X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FJalviewModelSequence.java;h=3ef30ad8e229a476a828c6595df02729dc181014;hb=65540422b57569f5bb9766742eccacc75f1368f0;hp=45f486b0da3e1755e55c9dcaf1db544d310ae7f8;hpb=65df62f4b048a1615d32ea2c3576082ad2b63af8;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/JalviewModelSequence.java b/src/jalview/schemabinding/version2/JalviewModelSequence.java
index 45f486b..3ef30ad 100755
--- a/src/jalview/schemabinding/version2/JalviewModelSequence.java
+++ b/src/jalview/schemabinding/version2/JalviewModelSequence.java
@@ -1,27 +1,29 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 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 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 JalviewModelSequence.
@@ -36,32 +38,32 @@ public class JalviewModelSequence implements java.io.Serializable {
     //--------------------------/
 
     /**
-     * Field _JSeqList
+     * Field _JSeqList.
      */
     private java.util.Vector _JSeqList;
 
     /**
-     * Field _JGroupList
+     * Field _JGroupList.
      */
     private java.util.Vector _JGroupList;
 
     /**
-     * Field _viewportList
+     * Field _viewportList.
      */
     private java.util.Vector _viewportList;
 
     /**
-     * Field _userColoursList
+     * Field _userColoursList.
      */
     private java.util.Vector _userColoursList;
 
     /**
-     * Field _treeList
+     * Field _treeList.
      */
     private java.util.Vector _treeList;
 
     /**
-     * Field _featureSettings
+     * Field _featureSettings.
      */
     private jalview.schemabinding.version2.FeatureSettings _featureSettings;
 
@@ -72,12 +74,12 @@ public class JalviewModelSequence implements java.io.Serializable {
 
     public JalviewModelSequence() {
         super();
-        _JSeqList = new Vector();
-        _JGroupList = new Vector();
-        _viewportList = new Vector();
-        _userColoursList = new Vector();
-        _treeList = new Vector();
-    } //-- jalview.schemabinding.version2.JalviewModelSequence()
+        this._JSeqList = new java.util.Vector();
+        this._JGroupList = new java.util.Vector();
+        this._viewportList = new java.util.Vector();
+        this._userColoursList = new java.util.Vector();
+        this._treeList = new java.util.Vector();
+    }
 
 
       //-----------/
@@ -85,820 +87,850 @@ public class JalviewModelSequence implements java.io.Serializable {
     //-----------/
 
     /**
-     * Method addJGroup
-     * 
      * 
      * 
      * @param vJGroup
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
      */
-    public void addJGroup(jalview.schemabinding.version2.JGroup vJGroup)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _JGroupList.addElement(vJGroup);
-    } //-- void addJGroup(jalview.schemabinding.version2.JGroup) 
+    public void addJGroup(
+            final jalview.schemabinding.version2.JGroup vJGroup)
+    throws java.lang.IndexOutOfBoundsException {
+        this._JGroupList.addElement(vJGroup);
+    }
 
     /**
-     * Method addJGroup
-     * 
      * 
      * 
      * @param index
      * @param vJGroup
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
      */
-    public void addJGroup(int index, jalview.schemabinding.version2.JGroup vJGroup)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _JGroupList.insertElementAt(vJGroup, index);
-    } //-- void addJGroup(int, jalview.schemabinding.version2.JGroup) 
+    public void addJGroup(
+            final int index,
+            final jalview.schemabinding.version2.JGroup vJGroup)
+    throws java.lang.IndexOutOfBoundsException {
+        this._JGroupList.add(index, vJGroup);
+    }
 
     /**
-     * Method addJSeq
-     * 
      * 
      * 
      * @param vJSeq
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
      */
-    public void addJSeq(jalview.schemabinding.version2.JSeq vJSeq)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _JSeqList.addElement(vJSeq);
-    } //-- void addJSeq(jalview.schemabinding.version2.JSeq) 
+    public void addJSeq(
+            final jalview.schemabinding.version2.JSeq vJSeq)
+    throws java.lang.IndexOutOfBoundsException {
+        this._JSeqList.addElement(vJSeq);
+    }
 
     /**
-     * Method addJSeq
-     * 
      * 
      * 
      * @param index
      * @param vJSeq
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
      */
-    public void addJSeq(int index, jalview.schemabinding.version2.JSeq vJSeq)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _JSeqList.insertElementAt(vJSeq, index);
-    } //-- void addJSeq(int, jalview.schemabinding.version2.JSeq) 
+    public void addJSeq(
+            final int index,
+            final jalview.schemabinding.version2.JSeq vJSeq)
+    throws java.lang.IndexOutOfBoundsException {
+        this._JSeqList.add(index, vJSeq);
+    }
 
