X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FVAMSAS.java;h=4ff836de5eb5107bd8736fa873b68d885ca56ca7;hb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;hp=03633d62f1091fbe83e2679a8e836ad180ffc7e2;hpb=48df59aa393e03aa7269b2df662ac1b8d58cbb25;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/VAMSAS.java b/src/jalview/schemabinding/version2/VAMSAS.java
index 03633d6..4ff836d 100755
--- a/src/jalview/schemabinding/version2/VAMSAS.java
+++ b/src/jalview/schemabinding/version2/VAMSAS.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 (Development 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 VAMSAS.
@@ -36,12 +38,12 @@ public class VAMSAS implements java.io.Serializable {
     //--------------------------/
 
     /**
-     * Field _treeList
+     * Field _treeList.
      */
     private java.util.Vector _treeList;
 
     /**
-     * Field _sequenceSetList
+     * Field _sequenceSetList.
      */
     private java.util.Vector _sequenceSetList;
 
@@ -52,9 +54,9 @@ public class VAMSAS implements java.io.Serializable {
 
     public VAMSAS() {
         super();
-        _treeList = new Vector();
-        _sequenceSetList = new Vector();
-    } //-- jalview.schemabinding.version2.VAMSAS()
+        this._treeList = new java.util.Vector();
+        this._sequenceSetList = new java.util.Vector();
+    }
 
 
       //-----------/
@@ -62,364 +64,377 @@ public class VAMSAS implements java.io.Serializable {
     //-----------/
 
     /**
-     * Method addSequenceSet
-     * 
      * 
      * 
      * @param vSequenceSet
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
      */
-    public void addSequenceSet(jalview.schemabinding.version2.SequenceSet vSequenceSet)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _sequenceSetList.addElement(vSequenceSet);
-    } //-- void addSequenceSet(jalview.schemabinding.version2.SequenceSet) 
+    public void addSequenceSet(
+            final jalview.schemabinding.version2.SequenceSet vSequenceSet)
+    throws java.lang.IndexOutOfBoundsException {
+        this._sequenceSetList.addElement(vSequenceSet);
+    }
 
     /**
-     * Method addSequenceSet
-     * 
      * 
      * 
      * @param index
      * @param vSequenceSet
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
      */
-    public void addSequenceSet(int index, jalview.schemabinding.version2.SequenceSet vSequenceSet)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _sequenceSetList.insertElementAt(vSequenceSet, index);
-    } //-- void addSequenceSet(int, jalview.schemabinding.version2.SequenceSet) 
+    public void addSequenceSet(
+            final int index,
+            final jalview.schemabinding.version2.SequenceSet vSequenceSet)
+    throws java.lang.IndexOutOfBoundsException {
+        this._sequenceSetList.add(index, vSequenceSet);
+    }
 
     /**
-     * Method addTree
-     * 
      * 
      * 
      * @param vTree
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
      */
-    public void addTree(java.lang.String vTree)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _treeList.addElement(vTree);
-    } //-- void addTree(java.lang.String) 
+    public void addTree(
+            final java.lang.String 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, java.lang.String vTree)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _treeList.insertElementAt(vTree, index);
-    } //-- void addTree(int, java.lang.String) 
+    public void addTree(
+            final int index,
+            final java.lang.String vTree)
+    throws java.lang.IndexOutOfBoundsException {
+        this._treeList.add(index, vTree);
+    }
 
     /**
-     * Method enumerateSequenceSet
-     * 
+     * Method enumerateSequenceSet.
      * 
-     * 
-     * @return Enumeration
+     * @return an Enumeration over all
+     * jalview.schemabinding.version2.SequenceSet elements
      */
-    public java.util.Enumeration enumerateSequenceSet()
-    {
-        return _sequenceSetList.elements();
-    } //-- java.util.Enumeration enumerateSequenceSet() 
+    public java.util.Enumeration enumerateSequenceSet(
+    ) {
+        return this._sequenceSetList.elements();
+    }
 
     /**
-     * Method enumerateTree
-     * 
+     * Method enumerateTree.
      * 
-     * 
-     * @return Enumeration
+     * @return an Enumeration over all java.lang.String elements
      */
-    public java.util.Enumeration enumerateTree()
-    {
-        return _treeList.elements();
-    } //-- java.util.Enumeration enumerateTree() 
+    public java.util.Enumeration enumerateTree(
+    ) {
+        return this._treeList.elements();
+    }
 
