X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FVAMSAS.java;h=a0b34602f8874457665e544101f0d125aeca1680;hb=78f929d85e95b6445f7fab46504abc394d8c3fe9;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..a0b3460 100755
--- a/src/jalview/schemabinding/version2/VAMSAS.java
+++ b/src/jalview/schemabinding/version2/VAMSAS.java
@@ -1,441 +1,464 @@
 /*
- * 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 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
-
 package jalview.schemabinding.version2;
 
 //---------------------------------/
 //- 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
+public class VAMSAS implements java.io.Serializable
 {
 
-  //--------------------------/
-  //- Class/Member Variables -/
-  //--------------------------/
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
 
   /**
-   * Field _treeList
+   * Field _treeList.
    */
   private java.util.Vector _treeList;
 
   /**
-   * Field _sequenceSetList
+   * Field _sequenceSetList.
    */
   private java.util.Vector _sequenceSetList;
 
-  //----------------/
-  //- Constructors -/
-  //----------------/
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
   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();
+  }
 
-  //-----------/
-  //- Methods -/
-  //-----------/
+  // -----------/
+  // - Methods -/
+  // -----------/
 
   /**
-   * 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
+  public void addSequenceSet(
+          final jalview.schemabinding.version2.SequenceSet vSequenceSet)
+          throws java.lang.IndexOutOfBoundsException
   {
-    _sequenceSetList.addElement(vSequenceSet);
-  } //-- void addSequenceSet(jalview.schemabinding.version2.SequenceSet)
+    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
+  public void addSequenceSet(final int index,
+          final jalview.schemabinding.version2.SequenceSet vSequenceSet)
+          throws java.lang.IndexOutOfBoundsException
   {
-    _sequenceSetList.insertElementAt(vSequenceSet, index);
-  } //-- void addSequenceSet(int, jalview.schemabinding.version2.SequenceSet)
+    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
+  public void addTree(final java.lang.String vTree)
+          throws java.lang.IndexOutOfBoundsException
   {
-    _treeList.addElement(vTree);
-  } //-- void addTree(java.lang.String)
+    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
+  public void addTree(final int index, final java.lang.String vTree)
+          throws java.lang.IndexOutOfBoundsException
   {
-    _treeList.insertElementAt(vTree, index);
-  } //-- void addTree(int, java.lang.String)
+    this._treeList.add(index, vTree);
+  }
 
   /**
-   * Method enumerateSequenceSet
-   *
-   *
-   *
-   * @return Enumeration
+   * Method enumerateSequenceSet.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.SequenceSet
+   *         elements
    */
   public java.util.Enumeration enumerateSequenceSet()
   {
-    return _sequenceSetList.elements();
-  } //-- java.util.Enumeration enumerateSequenceSet()
+    return this._sequenceSetList.elements();
+  }
 
   /**
-   * Method enumerateTree
-   *
-   *
-   *
-   * @return Enumeration
+   * Method enumerateTree.
+   * 
+   * @return an Enumeration over all java.lang.String elements
    */
   public java.util.Enumeration enumerateTree()
   {
-    return _treeList.elements();
-  } //-- 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
+  public jalview.schemabinding.version2.SequenceSet getSequenceSet(
+          final int index) throws java.lang.IndexOutOfBoundsException
   {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _sequenceSetList.size()))
+    // check bounds for index
+    if (index < 0 || index >= this._sequenceSetList.size())
     {
-      throw new IndexOutOfBoundsException();
+      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
-   *
-   *
-   *
-   * @return SequenceSet
+   * 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()
   {
-    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()
+    jalview.schemabinding.version2.SequenceSet[] array = new jalview.schemabinding.version2.SequenceSet[0];
+    return (jalview.schemabinding.version2.SequenceSet[]) this._sequenceSetList
+            .toArray(array);
+  }
 
   /**
-   * Method getSequenceSetCount
-   *
-   *
-   *
-   * @return int
+   * Method getSequenceSetCount.
+   * 
+   * @return the size of this collection
    */
   public int getSequenceSetCount()
   {
-    return _sequenceSetList.size();
-  } //-- 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
+  public java.lang.String getTree(final int index)
+          throws java.lang.IndexOutOfBoundsException
   {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _treeList.size()))
+    // check bounds for index
+    if (index < 0 || index >= this._treeList.size())
     {
-      throw new IndexOutOfBoundsException();
+      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
-   *
-   *
-   *
-   * @return String
+   * 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()
   {
-    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()
+    java.lang.String[] array = new java.lang.String[0];
+    return (java.lang.String[]) this._treeList.toArray(array);
+  }
 
   /**
-   * Method getTreeCount
-   *
-   *
-   *
-   * @return int
+   * Method getTreeCount.
+   * 
+   * @return the size of this collection
    */
   public int getTreeCount()
   {
-    return _treeList.size();
-  } //-- int getTreeCount()
+    return this._treeList.size();
+  }
 
   /**
-   * Method isValid
-   *
-   *
-   *
-   * @return boolean
+   * 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)
+    } 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()
+    this._sequenceSetList.clear();
+  }
 
   /**
-   * Method removeAllTree
-   *
-   */
+     */
   public void removeAllTree()
   {
-    _treeList.removeAllElements();
-  } //-- 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)
+  public jalview.schemabinding.version2.SequenceSet removeSequenceSetAt(
+          final int index)
   {
-    java.lang.Object obj = _sequenceSetList.elementAt(index);
-    _sequenceSetList.removeElementAt(index);
+    java.lang.Object obj = this._sequenceSetList.remove(index);
     return (jalview.schemabinding.version2.SequenceSet) obj;
-  } //-- jalview.schemabinding.version2.SequenceSet removeSequenceSet(int)
+  }
+
+  /**
+   * 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 removeTree
-   *
-   *
-   *
+   * Method removeTreeAt.
+   * 
    * @param index
-   * @return String
+   * @return the element removed from the collection
    */
-  public java.lang.String removeTree(int index)
+  public java.lang.String removeTreeAt(final int index)
   {
-    java.lang.Object obj = _treeList.elementAt(index);
-    _treeList.removeElementAt(index);
-    return (String) obj;
-  } //-- java.lang.String removeTree(int)
+    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
+  public void setSequenceSet(final int index,
+          final jalview.schemabinding.version2.SequenceSet vSequenceSet)
+          throws java.lang.IndexOutOfBoundsException
   {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _sequenceSetList.size()))
+    // check bounds for index
+    if (index < 0 || index >= this._sequenceSetList.size())
     {
-      throw new IndexOutOfBoundsException();
+      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++)
+    // -- copy array
+    _sequenceSetList.clear();
+
+    for (int i = 0; i < vSequenceSetArray.length; i++)
     {
-      _sequenceSetList.addElement(sequenceSetArray[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
+  public void setTree(final int index, final java.lang.String vTree)
+          throws java.lang.IndexOutOfBoundsException
   {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _treeList.size()))
+    // check bounds for index
+    if (index < 0 || index >= this._treeList.size())
     {
-      throw new IndexOutOfBoundsException();
+      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++)
+    // -- copy array
+    _treeList.clear();
+
+    for (int i = 0; i < vTreeArray.length; i++)
     {
-      _treeList.addElement(treeArray[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)
+            jalview.schemabinding.version2.VAMSAS.class, 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();
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
     validator.validate(this);
-  } //-- void validate()
+  }
 
 }