X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FTree.java;h=c73cb1213b0a31cfb396d0400516d535609c16dd;hb=ca384c307f32631d32ffd450d69a49abeff4f5df;hp=96b2e18602ce4c019ad4e84cccfc65598f3c36fc;hpb=48df59aa393e03aa7269b2df662ac1b8d58cbb25;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/Tree.java b/src/jalview/schemabinding/version2/Tree.java
index 96b2e18..c73cb12 100755
--- a/src/jalview/schemabinding/version2/Tree.java
+++ b/src/jalview/schemabinding/version2/Tree.java
@@ -1,6 +1,6 @@
 /*
  * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
  * Schema.
  * $Id$
  */
@@ -11,15 +11,8 @@ package jalview.schemabinding.version2;
  //- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
 
 /**
  * Class Tree.
@@ -34,7 +27,7 @@ public class Tree implements java.io.Serializable {
     //--------------------------/
 
     /**
-     * Field _width
+     * Field _width.
      */
     private int _width;
 
@@ -44,7 +37,7 @@ public class Tree implements java.io.Serializable {
     private boolean _has_width;
 
     /**
-     * Field _height
+     * Field _height.
      */
     private int _height;
 
@@ -54,7 +47,7 @@ public class Tree implements java.io.Serializable {
     private boolean _has_height;
 
     /**
-     * Field _xpos
+     * Field _xpos.
      */
     private int _xpos;
 
@@ -64,7 +57,7 @@ public class Tree implements java.io.Serializable {
     private boolean _has_xpos;
 
     /**
-     * Field _ypos
+     * Field _ypos.
      */
     private int _ypos;
 
@@ -74,12 +67,12 @@ public class Tree implements java.io.Serializable {
     private boolean _has_ypos;
 
     /**
-     * Field _fontName
+     * Field _fontName.
      */
     private java.lang.String _fontName;
 
     /**
-     * Field _fontSize
+     * Field _fontSize.
      */
     private int _fontSize;
 
@@ -89,7 +82,7 @@ public class Tree implements java.io.Serializable {
     private boolean _has_fontSize;
 
     /**
-     * Field _fontStyle
+     * Field _fontStyle.
      */
     private int _fontStyle;
 
@@ -99,7 +92,7 @@ public class Tree implements java.io.Serializable {
     private boolean _has_fontStyle;
 
     /**
-     * Field _threshold
+     * Field _threshold.
      */
     private float _threshold;
 
@@ -109,7 +102,7 @@ public class Tree implements java.io.Serializable {
     private boolean _has_threshold;
 
     /**
-     * Field _showBootstrap
+     * Field _showBootstrap.
      */
     private boolean _showBootstrap;
 
@@ -119,7 +112,7 @@ public class Tree implements java.io.Serializable {
     private boolean _has_showBootstrap;
 
     /**
-     * Field _showDistances
+     * Field _showDistances.
      */
     private boolean _showDistances;
 
@@ -129,7 +122,7 @@ public class Tree implements java.io.Serializable {
     private boolean _has_showDistances;
 
     /**
-     * Field _markUnlinked
+     * Field _markUnlinked.
      */
     private boolean _markUnlinked;
 
@@ -139,7 +132,7 @@ public class Tree implements java.io.Serializable {
     private boolean _has_markUnlinked;
 
     /**
-     * Field _fitToWindow
+     * Field _fitToWindow.
      */
     private boolean _fitToWindow;
 
@@ -149,7 +142,7 @@ public class Tree implements java.io.Serializable {
     private boolean _has_fitToWindow;
 
     /**
-     * Field _currentTree
+     * Field _currentTree.
      */
     private boolean _currentTree;
 
@@ -159,12 +152,18 @@ public class Tree implements java.io.Serializable {
     private boolean _has_currentTree;
 
     /**
-     * Field _title
+     * Tree ID added for binding tree visualization settings to
+     * vamsas document trees in jalview 2.4.1
+     */
+    private java.lang.String _id;
+
+    /**
+     * Field _title.
      */
     private java.lang.String _title;
 
     /**
-     * Field _newick
+     * Field _newick.
      */
     private java.lang.String _newick;
 
@@ -175,7 +174,7 @@ public class Tree implements java.io.Serializable {
 
     public Tree() {
         super();
-    } //-- jalview.schemabinding.version2.Tree()
+    }
 
 
       //-----------/
@@ -183,653 +182,671 @@ public class Tree implements java.io.Serializable {
     //-----------/
 
