X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FVAMSAS.java;h=ae8e17fe08c7d0d237fd2d9f3e51c1174b73e0e3;hb=22d4d2237b099daf76bd1a2ed324763972ed91aa;hp=8a4803c7dd0bcc3d3b45ed94d008dab3b055b011;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/VAMSAS.java b/src/jalview/schemabinding/version2/VAMSAS.java
index 8a4803c..ae8e17f 100755
--- a/src/jalview/schemabinding/version2/VAMSAS.java
+++ b/src/jalview/schemabinding/version2/VAMSAS.java
@@ -1,441 +1,429 @@
 /*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
  * Schema.
  * $Id$
  */
 
 package jalview.schemabinding.version2;
 
+  //---------------------------------/
+ //- Imported classes and packages -/
 //---------------------------------/
-//- Imported classes and packages -/
-//---------------------------------/
-
-import java.util.*;
 
-import org.exolab.castor.xml.*;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
 
 /**
  * Class VAMSAS.
- *
+ * 
  * @version $Revision$ $Date$
  */
-public class VAMSAS
-    implements java.io.Serializable
-{
-
-  //--------------------------/
-  //- Class/Member Variables -/
-  //--------------------------/
-
-  /**
-   * Field _treeList
-   */
-  private java.util.Vector _treeList;
-
-  /**
-   * Field _sequenceSetList
-   */
-  private java.util.Vector _sequenceSetList;
-
-  //----------------/
-  //- Constructors -/
-  //----------------/
-
-  public VAMSAS()
-  {
-    super();
-    _treeList = new Vector();
-    _sequenceSetList = new Vector();
-  } //-- jalview.schemabinding.version2.VAMSAS()
-
-  //-----------/
-  //- Methods -/
-  //-----------/
-
-  /**
-   * Method addSequenceSet
-   *
-   *
-   *
-   * @param vSequenceSet
-   */
-  public void addSequenceSet(jalview.schemabinding.version2.SequenceSet
-                             vSequenceSet)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _sequenceSetList.addElement(vSequenceSet);
-  } //-- void addSequenceSet(jalview.schemabinding.version2.SequenceSet)
-
-  /**
-   * Method addSequenceSet
-   *
-   *
-   *
-   * @param index
-   * @param vSequenceSet
-   */
-  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)
-
-  /**
-   * Method addTree
-   *
-   *
-   *
-   * @param vTree
-   */
-  public void addTree(java.lang.String vTree)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _treeList.addElement(vTree);
-  } //-- void addTree(java.lang.String)
-
-  /**
-   * Method addTree
-   *
-   *
-   *
-   * @param index
-   * @param vTree
-   */
-  public void addTree(int index, java.lang.String vTree)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _treeList.insertElementAt(vTree, index);
-  } //-- void addTree(int, java.lang.String)
-
-  /**
-   * Method enumerateSequenceSet
-   *
-   *
-   *
-   * @return Enumeration
-   */
-  public java.util.Enumeration enumerateSequenceSet()
-  {
-    return _sequenceSetList.elements();
-  } //-- java.util.Enumeration enumerateSequenceSet()
-
-  /**
-   * Method enumerateTree
-   *
-   *
-   *
-   * @return Enumeration
-   */
-  public java.util.Enumeration enumerateTree()
-  {
-    return _treeList.elements();
-  } //-- java.util.Enumeration enumerateTree()
-
-  /**
-   * Method getSequenceSet
-   *
-   *
-   *
-   * @param index
-   * @return SequenceSet
-   */
-  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 class VAMSAS implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _treeList.
+     */
+    private java.util.Vector _treeList;
+
+    /**
+     * Field _sequenceSetList.
+     */
+    private java.util.Vector _sequenceSetList;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public VAMSAS() {
+        super();
+        this._treeList = new java.util.Vector();
+        this._sequenceSetList = new java.util.Vector();
     }
 
