/*******************************************************************************
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
* Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* 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 .
*******************************************************************************/
/*
* This class was automatically generated with
* Castor 1.1, using an XML
* Schema.
* $Id$
*/
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);
}
}