     /**
-     * Method getSequenceSet
-     * 
-     * 
+     * Method getSequenceSet.
      * 
      * @param index
-     * @return SequenceSet
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     * @return the value of the
+     * jalview.schemabinding.version2.SequenceSet at the given index
      */
-    public jalview.schemabinding.version2.SequenceSet getSequenceSet(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _sequenceSetList.size())) {
-            throw new IndexOutOfBoundsException();
+    public jalview.schemabinding.version2.SequenceSet getSequenceSet(
+            final int index)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._sequenceSetList.size()) {
+            throw new IndexOutOfBoundsException("getSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]");
         }
         
-        return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.elementAt(index);
-    } //-- jalview.schemabinding.version2.SequenceSet getSequenceSet(int) 
+        return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.get(index);
+    }
 
     /**
-     * Method getSequenceSet
+     * Method getSequenceSet.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 SequenceSet
+     * @return this collection as an Array
      */
-    public jalview.schemabinding.version2.SequenceSet[] getSequenceSet()
-    {
-        int size = _sequenceSetList.size();
-        jalview.schemabinding.version2.SequenceSet[] mArray = new jalview.schemabinding.version2.SequenceSet[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.SequenceSet[] getSequenceSet() 
+    public jalview.schemabinding.version2.SequenceSet[] getSequenceSet(
+    ) {
+        jalview.schemabinding.version2.SequenceSet[] array = new jalview.schemabinding.version2.SequenceSet[0];
+        return (jalview.schemabinding.version2.SequenceSet[]) this._sequenceSetList.toArray(array);
+    }
 
     /**
-     * Method getSequenceSetCount
-     * 
+     * Method getSequenceSetCount.
      * 
-     * 
-     * @return int
+     * @return the size of this collection
      */
-    public int getSequenceSetCount()
-    {
-        return _sequenceSetList.size();
-    } //-- int getSequenceSetCount() 
+    public int getSequenceSetCount(
+    ) {
+        return this._sequenceSetList.size();
+    }
 
     /**
-     * Method getTree
-     * 
-     * 
+     * Method getTree.
      * 
      * @param index
-     * @return String
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     * @return the value of the java.lang.String at the given index
      */
-    public java.lang.String getTree(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _treeList.size())) {
-            throw new IndexOutOfBoundsException();
+    public java.lang.String 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 (String)_treeList.elementAt(index);
-    } //-- java.lang.String getTree(int) 
+        return (java.lang.String) _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 String
+     * @return this collection as an Array
      */
-    public java.lang.String[] getTree()
-    {
-        int size = _treeList.size();
-        java.lang.String[] mArray = new java.lang.String[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (String)_treeList.elementAt(index);
-        }
-        return mArray;
-    } //-- java.lang.String[] getTree() 
+    public java.lang.String[] getTree(
+    ) {
+        java.lang.String[] array = new java.lang.String[0];
+        return (java.lang.String[]) 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 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
+     * @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(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
+    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
+     * @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(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
+    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 removeAllSequenceSet
-     * 
      */
-    public void removeAllSequenceSet()
-    {
-        _sequenceSetList.removeAllElements();
-    } //-- void removeAllSequenceSet() 
+    public void removeAllSequenceSet(
+    ) {
+        this._sequenceSetList.clear();
+    }
 
     /**
-     * Method removeAllTree
-     * 
      */
-    public void removeAllTree()
-    {
-        _treeList.removeAllElements();
-    } //-- void removeAllTree() 
+    public void removeAllTree(
+    ) {
+        this._treeList.clear();
+    }
 
     /**
-     * Method removeSequenceSet
-     * 
+     * Method removeSequenceSet.
      * 
+     * @param vSequenceSet
+     * @return true if the object was removed from the collection.
+     */
+    public boolean removeSequenceSet(
+            final jalview.schemabinding.version2.SequenceSet vSequenceSet) {
+        boolean removed = _sequenceSetList.remove(vSequenceSet);
+        return removed;
+    }
+
+    /**
+     * Method removeSequenceSetAt.
      * 
      * @param index
-     * @return SequenceSet
+     * @return the element removed from the collection
      */
-    public jalview.schemabinding.version2.SequenceSet removeSequenceSet(int index)
-    {
-        java.lang.Object obj = _sequenceSetList.elementAt(index);
-        _sequenceSetList.removeElementAt(index);
+    public jalview.schemabinding.version2.SequenceSet removeSequenceSetAt(
+            final int index) {
+        java.lang.Object obj = this._sequenceSetList.remove(index);
         return (jalview.schemabinding.version2.SequenceSet) obj;
-    } //-- jalview.schemabinding.version2.SequenceSet removeSequenceSet(int) 
+    }
 
     /**
-     * Method removeTree
-     * 
+     * Method removeTree.
      * 
+     * @param vTree
+     * @return true if the object was removed from the collection.
+     */
+    public boolean removeTree(
+            final java.lang.String vTree) {
+        boolean removed = _treeList.remove(vTree);
+        return removed;
+    }
+
+    /**
+     * Method removeTreeAt.
      * 
      * @param index
-     * @return String
+     * @return the element removed from the collection
      */
-    public java.lang.String removeTree(int index)
-    {
-        java.lang.Object obj = _treeList.elementAt(index);
-        _treeList.removeElementAt(index);
-        return (String)obj;
-    } //-- java.lang.String removeTree(int) 
+    public java.lang.String removeTreeAt(
+            final int index) {
+        java.lang.Object obj = this._treeList.remove(index);
+        return (java.lang.String) obj;
+    }
 
     /**
-     * Method setSequenceSet
-     * 
      * 
      * 
      * @param index
      * @param vSequenceSet
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
      */
-    public void setSequenceSet(int index, jalview.schemabinding.version2.SequenceSet vSequenceSet)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _sequenceSetList.size())) {
-            throw new IndexOutOfBoundsException();
+    public void setSequenceSet(
+            final int index,
+            final jalview.schemabinding.version2.SequenceSet vSequenceSet)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._sequenceSetList.size()) {
+            throw new IndexOutOfBoundsException("setSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]");
         }
-        _sequenceSetList.setElementAt(vSequenceSet, index);
-    } //-- void setSequenceSet(int, jalview.schemabinding.version2.SequenceSet) 
+        
+        this._sequenceSetList.set(index, vSequenceSet);
+    }
 
     /**
-     * Method setSequenceSet
-     * 
      * 
      * 
-     * @param sequenceSetArray
+     * @param vSequenceSetArray
      */
-    public void setSequenceSet(jalview.schemabinding.version2.SequenceSet[] sequenceSetArray)
-    {
+    public void setSequenceSet(
+            final jalview.schemabinding.version2.SequenceSet[] vSequenceSetArray) {
         //-- copy array
-        _sequenceSetList.removeAllElements();
-        for (int i = 0; i < sequenceSetArray.length; i++) {
-            _sequenceSetList.addElement(sequenceSetArray[i]);
+        _sequenceSetList.clear();
+        
+        for (int i = 0; i < vSequenceSetArray.length; i++) {
+                this._sequenceSetList.add(vSequenceSetArray[i]);
         }
-    } //-- void setSequenceSet(jalview.schemabinding.version2.SequenceSet) 
+    }
 
     /**
-     * Method setTree
-     * 
      * 
      * 
      * @param index
      * @param vTree
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
      */
-    public void setTree(int index, java.lang.String vTree)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _treeList.size())) {
-            throw new IndexOutOfBoundsException();
+    public void setTree(
+            final int index,
+            final java.lang.String 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, java.lang.String) 
+        
+        this._treeList.set(index, vTree);
+    }
 
     /**
-     * Method setTree
      * 
      * 
-     * 
-     * @param treeArray
+     * @param vTreeArray
      */
-    public void setTree(java.lang.String[] treeArray)
-    {
+    public void setTree(
+            final java.lang.String[] 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(java.lang.String) 
+    }
 
     /**
-     * Method unmarshal
-     * 
-     * 
+     * Method unmarshal.
      * 
      * @param reader
-     * @return Object
+     * @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.VAMSAS
      */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
+    public static jalview.schemabinding.version2.VAMSAS unmarshal(
+            final java.io.Reader reader)
+    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
         return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(jalview.schemabinding.version2.VAMSAS.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() 
+    }
 
 }