X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FJGroup.java;h=83d3b9adc2279ccf5b1c57c388f0e8466d26b020;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=64731490614821768d01ee97f7039dede08e93c1;hpb=124589ea0c58cbb7b3788bbf13b687a0ece3c9e0;p=jalview.git

diff --git a/src/jalview/binding/JGroup.java b/src/jalview/binding/JGroup.java
old mode 100755
new mode 100644
index 6473149..83d3b9a
--- a/src/jalview/binding/JGroup.java
+++ b/src/jalview/binding/JGroup.java
@@ -1,750 +1,756 @@
-/*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package jalview.binding;
-
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-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 JGroup.
- * 
- * @version $Revision$ $Date$
- */
-public class JGroup implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _start
-     */
-    private int _start;
-
-    /**
-     * keeps track of state for field: _start
-     */
-    private boolean _has_start;
-
-    /**
-     * Field _end
-     */
-    private int _end;
-
-    /**
-     * keeps track of state for field: _end
-     */
-    private boolean _has_end;
-
-    /**
-     * Field _name
-     */
-    private java.lang.String _name;
-
-    /**
-     * Field _colour
-     */
-    private java.lang.String _colour;
-
-    /**
-     * Field _consThreshold
-     */
-    private int _consThreshold;
-
-    /**
-     * keeps track of state for field: _consThreshold
-     */
-    private boolean _has_consThreshold;
-
-    /**
-     * Field _pidThreshold
-     */
-    private int _pidThreshold;
-
-    /**
-     * keeps track of state for field: _pidThreshold
-     */
-    private boolean _has_pidThreshold;
-
-    /**
-     * Field _outlineColour
-     */
-    private int _outlineColour;
-
-    /**
-     * keeps track of state for field: _outlineColour
-     */
-    private boolean _has_outlineColour;
-
-    /**
-     * Field _displayBoxes
-     */
-    private boolean _displayBoxes;
-
-    /**
-     * keeps track of state for field: _displayBoxes
-     */
-    private boolean _has_displayBoxes;
-
-    /**
-     * Field _displayText
-     */
-    private boolean _displayText;
-
-    /**
-     * keeps track of state for field: _displayText
-     */
-    private boolean _has_displayText;
-
-    /**
-     * Field _colourText
-     */
-    private boolean _colourText;
-
-    /**
-     * keeps track of state for field: _colourText
-     */
-    private boolean _has_colourText;
-
-    /**
-     * Field _seqList
-     */
-    private java.util.Vector _seqList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JGroup() {
-        super();
-        _seqList = new Vector();
-    } //-- jalview.binding.JGroup()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addSeq
-     * 
-     * 
-     * 
-     * @param vSeq
-     */
-    public void addSeq(int vSeq)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _seqList.addElement(new java.lang.Integer(vSeq));
-    } //-- void addSeq(int) 
-
-    /**
-     * Method addSeq
-     * 
-     * 
-     * 
-     * @param index
-     * @param vSeq
-     */
-    public void addSeq(int index, int vSeq)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _seqList.insertElementAt(new java.lang.Integer(vSeq), index);
-    } //-- void addSeq(int, int) 
-
-    /**
-     * Method deleteColourText
-     * 
-     */
-    public void deleteColourText()
-    {
-        this._has_colourText= false;
-    } //-- void deleteColourText() 
-
-    /**
-     * Method deleteConsThreshold
-     * 
-     */
-    public void deleteConsThreshold()
-    {
-        this._has_consThreshold= false;
-    } //-- void deleteConsThreshold() 
-
-    /**
-     * Method deleteDisplayBoxes
-     * 
-     */
-    public void deleteDisplayBoxes()
-    {
-        this._has_displayBoxes= false;
-    } //-- void deleteDisplayBoxes() 
-
-    /**
-     * Method deleteDisplayText
-     * 
-     */
-    public void deleteDisplayText()
-    {
-        this._has_displayText= false;
-    } //-- void deleteDisplayText() 
-
-    /**
-     * Method deleteEnd
-     * 
-     */
-    public void deleteEnd()
-    {
-        this._has_end= false;
-    } //-- void deleteEnd() 
-
-    /**
-     * Method deleteOutlineColour
-     * 
-     */
-    public void deleteOutlineColour()
-    {
-        this._has_outlineColour= false;
-    } //-- void deleteOutlineColour() 
-
-    /**
-     * Method deletePidThreshold
-     * 
-     */
-    public void deletePidThreshold()
-    {
-        this._has_pidThreshold= false;
-    } //-- void deletePidThreshold() 
-
-    /**
-     * Method deleteStart
-     * 
-     */
-    public void deleteStart()
-    {
-        this._has_start= false;
-    } //-- void deleteStart() 
-
-    /**
-     * Method enumerateSeq
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateSeq()
-    {
-        return _seqList.elements();
-    } //-- java.util.Enumeration enumerateSeq() 
-
-    /**
-     * Returns the value of field 'colour'.
