X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FTree.java;h=94922ac051dc9a727c297bcac02cd21f001438cb;hb=76389b07e78f92b6db0aeaf2f964d9dcb6671543;hp=9fc63d24fb44e736c8a5a86c5a0df69771d9b384;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git diff --git a/src/jalview/binding/Tree.java b/src/jalview/binding/Tree.java index 9fc63d2..94922ac 100755 --- a/src/jalview/binding/Tree.java +++ b/src/jalview/binding/Tree.java @@ -1,102 +1,102 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ -package jalview.binding; - -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; +package jalview.binding; + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ -//- 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 -/ +public class Tree implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ //--------------------------/ /** - * Field _title + * Field _width */ - private java.lang.String _title; + private int _width; /** - * Field _currentTree + * keeps track of state for field: _width */ - private boolean _currentTree; + private boolean _has_width; /** - * keeps track of state for field: _currentTree + * Field _height */ - private boolean _has_currentTree; + private int _height; /** - * Field _fitToWindow + * keeps track of state for field: _height */ - private boolean _fitToWindow; + private boolean _has_height; /** - * keeps track of state for field: _fitToWindow + * Field _xpos */ - private boolean _has_fitToWindow; + private int _xpos; /** - * Field _showDistances + * keeps track of state for field: _xpos */ - private boolean _showDistances; + private boolean _has_xpos; /** - * keeps track of state for field: _showDistances + * Field _ypos */ - private boolean _has_showDistances; + private int _ypos; /** - * Field _showBootstrap + * keeps track of state for field: _ypos */ - private boolean _showBootstrap; + private boolean _has_ypos; /** - * keeps track of state for field: _showBootstrap + * Field _fontName */ - private boolean _has_showBootstrap; + private java.lang.String _fontName; /** - * Field _markUnlinked + * Field _fontSize */ - private boolean _markUnlinked; + private int _fontSize; /** - * keeps track of state for field: _markUnlinked + * keeps track of state for field: _fontSize */ - private boolean _has_markUnlinked; + private boolean _has_fontSize; /** - * Field _fontSize + * Field _fontStyle */ - private int _fontSize; + private int _fontStyle; /** - * keeps track of state for field: _fontSize + * keeps track of state for field: _fontStyle */ - private boolean _has_fontSize; + private boolean _has_fontStyle; /** * Field _threshold @@ -109,753 +109,727 @@ public class Tree implements java.io.Serializable private boolean _has_threshold; /** - * Field _xpos + * Field _showBootstrap */ - private int _xpos; + private boolean _showBootstrap; /** - * keeps track of state for field: _xpos + * keeps track of state for field: _showBootstrap */ - private boolean _has_xpos; + private boolean _has_showBootstrap; /** - * Field _ypos + * Field _showDistances */ - private int _ypos; + private boolean _showDistances; /** - * keeps track of state for field: _ypos + * keeps track of state for field: _showDistances */ - private boolean _has_ypos; + private boolean _has_showDistances; /** - * Field _width + * Field _markUnlinked */ - private int _width; + private boolean _markUnlinked; /** - * keeps track of state for field: _width + * keeps track of state for field: _markUnlinked */ - private boolean _has_width; + private boolean _has_markUnlinked; /** - * Field _height + * Field _fitToWindow */ - private int _height; + private boolean _fitToWindow; /** - * keeps track of state for field: _height + * keeps track of state for field: _fitToWindow */ - private boolean _has_height; + 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 -/ //----------------/ - //- Constructors -/ - //----------------/ - public Tree() - { + + public Tree() { super(); - } + } //-- jalview.binding.Tree() - //-- jalview.binding.Tree() + + //-----------/ + //- Methods -/ //-----------/ /** - * DOCUMENT ME! + * Method deleteCurrentTree + * */ public void deleteCurrentTree() { - this._has_currentTree = false; - } - - //-- void deleteCurrentTree() + this._has_currentTree= false; + } //-- void deleteCurrentTree() /** * Method deleteFitToWindow - * + * */ public void deleteFitToWindow() { - this._has_fitToWindow = false; - } - - //-- void deleteFitToWindow() + this._has_fitToWindow= false; + } //-- void deleteFitToWindow() /** * Method deleteFontSize - * + * */ public void deleteFontSize() { - this._has_fontSize = false; - } + this._has_fontSize= false; + } //-- void deleteFontSize() - //-- void deleteFontSize() + /** + * Method deleteFontStyle + * + */ + public void deleteFontStyle() + { + this._has_fontStyle= false; + } //-- void deleteFontStyle() /** * Method deleteHeight - * + * */ public void deleteHeight() { - this._has_height = false; - } - - //-- void deleteHeight() + this._has_height= false; + } //-- void deleteHeight() /** * Method deleteMarkUnlinked - * + * */ public void deleteMarkUnlinked() { - this._has_markUnlinked = false; - } - - //-- void deleteMarkUnlinked() + this._has_markUnlinked= false; + } //-- void deleteMarkUnlinked() /** * Method deleteShowBootstrap - * + * */ public void deleteShowBootstrap() { - this._has_showBootstrap = false; - } - - //-- void deleteShowBootstrap() + this._has_showBootstrap= false; + } //-- void deleteShowBootstrap() /** * Method deleteShowDistances - * + * */ public void deleteShowDistances() { - this._has_showDistances = false; - } - - //-- void deleteShowDistances() + this._has_showDistances= false; + } //-- void deleteShowDistances() /** * Method deleteThreshold - * + * */ public void deleteThreshold() { - this._has_threshold = false; - } - - //-- void deleteThreshold() + this._has_threshold= false; + } //-- void deleteThreshold() /** * Method deleteWidth - * + * */ public void deleteWidth() { - this._has_width = false; - } - - //-- void deleteWidth() + this._has_width= false; + } //-- void deleteWidth() /** * Method deleteXpos - * + * */ public void deleteXpos() { - this._has_xpos = false; - } - - //-- void deleteXpos() + this._has_xpos= false; + } //-- void deleteXpos() /** * Method deleteYpos - * + * */ public void deleteYpos() { - this._has_ypos = false; - } - - //-- 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() + } //-- boolean getCurrentTree() /** * Returns the value of field 'fitToWindow'. - * + * * @return boolean * @return the value of field 'fitToWindow'. */ public boolean getFitToWindow() { return this._fitToWindow; - } + } //-- boolean getFitToWindow() - //-- 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() - //-- 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() + } //-- int getHeight() /** * Returns the value of field 'markUnlinked'. - * + * * @return boolean * @return the value of field 'markUnlinked'. */ public boolean getMarkUnlinked() { return this._markUnlinked; - } - - //-- boolean getMarkUnlinked() + } //-- 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() + } //-- 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() + } //-- boolean getShowBootstrap() /** * Returns the value of field 'showDistances'. - * + * * @return boolean * @return the value of field 'showDistances'. */ public boolean getShowDistances() { return this._showDistances; - } - - //-- boolean getShowDistances() + } //-- boolean getShowDistances() /** * Returns the value of field 'threshold'. - * + * * @return float * @return the value of field 'threshold'. */ public float getThreshold() { return this._threshold; - } - - //-- float getThreshold() + } //-- 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() + } //-- 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() + } //-- int getWidth() /** * Returns the value of field 'xpos'. - * + * * @return int * @return the value of field 'xpos'. */ public int getXpos() { return this._xpos; - } - - //-- int getXpos() + } //-- int getXpos() /** * Returns the value of field 'ypos'. - * + * * @return int * @return the value of field 'ypos'. */ public int getYpos() { return this._ypos; - } - - //-- int getYpos() + } //-- int getYpos() /** * Method hasCurrentTree - * - * - * + * + * + * * @return boolean */ public boolean hasCurrentTree() { return this._has_currentTree; - } - - //-- boolean hasCurrentTree() + } //-- boolean hasCurrentTree() /** * Method hasFitToWindow - * - * - * + * + * + * * @return boolean */ public boolean hasFitToWindow() { return this._has_fitToWindow; - } - - //-- boolean hasFitToWindow() + } //-- boolean hasFitToWindow() /** * Method hasFontSize - * - * - * + * + * + * * @return boolean */ public boolean hasFontSize() { return this._has_fontSize; - } + } //-- boolean hasFontSize() - //-- 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() + } //-- boolean hasHeight() /** * Method hasMarkUnlinked - * - * - * + * + * + * * @return boolean */ public boolean hasMarkUnlinked() { return this._has_markUnlinked; - } - - //-- boolean hasMarkUnlinked() + } //-- boolean hasMarkUnlinked() /** * Method hasShowBootstrap - * - * - * + * + * + * * @return boolean */ public boolean hasShowBootstrap() { return this._has_showBootstrap; - } - - //-- boolean hasShowBootstrap() + } //-- boolean hasShowBootstrap() /** * Method hasShowDistances - * - * - * + * + * + * * @return boolean */ public boolean hasShowDistances() { return this._has_showDistances; - } - - //-- boolean hasShowDistances() + } //-- boolean hasShowDistances() /** * Method hasThreshold - * - * - * + * + * + * * @return boolean */ public boolean hasThreshold() { return this._has_threshold; - } - - //-- boolean hasThreshold() + } //-- boolean hasThreshold() /** * Method hasWidth - * - * - * + * + * + * * @return boolean */ public boolean hasWidth() { return this._has_width; - } - - //-- boolean hasWidth() + } //-- boolean hasWidth() /** * Method hasXpos - * - * - * + * + * + * * @return boolean */ public boolean hasXpos() { return this._has_xpos; - } - - //-- boolean hasXpos() + } //-- boolean hasXpos() /** * Method hasYpos - * - * - * + * + * + * * @return boolean */ public boolean hasYpos() { return this._has_ypos; - } - - //-- boolean hasYpos() + } //-- boolean hasYpos() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() { - try - { + try { validate(); } - catch (org.exolab.castor.xml.ValidationException vex) - { + catch (org.exolab.castor.xml.ValidationException vex) { return false; } - return true; - } - - //-- boolean isValid() + } //-- boolean isValid() /** * Method marshal - * - * - * + * + * + * * @param out */ public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); - } - - //-- void marshal(java.io.Writer) + } //-- 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 + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); - } - - //-- void marshal(org.xml.sax.ContentHandler) + } //-- 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) + } //-- 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) - //-- 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) - //-- 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) + } //-- 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) + } //-- 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) + } //-- 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) + } //-- 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) + } //-- 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) + } //-- 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) + } //-- 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) + } //-- 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) + } //-- 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) + } //-- 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 + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.binding.Tree) Unmarshaller.unmarshal(jalview.binding.Tree.class, - reader); - } - - //-- java.lang.Object unmarshal(java.io.Reader) + return (jalview.binding.Tree) Unmarshaller.unmarshal(jalview.binding.Tree.class, reader); + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ - public void validate() throws org.exolab.castor.xml.ValidationException + 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() - //-- void validate() }