X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FVAMSAS.java;h=b4237b85bf82880a9d5374673c94f37bae3243d0;hb=d4b1e4d0c74b1c6d0f3c3556b10be91a6aaea475;hp=5bc9b12fdef6baa7d8847618e6f1a4031afaef20;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/binding/VAMSAS.java b/src/jalview/binding/VAMSAS.java
index 5bc9b12..b4237b8 100755
--- a/src/jalview/binding/VAMSAS.java
+++ b/src/jalview/binding/VAMSAS.java
@@ -1,56 +1,38 @@
 /*
- * This class was automatically generated with
+ * 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
-* Copyright (C) 2005 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.binding;
-
-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;
+package jalview.binding;
 
+  //---------------------------------/
+ //- Imported classes and packages -/
 //---------------------------------/
-//- 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.
- *
+ * 
  * @version $Revision$ $Date$
  */
 public class VAMSAS implements java.io.Serializable {
-    //--------------------------/
-    //- Class/Member Variables -/
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -68,532 +50,527 @@ public class VAMSAS implements java.io.Serializable {
      */
     private java.util.Vector _sequenceSetList;
 
+
+      //----------------/
+     //- Constructors -/
     //----------------/
-    //- Constructors -/
-    //----------------/
+
     public VAMSAS() {
         super();
         _alignmentList = new Vector();
         _treeList = new Vector();
         _sequenceSetList = new Vector();
-    }
-     //-- jalview.binding.VAMSAS()
- //-----------/
+    } //-- jalview.binding.VAMSAS()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
 
+    /**
+     * Method addAlignment
+     * 
+     * 
+     * 
+     * @param vAlignment
+     */
     public void addAlignment(jalview.binding.Alignment vAlignment)
-        throws java.lang.IndexOutOfBoundsException {
+        throws java.lang.IndexOutOfBoundsException
+    {
         _alignmentList.addElement(vAlignment);
-    }
-     //-- void addAlignment(jalview.binding.Alignment)
+    } //-- void addAlignment(jalview.binding.Alignment) 
 
     /**
      * Method addAlignment
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @param vAlignment
      */
     public void addAlignment(int index, jalview.binding.Alignment vAlignment)
-        throws java.lang.IndexOutOfBoundsException {
+        throws java.lang.IndexOutOfBoundsException
+    {
         _alignmentList.insertElementAt(vAlignment, index);
-    }
-     //-- void addAlignment(int, jalview.binding.Alignment)
+    } //-- void addAlignment(int, jalview.binding.Alignment) 
 
     /**
      * Method addSequenceSet
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param vSequenceSet
      */
     public void addSequenceSet(jalview.binding.SequenceSet vSequenceSet)
-        throws java.lang.IndexOutOfBoundsException {
+        throws java.lang.IndexOutOfBoundsException
+    {
         _sequenceSetList.addElement(vSequenceSet);
-    }
-     //-- void addSequenceSet(jalview.binding.SequenceSet)
+    } //-- void addSequenceSet(jalview.binding.SequenceSet) 
 
     /**
      * Method addSequenceSet
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @param vSequenceSet
      */
-    public void addSequenceSet(int index,
-        jalview.binding.SequenceSet vSequenceSet)
-        throws java.lang.IndexOutOfBoundsException {
+    public void addSequenceSet(int index, jalview.binding.SequenceSet vSequenceSet)
+        throws java.lang.IndexOutOfBoundsException
+    {
         _sequenceSetList.insertElementAt(vSequenceSet, index);
-    }
-     //-- void addSequenceSet(int, jalview.binding.SequenceSet)
+    } //-- void addSequenceSet(int, jalview.binding.SequenceSet) 
 
     /**
      * Method addTree
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param vTree
      */
     public void addTree(java.lang.String vTree)
-        throws java.lang.IndexOutOfBoundsException {
+        throws java.lang.IndexOutOfBoundsException
+    {
         _treeList.addElement(vTree);
-    }
-     //-- void addTree(java.lang.String)
+    } //-- void addTree(java.lang.String) 
 
