X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FJSeq.java;h=a5dc2f7e23bcdc7627d7ae1c8e3cfe77468f152b;hb=a95b88b05400d7e841f9523d4c4228c678307654;hp=19e2e6dbf94148a3b0af4277f2d6faab7fadcb0c;hpb=48df59aa393e03aa7269b2df662ac1b8d58cbb25;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/JSeq.java b/src/jalview/schemabinding/version2/JSeq.java
index 19e2e6d..a5dc2f7 100755
--- a/src/jalview/schemabinding/version2/JSeq.java
+++ b/src/jalview/schemabinding/version2/JSeq.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.
  * $Id$
  */
@@ -11,17 +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 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 JSeq.
@@ -36,7 +27,7 @@ public class JSeq implements java.io.Serializable {
     //--------------------------/
 
     /**
-     * Field _colour
+     * Field _colour.
      */
     private int _colour;
 
@@ -46,7 +37,7 @@ public class JSeq implements java.io.Serializable {
     private boolean _has_colour;
 
     /**
-     * Field _start
+     * Field _start.
      */
     private int _start;
 
@@ -56,7 +47,7 @@ public class JSeq implements java.io.Serializable {
     private boolean _has_start;
 
     /**
-     * Field _end
+     * Field _end.
      */
     private int _end;
 
@@ -66,17 +57,12 @@ public class JSeq implements java.io.Serializable {
     private boolean _has_end;
 
     /**
-     * Field _id
+     * Field _id.
      */
-    private int _id;
+    private java.lang.String _id;
 
     /**
-     * keeps track of state for field: _id
-     */
-    private boolean _has_id;
-
-    /**
-     * Field _hidden
+     * Field _hidden.
      */
     private boolean _hidden;
 
@@ -86,17 +72,17 @@ public class JSeq implements java.io.Serializable {
     private boolean _has_hidden;
 
     /**
-     * Field _featuresList
+     * Field _featuresList.
      */
     private java.util.Vector _featuresList;
 
     /**
-     * Field _pdbidsList
+     * Field _pdbidsList.
      */
     private java.util.Vector _pdbidsList;
 
     /**
-     * Field _hiddenSequencesList
+     * Field _hiddenSequencesList.
      */
     private java.util.Vector _hiddenSequencesList;
 
@@ -107,10 +93,10 @@ public class JSeq implements java.io.Serializable {
 
     public JSeq() {
         super();
-        _featuresList = new Vector();
-        _pdbidsList = new Vector();
-        _hiddenSequencesList = new Vector();
-    } //-- jalview.schemabinding.version2.JSeq()
+        this._featuresList = new java.util.Vector();
+        this._pdbidsList = new java.util.Vector();
+        this._hiddenSequencesList = new java.util.Vector();
+    }
 
 
       //-----------/
@@ -118,724 +104,711 @@ public class JSeq implements java.io.Serializable {
     //-----------/
 
     /**
-     * Method addFeatures
-     * 
      * 
      * 
      * @param vFeatures
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
      */
-    public void addFeatures(jalview.schemabinding.version2.Features vFeatures)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _featuresList.addElement(vFeatures);
-    } //-- void addFeatures(jalview.schemabinding.version2.Features) 
+    public void addFeatures(
+            final jalview.schemabinding.version2.Features vFeatures)
+    throws java.lang.IndexOutOfBoundsException {
+        this._featuresList.addElement(vFeatures);
+    }
 
     /**
-     * Method addFeatures
-     * 
      * 
      * 
      * @param index
      * @param vFeatures
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
      */
-    public void addFeatures(int index, jalview.schemabinding.version2.Features vFeatures)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _featuresList.insertElementAt(vFeatures, index);
-    } //-- void addFeatures(int, jalview.schemabinding.version2.Features) 
+    public void addFeatures(
+            final int index,
+            final jalview.schemabinding.version2.Features vFeatures)
+    throws java.lang.IndexOutOfBoundsException {
+        this._featuresList.add(index, vFeatures);
+    }
 