-     * 
-     * @return String
-     * @return the value of field 'colour'.
-     */
-    public java.lang.String getColour()
-    {
-        return this._colour;
-    } //-- java.lang.String getColour() 
-
-    /**
-     * Returns the value of field 'colourText'.
-     * 
-     * @return boolean
-     * @return the value of field 'colourText'.
-     */
-    public boolean getColourText()
-    {
-        return this._colourText;
-    } //-- boolean getColourText() 
-
-    /**
-     * Returns the value of field 'consThreshold'.
-     * 
-     * @return int
-     * @return the value of field 'consThreshold'.
-     */
-    public int getConsThreshold()
-    {
-        return this._consThreshold;
-    } //-- int getConsThreshold() 
-
-    /**
-     * Returns the value of field 'displayBoxes'.
-     * 
-     * @return boolean
-     * @return the value of field 'displayBoxes'.
-     */
-    public boolean getDisplayBoxes()
-    {
-        return this._displayBoxes;
-    } //-- boolean getDisplayBoxes() 
-
-    /**
-     * Returns the value of field 'displayText'.
-     * 
-     * @return boolean
-     * @return the value of field 'displayText'.
-     */
-    public boolean getDisplayText()
-    {
-        return this._displayText;
-    } //-- boolean getDisplayText() 
-
-    /**
-     * Returns the value of field 'end'.
-     * 
-     * @return int
-     * @return the value of field 'end'.
-     */
-    public int getEnd()
-    {
-        return this._end;
-    } //-- int getEnd() 
-
-    /**
-     * Returns the value of field 'name'.
-     * 
-     * @return String
-     * @return the value of field 'name'.
-     */
-    public java.lang.String getName()
-    {
-        return this._name;
-    } //-- java.lang.String getName() 
-
-    /**
-     * Returns the value of field 'outlineColour'.
-     * 
-     * @return int
-     * @return the value of field 'outlineColour'.
-     */
-    public int getOutlineColour()
-    {
-        return this._outlineColour;
-    } //-- int getOutlineColour() 
-
-    /**
-     * Returns the value of field 'pidThreshold'.
-     * 
-     * @return int
-     * @return the value of field 'pidThreshold'.
-     */
-    public int getPidThreshold()
-    {
-        return this._pidThreshold;
-    } //-- int getPidThreshold() 
-
-    /**
-     * Method getSeq
-     * 
-     * 
-     * 
-     * @param index
-     * @return int
-     */
-    public int getSeq(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _seqList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return ((java.lang.Integer)_seqList.elementAt(index)).intValue();
-    } //-- int getSeq(int) 
-
-    /**
-     * Method getSeq
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int[] getSeq()
-    {
-        int size = _seqList.size();
-        int[] mArray = new int[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = ((java.lang.Integer)_seqList.elementAt(index)).intValue();
-        }
-        return mArray;
-    } //-- int[] getSeq() 
-
-    /**
-     * Method getSeqCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getSeqCount()
-    {
-        return _seqList.size();
-    } //-- int getSeqCount() 
-
-    /**
-     * Returns the value of field 'start'.