-    return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.
-        elementAt(index);
-  } //-- jalview.schemabinding.version2.SequenceSet getSequenceSet(int)
-
-  /**
-   * Method getSequenceSet
-   *
-   *
-   *
-   * @return SequenceSet
-   */
-  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);
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * 
+     * 
+     * @param vSequenceSet
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addSequenceSet(
+            final jalview.schemabinding.version2.SequenceSet vSequenceSet)
+    throws java.lang.IndexOutOfBoundsException {
+        this._sequenceSetList.addElement(vSequenceSet);
     }
-    return mArray;
-  } //-- jalview.schemabinding.version2.SequenceSet[] getSequenceSet()
-
-  /**
-   * Method getSequenceSetCount
-   *
-   *
-   *
-   * @return int
-   */
-  public int getSequenceSetCount()
-  {
-    return _sequenceSetList.size();
-  } //-- int getSequenceSetCount()
-
-  /**
-   * Method getTree
-   *
-   *
-   *
-   * @param index
-   * @return String
-   */
-  public java.lang.String getTree(int index)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _treeList.size()))
-    {
-      throw new IndexOutOfBoundsException();
+
+    /**
+     * 
+     * 
+     * @param index
+     * @param vSequenceSet
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addSequenceSet(
+            final int index,
+            final jalview.schemabinding.version2.SequenceSet vSequenceSet)
+    throws java.lang.IndexOutOfBoundsException {
+        this._sequenceSetList.add(index, vSequenceSet);
     }
 