     /**
-     * Method addHiddenSequences
-     * 
      * 
      * 
      * @param vHiddenSequences
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
      */
-    public void addHiddenSequences(int vHiddenSequences)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _hiddenSequencesList.addElement(new java.lang.Integer(vHiddenSequences));
-    } //-- void addHiddenSequences(int) 
+    public void addHiddenSequences(
+            final int vHiddenSequences)
+    throws java.lang.IndexOutOfBoundsException {
+        this._hiddenSequencesList.addElement(new java.lang.Integer(vHiddenSequences));
+    }
 
     /**
-     * Method addHiddenSequences
-     * 
      * 
      * 
      * @param index
      * @param vHiddenSequences
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
      */
-    public void addHiddenSequences(int index, int vHiddenSequences)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _hiddenSequencesList.insertElementAt(new java.lang.Integer(vHiddenSequences), index);
-    } //-- void addHiddenSequences(int, int) 
+    public void addHiddenSequences(
+            final int index,
+            final int vHiddenSequences)
+    throws java.lang.IndexOutOfBoundsException {
+        this._hiddenSequencesList.add(index, new java.lang.Integer(vHiddenSequences));
+    }
 
     /**
-     * Method addPdbids
-     * 
      * 
      * 
      * @param vPdbids
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
      */
-    public void addPdbids(jalview.schemabinding.version2.Pdbids vPdbids)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _pdbidsList.addElement(vPdbids);
-    } //-- void addPdbids(jalview.schemabinding.version2.Pdbids) 
+    public void addPdbids(
+            final jalview.schemabinding.version2.Pdbids vPdbids)
+    throws java.lang.IndexOutOfBoundsException {
+        this._pdbidsList.addElement(vPdbids);
+    }
 
     /**
-     * Method addPdbids
-     * 
      * 
      * 
      * @param index
      * @param vPdbids
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
      */
-    public void addPdbids(int index, jalview.schemabinding.version2.Pdbids vPdbids)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _pdbidsList.insertElementAt(vPdbids, index);
-    } //-- void addPdbids(int, jalview.schemabinding.version2.Pdbids) 
+    public void addPdbids(
+            final int index,
+            final jalview.schemabinding.version2.Pdbids vPdbids)
+    throws java.lang.IndexOutOfBoundsException {
+        this._pdbidsList.add(index, vPdbids);
+    }
 
     /**
-     * Method deleteColour
-     * 
      */
-    public void deleteColour()
-    {
+    public void deleteColour(
+    ) {
         this._has_colour= false;
-    } //-- void deleteColour() 
+    }
 
     /**
-     * Method deleteEnd
-     * 
      */
-    public void deleteEnd()
-    {
+    public void deleteEnd(
+    ) {
         this._has_end= false;
-    } //-- void deleteEnd() 
+    }
 
     /**
-     * Method deleteHidden
-     * 
      */
-    public void deleteHidden()
-    {
+    public void deleteHidden(
+    ) {
         this._has_hidden= false;
-    } //-- void deleteHidden() 
+    }
 
     /**
-     * Method deleteId
-     * 
      */
-    public void deleteId()
-    {
-        this._has_id= false;
-    } //-- void deleteId() 
-
-    /**
-     * Method deleteStart
-     * 
-     */
-    public void deleteStart()
-    {
+    public void deleteStart(
+    ) {
         this._has_start= false;
-    } //-- void deleteStart() 
+    }
 
     /**
-     * Method enumerateFeatures
-     * 
+     * Method enumerateFeatures.
      * 
-     * 
-     * @return Enumeration
+     * @return an Enumeration over all
+     * jalview.schemabinding.version2.Features elements
      */
-    public java.util.Enumeration enumerateFeatures()
-    {
-        return _featuresList.elements();
-    } //-- java.util.Enumeration enumerateFeatures() 
+    public java.util.Enumeration enumerateFeatures(
+    ) {
+        return this._featuresList.elements();
+    }
 
     /**
-     * Method enumerateHiddenSequences
-     * 
-     * 
+     * Method enumerateHiddenSequences.
      * 
-     * @return Enumeration
+     * @return an Enumeration over all int elements
      */
-    public java.util.Enumeration enumerateHiddenSequences()
-    {
-        return _hiddenSequencesList.elements();
-    } //-- java.util.Enumeration enumerateHiddenSequences() 
+    public java.util.Enumeration enumerateHiddenSequences(
+    ) {
+        return this._hiddenSequencesList.elements();
+    }
 