-     * 
-     * @return int
-     * @return the value of field 'start'.
-     */
-    public int getStart()
-    {
-        return this._start;
-    } //-- int getStart() 
-
-    /**
-     * Method hasColourText
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasColourText()
-    {
-        return this._has_colourText;
-    } //-- boolean hasColourText() 
-
-    /**
-     * Method hasConsThreshold
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasConsThreshold()
-    {
-        return this._has_consThreshold;
-    } //-- boolean hasConsThreshold() 
-
-    /**
-     * Method hasDisplayBoxes
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasDisplayBoxes()
-    {
-        return this._has_displayBoxes;
-    } //-- boolean hasDisplayBoxes() 
-
-    /**
-     * Method hasDisplayText
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasDisplayText()
-    {
-        return this._has_displayText;
-    } //-- boolean hasDisplayText() 
-
-    /**
-     * Method hasEnd
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasEnd()
-    {
-        return this._has_end;
-    } //-- boolean hasEnd() 
-
-    /**
-     * Method hasOutlineColour
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasOutlineColour()
-    {
-        return this._has_outlineColour;
-    } //-- boolean hasOutlineColour() 
-
-    /**
-     * Method hasPidThreshold
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasPidThreshold()
-    {
-        return this._has_pidThreshold;
-    } //-- boolean hasPidThreshold() 
-
-    /**
-     * Method hasStart
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasStart()
-    {
-        return this._has_start;
-    } //-- boolean hasStart() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        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
-    {
-        
-        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
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Method removeAllSeq
-     * 
-     */
-    public void removeAllSeq()
-    {
-        _seqList.removeAllElements();
-    } //-- void removeAllSeq() 
-
-    /**
-     * Method removeSeq
-     * 
-     * 
-     * 
-     * @param index
-     * @return int
-     */
-    public int removeSeq(int index)
-    {
-        java.lang.Object obj = _seqList.elementAt(index);
-        _seqList.removeElementAt(index);
-        return ((java.lang.Integer)obj).intValue();
-    } //-- int removeSeq(int) 
-
-    /**
-     * Sets the value of field 'colour'.
-     * 
-     * @param colour the value of field 'colour'.
-     */
-    public void setColour(java.lang.String colour)
-    {
-        this._colour = colour;
-    } //-- void setColour(java.lang.String) 
-
-    /**
-     * Sets the value of field 'colourText'.
-     * 
-     * @param colourText the value of field 'colourText'.
-     */
-    public void setColourText(boolean colourText)
-    {
-        this._colourText = colourText;
-        this._has_colourText = true;
-    } //-- void setColourText(boolean) 
-
-    /**
-     * Sets the value of field 'consThreshold'.
-     * 
-     * @param consThreshold the value of field 'consThreshold'.
-     */
-    public void setConsThreshold(int consThreshold)
-    {
-        this._consThreshold = consThreshold;
-        this._has_consThreshold = true;
-    } //-- void setConsThreshold(int) 
-
-    /**
-     * Sets the value of field 'displayBoxes'.
-     * 
-     * @param displayBoxes the value of field 'displayBoxes'.
-     */
-    public void setDisplayBoxes(boolean displayBoxes)
-    {
-        this._displayBoxes = displayBoxes;
-        this._has_displayBoxes = true;
-    } //-- void setDisplayBoxes(boolean) 
-
-    /**
-     * Sets the value of field 'displayText'.
-     * 
-     * @param displayText the value of field 'displayText'.
-     */
-    public void setDisplayText(boolean displayText)
-    {
-        this._displayText = displayText;
-        this._has_displayText = true;
-    } //-- void setDisplayText(boolean) 
-
-    /**
-     * Sets the value of field 'end'.
-     * 
-     * @param end the value of field 'end'.