     /**
-     * Method addTree
-     * 
      * 
      * 
      * @param vTree
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
      */
-    public void addTree(jalview.schemabinding.version2.Tree vTree)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _treeList.addElement(vTree);
-    } //-- void addTree(jalview.schemabinding.version2.Tree) 
+    public void addTree(
+            final jalview.schemabinding.version2.Tree vTree)
+    throws java.lang.IndexOutOfBoundsException {
+        this._treeList.addElement(vTree);
+    }
 
     /**
-     * Method addTree
-     * 
      * 
      * 
      * @param index
      * @param vTree
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
      */
-    public void addTree(int index, jalview.schemabinding.version2.Tree vTree)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _treeList.insertElementAt(vTree, index);
-    } //-- void addTree(int, jalview.schemabinding.version2.Tree) 
+    public void addTree(
+            final int index,
+            final jalview.schemabinding.version2.Tree vTree)
+    throws java.lang.IndexOutOfBoundsException {
+        this._treeList.add(index, vTree);
+    }
 
     /**
-     * Method addUserColours
-     * 
      * 
      * 
      * @param vUserColours
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
      */
-    public void addUserColours(jalview.schemabinding.version2.UserColours vUserColours)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _userColoursList.addElement(vUserColours);
-    } //-- void addUserColours(jalview.schemabinding.version2.UserColours) 
+    public void addUserColours(
+            final jalview.schemabinding.version2.UserColours vUserColours)
+    throws java.lang.IndexOutOfBoundsException {
+        this._userColoursList.addElement(vUserColours);
+    }
 
     /**
-     * Method addUserColours
-     * 
      * 
      * 
      * @param index
      * @param vUserColours
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
      */
-    public void addUserColours(int index, jalview.schemabinding.version2.UserColours vUserColours)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _userColoursList.insertElementAt(vUserColours, index);
-    } //-- void addUserColours(int, jalview.schemabinding.version2.UserColours) 
+    public void addUserColours(
+            final int index,
+            final jalview.schemabinding.version2.UserColours vUserColours)
+    throws java.lang.IndexOutOfBoundsException {
+        this._userColoursList.add(index, vUserColours);
+    }
 
     /**
-     * Method addViewport
-     * 
      * 
      * 
      * @param vViewport
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
      */
-    public void addViewport(jalview.schemabinding.version2.Viewport vViewport)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _viewportList.addElement(vViewport);
-    } //-- void addViewport(jalview.schemabinding.version2.Viewport) 
+    public void addViewport(
+            final jalview.schemabinding.version2.Viewport vViewport)
+    throws java.lang.IndexOutOfBoundsException {
+        this._viewportList.addElement(vViewport);
+    }
 
     /**
-     * Method addViewport
-     * 
      * 
      * 
      * @param index
      * @param vViewport
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
      */
-    public void addViewport(int index, jalview.schemabinding.version2.Viewport vViewport)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _viewportList.insertElementAt(vViewport, index);
-    } //-- void addViewport(int, jalview.schemabinding.version2.Viewport) 
+    public void addViewport(
+            final int index,
+            final jalview.schemabinding.version2.Viewport vViewport)
+    throws java.lang.IndexOutOfBoundsException {
+        this._viewportList.add(index, vViewport);
+    }
 
     /**
-     * Method enumerateJGroup
-     * 
-     * 
+     * Method enumerateJGroup.
      * 
-     * @return Enumeration
+     * @return an Enumeration over all
+     * jalview.schemabinding.version2.JGroup elements
      */
-    public java.util.Enumeration enumerateJGroup()
-    {
-        return _JGroupList.elements();
-    } //-- java.util.Enumeration enumerateJGroup() 
+    public java.util.Enumeration enumerateJGroup(
+    ) {
+        return this._JGroupList.elements();
+    }
 
     /**
-     * Method enumerateJSeq
+     * Method enumerateJSeq.
      * 
-     * 
-     * 
-     * @return Enumeration
+     * @return an Enumeration over all
+     * jalview.schemabinding.version2.JSeq elements
      */
-    public java.util.Enumeration enumerateJSeq()
-    {
-        return _JSeqList.elements();
-    } //-- java.util.Enumeration enumerateJSeq() 
+    public java.util.Enumeration enumerateJSeq(
+    ) {
+        return this._JSeqList.elements();
+    }
 
     /**
-     * Method enumerateTree
-     * 
-     * 
+     * Method enumerateTree.
      * 
-     * @return Enumeration
+     * @return an Enumeration over all
+     * jalview.schemabinding.version2.Tree elements
      */
-    public java.util.Enumeration enumerateTree()
-    {
-        return _treeList.elements();
-    } //-- java.util.Enumeration enumerateTree() 
+    public java.util.Enumeration enumerateTree(
+    ) {
+        return this._treeList.elements();
+    }
 