     /**
-     * Method enumeratePdbids
+     * Method enumeratePdbids.
      * 
-     * 
-     * 
-     * @return Enumeration
+     * @return an Enumeration over all
+     * jalview.schemabinding.version2.Pdbids elements
      */
-    public java.util.Enumeration enumeratePdbids()
-    {
-        return _pdbidsList.elements();
-    } //-- java.util.Enumeration enumeratePdbids() 
+    public java.util.Enumeration enumeratePdbids(
+    ) {
+        return this._pdbidsList.elements();
+    }
 
     /**
      * Returns the value of field 'colour'.
      * 
-     * @return int
-     * @return the value of field 'colour'.
+     * @return the value of field 'Colour'.
      */
-    public int getColour()
-    {
+    public int getColour(
+    ) {
         return this._colour;
-    } //-- int getColour() 
+    }
 
     /**
      * Returns the value of field 'end'.
      * 
-     * @return int
-     * @return the value of field 'end'.
+     * @return the value of field 'End'.
      */
-    public int getEnd()
-    {
+    public int getEnd(
+    ) {
         return this._end;
-    } //-- int getEnd() 
+    }
 
     /**
-     * Method getFeatures
-     * 
-     * 
+     * Method getFeatures.
      * 
      * @param index
-     * @return Features
-     */
-    public jalview.schemabinding.version2.Features getFeatures(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _featuresList.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.Features at the given index
+     */
+    public jalview.schemabinding.version2.Features getFeatures(
+            final int index)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._featuresList.size()) {
+            throw new IndexOutOfBoundsException("getFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");
         }
         
-        return (jalview.schemabinding.version2.Features) _featuresList.elementAt(index);
-    } //-- jalview.schemabinding.version2.Features getFeatures(int) 
+        return (jalview.schemabinding.version2.Features) _featuresList.get(index);
+    }
 
     /**
-     * Method getFeatures
-     * 
-     * 
+     * Method getFeatures.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 Features
+     * @return this collection as an Array
      */
-    public jalview.schemabinding.version2.Features[] getFeatures()
-    {
-        int size = _featuresList.size();
-        jalview.schemabinding.version2.Features[] mArray = new jalview.schemabinding.version2.Features[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.Features) _featuresList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.Features[] getFeatures() 
+    public jalview.schemabinding.version2.Features[] getFeatures(
+    ) {
+        jalview.schemabinding.version2.Features[] array = new jalview.schemabinding.version2.Features[0];
+        return (jalview.schemabinding.version2.Features[]) this._featuresList.toArray(array);
+    }
 
     /**
-     * Method getFeaturesCount
-     * 
-     * 
+     * Method getFeaturesCount.
      * 
-     * @return int
+     * @return the size of this collection
      */
-    public int getFeaturesCount()
-    {
-        return _featuresList.size();
-    } //-- int getFeaturesCount() 
+    public int getFeaturesCount(
+    ) {
+        return this._featuresList.size();
+    }
 
     /**
      * Returns the value of field 'hidden'.
      * 
-     * @return boolean
-     * @return the value of field 'hidden'.
+     * @return the value of field 'Hidden'.
      */
-    public boolean getHidden()
-    {
+    public boolean getHidden(
+    ) {
         return this._hidden;
-    } //-- boolean getHidden() 
+    }
 
     /**
-     * Method getHiddenSequences
-     * 
-     * 
+     * Method getHiddenSequences.
      * 
      * @param index
-     * @return int
-     */
-    public int getHiddenSequences(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _hiddenSequencesList.size())) {
-            throw new IndexOutOfBoundsException();
+     * @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 getHiddenSequences(
+            final int index)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._hiddenSequencesList.size()) {
+            throw new IndexOutOfBoundsException("getHiddenSequences: Index value '" + index + "' not in range [0.." + (this._hiddenSequencesList.size() - 1) + "]");
         }
         
