X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FAlignment.java;h=78fff89dc2a6285df130e8bda1f746824356d1c4;hb=258c0056231d8a97c1d40dd665260e7814d11206;hp=093ae6f690f7379868433291a6f80c8574d2720d;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/binding/Alignment.java b/src/jalview/binding/Alignment.java
index 093ae6f..78fff89 100755
--- a/src/jalview/binding/Alignment.java
+++ b/src/jalview/binding/Alignment.java
@@ -4,24 +4,6 @@
  * 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;
@@ -45,7 +27,8 @@ import java.io.Writer;
  *
  * @version $Revision$ $Date$
  */
-public class Alignment implements java.io.Serializable {
+public class Alignment implements java.io.Serializable
+{
     //--------------------------/
     //- Class/Member Variables -/
     //--------------------------/
@@ -63,16 +46,25 @@ public class Alignment implements java.io.Serializable {
     //----------------/
     //- Constructors -/
     //----------------/
-    public Alignment() {
+    public Alignment()
+    {
         super();
     }
-     //-- jalview.binding.Alignment()
- //-----------/
 
-    public jalview.binding.Annotation getAnnotation() {
+    //-- jalview.binding.Alignment()
+    //-----------/
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public jalview.binding.Annotation getAnnotation()
+    {
         return this._annotation;
     }
-     //-- jalview.binding.Annotation getAnnotation()
+
+    //-- jalview.binding.Annotation getAnnotation() 
 
     /**
      * Returns the value of field 'sequenceSet'.
@@ -80,10 +72,12 @@ public class Alignment implements java.io.Serializable {
      * @return SequenceSet
      * @return the value of field 'sequenceSet'.
      */
-    public jalview.binding.SequenceSet getSequenceSet() {
+    public jalview.binding.SequenceSet getSequenceSet()
+    {
         return this._sequenceSet;
     }
-     //-- jalview.binding.SequenceSet getSequenceSet()
+
+    //-- jalview.binding.SequenceSet getSequenceSet() 
 
     /**
      * Method isValid
@@ -92,16 +86,21 @@ public class Alignment implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean isValid() {
-        try {
+    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
@@ -112,10 +111,12 @@ public class Alignment implements java.io.Serializable {
      */
     public void marshal(java.io.Writer out)
         throws org.exolab.castor.xml.MarshalException, 
-            org.exolab.castor.xml.ValidationException {
+            org.exolab.castor.xml.ValidationException
+    {
         Marshaller.marshal(this, out);
     }
-     //-- void marshal(java.io.Writer)
+
+    //-- void marshal(java.io.Writer) 
 
     /**
      * Method marshal
@@ -126,30 +127,36 @@ public class Alignment implements java.io.Serializable {
      */
     public void marshal(org.xml.sax.ContentHandler handler)
         throws java.io.IOException, org.exolab.castor.xml.MarshalException, 
-            org.exolab.castor.xml.ValidationException {
+            org.exolab.castor.xml.ValidationException
+    {
         Marshaller.marshal(this, handler);
     }
-     //-- void marshal(org.xml.sax.ContentHandler)
+
+    //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
      * Sets the value of field 'annotation'.
      *
      * @param annotation the value of field 'annotation'.
      */
-    public void setAnnotation(jalview.binding.Annotation annotation) {
+    public void setAnnotation(jalview.binding.Annotation annotation)
+    {
         this._annotation = annotation;
     }
-     //-- void setAnnotation(jalview.binding.Annotation)
+
+    //-- void setAnnotation(jalview.binding.Annotation) 
 
     /**
      * Sets the value of field 'sequenceSet'.
      *
      * @param sequenceSet the value of field 'sequenceSet'.
      */
-    public void setSequenceSet(jalview.binding.SequenceSet sequenceSet) {
+    public void setSequenceSet(jalview.binding.SequenceSet sequenceSet)
+    {
         this._sequenceSet = sequenceSet;
     }
-     //-- void setSequenceSet(jalview.binding.SequenceSet)
+
+    //-- void setSequenceSet(jalview.binding.SequenceSet) 
 
     /**
      * Method unmarshal
@@ -161,19 +168,23 @@ public class Alignment implements java.io.Serializable {
      */
     public static java.lang.Object unmarshal(java.io.Reader reader)
         throws org.exolab.castor.xml.MarshalException, 
-            org.exolab.castor.xml.ValidationException {
+            org.exolab.castor.xml.ValidationException
+    {
         return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.class,
             reader);
     }
-     //-- java.lang.Object unmarshal(java.io.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() 
 }