From 9e69e298da663ca4c43f631bcca4dbb54da969f8 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 31 Jan 2007 15:33:00 +0000
Subject: [PATCH] aligned not used

---
 .../schemabinding/version2/SequenceSet.java        |   53 --------------------
 .../version2/SequenceSetDescriptor.java            |   41 ---------------
 2 files changed, 94 deletions(-)

diff --git a/src/jalview/schemabinding/version2/SequenceSet.java b/src/jalview/schemabinding/version2/SequenceSet.java
index 187139d..6f0342b 100755
--- a/src/jalview/schemabinding/version2/SequenceSet.java
+++ b/src/jalview/schemabinding/version2/SequenceSet.java
@@ -41,16 +41,6 @@ public class SequenceSet implements java.io.Serializable {
     private java.lang.String _gapChar;
 
     /**
-     * Field _aligned
-     */
-    private boolean _aligned;
-
-    /**
-     * keeps track of state for field: _aligned
-     */
-    private boolean _has_aligned;
-
-    /**
      * Field _sequenceList
      */
     private java.util.Vector _sequenceList;
@@ -131,15 +121,6 @@ public class SequenceSet implements java.io.Serializable {
     } //-- void addSequence(int, jalview.schemabinding.version2.Sequence) 
 
     /**
-     * Method deleteAligned
-     * 
-     */
-    public void deleteAligned()
-    {
-        this._has_aligned= false;
-    } //-- void deleteAligned() 
-
-    /**
      * Method enumerateAnnotation
      * 
      * 
@@ -164,17 +145,6 @@ public class SequenceSet implements java.io.Serializable {
     } //-- java.util.Enumeration enumerateSequence() 
 
     /**
-     * Returns the value of field 'aligned'.
-     * 
-     * @return boolean
-     * @return the value of field 'aligned'.
-     */
-    public boolean getAligned()
-    {
-        return this._aligned;
-    } //-- boolean getAligned() 
-
-    /**
      * Method getAnnotation
      * 
      * 
@@ -282,18 +252,6 @@ public class SequenceSet implements java.io.Serializable {
     } //-- int getSequenceCount() 
 
     /**
-     * Method hasAligned
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasAligned()
-    {
-        return this._has_aligned;
-    } //-- boolean hasAligned() 
-
-    /**
      * Method isValid
      * 
      * 
@@ -388,17 +346,6 @@ public class SequenceSet implements java.io.Serializable {
     } //-- jalview.schemabinding.version2.Sequence removeSequence(int) 
 
     /**
-     * Sets the value of field 'aligned'.
-     * 
-     * @param aligned the value of field 'aligned'.
-     */
-    public void setAligned(boolean aligned)
-    {
-        this._aligned = aligned;
-        this._has_aligned = true;
-    } //-- void setAligned(boolean) 
-
-    /**
      * Method setAnnotation
      * 
      * 
diff --git a/src/jalview/schemabinding/version2/SequenceSetDescriptor.java b/src/jalview/schemabinding/version2/SequenceSetDescriptor.java
index 81946b5..70ad2dc 100755
--- a/src/jalview/schemabinding/version2/SequenceSetDescriptor.java
+++ b/src/jalview/schemabinding/version2/SequenceSetDescriptor.java
@@ -103,47 +103,6 @@ public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDe
             fieldValidator.setValidator(typeValidator);
         }
         desc.setValidator(fieldValidator);
-        //-- _aligned
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_aligned", "aligned", org.exolab.castor.xml.NodeType.Attribute);
-        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                SequenceSet target = (SequenceSet) object;
-                if(!target.hasAligned())
-                    return null;
-                return (target.getAligned() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SequenceSet target = (SequenceSet) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteAligned();
-                        return;
-                    }
-                    target.setAligned( ((java.lang.Boolean)value).booleanValue());
-                }
-                catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance( java.lang.Object parent ) {
-                return null;
-            }
-        } );
-        desc.setHandler(handler);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _aligned
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            BooleanValidator typeValidator = new BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
         //-- initialize element descriptors
         
         //-- _sequenceList
-- 
1.7.10.2