     /**
-     * Method enumerateUserColours
+     * Method enumerateUserColours.
      * 
-     * 
-     * 
-     * @return Enumeration
+     * @return an Enumeration over all
+     * jalview.schemabinding.version2.UserColours elements
      */
-    public java.util.Enumeration enumerateUserColours()
-    {
-        return _userColoursList.elements();
-    } //-- java.util.Enumeration enumerateUserColours() 
+    public java.util.Enumeration enumerateUserColours(
+    ) {
+        return this._userColoursList.elements();
+    }
 
     /**
-     * Method enumerateViewport
-     * 
-     * 
+     * Method enumerateViewport.
      * 
-     * @return Enumeration
+     * @return an Enumeration over all
+     * jalview.schemabinding.version2.Viewport elements
      */
-    public java.util.Enumeration enumerateViewport()
-    {
-        return _viewportList.elements();
-    } //-- java.util.Enumeration enumerateViewport() 
+    public java.util.Enumeration enumerateViewport(
+    ) {
+        return this._viewportList.elements();
+    }
 
     /**
      * Returns the value of field 'featureSettings'.
      * 
-     * @return FeatureSettings
-     * @return the value of field 'featureSettings'.
+     * @return the value of field 'FeatureSettings'.
      */
-    public jalview.schemabinding.version2.FeatureSettings getFeatureSettings()
-    {
+    public jalview.schemabinding.version2.FeatureSettings getFeatureSettings(
+    ) {
         return this._featureSettings;
-    } //-- jalview.schemabinding.version2.FeatureSettings getFeatureSettings() 
+    }
 
     /**
-     * Method getJGroup
-     * 
-     * 
+     * Method getJGroup.
      * 
      * @param index
-     * @return JGroup
-     */
-    public jalview.schemabinding.version2.JGroup getJGroup(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _JGroupList.size())) {
-            throw new IndexOutOfBoundsException();
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     * @return the value of the
+     * jalview.schemabinding.version2.JGroup at the given index
+     */
+    public jalview.schemabinding.version2.JGroup getJGroup(
+            final int index)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._JGroupList.size()) {
+            throw new IndexOutOfBoundsException("getJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");
         }
         
-        return (jalview.schemabinding.version2.JGroup) _JGroupList.elementAt(index);
-    } //-- jalview.schemabinding.version2.JGroup getJGroup(int) 
+        return (jalview.schemabinding.version2.JGroup) _JGroupList.get(index);
+    }
 
     /**
-     * Method getJGroup
-     * 
-     * 
+     * Method getJGroup.Returns the contents of the collection in
+     * an Array.  <p>Note:  Just in case the collection contents
+     * are changing in another thread, we pass a 0-length Array of
+     * the correct type into the API call.  This way we <i>know</i>
+     * that the Array returned is of exactly the correct length.
      * 
-     * @return JGroup
+     * @return this collection as an Array
      */
-    public jalview.schemabinding.version2.JGroup[] getJGroup()
-    {
-        int size = _JGroupList.size();
-        jalview.schemabinding.version2.JGroup[] mArray = new jalview.schemabinding.version2.JGroup[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.JGroup) _JGroupList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.JGroup[] getJGroup() 
+    public jalview.schemabinding.version2.JGroup[] getJGroup(
+    ) {
+        jalview.schemabinding.version2.JGroup[] array = new jalview.schemabinding.version2.JGroup[0];
+        return (jalview.schemabinding.version2.JGroup[]) this._JGroupList.toArray(array);
+    }
 
     /**
-     * Method getJGroupCount
-     * 
+     * Method getJGroupCount.
      * 
-     * 
-     * @return int
+     * @return the size of this collection
      */
-    public int getJGroupCount()
-    {
-        return _JGroupList.size();
-    } //-- int getJGroupCount() 
+    public int getJGroupCount(
+    ) {
+        return this._JGroupList.size();
+    }
 
     /**
-     * Method getJSeq
-     * 
-     * 
+     * Method getJSeq.
      * 
      * @param index
-     * @return JSeq
-     */
-    public jalview.schemabinding.version2.JSeq getJSeq(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _JSeqList.size())) {
-            throw new IndexOutOfBoundsException();
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     * @return the value of the jalview.schemabinding.version2.JSeq
+     * at the given index
+     */
+    public jalview.schemabinding.version2.JSeq getJSeq(
+            final int index)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._JSeqList.size()) {
+            throw new IndexOutOfBoundsException("getJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
         }
         
