-/*\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 java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class Tree.\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
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Tree() {\r
- super();\r
- } //-- jalview.schemabinding.version2.Tree()\r
-\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
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * 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, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.schemabinding.version2.Tree) Unmarshaller.unmarshal(jalview.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.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+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 _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 _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 _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