X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FAlignment.java;h=9a38f10c1d7c794c3d3d412fca7cb8277693543d;hb=aad4f693fc478138fd225741acf1f8d44defd162;hp=093ae6f690f7379868433291a6f80c8574d2720d;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/binding/Alignment.java b/src/jalview/binding/Alignment.java
index 093ae6f..9a38f10 100755
--- a/src/jalview/binding/Alignment.java
+++ b/src/jalview/binding/Alignment.java
@@ -1,53 +1,36 @@
 /*
- * 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 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 Alignment.
- *
+ * 
  * @version $Revision$ $Date$
  */
 public class Alignment implements java.io.Serializable {
-    //--------------------------/
-    //- Class/Member Variables -/
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -60,120 +43,131 @@ public class Alignment implements java.io.Serializable {
      */
     private jalview.binding.SequenceSet _sequenceSet;
 
+
+      //----------------/
+     //- Constructors -/
     //----------------/
-    //- Constructors -/
-    //----------------/
+
     public Alignment() {
         super();
-    }
-     //-- jalview.binding.Alignment()
- //-----------/
+    } //-- jalview.binding.Alignment()
 
-    public jalview.binding.Annotation getAnnotation() {
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Returns the value of field 'annotation'.
+     * 
+     * @return Annotation
+     * @return the value of field 'annotation'.
+     */
+    public jalview.binding.Annotation getAnnotation()
+    {
         return this._annotation;
-    }
-     //-- jalview.binding.Annotation getAnnotation()
+    } //-- jalview.binding.Annotation getAnnotation() 
 
     /**
      * Returns the value of field 'sequenceSet'.
-     *
+     * 
      * @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
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @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) 
 
     /**
      * 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
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @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.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.class,
-            reader);
-    }
-     //-- java.lang.Object unmarshal(java.io.Reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.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() 
+
 }