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

diff --git a/src/jalview/binding/Alignment.java b/src/jalview/binding/Alignment.java
index 093ae6f..78fff89 100755 (executable)
--- a/src/jalview/binding/Alignment.java
+++ b/src/jalview/binding/Alignment.java
@@ -4,24 +4,6 @@
  * Schema.\r
  * $Id$\r
  */\r
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
-*/\r
 package jalview.binding;\r
 \r
 import org.exolab.castor.xml.MarshalException;\r
@@ -45,7 +27,8 @@ import java.io.Writer;
  *\r
  * @version $Revision$ $Date$\r
  */\r
-public class Alignment implements java.io.Serializable {\r
+public class Alignment implements java.io.Serializable\r
+{\r
     //--------------------------/\r
     //- Class/Member Variables -/\r
     //--------------------------/\r
@@ -63,16 +46,25 @@ public class Alignment implements java.io.Serializable {
     //----------------/\r
     //- Constructors -/\r
     //----------------/\r
-    public Alignment() {\r
+    public Alignment()\r
+    {\r
         super();\r
     }\r
-     //-- jalview.binding.Alignment()\r
- //-----------/\r
 \r
-    public jalview.binding.Annotation getAnnotation() {\r
+    //-- jalview.binding.Alignment()\r
+    //-----------/\r
+\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @return DOCUMENT ME!\r
+     */\r
+    public jalview.binding.Annotation getAnnotation()\r
+    {\r
         return this._annotation;\r
     }\r
-     //-- jalview.binding.Annotation getAnnotation()\r
+\r
+    //-- jalview.binding.Annotation getAnnotation() \r
 \r
     /**\r
      * Returns the value of field 'sequenceSet'.\r
@@ -80,10 +72,12 @@ public class Alignment implements java.io.Serializable {
      * @return SequenceSet\r
      * @return the value of field 'sequenceSet'.\r
      */\r
-    public jalview.binding.SequenceSet getSequenceSet() {\r
+    public jalview.binding.SequenceSet getSequenceSet()\r
+    {\r
         return this._sequenceSet;\r
     }\r
-     //-- jalview.binding.SequenceSet getSequenceSet()\r
+\r
+    //-- jalview.binding.SequenceSet getSequenceSet() \r
 \r
     /**\r
      * Method isValid\r
@@ -92,16 +86,21 @@ public class Alignment implements java.io.Serializable {
      *\r
      * @return boolean\r
      */\r
-    public boolean isValid() {\r
-        try {\r
+    public boolean isValid()\r
+    {\r
+        try\r
+        {\r
             validate();\r
-        } catch (org.exolab.castor.xml.ValidationException vex) {\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex)\r
+        {\r
             return false;\r
         }\r
 \r
         return true;\r
     }\r
-     //-- boolean isValid()\r
+\r
+    //-- boolean isValid() \r
 \r
     /**\r
      * Method marshal\r
@@ -112,10 +111,12 @@ public class Alignment implements java.io.Serializable {
      */\r
     public void marshal(java.io.Writer out)\r
         throws org.exolab.castor.xml.MarshalException, \r
-            org.exolab.castor.xml.ValidationException {\r
+            org.exolab.castor.xml.ValidationException\r
+    {\r
         Marshaller.marshal(this, out);\r
     }\r
-     //-- void marshal(java.io.Writer)\r
+\r
+    //-- void marshal(java.io.Writer) \r
 \r
     /**\r
      * Method marshal\r
@@ -126,30 +127,36 @@ public class Alignment implements java.io.Serializable {
      */\r
     public void marshal(org.xml.sax.ContentHandler handler)\r
         throws java.io.IOException, org.exolab.castor.xml.MarshalException, \r
-            org.exolab.castor.xml.ValidationException {\r
+            org.exolab.castor.xml.ValidationException\r
+    {\r
         Marshaller.marshal(this, handler);\r
     }\r
-     //-- void marshal(org.xml.sax.ContentHandler)\r
+\r
+    //-- void marshal(org.xml.sax.ContentHandler) \r
 \r
     /**\r
      * Sets the value of field 'annotation'.\r
      *\r
      * @param annotation the value of field 'annotation'.\r
      */\r
-    public void setAnnotation(jalview.binding.Annotation annotation) {\r
+    public void setAnnotation(jalview.binding.Annotation annotation)\r
+    {\r
         this._annotation = annotation;\r
     }\r
-     //-- void setAnnotation(jalview.binding.Annotation)\r
+\r
+    //-- void setAnnotation(jalview.binding.Annotation) \r
 \r
     /**\r
      * Sets the value of field 'sequenceSet'.\r
      *\r
      * @param sequenceSet the value of field 'sequenceSet'.\r
      */\r
-    public void setSequenceSet(jalview.binding.SequenceSet sequenceSet) {\r
+    public void setSequenceSet(jalview.binding.SequenceSet sequenceSet)\r
+    {\r
         this._sequenceSet = sequenceSet;\r
     }\r
-     //-- void setSequenceSet(jalview.binding.SequenceSet)\r
+\r
+    //-- void setSequenceSet(jalview.binding.SequenceSet) \r
 \r
     /**\r
      * Method unmarshal\r
@@ -161,19 +168,23 @@ public class Alignment implements java.io.Serializable {
      */\r
     public static java.lang.Object unmarshal(java.io.Reader reader)\r
         throws org.exolab.castor.xml.MarshalException, \r
-            org.exolab.castor.xml.ValidationException {\r
+            org.exolab.castor.xml.ValidationException\r
+    {\r
         return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.class,\r
             reader);\r
     }\r
-     //-- java.lang.Object unmarshal(java.io.Reader)\r
+\r
+    //-- java.lang.Object unmarshal(java.io.Reader) \r
 \r
     /**\r
      * Method validate\r
      *\r
      */\r
-    public void validate() throws org.exolab.castor.xml.ValidationException {\r
+    public void validate() throws org.exolab.castor.xml.ValidationException\r
+    {\r
         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
         validator.validate(this);\r
     }\r
-     //-- void validate()\r
+\r
+    //-- void validate() \r
 }\r