-        return ((java.lang.Integer)_hiddenSequencesList.elementAt(index)).intValue();
-    } //-- int getHiddenSequences(int) 
+        return ((java.lang.Integer) _hiddenSequencesList.get(index)).intValue();
+    }
 
     /**
-     * Method getHiddenSequences
-     * 
+     * Method getHiddenSequences.Returns the contents of the
+     * collection in an Array.  
      * 
-     * 
-     * @return int
+     * @return this collection as an Array
      */
-    public int[] getHiddenSequences()
-    {
-        int size = _hiddenSequencesList.size();
-        int[] mArray = new int[size];
+    public int[] getHiddenSequences(
+    ) {
+        int size = this._hiddenSequencesList.size();
+        int[] array = new int[size];
+        java.util.Iterator iter = _hiddenSequencesList.iterator();
         for (int index = 0; index < size; index++) {
-            mArray[index] = ((java.lang.Integer)_hiddenSequencesList.elementAt(index)).intValue();
+            array[index] = ((java.lang.Integer) iter.next()).intValue();
         }
-        return mArray;
-    } //-- int[] getHiddenSequences() 
+        return array;
+    }
 
     /**
-     * Method getHiddenSequencesCount
-     * 
-     * 
+     * Method getHiddenSequencesCount.
      * 
-     * @return int
+     * @return the size of this collection
      */
-    public int getHiddenSequencesCount()
-    {
-        return _hiddenSequencesList.size();
-    } //-- int getHiddenSequencesCount() 
+    public int getHiddenSequencesCount(
+    ) {
+        return this._hiddenSequencesList.size();
+    }
 
     /**
      * Returns the value of field 'id'.
      * 
-     * @return int
-     * @return the value of field 'id'.
+     * @return the value of field 'Id'.
      */
-    public int getId()
-    {
+    public java.lang.String getId(
+    ) {
         return this._id;
-    } //-- int getId() 
+    }
 
     /**
-     * Method getPdbids
-     * 
-     * 
+     * Method getPdbids.
      * 
      * @param index
-     * @return Pdbids
-     */
-    public jalview.schemabinding.version2.Pdbids getPdbids(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _pdbidsList.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.Pdbids at the given index
+     */
+    public jalview.schemabinding.version2.Pdbids getPdbids(
+            final int index)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._pdbidsList.size()) {
+            throw new IndexOutOfBoundsException("getPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");
         }
         
-        return (jalview.schemabinding.version2.Pdbids) _pdbidsList.elementAt(index);
-    } //-- jalview.schemabinding.version2.Pdbids getPdbids(int) 
+        return (jalview.schemabinding.version2.Pdbids) _pdbidsList.get(index);
+    }
 
     /**
-     * Method getPdbids
-     * 
+     * Method getPdbids.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 Pdbids
+     * @return this collection as an Array
      */
-    public jalview.schemabinding.version2.Pdbids[] getPdbids()
-    {
-        int size = _pdbidsList.size();
-        jalview.schemabinding.version2.Pdbids[] mArray = new jalview.schemabinding.version2.Pdbids[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.Pdbids) _pdbidsList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.Pdbids[] getPdbids() 
+    public jalview.schemabinding.version2.Pdbids[] getPdbids(
+    ) {
+        jalview.schemabinding.version2.Pdbids[] array = new jalview.schemabinding.version2.Pdbids[0];
+        return (jalview.schemabinding.version2.Pdbids[]) this._pdbidsList.toArray(array);
+    }
 
     /**
-     * Method getPdbidsCount
-     * 
+     * Method getPdbidsCount.
      * 
-     * 
-     * @return int
+     * @return the size of this collection
      */
-    public int getPdbidsCount()
-    {
-        return _pdbidsList.size();
-    } //-- int getPdbidsCount() 
+    public int getPdbidsCount(
+    ) {
+        return this._pdbidsList.size();
+    }
 
     /**
      * Returns the value of field 'start'.
      * 
-     * @return int
-     * @return the value of field 'start'.
+     * @return the value of field 'Start'.
      */
-    public int getStart()
-    {
+    public int getStart(
+    ) {
         return this._start;
-    } //-- int getStart() 
+    }
 
