNewick(\r
+ ) {\r
+ return this._newick;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showBootstrap'.\r
+ * \r
+ * @return the value of field 'ShowBootstrap'.\r
+ */\r
+ public boolean getShowBootstrap(\r
+ ) {\r
+ return this._showBootstrap;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showDistances'.\r
+ * \r
+ * @return the value of field 'ShowDistances'.\r
+ */\r
+ public boolean getShowDistances(\r
+ ) {\r
+ return this._showDistances;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'threshold'.\r
+ * \r
+ * @return the value of field 'Threshold'.\r
+ */\r
+ public float getThreshold(\r
+ ) {\r
+ return this._threshold;\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 '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 '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 hasCurrentTree.\r
+ * \r
+ * @return true if at least one CurrentTree has been added\r
+ */\r
+ public boolean hasCurrentTree(\r
+ ) {\r
+ return this._has_currentTree;\r
+ }\r
+\r
+ /**\r
+ * Method hasFitToWindow.\r
+ * \r
+ * @return true if at least one FitToWindow has been added\r
+ */\r
+ public boolean hasFitToWindow(\r
+ ) {\r
+ return this._has_fitToWindow;\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 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 hasMarkUnlinked.\r
+ * \r
+ * @return true if at least one MarkUnlinked has been added\r
+ */\r
+ public boolean hasMarkUnlinked(\r
+ ) {\r
+ return this._has_markUnlinked;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowBootstrap.\r
+ * \r
+ * @return true if at least one ShowBootstrap has been added\r
+ */\r
+ public boolean hasShowBootstrap(\r
+ ) {\r
+ return this._has_showBootstrap;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowDistances.\r
+ * \r
+ * @return true if at least one ShowDistances has been added\r
+ */\r
+ public boolean hasShowDistances(\r
+ ) {\r
+ return this._has_showDistances;\r
+ }\r
+\r
+ /**\r
+ * Method hasThreshold.\r
+ * \r
+ * @return true if at least one Threshold has been added\r
+ */\r
+ public boolean hasThreshold(\r
+ ) {\r
+ return this._has_threshold;\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 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 'currentTree'.\r
+ * \r
+ * @return the value of field 'CurrentTree'.\r
+ */\r
+ public boolean isCurrentTree(\r
+ ) {\r
+ return this._currentTree;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'fitToWindow'.\r
+ * \r
+ * @return the value of field 'FitToWindow'.\r
+ */\r
+ public boolean isFitToWindow(\r
+ ) {\r
+ return this._fitToWindow;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'markUnlinked'.\r
+ * \r
+ * @return the value of field 'MarkUnlinked'.\r
+ */\r
+ public boolean isMarkUnlinked(\r
+ ) {\r
+ return this._markUnlinked;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showBootstrap'.\r
+ * \r
+ * @return the value of field 'ShowBootstrap'.\r
+ */\r
+ public boolean isShowBootstrap(\r
+ ) {\r
+ return this._showBootstrap;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showDistances'.\r
+ * \r
+ * @return the value of field 'ShowDistances'.\r
+ */\r
+ public boolean isShowDistances(\r
+ ) {\r
+ return this._showDistances;\r
+ }\r
+\r
+ /**\r
+ * Method isValid.\r
+ * \r
+ * @return true if this object is valid according to the schema\r
+ */\r
+ public boolean isValid(\r
+ ) {\r
+ try {\r
+ validate();\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\r
+ }\r
+ return true;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param out\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ Marshaller.marshal(this, out);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param handler\r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ */\r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ Marshaller.marshal(this, handler);\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'currentTree'.\r
+ * \r
+ * @param currentTree the value of field 'currentTree'.\r
+ */\r
+ public void setCurrentTree(\r
+ final boolean currentTree) {\r
+ this._currentTree = currentTree;\r
+ this._has_currentTree = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'fitToWindow'.\r