     /**
      * Method addTree
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @param vTree
      */
     public void addTree(int index, java.lang.String vTree)
-        throws java.lang.IndexOutOfBoundsException {
+        throws java.lang.IndexOutOfBoundsException
+    {
         _treeList.insertElementAt(vTree, index);
-    }
-     //-- void addTree(int, java.lang.String)
+    } //-- void addTree(int, java.lang.String) 
 
     /**
      * Method enumerateAlignment
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateAlignment() {
+    public java.util.Enumeration enumerateAlignment()
+    {
         return _alignmentList.elements();
-    }
-     //-- java.util.Enumeration enumerateAlignment()
+    } //-- java.util.Enumeration enumerateAlignment() 
 
     /**
      * Method enumerateSequenceSet
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateSequenceSet() {
+    public java.util.Enumeration enumerateSequenceSet()
+    {
         return _sequenceSetList.elements();
-    }
-     //-- java.util.Enumeration enumerateSequenceSet()
+    } //-- java.util.Enumeration enumerateSequenceSet() 
 
     /**
      * Method enumerateTree
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateTree() {
+    public java.util.Enumeration enumerateTree()
+    {
         return _treeList.elements();
-    }
-     //-- java.util.Enumeration enumerateTree()
+    } //-- java.util.Enumeration enumerateTree() 
 
     /**
      * Method getAlignment
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @return Alignment
      */
     public jalview.binding.Alignment getAlignment(int index)
-        throws java.lang.IndexOutOfBoundsException {
+        throws java.lang.IndexOutOfBoundsException
+    {
         //-- check bounds for index
         if ((index < 0) || (index > _alignmentList.size())) {
             throw new IndexOutOfBoundsException();
         }
-
+        
         return (jalview.binding.Alignment) _alignmentList.elementAt(index);
-    }
-     //-- jalview.binding.Alignment getAlignment(int)
+    } //-- jalview.binding.Alignment getAlignment(int) 
 
     /**
      * Method getAlignment
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return Alignment
      */
-    public jalview.binding.Alignment[] getAlignment() {
+    public jalview.binding.Alignment[] getAlignment()
+    {
         int size = _alignmentList.size();
         jalview.binding.Alignment[] mArray = new jalview.binding.Alignment[size];
-
         for (int index = 0; index < size; index++) {
             mArray[index] = (jalview.binding.Alignment) _alignmentList.elementAt(index);
         }
-
         return mArray;
-    }
-     //-- jalview.binding.Alignment[] getAlignment()
+    } //-- jalview.binding.Alignment[] getAlignment() 
 
     /**
      * Method getAlignmentCount
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return int
      */
-    public int getAlignmentCount() {
+    public int getAlignmentCount()
+    {
         return _alignmentList.size();
-    }
-     //-- int getAlignmentCount()
+    } //-- int getAlignmentCount() 
 
     /**
      * Method getSequenceSet
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @return SequenceSet
      */
     public jalview.binding.SequenceSet getSequenceSet(int index)
-        throws java.lang.IndexOutOfBoundsException {
+        throws java.lang.IndexOutOfBoundsException
+    {
         //-- check bounds for index
         if ((index < 0) || (index > _sequenceSetList.size())) {
             throw new IndexOutOfBoundsException();
         }
-
+        
         return (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index);
-    }
-     //-- jalview.binding.SequenceSet getSequenceSet(int)
+    } //-- jalview.binding.SequenceSet getSequenceSet(int) 
 
     /**
      * Method getSequenceSet
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return SequenceSet
      */
-    public jalview.binding.SequenceSet[] getSequenceSet() {
+    public jalview.binding.SequenceSet[] getSequenceSet()
+    {
         int size = _sequenceSetList.size();
         jalview.binding.SequenceSet[] mArray = new jalview.binding.SequenceSet[size];
-
         for (int index = 0; index < size; index++) {
             mArray[index] = (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index);
         }
-
         return mArray;
-    }
-     //-- jalview.binding.SequenceSet[] getSequenceSet()
+    } //-- jalview.binding.SequenceSet[] getSequenceSet() 
 
