X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FTree.java;h=f9d7c13bf10b2a51ed8dc6dd62992c7e7aaab670;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=96b2e18602ce4c019ad4e84cccfc65598f3c36fc;hpb=48df59aa393e03aa7269b2df662ac1b8d58cbb25;p=jalview.git
diff --git a/src/jalview/schemabinding/version2/Tree.java b/src/jalview/schemabinding/version2/Tree.java
old mode 100755
new mode 100644
index 96b2e18..f9d7c13
--- a/src/jalview/schemabinding/version2/Tree.java
+++ b/src/jalview/schemabinding/version2/Tree.java
@@ -1,835 +1,889 @@
-/*
- * This class was automatically generated with
- * Castor 0.9.6, using an XML
- * Schema.
- * $Id$
- */
-
-package jalview.schemabinding.version2;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
-
-/**
- * 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;
-
- /**
- * Field _title
- */
- private java.lang.String _title;
-
- /**
- * Field _newick
- */
- private java.lang.String _newick;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Tree() {
- super();
- } //-- jalview.schemabinding.version2.Tree()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method deleteCurrentTree
- *
- */
- public void deleteCurrentTree()
- {
- this._has_currentTree= false;
- } //-- void deleteCurrentTree()
-
- /**
- * Method deleteFitToWindow
- *
- */
- public void deleteFitToWindow()
- {
- this._has_fitToWindow= false;
- } //-- void deleteFitToWindow()
-
- /**
- * Method deleteFontSize
- *
- */
- public void deleteFontSize()
- {
- this._has_fontSize= false;
- } //-- void deleteFontSize()
-
- /**
- * Method deleteFontStyle
- *
- */
- public void deleteFontStyle()
- {
- this._has_fontStyle= false;
- } //-- void deleteFontStyle()
-
- /**
- * Method deleteHeight
- *
- */
- public void deleteHeight()
- {
- this._has_height= false;
- } //-- void deleteHeight()
-
- /**
- * Method deleteMarkUnlinked
- *
- */
- public void deleteMarkUnlinked()
- {
- this._has_markUnlinked= false;
- } //-- void deleteMarkUnlinked()
-
- /**
- * Method deleteShowBootstrap
- *
- */
- public void deleteShowBootstrap()
- {
- this._has_showBootstrap= false;
- } //-- void deleteShowBootstrap()
-
- /**
- * Method deleteShowDistances
- *
- */
- public void deleteShowDistances()
- {
- this._has_showDistances= false;
- } //-- void deleteShowDistances()
-
- /**
- * Method deleteThreshold
- *
- */
- public void deleteThreshold()
- {
- this._has_threshold= false;
- } //-- void deleteThreshold()
-
- /**
- * Method deleteWidth
- *
- */
- public void deleteWidth()
- {
- this._has_width= false;
- } //-- void deleteWidth()
-
- /**
- * Method deleteXpos
- *
- */
- public void deleteXpos()
- {
- this._has_xpos= false;
- } //-- void deleteXpos()
-
- /**
- * Method deleteYpos
- *
- */
- public void deleteYpos()
- {
- this._has_ypos= false;
- } //-- void deleteYpos()
-
- /**
- * Returns the value of field 'currentTree'.
- *
- * @return boolean
- * @return the value of field 'currentTree'.
- */
- public boolean getCurrentTree()
- {
- return this._currentTree;
- } //-- boolean getCurrentTree()
-
- /**
- * Returns the value of field 'fitToWindow'.
- *
- * @return boolean
- * @return the value of field 'fitToWindow'.
- */
- public boolean getFitToWindow()
- {
- return this._fitToWindow;
- } //-- boolean getFitToWindow()
-
- /**
- * Returns the value of field 'fontName'.
- *
- * @return String
- * @return the value of field 'fontName'.
- */
- public java.lang.String getFontName()
- {
- return this._fontName;
- } //-- java.lang.String getFontName()
-
- /**
- * Returns the value of field 'fontSize'.
- *
- * @return int
- * @return the value of field 'fontSize'.
- */
- public int getFontSize()
- {
- return this._fontSize;
- } //-- int getFontSize()
-
- /**
- * Returns the value of field 'fontStyle'.
- *
- * @return int
- * @return the value of field 'fontStyle'.
- */
- public int getFontStyle()
- {
- return this._fontStyle;
- } //-- int getFontStyle()
-
- /**
- * Returns the value of field 'height'.
- *
- * @return int
- * @return the value of field 'height'.
- */
- public int getHeight()
- {
- return this._height;
- } //-- int getHeight()
-
- /**
- * Returns the value of field 'markUnlinked'.
- *
- * @return boolean
- * @return the value of field 'markUnlinked'.
- */
- public boolean getMarkUnlinked()
- {
- return this._markUnlinked;
- } //-- boolean getMarkUnlinked()
-
- /**
- * Returns the value of field 'newick'.
- *
- * @return String
- * @return the value of field 'newick'.
- */
- public java.lang.String getNewick()
- {
- return this._newick;
- } //-- java.lang.String getNewick()
-
- /**
- * Returns the value of field 'showBootstrap'.
- *
- * @return boolean
- * @return the value of field 'showBootstrap'.
- */
- public boolean getShowBootstrap()
- {
- return this._showBootstrap;
- } //-- boolean getShowBootstrap()
-
- /**
- * Returns the value of field 'showDistances'.
- *
- * @return boolean
- * @return the value of field 'showDistances'.
- */
- public boolean getShowDistances()
- {
- return this._showDistances;
- } //-- boolean getShowDistances()
-
- /**
- * Returns the value of field 'threshold'.
- *
- * @return float
- * @return the value of field 'threshold'.
- */
- public float getThreshold()
- {
- return this._threshold;
- } //-- float getThreshold()
-
- /**
- * Returns the value of field 'title'.
- *
- * @return String
- * @return the value of field 'title'.
- */
- public java.lang.String getTitle()
- {
- return this._title;
- } //-- java.lang.String getTitle()
-
- /**
- * Returns the value of field 'width'.
- *
- * @return int
- * @return the value of field 'width'.
- */
- public int getWidth()
- {
- return this._width;
- } //-- int getWidth()
-
- /**
- * Returns the value of field 'xpos'.
- *
- * @return int
- * @return the value of field 'xpos'.
- */
- public int getXpos()
- {
- return this._xpos;
- } //-- int getXpos()
-
- /**
- * Returns the value of field 'ypos'.
- *
- * @return int
- * @return the value of field 'ypos'.
- */
- public int getYpos()
- {
- return this._ypos;
- } //-- int getYpos()
-
- /**
- * Method hasCurrentTree
- *
- *
- *
- * @return boolean
- */
- public boolean hasCurrentTree()
- {
- return this._has_currentTree;
- } //-- boolean hasCurrentTree()
-
- /**
- * Method hasFitToWindow
- *
- *
- *
- * @return boolean
- */
- public boolean hasFitToWindow()
- {
- return this._has_fitToWindow;
- } //-- boolean hasFitToWindow()
-
- /**
- * Method hasFontSize
- *
- *
- *
- * @return boolean
- */
- public boolean hasFontSize()
- {
- return this._has_fontSize;
- } //-- boolean hasFontSize()
-
- /**
- * Method hasFontStyle
- *
- *
- *
- * @return boolean
- */
- public boolean hasFontStyle()
- {
- return this._has_fontStyle;
- } //-- boolean hasFontStyle()
-
- /**
- * Method hasHeight
- *
- *
- *
- * @return boolean
- */
- public boolean hasHeight()
- {
- return this._has_height;
- } //-- boolean hasHeight()
-
- /**
- * Method hasMarkUnlinked
- *
- *
- *
- * @return boolean
- */
- public boolean hasMarkUnlinked()
- {
- return this._has_markUnlinked;
- } //-- boolean hasMarkUnlinked()
-
- /**
- * Method hasShowBootstrap
- *
- *
- *
- * @return boolean
- */
- public boolean hasShowBootstrap()
- {
- return this._has_showBootstrap;
- } //-- boolean hasShowBootstrap()
-
- /**
- * Method hasShowDistances
- *
- *
- *
- * @return boolean
- */
- public boolean hasShowDistances()
- {
- return this._has_showDistances;
- } //-- boolean hasShowDistances()
-
- /**
- * Method hasThreshold
- *
- *
- *
- * @return boolean
- */
- public boolean hasThreshold()
- {
- return this._has_threshold;
- } //-- boolean hasThreshold()
-
- /**
- * Method hasWidth
- *
- *
- *
- * @return boolean
- */
- public boolean hasWidth()
- {
- return this._has_width;
- } //-- boolean hasWidth()
-
- /**
- * Method hasXpos
- *
- *
- *
- * @return boolean
- */
- public boolean hasXpos()
- {
- return this._has_xpos;
- } //-- boolean hasXpos()
-
- /**
- * Method hasYpos
- *
- *
- *
- * @return boolean
- */
- public boolean hasYpos()
- {
- return this._has_ypos;
- } //-- boolean hasYpos()
-
- /**
- * Method isValid
- *
- *
- *
- * @return boolean
- */
- public boolean isValid()
- {
- try {
- validate();
- }
- catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- } //-- boolean isValid()
-
- /**
- * Method marshal
- *
- *
- *
- * @param out
- */
- public void marshal(java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
- Marshaller.marshal(this, out);
- } //-- void marshal(java.io.Writer)
-
- /**
- * Method marshal
- *
- *
- *
- * @param handler
- */
- public void marshal(org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
- Marshaller.marshal(this, handler);
- } //-- void marshal(org.xml.sax.ContentHandler)
-
- /**
- * Sets the value of field 'currentTree'.
- *
- * @param currentTree the value of field 'currentTree'.
- */
- public void setCurrentTree(boolean currentTree)
- {
- this._currentTree = currentTree;
- this._has_currentTree = true;
- } //-- void setCurrentTree(boolean)
-
- /**
- * Sets the value of field 'fitToWindow'.
- *
- * @param fitToWindow the value of field 'fitToWindow'.
- */
- public void setFitToWindow(boolean fitToWindow)
- {
- this._fitToWindow = fitToWindow;
- this._has_fitToWindow = true;
- } //-- void setFitToWindow(boolean)
-
- /**
- * Sets the value of field 'fontName'.
- *
- * @param fontName the value of field 'fontName'.
- */
- public void setFontName(java.lang.String fontName)
- {
- this._fontName = fontName;
- } //-- void setFontName(java.lang.String)
-
- /**
- * Sets the value of field 'fontSize'.
- *
- * @param fontSize the value of field 'fontSize'.
- */
- public void setFontSize(int fontSize)
- {
- this._fontSize = fontSize;
- this._has_fontSize = true;
- } //-- void setFontSize(int)
-
- /**
- * Sets the value of field 'fontStyle'.
- *
- * @param fontStyle the value of field 'fontStyle'.
- */
- public void setFontStyle(int fontStyle)
- {
- this._fontStyle = fontStyle;
- this._has_fontStyle = true;
- } //-- void setFontStyle(int)
-
- /**
- * Sets the value of field 'height'.
- *
- * @param height the value of field 'height'.
- */
- public void setHeight(int height)
- {
- this._height = height;
- this._has_height = true;
- } //-- void setHeight(int)
-
- /**
- * Sets the value of field 'markUnlinked'.
- *
- * @param markUnlinked the value of field 'markUnlinked'.
- */
- public void setMarkUnlinked(boolean markUnlinked)
- {
- this._markUnlinked = markUnlinked;
- this._has_markUnlinked = true;
- } //-- void setMarkUnlinked(boolean)
-
- /**
- * Sets the value of field 'newick'.
- *
- * @param newick the value of field 'newick'.
- */
- public void setNewick(java.lang.String newick)
- {
- this._newick = newick;
- } //-- void setNewick(java.lang.String)
-
- /**
- * Sets the value of field 'showBootstrap'.
- *
- * @param showBootstrap the value of field 'showBootstrap'.
- */
- public void setShowBootstrap(boolean showBootstrap)
- {
- this._showBootstrap = showBootstrap;
- this._has_showBootstrap = true;
- } //-- void setShowBootstrap(boolean)
-
- /**
- * Sets the value of field 'showDistances'.
- *
- * @param showDistances the value of field 'showDistances'.
- */
- public void setShowDistances(boolean showDistances)
- {
- this._showDistances = showDistances;
- this._has_showDistances = true;
- } //-- void setShowDistances(boolean)
-
- /**
- * Sets the value of field 'threshold'.
- *
- * @param threshold the value of field 'threshold'.
- */
- public void setThreshold(float threshold)
- {
- this._threshold = threshold;
- this._has_threshold = true;
- } //-- void setThreshold(float)
-
- /**
- * Sets the value of field 'title'.
- *
- * @param title the value of field 'title'.
- */
- public void setTitle(java.lang.String title)
- {
- this._title = title;
- } //-- void setTitle(java.lang.String)
-
- /**
- * Sets the value of field 'width'.
- *
- * @param width the value of field 'width'.
- */
- public void setWidth(int width)
- {
- this._width = width;
- this._has_width = true;
- } //-- void setWidth(int)
-
- /**
- * Sets the value of field 'xpos'.
- *
- * @param xpos the value of field 'xpos'.
- */
- public void setXpos(int xpos)
- {
- this._xpos = xpos;
- this._has_xpos = true;
- } //-- void setXpos(int)
-
- /**
- * Sets the value of field 'ypos'.
- *
- * @param ypos the value of field 'ypos'.
- */
- public void setYpos(int ypos)
- {
- this._ypos = ypos;
- this._has_ypos = true;
- } //-- void setYpos(int)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return Object
- */
- public static java.lang.Object unmarshal(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);
- } //-- java.lang.Object unmarshal(java.io.Reader)
-
- /**
- * Method validate
- *
- */
- public void validate()
- throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- } //-- void validate()
-
-}
+/*
+ * 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 .
+ * 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);
+ }
+
+}