     /**
-     * Method deleteCurrentTree
-     * 
      */
-    public void deleteCurrentTree()
-    {
+    public void deleteCurrentTree(
+    ) {
         this._has_currentTree= false;
-    } //-- void deleteCurrentTree() 
+    }
 
     /**
-     * Method deleteFitToWindow
-     * 
      */
-    public void deleteFitToWindow()
-    {
+    public void deleteFitToWindow(
+    ) {
         this._has_fitToWindow= false;
-    } //-- void deleteFitToWindow() 
+    }
 
     /**
-     * Method deleteFontSize
-     * 
      */
-    public void deleteFontSize()
-    {
+    public void deleteFontSize(
+    ) {
         this._has_fontSize= false;
-    } //-- void deleteFontSize() 
+    }
 
     /**
-     * Method deleteFontStyle
-     * 
      */
-    public void deleteFontStyle()
-    {
+    public void deleteFontStyle(
+    ) {
         this._has_fontStyle= false;
-    } //-- void deleteFontStyle() 
+    }
 
     /**
-     * Method deleteHeight
-     * 
      */
-    public void deleteHeight()
-    {
+    public void deleteHeight(
+    ) {
         this._has_height= false;
-    } //-- void deleteHeight() 
+    }
 
     /**
-     * Method deleteMarkUnlinked
-     * 
      */
-    public void deleteMarkUnlinked()
-    {
+    public void deleteMarkUnlinked(
+    ) {
         this._has_markUnlinked= false;
-    } //-- void deleteMarkUnlinked() 
+    }
 
     /**
-     * Method deleteShowBootstrap
-     * 
      */
-    public void deleteShowBootstrap()
-    {
+    public void deleteShowBootstrap(
+    ) {
         this._has_showBootstrap= false;
-    } //-- void deleteShowBootstrap() 
+    }
 
     /**
-     * Method deleteShowDistances
-     * 
      */
-    public void deleteShowDistances()
-    {
+    public void deleteShowDistances(
+    ) {
         this._has_showDistances= false;
-    } //-- void deleteShowDistances() 
+    }
 
     /**
-     * Method deleteThreshold
-     * 
      */
-    public void deleteThreshold()
-    {
+    public void deleteThreshold(
+    ) {
         this._has_threshold= false;
-    } //-- void deleteThreshold() 
+    }
 
     /**
-     * Method deleteWidth
-     * 
      */
-    public void deleteWidth()
-    {
+    public void deleteWidth(
+    ) {
         this._has_width= false;
-    } //-- void deleteWidth() 
+    }
 
     /**
-     * Method deleteXpos
-     * 
      */
-    public void deleteXpos()
-    {
+    public void deleteXpos(
+    ) {
         this._has_xpos= false;
-    } //-- void deleteXpos() 
+    }
 
     /**
-     * Method deleteYpos
-     * 
      */
-    public void deleteYpos()
-    {
+    public void deleteYpos(
+    ) {
         this._has_ypos= false;
-    } //-- void deleteYpos() 
+    }
 
     /**
      * Returns the value of field 'currentTree'.
      * 
-     * @return boolean
-     * @return the value of field 'currentTree'.
+     * @return the value of field 'CurrentTree'.
      */
-    public boolean getCurrentTree()
-    {
+    public boolean getCurrentTree(
+    ) {
         return this._currentTree;
-    } //-- boolean getCurrentTree() 
+    }
 
     /**
      * Returns the value of field 'fitToWindow'.
      * 
-     * @return boolean
-     * @return the value of field 'fitToWindow'.
+     * @return the value of field 'FitToWindow'.
      */
-    public boolean getFitToWindow()
-    {
+    public boolean getFitToWindow(
+    ) {
         return this._fitToWindow;
-    } //-- boolean getFitToWindow() 
+    }
 
     /**
      * Returns the value of field 'fontName'.
      * 
-     * @return String
-     * @return the value of field 'fontName'.
+     * @return the value of field 'FontName'.
      */
-    public java.lang.String getFontName()
-    {
+    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'.
+     * @return the value of field 'FontSize'.
      */
-    public int getFontSize()
-    {
+    public int getFontSize(
+    ) {
         return this._fontSize;
-    } //-- int getFontSize() 
+    }
 
     /**
      * Returns the value of field 'fontStyle'.
      * 
-     * @return int
-     * @return the value of field 'fontStyle'.
+     * @return the value of field 'FontStyle'.
      */
-    public int getFontStyle()
-    {
+    public int getFontStyle(
+    ) {
         return this._fontStyle;
-    } //-- int getFontStyle() 
+    }
 
