X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FAlignment.java;h=0116b44393eba47157843ede0032ccc5e7b532e8;hb=382f5ff058a4c2fed1e9874bb712b40f16ec1a4e;hp=96812e3d545995a529db0cc57043f126fc6a637e;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/binding/Alignment.java b/src/jalview/binding/Alignment.java
old mode 100755
new mode 100644
index 96812e3..0116b44
--- a/src/jalview/binding/Alignment.java
+++ b/src/jalview/binding/Alignment.java
@@ -1,26 +1,15 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 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
+ * 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 -/
-// ---------------------------------/
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -102,11 +91,10 @@ public class Alignment implements java.io.Serializable
    * 
    * @param out
    * @throws org.exolab.castor.xml.MarshalException
-   *                 if object is null or if any SAXException is thrown during
-   *                 marshaling
+   *           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
+   *           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,
@@ -120,13 +108,12 @@ public class Alignment implements java.io.Serializable
    * 
    * @param handler
    * @throws java.io.IOException
-   *                 if an IOException occurs during marshaling
+   *           if an IOException occurs during marshaling
    * @throws org.exolab.castor.xml.ValidationException
-   *                 if this object is an invalid instance according to the
-   *                 schema
+   *           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
+   *           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,
@@ -140,7 +127,7 @@ public class Alignment implements java.io.Serializable
    * Sets the value of field 'annotation'.
    * 
    * @param annotation
-   *                the value of field 'annotation'.
+   *          the value of field 'annotation'.
    */
   public void setAnnotation(final jalview.binding.Annotation annotation)
   {
@@ -151,7 +138,7 @@ public class Alignment implements java.io.Serializable
    * Sets the value of field 'sequenceSet'.
    * 
    * @param sequenceSet
-   *                the value of field 'sequenceSet'.
+   *          the value of field 'sequenceSet'.
    */
   public void setSequenceSet(final jalview.binding.SequenceSet sequenceSet)
   {
@@ -163,11 +150,10 @@ public class Alignment implements java.io.Serializable
    * 
    * @param reader
    * @throws org.exolab.castor.xml.MarshalException
-   *                 if object is null or if any SAXException is thrown during
-   *                 marshaling
+   *           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
+   *           if this object is an invalid instance according to the schema
    * @return the unmarshaled jalview.binding.Alignment
    */
   public static jalview.binding.Alignment unmarshal(
@@ -175,16 +161,15 @@ public class Alignment implements java.io.Serializable
           throws org.exolab.castor.xml.MarshalException,
           org.exolab.castor.xml.ValidationException
   {
-    return (jalview.binding.Alignment) Unmarshaller.unmarshal(
-            jalview.binding.Alignment.class, reader);
+    return (jalview.binding.Alignment) Unmarshaller
+            .unmarshal(jalview.binding.Alignment.class, reader);
   }
 
   /**
    * 
    * 
    * @throws org.exolab.castor.xml.ValidationException
-   *                 if this object is an invalid instance according to the
-   *                 schema
+   *           if this object is an invalid instance according to the schema
    */
   public void validate() throws org.exolab.castor.xml.ValidationException
   {