-        return (jalview.schemabinding.version2.JSeq) _JSeqList.elementAt(index);
-    } //-- jalview.schemabinding.version2.JSeq getJSeq(int) 
+        return (jalview.schemabinding.version2.JSeq) _JSeqList.get(index);
+    }
 
     /**
-     * Method getJSeq
-     * 
+     * Method getJSeq.Returns the contents of the collection in an
+     * Array.  <p>Note:  Just in case the collection contents are
+     * changing in another thread, we pass a 0-length Array of the
+     * correct type into the API call.  This way we <i>know</i>
+     * that the Array returned is of exactly the correct length.
      * 
-     * 
-     * @return JSeq
+     * @return this collection as an Array
      */
-    public jalview.schemabinding.version2.JSeq[] getJSeq()
-    {
-        int size = _JSeqList.size();
-        jalview.schemabinding.version2.JSeq[] mArray = new jalview.schemabinding.version2.JSeq[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.JSeq) _JSeqList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.JSeq[] getJSeq() 
+    public jalview.schemabinding.version2.JSeq[] getJSeq(
+    ) {
+        jalview.schemabinding.version2.JSeq[] array = new jalview.schemabinding.version2.JSeq[0];
+        return (jalview.schemabinding.version2.JSeq[]) this._JSeqList.toArray(array);
+    }
 
     /**
-     * Method getJSeqCount
+     * Method getJSeqCount.
      * 
-     * 
-     * 
-     * @return int
+     * @return the size of this collection
      */
-    public int getJSeqCount()
-    {
-        return _JSeqList.size();
-    } //-- int getJSeqCount() 
+    public int getJSeqCount(
+    ) {
+        return this._JSeqList.size();
+    }
 
     /**
-     * Method getTree
-     * 
-     * 
+     * Method getTree.
      * 
      * @param index
-     * @return Tree
-     */
-    public jalview.schemabinding.version2.Tree getTree(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _treeList.size())) {
-            throw new IndexOutOfBoundsException();
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     * @return the value of the jalview.schemabinding.version2.Tree
+     * at the given index
+     */
+    public jalview.schemabinding.version2.Tree getTree(
+            final int index)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._treeList.size()) {
+            throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
         }
         
-        return (jalview.schemabinding.version2.Tree) _treeList.elementAt(index);
-    } //-- jalview.schemabinding.version2.Tree getTree(int) 
+        return (jalview.schemabinding.version2.Tree) _treeList.get(index);
+    }
 
     /**
-     * Method getTree
+     * Method getTree.Returns the contents of the collection in an
+     * Array.  <p>Note:  Just in case the collection contents are
+     * changing in another thread, we pass a 0-length Array of the
+     * correct type into the API call.  This way we <i>know</i>
+     * that the Array returned is of exactly the correct length.
      * 
-     * 
-     * 
-     * @return Tree
+     * @return this collection as an Array
      */
-    public jalview.schemabinding.version2.Tree[] getTree()
-    {
-        int size = _treeList.size();
-        jalview.schemabinding.version2.Tree[] mArray = new jalview.schemabinding.version2.Tree[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.Tree) _treeList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.Tree[] getTree() 
+    public jalview.schemabinding.version2.Tree[] getTree(
+    ) {
+        jalview.schemabinding.version2.Tree[] array = new jalview.schemabinding.version2.Tree[0];
+        return (jalview.schemabinding.version2.Tree[]) this._treeList.toArray(array);
+    }
 
     /**
-     * Method getTreeCount
-     * 
+     * Method getTreeCount.
      * 
-     * 
-     * @return int
+     * @return the size of this collection
      */
-    public int getTreeCount()
-    {
-        return _treeList.size();
-    } //-- int getTreeCount() 
+    public int getTreeCount(
+    ) {
+        return this._treeList.size();
+    }
 
     /**
-     * Method getUserColours
-     * 
-     * 
+     * Method getUserColours.
      * 
      * @param index
-     * @return UserColours
-     */
-    public jalview.schemabinding.version2.UserColours getUserColours(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _userColoursList.size())) {
-            throw new IndexOutOfBoundsException();
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     * @return the value of the
+     * jalview.schemabinding.version2.UserColours at the given index
+     */
+    public jalview.schemabinding.version2.UserColours getUserColours(
+            final int index)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._userColoursList.size()) {
+            throw new IndexOutOfBoundsException("getUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");
         }
         
-        return (jalview.schemabinding.version2.UserColours) _userColoursList.elementAt(index);
-    } //-- jalview.schemabinding.version2.UserColours getUserColours(int) 
+        return (jalview.schemabinding.version2.UserColours) _userColoursList.get(index);
+    }
 