-    return (String) _treeList.elementAt(index);
-  } //-- java.lang.String getTree(int)
-
-  /**
-   * Method getTree
-   *
-   *
-   *
-   * @return String
-   */
-  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);
+    /**
+     * 
+     * 
+     * @param vTree
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addTree(
+            final java.lang.String vTree)
+    throws java.lang.IndexOutOfBoundsException {
+        this._treeList.addElement(vTree);
     }
-    return mArray;
-  } //-- java.lang.String[] getTree()
-
-  /**
-   * Method getTreeCount
-   *
-   *
-   *
-   * @return int
-   */
-  public int getTreeCount()
-  {
-    return _treeList.size();
-  } //-- int getTreeCount()
-
-  /**
-   * Method isValid
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean isValid()
-  {
-    try
-    {
-      validate();
+
+    /**
+     * 
+     * 
+     * @param index
+     * @param vTree
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addTree(
+            final int index,
+            final java.lang.String vTree)
+    throws java.lang.IndexOutOfBoundsException {
+        this._treeList.add(index, vTree);
     }
-    catch (org.exolab.castor.xml.ValidationException vex)
-    {
-      return false;
+
+    /**
+     * Method enumerateSequenceSet.
+     * 
+     * @return an Enumeration over all
+     * jalview.schemabinding.version2.SequenceSet elements
+     */
+    public java.util.Enumeration enumerateSequenceSet(
+    ) {
+        return this._sequenceSetList.elements();
     }
-    return true;
-  } //-- boolean isValid()
-
-  /**
-   * Method marshal
-   *
-   *
-   *
-   * @param out
-   */
-  public void marshal(java.io.Writer out)
-      throws org.exolab.castor.xml.MarshalException,
-      org.exolab.castor.xml.ValidationException
-  {
-
-    Marshaller.marshal(this, out);
-  } //-- void marshal(java.io.Writer)
-
-  /**
-   * Method marshal
-   *
-   *
-   *
-   * @param handler
-   */
-  public void marshal(org.xml.sax.ContentHandler handler)
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
-      org.exolab.castor.xml.ValidationException
-  {
-
-    Marshaller.marshal(this, handler);
-  } //-- void marshal(org.xml.sax.ContentHandler)
-
-  /**
-   * Method removeAllSequenceSet
-   *
-   */
-  public void removeAllSequenceSet()
-  {
-    _sequenceSetList.removeAllElements();
-  } //-- void removeAllSequenceSet()
-
-  /**
-   * Method removeAllTree
-   *
-   */
-  public void removeAllTree()
-  {
-    _treeList.removeAllElements();
-  } //-- void removeAllTree()
-
-  /**
-   * Method removeSequenceSet
-   *
-   *
-   *
-   * @param index
-   * @return SequenceSet
-   */
-  public jalview.schemabinding.version2.SequenceSet removeSequenceSet(int index)
-  {
-    java.lang.Object obj = _sequenceSetList.elementAt(index);
-    _sequenceSetList.removeElementAt(index);
-    return (jalview.schemabinding.version2.SequenceSet) obj;
-  } //-- jalview.schemabinding.version2.SequenceSet removeSequenceSet(int)
-
-  /**
-   * Method removeTree
-   *
-   *
-   *
-   * @param index
-   * @return String
-   */
-  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)
-
-  /**
-   * Method setSequenceSet
-   *
-   *
-   *
-   * @param index
-   * @param vSequenceSet
-   */
-  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();
+
+    /**
+     * Method enumerateTree.
+     * 
+     * @return an Enumeration over all java.lang.String elements
+     */
+    public java.util.Enumeration enumerateTree(
+    ) {
+        return this._treeList.elements();
     }
-    _sequenceSetList.setElementAt(vSequenceSet, index);
-  } //-- void setSequenceSet(int, jalview.schemabinding.version2.SequenceSet)
-
-  /**
-   * Method setSequenceSet
-   *
-   *
-   *
-   * @param sequenceSetArray
-   */
-  public void setSequenceSet(jalview.schemabinding.version2.SequenceSet[]
-                             sequenceSetArray)
-  {
-    //-- copy array
-    _sequenceSetList.removeAllElements();
-    for (int i = 0; i < sequenceSetArray.length; i++)
-    {
-      _sequenceSetList.addElement(sequenceSetArray[i]);
+
+    /**
+     * Method getSequenceSet.
+     * 
+     * @param index
+     * @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(
+            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.get(index);
+    }
+
+    /**
+     * 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 this collection as an Array
+     */
+    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);
     }
-  } //-- void setSequenceSet(jalview.schemabinding.version2.SequenceSet)
-
-  /**
-   * Method setTree
-   *
-   *
-   *
-   * @param index
-   * @param vTree
-   */
-  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();
+
+    /**
+     * Method getSequenceSetCount.
+     * 
+     * @return the size of this collection
+     */
+    public int getSequenceSetCount(
+    ) {
+        return this._sequenceSetList.size();
     }
-    _treeList.setElementAt(vTree, index);
-  } //-- void setTree(int, java.lang.String)
-
-  /**
-   * Method setTree
-   *
-   *
-   *
-   * @param treeArray
-   */
-  public void setTree(java.lang.String[] treeArray)
-  {
-    //-- copy array
-    _treeList.removeAllElements();
-    for (int i = 0; i < treeArray.length; i++)
-    {
-      _treeList.addElement(treeArray[i]);
+
+    /**
+     * Method getTree.
+     * 
+     * @param index
+     * @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(
+            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 (java.lang.String) _treeList.get(index);
+    }
+
+    /**