     /**
      * Method getSequenceSetCount
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return int
      */
-    public int getSequenceSetCount() {
+    public int getSequenceSetCount()
+    {
         return _sequenceSetList.size();
-    }
-     //-- int getSequenceSetCount()
+    } //-- int getSequenceSetCount() 
 
     /**
      * Method getTree
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @return String
      */
     public java.lang.String getTree(int index)
-        throws java.lang.IndexOutOfBoundsException {
+        throws java.lang.IndexOutOfBoundsException
+    {
         //-- check bounds for index
         if ((index < 0) || (index > _treeList.size())) {
             throw new IndexOutOfBoundsException();
         }
-
-        return (String) _treeList.elementAt(index);
-    }
-     //-- java.lang.String getTree(int)
+        
+        return (String)_treeList.elementAt(index);
+    } //-- java.lang.String getTree(int) 
 
     /**
      * Method getTree
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return String
      */
-    public java.lang.String[] getTree() {
+    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);
+            mArray[index] = (String)_treeList.elementAt(index);
         }
-
         return mArray;
-    }
-     //-- java.lang.String[] getTree()
+    } //-- java.lang.String[] getTree() 
 
     /**
      * Method getTreeCount
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return int
      */
-    public int getTreeCount() {
+    public int getTreeCount()
+    {
         return _treeList.size();
-    }
-     //-- int getTreeCount()
+    } //-- int getTreeCount() 
 
     /**
      * Method isValid
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return boolean
      */
-    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()
+    } //-- 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, org.exolab.castor.xml.ValidationException
+    {
+        
         Marshaller.marshal(this, out);
-    }
-     //-- void marshal(java.io.Writer)
+    } //-- 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, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
         Marshaller.marshal(this, handler);
-    }
-     //-- void marshal(org.xml.sax.ContentHandler)
+    } //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
      * Method removeAlignment
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @return Alignment
      */
-    public jalview.binding.Alignment removeAlignment(int index) {
+    public jalview.binding.Alignment removeAlignment(int index)
+    {
         java.lang.Object obj = _alignmentList.elementAt(index);
         _alignmentList.removeElementAt(index);
-
         return (jalview.binding.Alignment) obj;
-    }
-     //-- jalview.binding.Alignment removeAlignment(int)
+    } //-- jalview.binding.Alignment removeAlignment(int) 
 
     /**
      * Method removeAllAlignment
-     *
+     * 
      */
-    public void removeAllAlignment() {
+    public void removeAllAlignment()
+    {
         _alignmentList.removeAllElements();
-    }
-     //-- void removeAllAlignment()
+    } //-- void removeAllAlignment() 
 
     /**
      * Method removeAllSequenceSet
-     *
+     * 
      */
-    public void removeAllSequenceSet() {
+    public void removeAllSequenceSet()
+    {
         _sequenceSetList.removeAllElements();
-    }
-     //-- void removeAllSequenceSet()
+    } //-- void removeAllSequenceSet() 
 
     /**
      * Method removeAllTree
-     *
+     * 
      */
-    public void removeAllTree() {
+    public void removeAllTree()
+    {
         _treeList.removeAllElements();
-    }
-     //-- void removeAllTree()
+    } //-- void removeAllTree() 
 
     /**
      * Method removeSequenceSet
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @return SequenceSet
      */
-    public jalview.binding.SequenceSet removeSequenceSet(int index) {
+    public jalview.binding.SequenceSet removeSequenceSet(int index)
+    {
         java.lang.Object obj = _sequenceSetList.elementAt(index);
         _sequenceSetList.removeElementAt(index);
-
         return (jalview.binding.SequenceSet) obj;
-    }
-     //-- jalview.binding.SequenceSet removeSequenceSet(int)
+    } //-- jalview.binding.SequenceSet removeSequenceSet(int) 
 