     /**
-     * Method getUserColours
-     * 
+     * Method getUserColours.Returns the contents of the collection
+     * in an Array.  <p>Note:  Just in case the collection contents
+     * are changing in another thread, we pass a 0-length Array of
+     * the correct type into the API call.  This way we <i>know</i>
+     * that the Array returned is of exactly the correct length.
      * 
-     * 
-     * @return UserColours
+     * @return this collection as an Array
      */
-    public jalview.schemabinding.version2.UserColours[] getUserColours()
-    {
-        int size = _userColoursList.size();
-        jalview.schemabinding.version2.UserColours[] mArray = new jalview.schemabinding.version2.UserColours[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.UserColours) _userColoursList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.UserColours[] getUserColours() 
+    public jalview.schemabinding.version2.UserColours[] getUserColours(
+    ) {
+        jalview.schemabinding.version2.UserColours[] array = new jalview.schemabinding.version2.UserColours[0];
+        return (jalview.schemabinding.version2.UserColours[]) this._userColoursList.toArray(array);
+    }
 
     /**
-     * Method getUserColoursCount
-     * 
-     * 
+     * Method getUserColoursCount.
      * 
-     * @return int
+     * @return the size of this collection
      */
-    public int getUserColoursCount()
-    {
-        return _userColoursList.size();
-    } //-- int getUserColoursCount() 
+    public int getUserColoursCount(
+    ) {
+        return this._userColoursList.size();
+    }
 
     /**
-     * Method getViewport
-     * 
-     * 
+     * Method getViewport.
      * 
      * @param index
-     * @return Viewport
-     */
-    public jalview.schemabinding.version2.Viewport getViewport(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _viewportList.size())) {
-            throw new IndexOutOfBoundsException();
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     * @return the value of the
+     * jalview.schemabinding.version2.Viewport at the given index
+     */
+    public jalview.schemabinding.version2.Viewport getViewport(
+            final int index)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._viewportList.size()) {
+            throw new IndexOutOfBoundsException("getViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");
         }
         
-        return (jalview.schemabinding.version2.Viewport) _viewportList.elementAt(index);
-    } //-- jalview.schemabinding.version2.Viewport getViewport(int) 
+        return (jalview.schemabinding.version2.Viewport) _viewportList.get(index);
+    }
 
     /**
-     * Method getViewport
-     * 
-     * 
+     * Method getViewport.Returns the contents of the collection in
+     * an Array.  <p>Note:  Just in case the collection contents
+     * are changing in another thread, we pass a 0-length Array of
+     * the correct type into the API call.  This way we <i>know</i>
+     * that the Array returned is of exactly the correct length.
      * 
-     * @return Viewport
+     * @return this collection as an Array
      */
-    public jalview.schemabinding.version2.Viewport[] getViewport()
-    {
-        int size = _viewportList.size();
-        jalview.schemabinding.version2.Viewport[] mArray = new jalview.schemabinding.version2.Viewport[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.Viewport) _viewportList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.Viewport[] getViewport() 
+    public jalview.schemabinding.version2.Viewport[] getViewport(
+    ) {
+        jalview.schemabinding.version2.Viewport[] array = new jalview.schemabinding.version2.Viewport[0];
+        return (jalview.schemabinding.version2.Viewport[]) this._viewportList.toArray(array);
+    }
 
     /**
-     * Method getViewportCount
-     * 
+     * Method getViewportCount.
      * 
-     * 
-     * @return int
+     * @return the size of this collection
      */
-    public int getViewportCount()
-    {
-        return _viewportList.size();
-    } //-- int getViewportCount() 
+    public int getViewportCount(
+    ) {
+        return this._viewportList.size();
+    }
 
     /**
-     * Method isValid
-     * 
+     * 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) 
+    }
 
     /**
-     * Method removeAllJGroup
-     * 
      */
-    public void removeAllJGroup()
-    {
-        _JGroupList.removeAllElements();
-    } //-- void removeAllJGroup() 
+    public void removeAllJGroup(
+    ) {
+        this._JGroupList.clear();
+    }
 
     /**
-     * Method removeAllJSeq
-     * 
      */
-    public void removeAllJSeq()
-    {
-        _JSeqList.removeAllElements();
-    } //-- void removeAllJSeq() 
+    public void removeAllJSeq(
+    ) {
+        this._JSeqList.clear();
+    }
 
     /**
-     * Method removeAllTree
-     * 
      */
-    public void removeAllTree()
-    {
-        _treeList.removeAllElements();
-    } //-- void removeAllTree() 
+    public void removeAllTree(
+    ) {
+        this._treeList.clear();
+    }
 
