JAL-1620 version bump and release notes

[jalview.git] / src / jalview / binding / Alignment.java

diff --git a/src/jalview/binding/Alignment.java b/src/jalview/binding/Alignment.java
old mode 100755 (executable)
new mode 100644 (file)
index 96812e3..9627b20
--- a/src/jalview/binding/Alignment.java
+++ b/src/jalview/binding/Alignment.java
@@ -1,26 +1,28 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
- * 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 file is part of Jalview.
  * 
- * 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.
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview 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
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 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 +104,10 @@ 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 +121,12 @@ 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 +140,7 @@ 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 +151,7 @@ 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 +163,10 @@ 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(
@@ -183,8 +182,7 @@ public class Alignment implements java.io.Serializable
    * 
    * 
    * @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
   {