     /**
      * Returns the value of field 'height'.
      * 
-     * @return int
-     * @return the value of field 'height'.
+     * @return the value of field 'Height'.
      */
-    public int getHeight()
-    {
+    public int getHeight(
+    ) {
         return this._height;
-    } //-- int getHeight() 
+    }
+
+    /**
+     * 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 boolean
-     * @return the value of field 'markUnlinked'.
+     * @return the value of field 'MarkUnlinked'.
      */
-    public boolean getMarkUnlinked()
-    {
+    public boolean getMarkUnlinked(
+    ) {
         return this._markUnlinked;
-    } //-- boolean getMarkUnlinked() 
+    }
 
     /**
      * Returns the value of field 'newick'.
      * 
-     * @return String
-     * @return the value of field 'newick'.
+     * @return the value of field 'Newick'.
      */
-    public java.lang.String getNewick()
-    {
+    public java.lang.String getNewick(
+    ) {
         return this._newick;
-    } //-- java.lang.String getNewick() 
+    }
 
     /**
      * Returns the value of field 'showBootstrap'.
      * 
-     * @return boolean
-     * @return the value of field 'showBootstrap'.
+     * @return the value of field 'ShowBootstrap'.
      */
-    public boolean getShowBootstrap()
-    {
+    public boolean getShowBootstrap(
+    ) {
         return this._showBootstrap;
-    } //-- boolean getShowBootstrap() 
+    }
 
     /**
      * Returns the value of field 'showDistances'.
      * 
-     * @return boolean
-     * @return the value of field 'showDistances'.
+     * @return the value of field 'ShowDistances'.
      */
-    public boolean getShowDistances()
-    {
+    public boolean getShowDistances(
+    ) {
         return this._showDistances;
-    } //-- boolean getShowDistances() 
+    }
 
     /**
      * Returns the value of field 'threshold'.
      * 
-     * @return float
-     * @return the value of field 'threshold'.
+     * @return the value of field 'Threshold'.
      */
-    public float getThreshold()
-    {
+    public float getThreshold(
+    ) {
         return this._threshold;
-    } //-- float getThreshold() 
+    }
 
     /**
      * Returns the value of field 'title'.
      * 
-     * @return String
-     * @return the value of field 'title'.
+     * @return the value of field 'Title'.
      */
-    public java.lang.String getTitle()
-    {
+    public java.lang.String getTitle(
+    ) {
         return this._title;
-    } //-- java.lang.String getTitle() 
+    }
 
     /**
      * Returns the value of field 'width'.
      * 
-     * @return int
-     * @return the value of field 'width'.
+     * @return the value of field 'Width'.
      */
-    public int getWidth()
-    {
+    public int getWidth(
+    ) {
         return this._width;
-    } //-- int getWidth() 
+    }
 
     /**
      * Returns the value of field 'xpos'.
      * 
-     * @return int
-     * @return the value of field 'xpos'.
+     * @return the value of field 'Xpos'.
      */
-    public int getXpos()
-    {
+    public int getXpos(
+    ) {
         return this._xpos;
-    } //-- int getXpos() 
+    }
 
     /**
      * Returns the value of field 'ypos'.
      * 
-     * @return int
-     * @return the value of field 'ypos'.
+     * @return the value of field 'Ypos'.
      */
-    public int getYpos()
-    {
+    public int getYpos(
+    ) {
         return this._ypos;
-    } //-- int getYpos() 
+    }
 
     /**
-     * Method hasCurrentTree
-     * 
-     * 
+     * Method hasCurrentTree.
      * 
-     * @return boolean
+     * @return true if at least one CurrentTree has been added
      */
-    public boolean hasCurrentTree()
-    {
+    public boolean hasCurrentTree(
+    ) {
         return this._has_currentTree;
-    } //-- boolean hasCurrentTree() 
+    }
 
     /**
-     * Method hasFitToWindow
+     * Method hasFitToWindow.
      * 
-     * 
-     * 
-     * @return boolean
+     * @return true if at least one FitToWindow has been added
      */
-    public boolean hasFitToWindow()
-    {
+    public boolean hasFitToWindow(
+    ) {
         return this._has_fitToWindow;
-    } //-- boolean hasFitToWindow() 
+    }
 