+     * 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 this collection as an Array
+     */
+    public java.lang.String[] getTree(
+    ) {
+        java.lang.String[] array = new java.lang.String[0];
+        return (java.lang.String[]) this._treeList.toArray(array);
+    }
+
+    /**
+     * Method getTreeCount.
+     * 
+     * @return the size of this collection
+     */
+    public int getTreeCount(
+    ) {
+        return this._treeList.size();
+    }
+
+    /**
+     * Method isValid.
+     * 
+     * @return true if this object is valid according to the schema
+     */
+    public boolean isValid(
+    ) {
+        try {
+            validate();
+        } catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    }
+
+    /**
+     * 
+     * 
+     * @param out
+     * @throws org.exolab.castor.xml.MarshalException if object is
+     * null or if any SAXException is thrown during marshaling
+     * @throws org.exolab.castor.xml.ValidationException if this
+     * object is an invalid instance according to the schema
+     */
+    public void marshal(
+            final java.io.Writer out)
+    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+        Marshaller.marshal(this, out);
+    }
+
+    /**
+     * 
+     * 
+     * @param handler
+     * @throws java.io.IOException if an IOException occurs during
+     * marshaling
+     * @throws org.exolab.castor.xml.ValidationException if this
+     * object is an invalid instance according to the schema
+     * @throws org.exolab.castor.xml.MarshalException if object is
+     * null or if any SAXException is thrown during marshaling
+     */
+    public void marshal(
+            final org.xml.sax.ContentHandler handler)
+    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+        Marshaller.marshal(this, handler);
+    }
+
+    /**
+     */
+    public void removeAllSequenceSet(
+    ) {
+        this._sequenceSetList.clear();
+    }
+
+    /**
+     */
+    public void removeAllTree(
+    ) {
+        this._treeList.clear();
+    }
+
+    /**
+     * 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 the element removed from the collection
+     */
+    public jalview.schemabinding.version2.SequenceSet removeSequenceSetAt(
+            final int index) {
+        java.lang.Object obj = this._sequenceSetList.remove(index);
+        return (jalview.schemabinding.version2.SequenceSet) obj;
+    }
+
+    /**
+     * 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 the element removed from the collection
+     */
+    public java.lang.String removeTreeAt(
+            final int index) {
+        java.lang.Object obj = this._treeList.remove(index);
+        return (java.lang.String) obj;
+    }
+
+    /**
+     * 
+     * 
+     * @param index
+     * @param vSequenceSet
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    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) + "]");
+        }
+        
+        this._sequenceSetList.set(index, vSequenceSet);
+    }
+
+    /**
+     * 
+     * 
+     * @param vSequenceSetArray
+     */
+    public void setSequenceSet(
+            final jalview.schemabinding.version2.SequenceSet[] vSequenceSetArray) {
+        //-- copy array
+        _sequenceSetList.clear();
+        
+        for (int i = 0; i < vSequenceSetArray.length; i++) {
+                this._sequenceSetList.add(vSequenceSetArray[i]);
+        }
+    }
+
+    /**
+     * 
+     * 
+     * @param index
+     * @param vTree
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    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) + "]");
+        }
+        
+        this._treeList.set(index, vTree);
+    }
+
+    /**
+     * 
+     * 
+     * @param vTreeArray
+     */
+    public void setTree(
+            final java.lang.String[] vTreeArray) {
+        //-- copy array
+        _treeList.clear();
+        
+        for (int i = 0; i < vTreeArray.length; i++) {
+                this._treeList.add(vTreeArray[i]);
+        }
+    }
+
+    /**
+     * Method unmarshal.
+     * 
+     * @param reader
+     * @throws org.exolab.castor.xml.MarshalException if object is
+     * null or if any SAXException is thrown during marshaling
+     * @throws org.exolab.castor.xml.ValidationException if this
+     * object is an invalid instance according to the schema
+     * @return the unmarshaled jalview.schemabinding.version2.VAMSAS
+     */
+    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);
+    }
+
+    /**
+     * 
+     * 
+     * @throws org.exolab.castor.xml.ValidationException if this
+     * object is an invalid instance according to the schema
+     */
+    public void validate(
+    )
+    throws org.exolab.castor.xml.ValidationException {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
     }
-  } //-- void setTree(java.lang.String)
-
-  /**
-   * Method unmarshal
-   *
-   *
-   *
-   * @param reader
-   * @return Object
-   */
-  public static java.lang.Object unmarshal(java.io.Reader reader)
-      throws org.exolab.castor.xml.MarshalException,
-      org.exolab.castor.xml.ValidationException
-  {
-    return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(
-        jalview.schemabinding.version2.VAMSAS.class, reader);
-  } //-- java.lang.Object unmarshal(java.io.Reader)
-
-  /**
-   * Method validate
-   *
-   */
-  public void validate()
-      throws org.exolab.castor.xml.ValidationException
-  {
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
-        Validator();
-    validator.validate(this);
-  } //-- void validate()
 
 }