Formatted source

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

diff --git a/src/jalview/binding/Alignment.java b/src/jalview/binding/Alignment.java
index 644cd03..093ae6f 100755 (executable)
--- a/src/jalview/binding/Alignment.java
+++ b/src/jalview/binding/Alignment.java
@@ -4,7 +4,6 @@
  * Schema.\r
  * $Id$\r
  */\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
@@ -23,33 +22,32 @@
 * 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
-\r
 package jalview.binding;\r
 \r
-  //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
 import org.exolab.castor.xml.MarshalException;\r
 import org.exolab.castor.xml.Marshaller;\r
 import org.exolab.castor.xml.Unmarshaller;\r
 import org.exolab.castor.xml.ValidationException;\r
+\r
 import org.xml.sax.ContentHandler;\r
 \r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
+//---------------------------------/\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+\r
+\r
 /**\r
  * Class Alignment.\r
  *\r
  * @version $Revision$ $Date$\r
  */\r
 public class Alignment implements java.io.Serializable {\r
-\r
-\r
-      //--------------------------/\r
-     //- Class/Member Variables -/\r
+    //--------------------------/\r
+    //- Class/Member Variables -/\r
     //--------------------------/\r
 \r
     /**\r
@@ -62,30 +60,19 @@ public class Alignment implements java.io.Serializable {
      */\r
     private jalview.binding.SequenceSet _sequenceSet;\r
 \r
-\r
-      //----------------/\r
-     //- Constructors -/\r
     //----------------/\r
-\r
+    //- Constructors -/\r
+    //----------------/\r
     public Alignment() {\r
         super();\r
-    } //-- jalview.binding.Alignment()\r
-\r
-\r
-      //-----------/\r
-     //- Methods -/\r
-    //-----------/\r
+    }\r
+     //-- jalview.binding.Alignment()\r
+ //-----------/\r
 \r
-    /**\r
-     * Returns the value of field 'annotation'.\r
-     *\r
-     * @return Annotation\r
-     * @return the value of field 'annotation'.\r
-     */\r
-    public jalview.binding.Annotation getAnnotation()\r
-    {\r
+    public jalview.binding.Annotation getAnnotation() {\r
         return this._annotation;\r
-    } //-- jalview.binding.Annotation getAnnotation()\r
+    }\r
+     //-- jalview.binding.Annotation getAnnotation()\r
 \r
     /**\r
      * Returns the value of field 'sequenceSet'.\r
@@ -93,10 +80,10 @@ public class Alignment implements java.io.Serializable {
      * @return SequenceSet\r
      * @return the value of field 'sequenceSet'.\r
      */\r
-    public jalview.binding.SequenceSet getSequenceSet()\r
-    {\r
+    public jalview.binding.SequenceSet getSequenceSet() {\r
         return this._sequenceSet;\r
-    } //-- jalview.binding.SequenceSet getSequenceSet()\r
+    }\r
+     //-- jalview.binding.SequenceSet getSequenceSet()\r
 \r
     /**\r
      * Method isValid\r
@@ -105,16 +92,16 @@ public class Alignment implements java.io.Serializable {
      *\r
      * @return boolean\r
      */\r
-    public boolean isValid()\r
-    {\r
+    public boolean isValid() {\r
         try {\r
             validate();\r
-        }\r
-        catch (org.exolab.castor.xml.ValidationException vex) {\r
+        } catch (org.exolab.castor.xml.ValidationException vex) {\r
             return false;\r
         }\r
+\r
         return true;\r
-    } //-- boolean isValid()\r
+    }\r
+     //-- boolean isValid()\r
 \r
     /**\r
      * Method marshal\r
@@ -124,11 +111,11 @@ public class Alignment implements java.io.Serializable {
      * @param out\r
      */\r
     public void marshal(java.io.Writer out)\r
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
-    {\r
-\r
+        throws org.exolab.castor.xml.MarshalException, \r
+            org.exolab.castor.xml.ValidationException {\r
         Marshaller.marshal(this, out);\r
-    } //-- void marshal(java.io.Writer)\r
+    }\r
+     //-- void marshal(java.io.Writer)\r
 \r
     /**\r
      * Method marshal\r
@@ -138,31 +125,31 @@ public class Alignment implements java.io.Serializable {
      * @param handler\r
      */\r
     public void marshal(org.xml.sax.ContentHandler handler)\r
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
-    {\r
-\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, \r
+            org.exolab.castor.xml.ValidationException {\r
         Marshaller.marshal(this, handler);\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
-    {\r
+    public void setAnnotation(jalview.binding.Annotation annotation) {\r
         this._annotation = annotation;\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
-    {\r
+    public void setSequenceSet(jalview.binding.SequenceSet sequenceSet) {\r
         this._sequenceSet = sequenceSet;\r
-    } //-- void setSequenceSet(jalview.binding.SequenceSet)\r
+    }\r
+     //-- void setSequenceSet(jalview.binding.SequenceSet)\r
 \r
     /**\r
      * Method unmarshal\r
@@ -173,20 +160,20 @@ public class Alignment implements java.io.Serializable {
      * @return Object\r
      */\r
     public static java.lang.Object unmarshal(java.io.Reader reader)\r
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
-    {\r
-        return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.class, reader);\r
-    } //-- java.lang.Object unmarshal(java.io.Reader)\r
+        throws org.exolab.castor.xml.MarshalException, \r
+            org.exolab.castor.xml.ValidationException {\r
+        return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.class,\r
+            reader);\r
+    }\r
+     //-- java.lang.Object unmarshal(java.io.Reader)\r
 \r
     /**\r
      * Method validate\r
      *\r
      */\r
-    public void validate()\r
-        throws org.exolab.castor.xml.ValidationException\r
-    {\r
+    public void validate() throws org.exolab.castor.xml.ValidationException {\r
         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
         validator.validate(this);\r
-    } //-- void validate()\r
-\r
+    }\r
+     //-- void validate()\r
 }\r