     /**
-     * Method hasColour
-     * 
-     * 
+     * Method hasColour.
      * 
-     * @return boolean
+     * @return true if at least one Colour has been added
      */
-    public boolean hasColour()
-    {
+    public boolean hasColour(
+    ) {
         return this._has_colour;
-    } //-- boolean hasColour() 
+    }
 
     /**
-     * Method hasEnd
+     * Method hasEnd.
      * 
-     * 
-     * 
-     * @return boolean
+     * @return true if at least one End has been added
      */
-    public boolean hasEnd()
-    {
+    public boolean hasEnd(
+    ) {
         return this._has_end;
-    } //-- boolean hasEnd() 
+    }
 
     /**
-     * Method hasHidden
-     * 
+     * Method hasHidden.
      * 
-     * 
-     * @return boolean
+     * @return true if at least one Hidden has been added
      */
-    public boolean hasHidden()
-    {
+    public boolean hasHidden(
+    ) {
         return this._has_hidden;
-    } //-- boolean hasHidden() 
+    }
 
     /**
-     * Method hasId
-     * 
-     * 
+     * Method hasStart.
      * 
-     * @return boolean
+     * @return true if at least one Start has been added
      */
-    public boolean hasId()
-    {
-        return this._has_id;
-    } //-- boolean hasId() 
+    public boolean hasStart(
+    ) {
+        return this._has_start;
+    }
 
     /**
-     * Method hasStart
-     * 
-     * 
+     * Returns the value of field 'hidden'.
      * 
-     * @return boolean
+     * @return the value of field 'Hidden'.
      */
-    public boolean hasStart()
-    {
-        return this._has_start;
-    } //-- boolean hasStart() 
+    public boolean isHidden(
+    ) {
+        return this._hidden;
+    }
 
     /**
-     * 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 removeAllFeatures
-     * 
      */
-    public void removeAllFeatures()
-    {
-        _featuresList.removeAllElements();
-    } //-- void removeAllFeatures() 
+    public void removeAllFeatures(
+    ) {
+        this._featuresList.clear();
+    }
 
     /**
-     * Method removeAllHiddenSequences
-     * 
      */
-    public void removeAllHiddenSequences()
-    {
-        _hiddenSequencesList.removeAllElements();
-    } //-- void removeAllHiddenSequences() 
+    public void removeAllHiddenSequences(
+    ) {
+        this._hiddenSequencesList.clear();
+    }
 
     /**
-     * Method removeAllPdbids
-     * 
      */
-    public void removeAllPdbids()
-    {
-        _pdbidsList.removeAllElements();
-    } //-- void removeAllPdbids() 
+    public void removeAllPdbids(
+    ) {
+        this._pdbidsList.clear();
+    }
 
     /**
-     * Method removeFeatures
-     * 
+     * Method removeFeatures.
      * 
+     * @param vFeatures
+     * @return true if the object was removed from the collection.
+     */
+    public boolean removeFeatures(
+            final jalview.schemabinding.version2.Features vFeatures) {
+        boolean removed = _featuresList.remove(vFeatures);
+        return removed;
+    }
+
+    /**
+     * Method removeFeaturesAt.
      * 
      * @param index
-     * @return Features
+     * @return the element removed from the collection
      */
-    public jalview.schemabinding.version2.Features removeFeatures(int index)
-    {
-        java.lang.Object obj = _featuresList.elementAt(index);
-        _featuresList.removeElementAt(index);
+    public jalview.schemabinding.version2.Features removeFeaturesAt(
+            final int index) {
+        java.lang.Object obj = this._featuresList.remove(index);
         return (jalview.schemabinding.version2.Features) obj;
-    } //-- jalview.schemabinding.version2.Features removeFeatures(int) 
+    }
 
