X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FSequence.java;h=993ad23609b227ec32ae07d817e49cd2abed549c;hb=0fc704a18faa7d11b6d02876bb6c1e8bc19f343c;hp=7a1533276062ff12ab51c19652ebaecdc2494e5a;hpb=65df62f4b048a1615d32ea2c3576082ad2b63af8;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/Sequence.java b/src/jalview/schemabinding/version2/Sequence.java
index 7a15332..993ad23 100755
--- a/src/jalview/schemabinding/version2/Sequence.java
+++ b/src/jalview/schemabinding/version2/Sequence.java
@@ -15,6 +15,8 @@ import java.io.IOException;
 import java.io.Reader;
 import java.io.Serializable;
 import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
 import org.exolab.castor.xml.MarshalException;
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -26,17 +28,28 @@ import org.xml.sax.ContentHandler;
  * 
  * @version $Revision$ $Date$
  */
-public class Sequence extends SequenceType 
+public class Sequence extends jalview.schemabinding.version2.SequenceType 
 implements java.io.Serializable
 {
 
 
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _DBRefList
+     */
+    private java.util.Vector _DBRefList;
+
+
       //----------------/
      //- Constructors -/
     //----------------/
 
     public Sequence() {
         super();
+        _DBRefList = new Vector();
     } //-- jalview.schemabinding.version2.Sequence()
 
 
@@ -45,6 +58,93 @@ implements java.io.Serializable
     //-----------/
 
     /**
+     * Method addDBRef
+     * 
+     * 
+     * 
+     * @param vDBRef
+     */
+    public void addDBRef(jalview.schemabinding.version2.DBRef vDBRef)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _DBRefList.addElement(vDBRef);
+    } //-- void addDBRef(jalview.schemabinding.version2.DBRef) 
+
+    /**
+     * Method addDBRef
+     * 
+     * 
+     * 
+     * @param index
+     * @param vDBRef
+     */
+    public void addDBRef(int index, jalview.schemabinding.version2.DBRef vDBRef)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _DBRefList.insertElementAt(vDBRef, index);
+    } //-- void addDBRef(int, jalview.schemabinding.version2.DBRef) 
+
+    /**
+     * Method enumerateDBRef
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateDBRef()
+    {
+        return _DBRefList.elements();
+    } //-- java.util.Enumeration enumerateDBRef() 
+
+    /**
+     * Method getDBRef
+     * 
+     * 
+     * 
+     * @param index
+     * @return DBRef
+     */
+    public jalview.schemabinding.version2.DBRef getDBRef(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _DBRefList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.schemabinding.version2.DBRef) _DBRefList.elementAt(index);
+    } //-- jalview.schemabinding.version2.DBRef getDBRef(int) 
+
+    /**
+     * Method getDBRef
+     * 
+     * 
+     * 
+     * @return DBRef
+     */
+    public jalview.schemabinding.version2.DBRef[] getDBRef()
+    {
+        int size = _DBRefList.size();
+        jalview.schemabinding.version2.DBRef[] mArray = new jalview.schemabinding.version2.DBRef[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.schemabinding.version2.DBRef) _DBRefList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.schemabinding.version2.DBRef[] getDBRef() 
+
+    /**
+     * Method getDBRefCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getDBRefCount()
+    {
+        return _DBRefList.size();
+    } //-- int getDBRefCount() 
+
+    /**
      * Method isValid
      * 
      * 
@@ -91,6 +191,64 @@ implements java.io.Serializable
     } //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
+     * Method removeAllDBRef
+     * 
+     */
+    public void removeAllDBRef()
+    {
+        _DBRefList.removeAllElements();
+    } //-- void removeAllDBRef() 
+
+    /**
+     * