-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package jalview.schemabinding.version2;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\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
- }\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
- 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 '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
+/*
+ * 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