     /**
-     * Method removeHiddenSequences
-     * 
+     * Method removeHiddenSequences.
      * 
+     * @param vHiddenSequences
+     * @return true if the object was removed from the collection.
+     */
+    public boolean removeHiddenSequences(
+            final int vHiddenSequences) {
+        boolean removed = _hiddenSequencesList.remove(new java.lang.Integer(vHiddenSequences));
+        return removed;
+    }
+
+    /**
+     * Method removeHiddenSequencesAt.
      * 
      * @param index
-     * @return int
+     * @return the element removed from the collection
      */
-    public int removeHiddenSequences(int index)
-    {
-        java.lang.Object obj = _hiddenSequencesList.elementAt(index);
-        _hiddenSequencesList.removeElementAt(index);
-        return ((java.lang.Integer)obj).intValue();
-    } //-- int removeHiddenSequences(int) 
+    public int removeHiddenSequencesAt(
+            final int index) {
+        java.lang.Object obj = this._hiddenSequencesList.remove(index);
+        return ((java.lang.Integer) obj).intValue();
+    }
 
     /**
-     * Method removePdbids
-     * 
+     * Method removePdbids.
      * 
+     * @param vPdbids
+     * @return true if the object was removed from the collection.
+     */
+    public boolean removePdbids(
+            final jalview.schemabinding.version2.Pdbids vPdbids) {
+        boolean removed = _pdbidsList.remove(vPdbids);
+        return removed;
+    }
+
+    /**
+     * Method removePdbidsAt.
      * 
      * @param index
-     * @return Pdbids
+     * @return the element removed from the collection
      */
-    public jalview.schemabinding.version2.Pdbids removePdbids(int index)
-    {
-        java.lang.Object obj = _pdbidsList.elementAt(index);
-        _pdbidsList.removeElementAt(index);
+    public jalview.schemabinding.version2.Pdbids removePdbidsAt(
+            final int index) {
+        java.lang.Object obj = this._pdbidsList.remove(index);
         return (jalview.schemabinding.version2.Pdbids) obj;
-    } //-- jalview.schemabinding.version2.Pdbids removePdbids(int) 
+    }
 
     /**
      * Sets the value of field 'colour'.
      * 
      * @param colour the value of field 'colour'.
      */
-    public void setColour(int colour)
-    {
+    public void setColour(
+            final int colour) {
         this._colour = colour;
         this._has_colour = true;
-    } //-- void setColour(int) 
+    }
 
     /**
      * Sets the value of field 'end'.
      * 
      * @param end the value of field 'end'.
      */
-    public void setEnd(int end)
-    {
+    public void setEnd(
+            final int end) {
         this._end = end;
         this._has_end = true;
-    } //-- void setEnd(int) 
+    }
 
     /**
-     * Method setFeatures
-     * 
      * 
      * 
      * @param index
      * @param vFeatures
-     */
-    public void setFeatures(int index, jalview.schemabinding.version2.Features vFeatures)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _featuresList.size())) {
-            throw new IndexOutOfBoundsException();
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void setFeatures(
+            final int index,
+            final jalview.schemabinding.version2.Features vFeatures)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._featuresList.size()) {
+            throw new IndexOutOfBoundsException("setFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");
         }
-        _featuresList.setElementAt(vFeatures, index);
-    } //-- void setFeatures(int, jalview.schemabinding.version2.Features) 
+        
+        this._featuresList.set(index, vFeatures);
+    }
 
     /**
-     * Method setFeatures
      * 
      * 
-     * 
-     * @param featuresArray
+     * @param vFeaturesArray
      */
-    public void setFeatures(jalview.schemabinding.version2.Features[] featuresArray)
-    {
+    public void setFeatures(
+            final jalview.schemabinding.version2.Features[] vFeaturesArray) {
         //-- copy array
-        _featuresList.removeAllElements();
-        for (int i = 0; i < featuresArray.length; i++) {
-            _featuresList.addElement(featuresArray[i]);
+        _featuresList.clear();
+        
+        for (int i = 0; i < vFeaturesArray.length; i++) {
+                this._featuresList.add(vFeaturesArray[i]);
         }
-    } //-- void setFeatures(jalview.schemabinding.version2.Features) 
+    }
 
     /**
      * Sets the value of field 'hidden'.
      * 
      * @param hidden the value of field 'hidden'.
      */
-    public void setHidden(boolean hidden)
-    {
+    public void setHidden(
+            final boolean hidden) {
         this._hidden = hidden;
         this._has_hidden = true;
-    } //-- void setHidden(boolean) 
+    }
 