     /**
-     * Method removeAllUserColours
-     * 
      */
-    public void removeAllUserColours()
-    {
-        _userColoursList.removeAllElements();
-    } //-- void removeAllUserColours() 
+    public void removeAllUserColours(
+    ) {
+        this._userColoursList.clear();
+    }
 
     /**
-     * Method removeAllViewport
-     * 
      */
-    public void removeAllViewport()
-    {
-        _viewportList.removeAllElements();
-    } //-- void removeAllViewport() 
+    public void removeAllViewport(
+    ) {
+        this._viewportList.clear();
+    }
 
     /**
-     * Method removeJGroup
-     * 
+     * Method removeJGroup.
      * 
+     * @param vJGroup
+     * @return true if the object was removed from the collection.
+     */
+    public boolean removeJGroup(
+            final jalview.schemabinding.version2.JGroup vJGroup) {
+        boolean removed = _JGroupList.remove(vJGroup);
+        return removed;
+    }
+
+    /**
+     * Method removeJGroupAt.
      * 
      * @param index
-     * @return JGroup
+     * @return the element removed from the collection
      */
-    public jalview.schemabinding.version2.JGroup removeJGroup(int index)
-    {
-        java.lang.Object obj = _JGroupList.elementAt(index);
-        _JGroupList.removeElementAt(index);
+    public jalview.schemabinding.version2.JGroup removeJGroupAt(
+            final int index) {
+        java.lang.Object obj = this._JGroupList.remove(index);
         return (jalview.schemabinding.version2.JGroup) obj;
-    } //-- jalview.schemabinding.version2.JGroup removeJGroup(int) 
+    }
 
     /**
-     * Method removeJSeq
-     * 
+     * Method removeJSeq.
      * 
+     * @param vJSeq
+     * @return true if the object was removed from the collection.
+     */
+    public boolean removeJSeq(
+            final jalview.schemabinding.version2.JSeq vJSeq) {
+        boolean removed = _JSeqList.remove(vJSeq);
+        return removed;
+    }
+
+    /**
+     * Method removeJSeqAt.
      * 
      * @param index
-     * @return JSeq
+     * @return the element removed from the collection
      */
-    public jalview.schemabinding.version2.JSeq removeJSeq(int index)
-    {
-        java.lang.Object obj = _JSeqList.elementAt(index);
-        _JSeqList.removeElementAt(index);
+    public jalview.schemabinding.version2.JSeq removeJSeqAt(
+            final int index) {
+        java.lang.Object obj = this._JSeqList.remove(index);
         return (jalview.schemabinding.version2.JSeq) obj;
-    } //-- jalview.schemabinding.version2.JSeq removeJSeq(int) 
+    }
 
     /**
-     * Method removeTree
-     * 
+     * Method removeTree.
      * 
+     * @param vTree
+     * @return true if the object was removed from the collection.
+     */
+    public boolean removeTree(
+            final jalview.schemabinding.version2.Tree vTree) {
+        boolean removed = _treeList.remove(vTree);
+        return removed;
+    }
+
+    /**
+     * Method removeTreeAt.
      * 
      * @param index
-     * @return Tree
+     * @return the element removed from the collection
      */
-    public jalview.schemabinding.version2.Tree removeTree(int index)
-    {
-        java.lang.Object obj = _treeList.elementAt(index);
-        _treeList.removeElementAt(index);
+    public jalview.schemabinding.version2.Tree removeTreeAt(
+            final int index) {
+        java.lang.Object obj = this._treeList.remove(index);
         return (jalview.schemabinding.version2.Tree) obj;
-    } //-- jalview.schemabinding.version2.Tree removeTree(int) 
+    }
 
     /**
-     * Method removeUserColours
-     * 
+     * Method removeUserColours.
      * 
+     * @param vUserColours
+     * @return true if the object was removed from the collection.
+     */
+    public boolean removeUserColours(
+            final jalview.schemabinding.version2.UserColours vUserColours) {
+        boolean removed = _userColoursList.remove(vUserColours);
+        return removed;
+    }
+
+    /**
+     * Method removeUserColoursAt.
      * 
      * @param index
-     * @return UserColours
+     * @return the element removed from the collection
      */
-    public jalview.schemabinding.version2.UserColours removeUserColours(int index)
-    {
-        java.lang.Object obj = _userColoursList.elementAt(index);
-        _userColoursList.removeElementAt(index);
+    public jalview.schemabinding.version2.UserColours removeUserColoursAt(
+            final int index) {
+        java.lang.Object obj = this._userColoursList.remove(index);
         return (jalview.schemabinding.version2.UserColours) obj;
-    } //-- jalview.schemabinding.version2.UserColours removeUserColours(int) 
+    }
 