     /**
-     * Method hasFontSize
-     * 
+     * Method hasFontSize.
      * 
-     * 
-     * @return boolean
+     * @return true if at least one FontSize has been added
      */
-    public boolean hasFontSize()
-    {
+    public boolean hasFontSize(
+    ) {
         return this._has_fontSize;
-    } //-- boolean hasFontSize() 
+    }
 
     /**
-     * Method hasFontStyle
-     * 
+     * Method hasFontStyle.
      * 
-     * 
-     * @return boolean
+     * @return true if at least one FontStyle has been added
      */
-    public boolean hasFontStyle()
-    {
+    public boolean hasFontStyle(
+    ) {
         return this._has_fontStyle;
-    } //-- boolean hasFontStyle() 
+    }
 
     /**
-     * Method hasHeight
-     * 
-     * 
+     * Method hasHeight.
      * 
-     * @return boolean
+     * @return true if at least one Height has been added
      */
-    public boolean hasHeight()
-    {
+    public boolean hasHeight(
+    ) {
         return this._has_height;
-    } //-- boolean hasHeight() 
+    }
 
     /**
-     * Method hasMarkUnlinked
-     * 
-     * 
+     * Method hasMarkUnlinked.
      * 
-     * @return boolean
+     * @return true if at least one MarkUnlinked has been added
      */
-    public boolean hasMarkUnlinked()
-    {
+    public boolean hasMarkUnlinked(
+    ) {
         return this._has_markUnlinked;
-    } //-- boolean hasMarkUnlinked() 
+    }
 
     /**
-     * Method hasShowBootstrap
+     * Method hasShowBootstrap.
      * 
-     * 
-     * 
-     * @return boolean
+     * @return true if at least one ShowBootstrap has been added
      */
-    public boolean hasShowBootstrap()
-    {
+    public boolean hasShowBootstrap(
+    ) {
         return this._has_showBootstrap;
-    } //-- boolean hasShowBootstrap() 
+    }
 
     /**
-     * Method hasShowDistances
-     * 
+     * Method hasShowDistances.
      * 
-     * 
-     * @return boolean
+     * @return true if at least one ShowDistances has been added
      */
-    public boolean hasShowDistances()
-    {
+    public boolean hasShowDistances(
+    ) {
         return this._has_showDistances;
-    } //-- boolean hasShowDistances() 
+    }
 
     /**
-     * Method hasThreshold
-     * 
+     * Method hasThreshold.
      * 
-     * 
-     * @return boolean
+     * @return true if at least one Threshold has been added
      */
-    public boolean hasThreshold()
-    {
+    public boolean hasThreshold(
+    ) {
         return this._has_threshold;
-    } //-- boolean hasThreshold() 
+    }
 
     /**
-     * Method hasWidth
-     * 
-     * 
+     * Method hasWidth.
      * 
-     * @return boolean
+     * @return true if at least one Width has been added
      */
-    public boolean hasWidth()
-    {
+    public boolean hasWidth(
+    ) {
         return this._has_width;
-    } //-- boolean hasWidth() 
+    }
 
     /**
-     * Method hasXpos
-     * 
-     * 
+     * Method hasXpos.
      * 
-     * @return boolean
+     * @return true if at least one Xpos has been added
      */
-    public boolean hasXpos()
-    {
+    public boolean hasXpos(
+    ) {
         return this._has_xpos;
-    } //-- boolean hasXpos() 
+    }
 
     /**
-     * Method hasYpos
+     * 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 boolean
+     * @return the value of field 'FitToWindow'.
      */
-    public boolean hasYpos()
-    {
-        return this._has_ypos;
-    } //-- boolean hasYpos() 
+    public boolean isFitToWindow(
+    ) {
+        return this._fitToWindow;
+    }
 
     /**
-     * Method isValid
+     * 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 boolean
+     * @return true if this object is valid according to the schema
      */
-    public boolean isValid()
-    {
+    public boolean isValid(
+    ) {
         try {
             validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
+        } catch (org.exolab.castor.xml.ValidationException vex) {
             return false;
         }
         return true;
-    } //-- boolean isValid() 
+    }
 
     /**
-     * Method marshal
-     * 
      * 
      * 
      * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
+     * @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);
-    } //-- 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 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);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
+    }
 
     /**
      * Sets the value of field 'currentTree'.
      * 
      * @param currentTree the value of field 'currentTree'.
      */
-    public void setCurrentTree(boolean currentTree)
-    {
+    public void setCurrentTree(
+            final boolean currentTree) {
         this._currentTree = currentTree;
         this._has_currentTree = true;
-    } //-- void setCurrentTree(boolean) 
+    }
 