-     */
-    public void setEnd(int end)
-    {
-        this._end = end;
-        this._has_end = true;
-    } //-- void setEnd(int) 
-
-    /**
-     * Sets the value of field 'name'.
-     * 
-     * @param name the value of field 'name'.
-     */
-    public void setName(java.lang.String name)
-    {
-        this._name = name;
-    } //-- void setName(java.lang.String) 
-
-    /**
-     * Sets the value of field 'outlineColour'.
-     * 
-     * @param outlineColour the value of field 'outlineColour'.
-     */
-    public void setOutlineColour(int outlineColour)
-    {
-        this._outlineColour = outlineColour;
-        this._has_outlineColour = true;
-    } //-- void setOutlineColour(int) 
-
-    /**
-     * Sets the value of field 'pidThreshold'.
-     * 
-     * @param pidThreshold the value of field 'pidThreshold'.
-     */
-    public void setPidThreshold(int pidThreshold)
-    {
-        this._pidThreshold = pidThreshold;
-        this._has_pidThreshold = true;
-    } //-- void setPidThreshold(int) 
-
-    /**
-     * Method setSeq
-     * 
-     * 
-     * 
-     * @param index
-     * @param vSeq
-     */
-    public void setSeq(int index, int vSeq)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _seqList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _seqList.setElementAt(new java.lang.Integer(vSeq), index);
-    } //-- void setSeq(int, int) 
-
-    /**
-     * Method setSeq
-     * 
-     * 
-     * 
-     * @param seqArray
-     */
-    public void setSeq(int[] seqArray)
-    {
-        //-- copy array
-        _seqList.removeAllElements();
-        for (int i = 0; i < seqArray.length; i++) {
-            _seqList.addElement(new java.lang.Integer(seqArray[i]));
-        }
-    } //-- void setSeq(int) 
-
-    /**
-     * Sets the value of field 'start'.
-     * 
-     * @param start the value of field 'start'.
-     */
-    public void setStart(int start)
-    {
-        this._start = start;
-        this._has_start = true;
-    } //-- void setStart(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
-    {
-        return (jalview.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    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() 
-
-}
+/*******************************************************************************
+ * 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 <http://www.gnu.org/licenses/>.
+ *******************************************************************************/
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class JGroup.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class JGroup implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _start.
+     */
+    private int _start;
+
+    /**
+     * keeps track of state for field: _start
+     */
+    private boolean _has_start;
+
+    /**
+     * Field _end.
+     */
+    private int _end;
+
+    /**
+     * keeps track of state for field: _end
+     */
+    private boolean _has_end;
+
+    /**
+     * Field _name.
+     */
+    private java.lang.String _name;
+
+    /**
+     * Field _colour.
+     */
+    private java.lang.String _colour;
+
+    /**
+     * Field _consThreshold.
+     */
+    private int _consThreshold;
+
+    /**
+     * keeps track of state for field: _consThreshold
+     */
+    private boolean _has_consThreshold;
+
+    /**
+     * Field _pidThreshold.
+     */
+    private int _pidThreshold;
+
+    /**
+     * keeps track of state for field: _pidThreshold
+     */
+    private boolean _has_pidThreshold;
+
+    /**
+     * Field _outlineColour.
+     */
+    private int _outlineColour;
+
+    /**
+     * keeps track of state for field: _outlineColour
+     */
+    private boolean _has_outlineColour;
+
+    /**
+     * Field _displayBoxes.
+     */
+    private boolean _displayBoxes;
+
+    /**
+     * keeps track of state for field: _displayBoxes
+     */
+    private boolean _has_displayBoxes;
+
+    /**
+     * Field _displayText.
+     */
+    private boolean _displayText;
+
+    /**
+     * keeps track of state for field: _displayText
+     */
+    private boolean _has_displayText;
+
+    /**
+     * Field _colourText.
+     */
+    private boolean _colourText;
+
+    /**
+     * keeps track of state for field: _colourText
+     */
+    private boolean _has_colourText;
+
+    /**
+     * Field _seqList.