     /**
-     * Method removeViewport
-     * 
+     * Method removeViewport.
      * 
+     * @param vViewport
+     * @return true if the object was removed from the collection.
+     */
+    public boolean removeViewport(
+            final jalview.schemabinding.version2.Viewport vViewport) {
+        boolean removed = _viewportList.remove(vViewport);
+        return removed;
+    }
+
+    /**
+     * Method removeViewportAt.
      * 
      * @param index
-     * @return Viewport
+     * @return the element removed from the collection
      */
-    public jalview.schemabinding.version2.Viewport removeViewport(int index)
-    {
-        java.lang.Object obj = _viewportList.elementAt(index);
-        _viewportList.removeElementAt(index);
+    public jalview.schemabinding.version2.Viewport removeViewportAt(
+            final int index) {
+        java.lang.Object obj = this._viewportList.remove(index);
         return (jalview.schemabinding.version2.Viewport) obj;
-    } //-- jalview.schemabinding.version2.Viewport removeViewport(int) 
+    }
 
     /**
      * Sets the value of field 'featureSettings'.
      * 
      * @param featureSettings the value of field 'featureSettings'.
      */
-    public void setFeatureSettings(jalview.schemabinding.version2.FeatureSettings featureSettings)
-    {
+    public void setFeatureSettings(
+            final jalview.schemabinding.version2.FeatureSettings featureSettings) {
         this._featureSettings = featureSettings;
-    } //-- void setFeatureSettings(jalview.schemabinding.version2.FeatureSettings) 
+    }
 
     /**
-     * Method setJGroup
-     * 
      * 
      * 
      * @param index
      * @param vJGroup
-     */
-    public void setJGroup(int index, jalview.schemabinding.version2.JGroup vJGroup)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _JGroupList.size())) {
-            throw new IndexOutOfBoundsException();
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void setJGroup(
+            final int index,
+            final jalview.schemabinding.version2.JGroup vJGroup)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._JGroupList.size()) {
+            throw new IndexOutOfBoundsException("setJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");
         }
-        _JGroupList.setElementAt(vJGroup, index);
-    } //-- void setJGroup(int, jalview.schemabinding.version2.JGroup) 
+        
+        this._JGroupList.set(index, vJGroup);
+    }
 
     /**
-     * Method setJGroup
-     * 
      * 
      * 
-     * @param JGroupArray
+     * @param vJGroupArray
      */
-    public void setJGroup(jalview.schemabinding.version2.JGroup[] JGroupArray)
-    {
+    public void setJGroup(
+            final jalview.schemabinding.version2.JGroup[] vJGroupArray) {
         //-- copy array
-        _JGroupList.removeAllElements();
-        for (int i = 0; i < JGroupArray.length; i++) {
-            _JGroupList.addElement(JGroupArray[i]);
+        _JGroupList.clear();
+        
+        for (int i = 0; i < vJGroupArray.length; i++) {
+                this._JGroupList.add(vJGroupArray[i]);
         }
-    } //-- void setJGroup(jalview.schemabinding.version2.JGroup) 
+    }
 
     /**
-     * Method setJSeq
-     * 
      * 
      * 
      * @param index
      * @param vJSeq
-     */
-    public void setJSeq(int index, jalview.schemabinding.version2.JSeq vJSeq)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _JSeqList.size())) {
-            throw new IndexOutOfBoundsException();
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void setJSeq(
+            final int index,
+            final jalview.schemabinding.version2.JSeq vJSeq)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._JSeqList.size()) {
+            throw new IndexOutOfBoundsException("setJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
         }
-        _JSeqList.setElementAt(vJSeq, index);
-    } //-- void setJSeq(int, jalview.schemabinding.version2.JSeq) 
+        
+        this._JSeqList.set(index, vJSeq);
+    }
 
     /**
-     * Method setJSeq
      * 
      * 
-     * 
-     * @param JSeqArray
+     * @param vJSeqArray
      */
-    public void setJSeq(jalview.schemabinding.version2.JSeq[] JSeqArray)
-    {
+    public void setJSeq(
+            final jalview.schemabinding.version2.JSeq[] vJSeqArray) {
         //-- copy array
-        _JSeqList.removeAllElements();
-        for (int i = 0; i < JSeqArray.length; i++) {
-            _JSeqList.addElement(JSeqArray[i]);
+        _JSeqList.clear();
+        
+        for (int i = 0; i < vJSeqArray.length; i++) {
+                this._JSeqList.add(vJSeqArray[i]);
         }
-    } //-- void setJSeq(jalview.schemabinding.version2.JSeq) 
+    }
 