     /**
-     * Method setHiddenSequences
-     * 
      * 
      * 
      * @param index
      * @param vHiddenSequences
-     */
-    public void setHiddenSequences(int index, int vHiddenSequences)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _hiddenSequencesList.size())) {
-            throw new IndexOutOfBoundsException();
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void setHiddenSequences(
+            final int index,
+            final int vHiddenSequences)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._hiddenSequencesList.size()) {
+            throw new IndexOutOfBoundsException("setHiddenSequences: Index value '" + index + "' not in range [0.." + (this._hiddenSequencesList.size() - 1) + "]");
         }
-        _hiddenSequencesList.setElementAt(new java.lang.Integer(vHiddenSequences), index);
-    } //-- void setHiddenSequences(int, int) 
+        
+        this._hiddenSequencesList.set(index, new java.lang.Integer(vHiddenSequences));
+    }
 
     /**
-     * Method setHiddenSequences
      * 
      * 
-     * 
-     * @param hiddenSequencesArray
+     * @param vHiddenSequencesArray
      */
-    public void setHiddenSequences(int[] hiddenSequencesArray)
-    {
+    public void setHiddenSequences(
+            final int[] vHiddenSequencesArray) {
         //-- copy array
-        _hiddenSequencesList.removeAllElements();
-        for (int i = 0; i < hiddenSequencesArray.length; i++) {
-            _hiddenSequencesList.addElement(new java.lang.Integer(hiddenSequencesArray[i]));
+        _hiddenSequencesList.clear();
+        
+        for (int i = 0; i < vHiddenSequencesArray.length; i++) {
+                this._hiddenSequencesList.add(new java.lang.Integer(vHiddenSequencesArray[i]));
         }
-    } //-- void setHiddenSequences(int) 
+    }
 
     /**
      * Sets the value of field 'id'.
      * 
      * @param id the value of field 'id'.
      */
-    public void setId(int id)
-    {
+    public void setId(
+            final java.lang.String id) {
         this._id = id;
-        this._has_id = true;
-    } //-- void setId(int) 
+    }
 
     /**
-     * Method setPdbids
-     * 
      * 
      * 
      * @param index
      * @param vPdbids
-     */
-    public void setPdbids(int index, jalview.schemabinding.version2.Pdbids vPdbids)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _pdbidsList.size())) {
-            throw new IndexOutOfBoundsException();
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void setPdbids(
+            final int index,
+            final jalview.schemabinding.version2.Pdbids vPdbids)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._pdbidsList.size()) {
+            throw new IndexOutOfBoundsException("setPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");
         }
-        _pdbidsList.setElementAt(vPdbids, index);
-    } //-- void setPdbids(int, jalview.schemabinding.version2.Pdbids) 
+        
+        this._pdbidsList.set(index, vPdbids);
+    }
 
     /**
-     * Method setPdbids
      * 
      * 
-     * 
-     * @param pdbidsArray
+     * @param vPdbidsArray
      */
-    public void setPdbids(jalview.schemabinding.version2.Pdbids[] pdbidsArray)
-    {
+    public void setPdbids(
+            final jalview.schemabinding.version2.Pdbids[] vPdbidsArray) {
         //-- copy array
-        _pdbidsList.removeAllElements();
-        for (int i = 0; i < pdbidsArray.length; i++) {
-            _pdbidsList.addElement(pdbidsArray[i]);
+        _pdbidsList.clear();
+        
+        for (int i = 0; i < vPdbidsArray.length; i++) {
+                this._pdbidsList.add(vPdbidsArray[i]);
         }
-    } //-- void setPdbids(jalview.schemabinding.version2.Pdbids) 
+    }
 
     /**
      * Sets the value of field 'start'.
      * 
      * @param start the value of field 'start'.
      */
-    public void setStart(int start)
-    {
+    public void setStart(
+            final int start) {
         this._start = start;
         this._has_start = true;
-    } //-- void setStart(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.JSeq
+     */
+    public static jalview.schemabinding.version2.JSeq unmarshal(
+            final java.io.Reader reader)
+    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
         return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal(jalview.schemabinding.version2.JSeq.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() 
+    }
 
 }