X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FSequenceSet.java;h=91b00577d5bddcbb712889706edbfe27c33ede1b;hb=682c69b6a050a742d20f643459d8d8fbfecf40e1;hp=187139dac98b87b290136d9337a706b2d3bdbd60;hpb=65df62f4b048a1615d32ea2c3576082ad2b63af8;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/SequenceSet.java b/src/jalview/schemabinding/version2/SequenceSet.java
index 187139d..91b0057 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;
@@ -60,6 +50,11 @@ public class SequenceSet implements java.io.Serializable {
      */
     private java.util.Vector _annotationList;
 
+    /**
+     * Field _sequenceSetPropertiesList
+     */
+    private java.util.Vector _sequenceSetPropertiesList;
+
 
       //----------------/
      //- Constructors -/
@@ -69,6 +64,7 @@ public class SequenceSet implements java.io.Serializable {
         super();
         _sequenceList = new Vector();
         _annotationList = new Vector();
+        _sequenceSetPropertiesList = new Vector();
     } //-- jalview.schemabinding.version2.SequenceSet()
 
 
@@ -131,13 +127,31 @@ public class SequenceSet implements java.io.Serializable {
     } //-- void addSequence(int, jalview.schemabinding.version2.Sequence) 
 
     /**
-     * Method deleteAligned
+     * Method addSequenceSetProperties
+     * 
+     * 
+     * 
+     * @param vSequenceSetProperties
+     */
+    public void addSequenceSetProperties(jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _sequenceSetPropertiesList.addElement(vSequenceSetProperties);
+    } //-- void addSequenceSetProperties(jalview.schemabinding.version2.SequenceSetProperties) 
+
+    /**
+     * Method addSequenceSetProperties
+     * 
      * 
+     * 
+     * @param index
+     * @param vSequenceSetProperties
      */
-    public void deleteAligned()
+    public void addSequenceSetProperties(int index, jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
+        throws java.lang.IndexOutOfBoundsException
     {
-        this._has_aligned= false;
-    } //-- void deleteAligned() 
+        _sequenceSetPropertiesList.insertElementAt(vSequenceSetProperties, index);
+    } //-- void addSequenceSetProperties(int, jalview.schemabinding.version2.SequenceSetProperties) 
 
     /**
      * Method enumerateAnnotation
@@ -164,15 +178,16 @@ public class SequenceSet implements java.io.Serializable {
     } //-- java.util.Enumeration enumerateSequence() 
 
     /**
-     * Returns the value of field 'aligned'.
+     * Method enumerateSequenceSetProperties
      * 
-     * @return boolean
-     * @return the value of field 'aligned'.
+     * 
+     * 
+     * @return Enumeration
      */
-    public boolean getAligned()
+    public java.util.Enumeration enumerateSequenceSetProperties()
     {
-        return this._aligned;
-    } //-- boolean getAligned() 
+        return _sequenceSetPropertiesList.elements();
+    } //-- java.util.Enumeration enumerateSequenceSetProperties() 
 
     /**
      * Method getAnnotation
@@ -282,16 +297,52 @@ public class SequenceSet implements java.io.Serializable {
     } //-- int getSequenceCount() 
 
     /**
-     * Method hasAligned
+     * Method getSequenceSetProperties
      * 
      * 
      * 
-     * @return boolean
+     * @param index
+     * @return SequenceSetProperties
      */
-    public boolean hasAligned()
+    public jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties(int index)
+        throws java.lang.IndexOutOfBoundsException
     {
-        return this._has_aligned;
-    } //-- boolean hasAligned() 
+        //-- check bounds for index
+        if ((index < 0) || (index > _sequenceSetPropertiesList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList.elementAt(index);
+    } //-- jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties(int) 
+
+    /**
+     * Method getSequenceSetProperties
+     * 
+     * 
+     * 
+     * @return SequenceSetProperties
+     */
+    public jalview.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties()
+    {
+        int size = _sequenceSetPropertiesList.size();
+        jalview.schemabinding.version2.SequenceSetProperties[] mArray = new jalview.schemabinding.version2.SequenceSetProperties[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties() 
+
+    /**
+     * Method getSequenceSetPropertiesCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getSequenceSetPropertiesCount()
+    {
+        return _sequenceSetPropertiesList.size();
+    } //-- int getSequenceSetPropertiesCount() 
 
     /**
      * Method isValid
@@ -358,6 +409,15 @@ public class SequenceSet implements java.io.Serializable {
     } //-- void removeAllSequence() 
 
     /**
+     * Method removeAllSequenceSetProperties
+     * 
+     */
+    public void removeAllSequenceSetProperties()
+    {
+        _sequenceSetPropertiesList.removeAllElements();
+    } //-- void removeAllSequenceSetProperties() 
+
+    /**
      * Method removeAnnotation
      * 
      * 
@@ -388,15 +448,19 @@ public class SequenceSet implements java.io.Serializable {
     } //-- jalview.schemabinding.version2.Sequence removeSequence(int) 
 
     /**
-     * Sets the value of field 'aligned'.
+     * Method removeSequenceSetProperties
      * 
-     * @param aligned the value of field 'aligned'.
+     * 
+     * 
+     * @param index
+     * @return SequenceSetProperties
      */
-    public void setAligned(boolean aligned)
+    public jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetProperties(int index)
     {
-        this._aligned = aligned;
-        this._has_aligned = true;
-    } //-- void setAligned(boolean) 
+        java.lang.Object obj = _sequenceSetPropertiesList.elementAt(index);
+        _sequenceSetPropertiesList.removeElementAt(index);
+        return (jalview.schemabinding.version2.SequenceSetProperties) obj;
+    } //-- jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetProperties(int) 
 
     /**
      * Method setAnnotation
@@ -477,6 +541,40 @@ public class SequenceSet implements java.io.Serializable {
     } //-- void setSequence(jalview.schemabinding.version2.Sequence) 
 
     /**
+     * Method setSequenceSetProperties
+     * 
+     * 
+     * 
+     * @param index
+     * @param vSequenceSetProperties
+     */
+    public void setSequenceSetProperties(int index, jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _sequenceSetPropertiesList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _sequenceSetPropertiesList.setElementAt(vSequenceSetProperties, index);
+    } //-- void setSequenceSetProperties(int, jalview.schemabinding.version2.SequenceSetProperties) 
+
+    /**
+     * Method setSequenceSetProperties
+     * 
+     * 
+     * 
+     * @param sequenceSetPropertiesArray
+     */
+    public void setSequenceSetProperties(jalview.schemabinding.version2.SequenceSetProperties[] sequenceSetPropertiesArray)
+    {
+        //-- copy array
+        _sequenceSetPropertiesList.removeAllElements();
+        for (int i = 0; i < sequenceSetPropertiesArray.length; i++) {
+            _sequenceSetPropertiesList.addElement(sequenceSetPropertiesArray[i]);
+        }
+    } //-- void setSequenceSetProperties(jalview.schemabinding.version2.SequenceSetProperties) 
+
+    /**
      * Method unmarshal
      * 
      *