     /**
      * Method removeTree
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @return String
      */
-    public java.lang.String removeTree(int index) {
+    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)
+        return (String)obj;
+    } //-- java.lang.String removeTree(int) 
 
     /**
      * Method setAlignment
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @param vAlignment
      */
     public void setAlignment(int index, jalview.binding.Alignment vAlignment)
-        throws java.lang.IndexOutOfBoundsException {
+        throws java.lang.IndexOutOfBoundsException
+    {
         //-- check bounds for index
         if ((index < 0) || (index > _alignmentList.size())) {
             throw new IndexOutOfBoundsException();
         }
-
         _alignmentList.setElementAt(vAlignment, index);
-    }
-     //-- void setAlignment(int, jalview.binding.Alignment)
+    } //-- void setAlignment(int, jalview.binding.Alignment) 
 
     /**
      * Method setAlignment
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param alignmentArray
      */
-    public void setAlignment(jalview.binding.Alignment[] alignmentArray) {
+    public void setAlignment(jalview.binding.Alignment[] alignmentArray)
+    {
         //-- copy array
         _alignmentList.removeAllElements();
-
         for (int i = 0; i < alignmentArray.length; i++) {
             _alignmentList.addElement(alignmentArray[i]);
         }
-    }
-     //-- void setAlignment(jalview.binding.Alignment)
+    } //-- void setAlignment(jalview.binding.Alignment) 
 
     /**
      * Method setSequenceSet
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @param vSequenceSet
      */
-    public void setSequenceSet(int index,
-        jalview.binding.SequenceSet vSequenceSet)
-        throws java.lang.IndexOutOfBoundsException {
+    public void setSequenceSet(int index, jalview.binding.SequenceSet vSequenceSet)
+        throws java.lang.IndexOutOfBoundsException
+    {
         //-- check bounds for index
         if ((index < 0) || (index > _sequenceSetList.size())) {
             throw new IndexOutOfBoundsException();
         }
-
         _sequenceSetList.setElementAt(vSequenceSet, index);
-    }
-     //-- void setSequenceSet(int, jalview.binding.SequenceSet)
+    } //-- void setSequenceSet(int, jalview.binding.SequenceSet) 
 
     /**
      * Method setSequenceSet
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param sequenceSetArray
      */
-    public void setSequenceSet(jalview.binding.SequenceSet[] sequenceSetArray) {
+    public void setSequenceSet(jalview.binding.SequenceSet[] sequenceSetArray)
+    {
         //-- copy array
         _sequenceSetList.removeAllElements();
-
         for (int i = 0; i < sequenceSetArray.length; i++) {
             _sequenceSetList.addElement(sequenceSetArray[i]);
         }
-    }
-     //-- void setSequenceSet(jalview.binding.SequenceSet)
+    } //-- void setSequenceSet(jalview.binding.SequenceSet) 
 
     /**
      * Method setTree
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @param vTree
      */
     public void setTree(int index, java.lang.String vTree)
-        throws java.lang.IndexOutOfBoundsException {
+        throws java.lang.IndexOutOfBoundsException
+    {
         //-- check bounds for index
         if ((index < 0) || (index > _treeList.size())) {
             throw new IndexOutOfBoundsException();
         }
-
         _treeList.setElementAt(vTree, index);
-    }
-     //-- void setTree(int, java.lang.String)
+    } //-- void setTree(int, java.lang.String) 
 
     /**
      * Method setTree
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param treeArray
      */
-    public void setTree(java.lang.String[] treeArray) {
+    public void setTree(java.lang.String[] treeArray)
+    {
         //-- copy array
         _treeList.removeAllElements();
-
         for (int i = 0; i < treeArray.length; i++) {
             _treeList.addElement(treeArray[i]);
         }
-    }
-     //-- void setTree(java.lang.String)
+    } //-- 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.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VAMSAS.class,
-            reader);
-    }
-     //-- java.lang.Object unmarshal(java.io.Reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VAMSAS.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
 
     /**
      * Method validate
-     *
+     * 
      */
-    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()
+    } //-- void validate() 
+
 }