+     */
+    private java.util.Vector _seqList;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public JGroup() {
+        super();
+        this._seqList = new java.util.Vector();
+    }
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * 
+     * 
+     * @param vSeq
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addSeq(
+            final int vSeq)
+    throws java.lang.IndexOutOfBoundsException {
+        this._seqList.addElement(new java.lang.Integer(vSeq));
+    }
+
+    /**
+     * 
+     * 
+     * @param index
+     * @param vSeq
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addSeq(
+            final int index,
+            final int vSeq)
+    throws java.lang.IndexOutOfBoundsException {
+        this._seqList.add(index, new java.lang.Integer(vSeq));
+    }
+
+    /**
+     */
+    public void deleteColourText(
+    ) {
+        this._has_colourText= false;
+    }
+
+    /**
+     */
+    public void deleteConsThreshold(
+    ) {
+        this._has_consThreshold= false;
+    }
+
+    /**
+     */
+    public void deleteDisplayBoxes(
+    ) {
+        this._has_displayBoxes= false;
+    }
+
+    /**
+     */
+    public void deleteDisplayText(
+    ) {
+        this._has_displayText= false;
+    }
+
+    /**
+     */
+    public void deleteEnd(
+    ) {
+        this._has_end= false;
+    }
+
+    /**
+     */
+    public void deleteOutlineColour(
+    ) {
+        this._has_outlineColour= false;
+    }
+
+    /**
+     */
+    public void deletePidThreshold(
+    ) {
+        this._has_pidThreshold= false;
+    }
+
+    /**
+     */
+    public void deleteStart(
+    ) {
+        this._has_start= false;
+    }
+
+    /**
+     * Method enumerateSeq.
+     * 
+     * @return an Enumeration over all int elements
+     */
+    public java.util.Enumeration enumerateSeq(
+    ) {
+        return this._seqList.elements();
+    }
+
+    /**
+     * Returns the value of field 'colour'.
+     * 
+     * @return the value of field 'Colour'.
+     */
+    public java.lang.String getColour(
+    ) {
+        return this._colour;
+    }
+
+    /**
+     * Returns the value of field 'colourText'.
+     * 
+     * @return the value of field 'ColourText'.
+     */
+    public boolean getColourText(
+    ) {
+        return this._colourText;
+    }
+
+    /**
+     * Returns the value of field 'consThreshold'.
+     * 
+     * @return the value of field 'ConsThreshold'.
+     */
+    public int getConsThreshold(
+    ) {
+        return this._consThreshold;
+    }
+
+    /**
+     * Returns the value of field 'displayBoxes'.
+     * 
+     * @return the value of field 'DisplayBoxes'.
+     */
+    public boolean getDisplayBoxes(
+    ) {
+        return this._displayBoxes;
+    }
+
+    /**
+     * Returns the value of field 'displayText'.
+     * 
+     * @return the value of field 'DisplayText'.
+     */
+    public boolean getDisplayText(
+    ) {
+        return this._displayText;
+    }
+
+    /**
+     * Returns the value of field 'end'.
+     * 
+     * @return the value of field 'End'.
+     */
+    public int getEnd(
+    ) {
+        return this._end;
+    }
+
+    /**
+     * Returns the value of field 'name'.
+     * 
+     * @return the value of field 'Name'.
+     */
+    public java.lang.String getName(
+    ) {
+        return this._name;
+    }
+
+    /**
+     * Returns the value of field 'outlineColour'.
+     * 
+     * @return the value of field 'OutlineColour'.
+     */
+    public int getOutlineColour(
+    ) {
+        return this._outlineColour;
+    }
+
+    /**
+     * Returns the value of field 'pidThreshold'.
+     * 
+     * @return the value of field 'PidThreshold'.
+     */
+    public int getPidThreshold(
+    ) {
+        return this._pidThreshold;
+    }
+
+    /**
+     * Method getSeq.
