X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FVAMSAS.java;fp=src%2Fjalview%2Fbinding%2FVAMSAS.java;h=0000000000000000000000000000000000000000;hb=ca8504cf9d10874dce9f07cf7a9d933853fe0dd0;hp=b5a32da99851eb7d9a7b909dc3cdb9f22cd8211c;hpb=775e7bc104584e88dddcea73fbf02c66f5200c16;p=jalview.git

diff --git a/src/jalview/binding/VAMSAS.java b/src/jalview/binding/VAMSAS.java
deleted file mode 100644
index b5a32da..0000000
--- a/src/jalview/binding/VAMSAS.java
+++ /dev/null
@@ -1,605 +0,0 @@
-/*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package jalview.binding;
-
-//---------------------------------/
-//- Imported classes and packages -/
-//---------------------------------/
-
-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 _alignmentList.
-   */
-  private java.util.Vector _alignmentList;
-
-  /**
-   * Field _treeList.
-   */
-  private java.util.Vector _treeList;
-
-  /**
-   * Field _sequenceSetList.
-   */
-  private java.util.Vector _sequenceSetList;
-
-  // ----------------/
-  // - Constructors -/
-  // ----------------/
-
-  public VAMSAS()
-  {
-    super();
-    this._alignmentList = new java.util.Vector();
-    this._treeList = new java.util.Vector();
-    this._sequenceSetList = new java.util.Vector();
-  }
-
-  // -----------/
-  // - Methods -/
-  // -----------/
-
-  /**
-   * 
-   * 
-   * @param vAlignment
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void addAlignment(final Alignment vAlignment)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    this._alignmentList.addElement(vAlignment);
-  }
-
-  /**
-   * 
-   * 
-   * @param index
-   * @param vAlignment
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void addAlignment(final int index, final Alignment vAlignment)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    this._alignmentList.add(index, vAlignment);
-  }
-
-  /**
-   * 
-   * 
-   * @param vSequenceSet
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void addSequenceSet(final SequenceSet vSequenceSet)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    this._sequenceSetList.addElement(vSequenceSet);
-  }
-
-  /**
-   * 
-   * 
-   * @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 SequenceSet vSequenceSet)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    this._sequenceSetList.add(index, vSequenceSet);
-  }
-
-  /**
-   * 
-   * 
-   * @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);
-  }
-
-  /**
-   * 
-   * 
-   * @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);
-  }
-
-  /**
-   * Method enumerateAlignment.
-   * 
-   * @return an Enumeration over all Alignment elements
-   */
-  public java.util.Enumeration enumerateAlignment()
-  {
-    return this._alignmentList.elements();
-  }
-
-  /**
-   * Method enumerateSequenceSet.
-   * 
-   * @return an Enumeration over all SequenceSet elements
-   */
-  public java.util.Enumeration enumerateSequenceSet()
-  {
-    return this._sequenceSetList.elements();
-  }
-
-  /**
-   * Method enumerateTree.
-   * 
-   * @return an Enumeration over all java.lang.String elements
-   */
-  public java.util.Enumeration enumerateTree()
-  {
-    return this._treeList.elements();
-  }
-
-  /**
-   * Method getAlignment.
-   * 
-   * @param index
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   * @return the value of the Alignment at the given index
-   */
-  public Alignment getAlignment(final int index)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    // check bounds for index
-    if (index < 0 || index >= this._alignmentList.size())
-    {
-      throw new IndexOutOfBoundsException(
-              "getAlignment: Index value '" + index + "' not in range [0.."
-                      + (this._alignmentList.size() - 1) + "]");
-    }
-
-    return (Alignment) _alignmentList.get(index);
-  }
-
-  /**
-   * Method getAlignment.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 Alignment[] getAlignment()
-  {
-    Alignment[] array = new Alignment[0];
-    return (Alignment[]) this._alignmentList.toArray(array);
-  }
-
-  /**
-   * Method getAlignmentCount.
-   * 
-   * @return the size of this collection
-   */
-  public int getAlignmentCount()
-  {
-    return this._alignmentList.size();
-  }
-
-  /**
-   * Method getSequenceSet.
-   * 
-   * @param index
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   * @return the value of the SequenceSet at the given index
-   */
-  public 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 (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 SequenceSet[] getSequenceSet()
-  {
-    SequenceSet[] array = new SequenceSet[0];
-    return (SequenceSet[]) this._sequenceSetList.toArray(array);
-  }
-
-  /**
-   * Method getSequenceSetCount.
-   * 
-   * @return the size of this collection
-   */
-  public int getSequenceSetCount()
-  {
-    return this._sequenceSetList.size();
-  }
-
-  /**
-   * 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);
-  }
-
-  /**
-   * Method removeAlignment.
-   * 
-   * @param vAlignment
-   * @return true if the object was removed from the collection.
-   */
-  public boolean removeAlignment(final Alignment vAlignment)
-  {
-    boolean removed = _alignmentList.remove(vAlignment);
-    return removed;
-  }
-
-  /**
-   * Method removeAlignmentAt.
-   * 
-   * @param index
-   * @return the element removed from the collection
-   */
-  public Alignment removeAlignmentAt(final int index)
-  {
-    java.lang.Object obj = this._alignmentList.remove(index);
-    return (Alignment) obj;
-  }
-
-  /**
-     */
-  public void removeAllAlignment()
-  {
-    this._alignmentList.clear();
-  }
-
-  /**
-     */
-  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 SequenceSet vSequenceSet)
-  {
-    boolean removed = _sequenceSetList.remove(vSequenceSet);
-    return removed;
-  }
-
-  /**
-   * Method removeSequenceSetAt.
-   * 
-   * @param index
-   * @return the element removed from the collection
-   */
-  public SequenceSet removeSequenceSetAt(final int index)
-  {
-    java.lang.Object obj = this._sequenceSetList.remove(index);
-    return (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 vAlignment
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void setAlignment(final int index, final Alignment vAlignment)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    // check bounds for index
-    if (index < 0 || index >= this._alignmentList.size())
-    {
-      throw new IndexOutOfBoundsException(
-              "setAlignment: Index value '" + index + "' not in range [0.."
-                      + (this._alignmentList.size() - 1) + "]");
-    }
-
-    this._alignmentList.set(index, vAlignment);
-  }
-
-  /**
-   * 
-   * 
-   * @param vAlignmentArray
-   */
-  public void setAlignment(final Alignment[] vAlignmentArray)
-  {
-    // -- copy array
-    _alignmentList.clear();
-
-    for (int i = 0; i < vAlignmentArray.length; i++)
-    {
-      this._alignmentList.add(vAlignmentArray[i]);
-    }
-  }
-
-  /**
-   * 
-   * 
-   * @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 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 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.binding.VAMSAS
-   */
-  public static jalview.binding.VAMSAS unmarshal(
-          final java.io.Reader reader)
-          throws org.exolab.castor.xml.MarshalException,
-          org.exolab.castor.xml.ValidationException
-  {
-    return (jalview.binding.VAMSAS) Unmarshaller
-            .unmarshal(jalview.binding.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);
-  }
-
-}