X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FAlignment.java;h=093ae6f690f7379868433291a6f80c8574d2720d;hb=61195dcb4558671895db385fd00f0f3680636fcf;hp=9a38f10c1d7c794c3d3d412fca7cb8277693543d;hpb=124589ea0c58cbb7b3788bbf13b687a0ece3c9e0;p=jalview.git

diff --git a/src/jalview/binding/Alignment.java b/src/jalview/binding/Alignment.java
index 9a38f10..093ae6f 100755
--- a/src/jalview/binding/Alignment.java
+++ b/src/jalview/binding/Alignment.java
@@ -1,36 +1,53 @@
 /*
- * 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;
 
-  //---------------------------------/
- //- 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;
 
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+
+
 /**
  * Class Alignment.
- * 
+ *
  * @version $Revision$ $Date$
  */
 public class Alignment implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -43,131 +60,120 @@ public class Alignment implements java.io.Serializable {
      */
     private jalview.binding.SequenceSet _sequenceSet;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
+    //- Constructors -/
+    //----------------/
     public Alignment() {
         super();
-    } //-- jalview.binding.Alignment()
+    }
+     //-- jalview.binding.Alignment()
+ //-----------/
 
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'annotation'.
-     * 
-     * @return Annotation
-     * @return the value of field 'annotation'.
-     */
-    public jalview.binding.Annotation getAnnotation()
-    {
+    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()
 }