+     * 
+     * @param index
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     * @return the value of the int at the given index
+     */
+    public int getSeq(
+            final int index)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._seqList.size()) {
+            throw new IndexOutOfBoundsException("getSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");
+        }
+        
+        return ((java.lang.Integer) _seqList.get(index)).intValue();
+    }
+
+    /**
+     * Method getSeq.Returns the contents of the collection in an
+     * Array.  
+     * 
+     * @return this collection as an Array
+     */
+    public int[] getSeq(
+    ) {
+        int size = this._seqList.size();
+        int[] array = new int[size];
+        java.util.Iterator iter = _seqList.iterator();
+        for (int index = 0; index < size; index++) {
+            array[index] = ((java.lang.Integer) iter.next()).intValue();
+        }
+        return array;
+    }
+
+    /**
+     * Method getSeqCount.
+     * 
+     * @return the size of this collection
+     */
+    public int getSeqCount(
+    ) {
+        return this._seqList.size();
+    }
+
+    /**
+     * Returns the value of field 'start'.
+     * 
+     * @return the value of field 'Start'.
+     */
+    public int getStart(
+    ) {
+        return this._start;
+    }
+
+    /**
+     * Method hasColourText.
+     * 
+     * @return true if at least one ColourText has been added
+     */
+    public boolean hasColourText(
+    ) {
+        return this._has_colourText;
+    }
+
+    /**
+     * Method hasConsThreshold.
+     * 
+     * @return true if at least one ConsThreshold has been added
+     */
+    public boolean hasConsThreshold(
+    ) {
+        return this._has_consThreshold;
+    }
+
+    /**
+     * Method hasDisplayBoxes.
+     * 
+     * @return true if at least one DisplayBoxes has been added
+     */
+    public boolean hasDisplayBoxes(
+    ) {
+        return this._has_displayBoxes;
+    }
+
+    /**
+     * Method hasDisplayText.
+     * 
+     * @return true if at least one DisplayText has been added
+     */
+    public boolean hasDisplayText(
+    ) {
+        return this._has_displayText;
+    }
+
+    /**
+     * Method hasEnd.
+     * 
+     * @return true if at least one End has been added
+     */
+    public boolean hasEnd(
+    ) {
+        return this._has_end;
+    }
+
+    /**
+     * Method hasOutlineColour.
+     * 
+     * @return true if at least one OutlineColour has been added
+     */
+    public boolean hasOutlineColour(
+    ) {
+        return this._has_outlineColour;
+    }
+
+    /**
+     * Method hasPidThreshold.
+     * 
+     * @return true if at least one PidThreshold has been added
+     */
+    public boolean hasPidThreshold(
+    ) {
+        return this._has_pidThreshold;
+    }
+
+    /**
+     * Method hasStart.
+     * 
+     * @return true if at least one Start has been added
+     */
+    public boolean hasStart(
+    ) {
+        return this._has_start;
+    }
+
+    /**
+     * Returns the value of field 'colourText'.
+     * 
+     * @return the value of field 'ColourText'.
+     */
+    public boolean isColourText(
+    ) {
+        return this._colourText;
+    }
+
+    /**
+     * Returns the value of field 'displayBoxes'.
+     * 
+     * @return the value of field 'DisplayBoxes'.
+     */
+    public boolean isDisplayBoxes(
+    ) {
+        return this._displayBoxes;
+    }
+
+    /**
+     * Returns the value of field 'displayText'.
+     * 
+     * @return the value of field 'DisplayText'.
+     */
+    public boolean isDisplayText(
+    ) {
+        return this._displayText;
+    }
+
+    /**
+     * 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);
+    }
+
+    /**
+     */
+    public void removeAllSeq(
+    ) {
+        this._seqList.clear();
+    }
+
+    /**
+     * Method removeSeq.
+     * 
+     * @param vSeq
+     * @return true if the object was removed from the collection.