     /**
      * Sets the value of field 'fitToWindow'.
      * 
      * @param fitToWindow the value of field 'fitToWindow'.
      */
-    public void setFitToWindow(boolean fitToWindow)
-    {
+    public void setFitToWindow(
+            final boolean fitToWindow) {
         this._fitToWindow = fitToWindow;
         this._has_fitToWindow = true;
-    } //-- void setFitToWindow(boolean) 
+    }
 
     /**
      * Sets the value of field 'fontName'.
      * 
      * @param fontName the value of field 'fontName'.
      */
-    public void setFontName(java.lang.String fontName)
-    {
+    public void setFontName(
+            final 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)
-    {
+    public void setFontSize(
+            final int fontSize) {
         this._fontSize = fontSize;
         this._has_fontSize = true;
-    } //-- void setFontSize(int) 
+    }
 
     /**
      * Sets the value of field 'fontStyle'.
      * 
      * @param fontStyle the value of field 'fontStyle'.
      */
-    public void setFontStyle(int fontStyle)
-    {
+    public void setFontStyle(
+            final 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)
-    {
+    public void setHeight(
+            final int height) {
         this._height = height;
         this._has_height = true;
-    } //-- void setHeight(int) 
+    }
+
+    /**
+     * 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(boolean markUnlinked)
-    {
+    public void setMarkUnlinked(
+            final boolean markUnlinked) {
         this._markUnlinked = markUnlinked;
         this._has_markUnlinked = true;
-    } //-- void setMarkUnlinked(boolean) 
+    }
 
     /**
      * Sets the value of field 'newick'.
      * 
      * @param newick the value of field 'newick'.
      */
-    public void setNewick(java.lang.String newick)
-    {
+    public void setNewick(
+            final java.lang.String newick) {
         this._newick = newick;
-    } //-- void setNewick(java.lang.String) 
+    }
 
     /**
      * Sets the value of field 'showBootstrap'.
      * 
      * @param showBootstrap the value of field 'showBootstrap'.
      */
-    public void setShowBootstrap(boolean showBootstrap)
-    {
+    public void setShowBootstrap(
+            final boolean showBootstrap) {
         this._showBootstrap = showBootstrap;
         this._has_showBootstrap = true;
-    } //-- void setShowBootstrap(boolean) 
+    }
 
     /**
      * Sets the value of field 'showDistances'.
      * 
      * @param showDistances the value of field 'showDistances'.
      */
-    public void setShowDistances(boolean showDistances)
-    {
+    public void setShowDistances(
+            final boolean showDistances) {
         this._showDistances = showDistances;
         this._has_showDistances = true;
-    } //-- void setShowDistances(boolean) 
+    }
 
     /**
      * Sets the value of field 'threshold'.
      * 
      * @param threshold the value of field 'threshold'.
      */
-    public void setThreshold(float threshold)
-    {
+    public void setThreshold(
+            final float threshold) {
         this._threshold = threshold;
         this._has_threshold = true;
-    } //-- void setThreshold(float) 
+    }
 
     /**
      * Sets the value of field 'title'.
      * 
      * @param title the value of field 'title'.
      */
-    public void setTitle(java.lang.String title)
-    {
+    public void setTitle(
+            final java.lang.String title) {
         this._title = title;
-    } //-- void setTitle(java.lang.String) 
+    }
 
     /**
      * Sets the value of field 'width'.
      * 
      * @param width the value of field 'width'.
      */
-    public void setWidth(int width)
-    {
+    public void setWidth(
+            final int width) {
         this._width = width;
         this._has_width = true;
-    } //-- void setWidth(int) 
+    }
 
     /**
      * Sets the value of field 'xpos'.
      * 
      * @param xpos the value of field 'xpos'.
      */
-    public void setXpos(int xpos)
-    {
+    public void setXpos(
+            final int xpos) {
         this._xpos = xpos;
         this._has_xpos = true;
-    } //-- void setXpos(int) 
+    }
 
     /**
      * Sets the value of field 'ypos'.
      * 
      * @param ypos the value of field 'ypos'.
      */
-    public void setYpos(int ypos)
-    {
+    public void setYpos(
+            final int ypos) {
         this._ypos = ypos;
         this._has_ypos = true;
-    } //-- void setYpos(int) 
+    }
 
     /**
-     * Method unmarshal
-     * 
-     * 
+     * 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 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);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
+    }
 
     /**
-     * Method validate
      * 
+     * 
+     * @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
-    {
+    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() 
+    }
 
 }