+ * \r
+ * @param fitToWindow the value of field 'fitToWindow'.\r
+ */\r
+ public void setFitToWindow(\r
+ final boolean fitToWindow) {\r
+ this._fitToWindow = fitToWindow;\r
+ this._has_fitToWindow = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'fontName'.\r
+ * \r
+ * @param fontName the value of field 'fontName'.\r
+ */\r
+ public void setFontName(\r
+ final java.lang.String fontName) {\r
+ this._fontName = fontName;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'fontSize'.\r
+ * \r
+ * @param fontSize the value of field 'fontSize'.\r
+ */\r
+ public void setFontSize(\r
+ final int fontSize) {\r
+ this._fontSize = fontSize;\r
+ this._has_fontSize = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'fontStyle'.\r
+ * \r
+ * @param fontStyle the value of field 'fontStyle'.\r
+ */\r
+ public void setFontStyle(\r
+ final int fontStyle) {\r
+ this._fontStyle = fontStyle;\r
+ this._has_fontStyle = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'height'.\r
+ * \r
+ * @param height the value of field 'height'.\r
+ */\r
+ public void setHeight(\r
+ final int height) {\r
+ this._height = height;\r
+ this._has_height = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'id'. The field 'id' has the\r
+ * following description: Tree ID added for binding tree\r
+ * visualization settings to vamsas document trees in jalview\r
+ * 2.4.1\r
+ * \r
+ * @param id the value of field 'id'.\r
+ */\r
+ public void setId(\r
+ final java.lang.String id) {\r
+ this._id = id;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'markUnlinked'.\r
+ * \r
+ * @param markUnlinked the value of field 'markUnlinked'.\r
+ */\r
+ public void setMarkUnlinked(\r
+ final boolean markUnlinked) {\r
+ this._markUnlinked = markUnlinked;\r
+ this._has_markUnlinked = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'newick'.\r
+ * \r
+ * @param newick the value of field 'newick'.\r
+ */\r
+ public void setNewick(\r
+ final java.lang.String newick) {\r
+ this._newick = newick;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showBootstrap'.\r
+ * \r
+ * @param showBootstrap the value of field 'showBootstrap'.\r
+ */\r
+ public void setShowBootstrap(\r
+ final boolean showBootstrap) {\r
+ this._showBootstrap = showBootstrap;\r
+ this._has_showBootstrap = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showDistances'.\r
+ * \r
+ * @param showDistances the value of field 'showDistances'.\r
+ */\r
+ public void setShowDistances(\r
+ final boolean showDistances) {\r
+ this._showDistances = showDistances;\r
+ this._has_showDistances = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'threshold'.\r
+ * \r
+ * @param threshold the value of field 'threshold'.\r
+ */\r
+ public void setThreshold(\r
+ final float threshold) {\r
+ this._threshold = threshold;\r
+ this._has_threshold = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'title'.\r
+ * \r
+ * @param title the value of field 'title'.\r
+ */\r
+ public void setTitle(\r
+ final java.lang.String title) {\r
+ this._title = title;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'width'.\r
+ * \r
+ * @param width the value of field 'width'.\r
+ */\r
+ public void setWidth(\r
+ final int width) {\r
+ this._width = width;\r
+ this._has_width = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'xpos'.\r
+ * \r
+ * @param xpos the value of field 'xpos'.\r
+ */\r
+ public void setXpos(\r
+ final int xpos) {\r
+ this._xpos = xpos;\r
+ this._has_xpos = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'ypos'.\r
+ * \r
+ * @param ypos the value of field 'ypos'.\r
+ */\r
+ public void setYpos(\r
+ final int ypos) {\r
+ this._ypos = ypos;\r
+ this._has_ypos = true;\r
+ }\r
+\r
+ /**\r
+ * Method unmarshal.\r
+ * \r
+ * @param reader\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled jalview.schemabinding.version2.Tree\r
+ */\r
+ public static jalview.schemabinding.version2.Tree unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.Tree) Unmarshaller.unmarshal(jalview.schemabinding.version2.Tree.class, reader);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ }\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff