X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FTree.java;h=aafef57311f03a4179444081507e9f3f39c153c2;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=7fd6238327a12476dc4a921abeffe35655768b1a;hpb=77441185ddcb1e85b0de8336ce513b2130c6b98b;p=jalview.git diff --git a/src/jalview/schemabinding/version2/Tree.java b/src/jalview/schemabinding/version2/Tree.java index 7fd6238..aafef57 100644 --- a/src/jalview/schemabinding/version2/Tree.java +++ b/src/jalview/schemabinding/version2/Tree.java @@ -1,14 +1,27 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) + * 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 -/ +//---------------------------------/ +//- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -19,838 +32,860 @@ import org.exolab.castor.xml.Unmarshaller; * * @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); - } +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); + } }