     /**
-     * Method setTree
-     * 
      * 
      * 
      * @param index
      * @param vTree
-     */
-    public void setTree(int index, jalview.schemabinding.version2.Tree vTree)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _treeList.size())) {
-            throw new IndexOutOfBoundsException();
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void setTree(
+            final int index,
+            final jalview.schemabinding.version2.Tree vTree)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._treeList.size()) {
+            throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
         }
-        _treeList.setElementAt(vTree, index);
-    } //-- void setTree(int, jalview.schemabinding.version2.Tree) 
+        
+        this._treeList.set(index, vTree);
+    }
 
     /**
-     * Method setTree
-     * 
      * 
      * 
-     * @param treeArray
+     * @param vTreeArray
      */
-    public void setTree(jalview.schemabinding.version2.Tree[] treeArray)
-    {
+    public void setTree(
+            final jalview.schemabinding.version2.Tree[] vTreeArray) {
         //-- copy array
-        _treeList.removeAllElements();
-        for (int i = 0; i < treeArray.length; i++) {
-            _treeList.addElement(treeArray[i]);
+        _treeList.clear();
+        
+        for (int i = 0; i < vTreeArray.length; i++) {
+                this._treeList.add(vTreeArray[i]);
         }
-    } //-- void setTree(jalview.schemabinding.version2.Tree) 
+    }
 
     /**
-     * Method setUserColours
-     * 
      * 
      * 
      * @param index
      * @param vUserColours
-     */
-    public void setUserColours(int index, jalview.schemabinding.version2.UserColours vUserColours)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _userColoursList.size())) {
-            throw new IndexOutOfBoundsException();
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void setUserColours(
+            final int index,
+            final jalview.schemabinding.version2.UserColours vUserColours)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._userColoursList.size()) {
+            throw new IndexOutOfBoundsException("setUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");
         }
-        _userColoursList.setElementAt(vUserColours, index);
-    } //-- void setUserColours(int, jalview.schemabinding.version2.UserColours) 
+        
+        this._userColoursList.set(index, vUserColours);
+    }
 
     /**
-     * Method setUserColours
      * 
      * 
-     * 
-     * @param userColoursArray
+     * @param vUserColoursArray
      */
-    public void setUserColours(jalview.schemabinding.version2.UserColours[] userColoursArray)
-    {
+    public void setUserColours(
+            final jalview.schemabinding.version2.UserColours[] vUserColoursArray) {
         //-- copy array
-        _userColoursList.removeAllElements();
-        for (int i = 0; i < userColoursArray.length; i++) {
-            _userColoursList.addElement(userColoursArray[i]);
+        _userColoursList.clear();
+        
+        for (int i = 0; i < vUserColoursArray.length; i++) {
+                this._userColoursList.add(vUserColoursArray[i]);
         }
-    } //-- void setUserColours(jalview.schemabinding.version2.UserColours) 
+    }
 
     /**
-     * Method setViewport
-     * 
      * 
      * 
      * @param index
      * @param vViewport
-     */
-    public void setViewport(int index, jalview.schemabinding.version2.Viewport vViewport)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _viewportList.size())) {
-            throw new IndexOutOfBoundsException();
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void setViewport(
+            final int index,
+            final jalview.schemabinding.version2.Viewport vViewport)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._viewportList.size()) {
+            throw new IndexOutOfBoundsException("setViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");
         }
-        _viewportList.setElementAt(vViewport, index);
-    } //-- void setViewport(int, jalview.schemabinding.version2.Viewport) 
+        
+        this._viewportList.set(index, vViewport);
+    }
 
     /**
-     * Method setViewport
-     * 
      * 
      * 
-     * @param viewportArray
+     * @param vViewportArray
      */
-    public void setViewport(jalview.schemabinding.version2.Viewport[] viewportArray)
-    {
+    public void setViewport(
+            final jalview.schemabinding.version2.Viewport[] vViewportArray) {
         //-- copy array
-        _viewportList.removeAllElements();
-        for (int i = 0; i < viewportArray.length; i++) {
-            _viewportList.addElement(viewportArray[i]);
+        _viewportList.clear();
+        
+        for (int i = 0; i < vViewportArray.length; i++) {
+                this._viewportList.add(vViewportArray[i]);
         }
-    } //-- void setViewport(jalview.schemabinding.version2.Viewport) 
+    }
 
     /**
-     * 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.JalviewModelSequence
+     */
+    public static jalview.schemabinding.version2.JalviewModelSequence unmarshal(
+            final java.io.Reader reader)
+    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
         return (jalview.schemabinding.version2.JalviewModelSequence) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewModelSequence.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() 
+    }
 
 }