aligned not used

diff --git a/src/jalview/schemabinding/version2/SequenceSet.java b/src/jalview/schemabinding/version2/SequenceSet.java
index 187139d..6f0342b 100755 (executable)
--- 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;\r
 \r
     /**\r
-     * Field _aligned\r
-     */\r
-    private boolean _aligned;\r
-\r
-    /**\r
-     * keeps track of state for field: _aligned\r
-     */\r
-    private boolean _has_aligned;\r
-\r
-    /**\r
      * Field _sequenceList\r
      */\r
     private java.util.Vector _sequenceList;\r
@@ -131,15 +121,6 @@ public class SequenceSet implements java.io.Serializable {
     } //-- void addSequence(int, jalview.schemabinding.version2.Sequence) \r
 \r
     /**\r
-     * Method deleteAligned\r
-     * \r
-     */\r
-    public void deleteAligned()\r
-    {\r
-        this._has_aligned= false;\r
-    } //-- void deleteAligned() \r
-\r
-    /**\r
      * Method enumerateAnnotation\r
      * \r
      * \r
@@ -164,17 +145,6 @@ public class SequenceSet implements java.io.Serializable {
     } //-- java.util.Enumeration enumerateSequence() \r
 \r
     /**\r
-     * Returns the value of field 'aligned'.\r
-     * \r
-     * @return boolean\r
-     * @return the value of field 'aligned'.\r
-     */\r
-    public boolean getAligned()\r
-    {\r
-        return this._aligned;\r
-    } //-- boolean getAligned() \r
-\r
-    /**\r
      * Method getAnnotation\r
      * \r
      * \r
@@ -282,18 +252,6 @@ public class SequenceSet implements java.io.Serializable {
     } //-- int getSequenceCount() \r
 \r
     /**\r
-     * Method hasAligned\r
-     * \r
-     * \r
-     * \r
-     * @return boolean\r
-     */\r
-    public boolean hasAligned()\r
-    {\r
-        return this._has_aligned;\r
-    } //-- boolean hasAligned() \r
-\r
-    /**\r
      * Method isValid\r
      * \r
      * \r
@@ -388,17 +346,6 @@ public class SequenceSet implements java.io.Serializable {
     } //-- jalview.schemabinding.version2.Sequence removeSequence(int) \r
 \r
     /**\r
-     * Sets the value of field 'aligned'.\r
-     * \r
-     * @param aligned the value of field 'aligned'.\r
-     */\r
-    public void setAligned(boolean aligned)\r
-    {\r
-        this._aligned = aligned;\r
-        this._has_aligned = true;\r
-    } //-- void setAligned(boolean) \r
-\r
-    /**\r
      * Method setAnnotation\r
      * \r
      * \r

diff --git a/src/jalview/schemabinding/version2/SequenceSetDescriptor.java b/src/jalview/schemabinding/version2/SequenceSetDescriptor.java
index 81946b5..70ad2dc 100755 (executable)
--- 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);\r
         }\r
         desc.setValidator(fieldValidator);\r
-        //-- _aligned\r
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_aligned", "aligned", org.exolab.castor.xml.NodeType.Attribute);\r
-        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
-            public java.lang.Object getValue( java.lang.Object object ) \r
-                throws IllegalStateException\r
-            {\r
-                SequenceSet target = (SequenceSet) object;\r
-                if(!target.hasAligned())\r
-                    return null;\r
-                return (target.getAligned() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
-            }\r
-            public void setValue( java.lang.Object object, java.lang.Object value) \r
-                throws IllegalStateException, IllegalArgumentException\r
-            {\r
-                try {\r
-                    SequenceSet target = (SequenceSet) object;\r
-                    // if null, use delete method for optional primitives \r
-                    if (value == null) {\r
-                        target.deleteAligned();\r
-                        return;\r
-                    }\r
-                    target.setAligned( ((java.lang.Boolean)value).booleanValue());\r
-                }\r
-                catch (java.lang.Exception ex) {\r
-                    throw new IllegalStateException(ex.toString());\r
-                }\r
-            }\r
-            public java.lang.Object newInstance( java.lang.Object parent ) {\r
-                return null;\r
-            }\r
-        } );\r
-        desc.setHandler(handler);\r
-        addFieldDescriptor(desc);\r
-        \r
-        //-- validation code for: _aligned\r
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-        { //-- local scope\r
-            BooleanValidator typeValidator = new BooleanValidator();\r
-            fieldValidator.setValidator(typeValidator);\r
-        }\r
-        desc.setValidator(fieldValidator);\r
         //-- initialize element descriptors\r
         \r
         //-- _sequenceList\r