+     */
+    public boolean removeSeq(
+            final int vSeq) {
+        boolean removed = _seqList.remove(new java.lang.Integer(vSeq));
+        return removed;
+    }
+
+    /**
+     * Method removeSeqAt.
+     * 
+     * @param index
+     * @return the element removed from the collection
+     */
+    public int removeSeqAt(
+            final int index) {
+        java.lang.Object obj = this._seqList.remove(index);
+        return ((java.lang.Integer) obj).intValue();
+    }
+
+    /**
+     * Sets the value of field 'colour'.
+     * 
+     * @param colour the value of field 'colour'.
+     */
+    public void setColour(
+            final java.lang.String colour) {
+        this._colour = colour;
+    }
+
+    /**
+     * Sets the value of field 'colourText'.
+     * 
+     * @param colourText the value of field 'colourText'.
+     */
+    public void setColourText(
+            final boolean colourText) {
+        this._colourText = colourText;
+        this._has_colourText = true;
+    }
+
+    /**
+     * Sets the value of field 'consThreshold'.
+     * 
+     * @param consThreshold the value of field 'consThreshold'.
+     */
+    public void setConsThreshold(
+            final int consThreshold) {
+        this._consThreshold = consThreshold;
+        this._has_consThreshold = true;
+    }
+
+    /**
+     * Sets the value of field 'displayBoxes'.
+     * 
+     * @param displayBoxes the value of field 'displayBoxes'.
+     */
+    public void setDisplayBoxes(
+            final boolean displayBoxes) {
+        this._displayBoxes = displayBoxes;
+        this._has_displayBoxes = true;
+    }
+
+    /**
+     * Sets the value of field 'displayText'.
+     * 
+     * @param displayText the value of field 'displayText'.
+     */
+    public void setDisplayText(
+            final boolean displayText) {
+        this._displayText = displayText;
+        this._has_displayText = true;
+    }
+
+    /**
+     * Sets the value of field 'end'.
+     * 
+     * @param end the value of field 'end'.
+     */
+    public void setEnd(
+            final int end) {
+        this._end = end;
+        this._has_end = true;
+    }
+
+    /**
+     * Sets the value of field 'name'.
+     * 
+     * @param name the value of field 'name'.
+     */
+    public void setName(
+            final java.lang.String name) {
+        this._name = name;
+    }
+
+    /**
+     * Sets the value of field 'outlineColour'.
+     * 
+     * @param outlineColour the value of field 'outlineColour'.
+     */
+    public void setOutlineColour(
+            final int outlineColour) {
+        this._outlineColour = outlineColour;
+        this._has_outlineColour = true;
+    }
+
+    /**
+     * Sets the value of field 'pidThreshold'.
+     * 
+     * @param pidThreshold the value of field 'pidThreshold'.
+     */
+    public void setPidThreshold(
+            final int pidThreshold) {
+        this._pidThreshold = pidThreshold;
+        this._has_pidThreshold = true;
+    }
+
+    /**
+     * 
+     * 
+     * @param index
+     * @param vSeq
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void setSeq(
+            final int index,
+            final int vSeq)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._seqList.size()) {
+            throw new IndexOutOfBoundsException("setSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");
+        }
+        
+        this._seqList.set(index, new java.lang.Integer(vSeq));
+    }
+
+    /**
+     * 
+     * 
+     * @param vSeqArray
+     */
+    public void setSeq(
+            final int[] vSeqArray) {
+        //-- copy array
+        _seqList.clear();
+        
+        for (int i = 0; i < vSeqArray.length; i++) {
+                this._seqList.add(new java.lang.Integer(vSeqArray[i]));
+        }
+    }
+
+    /**
+     * Sets the value of field 'start'.
+     * 
+     * @param start the value of field 'start'.
+     */
+    public void setStart(
+            final int start) {
+        this._start = start;
+        this._has_start = 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.binding.JGroup
+     */
+    public static jalview.binding.JGroup unmarshal(
+            final java.io.Reader reader)
+    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+        return (jalview.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.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);
+    }
+
+}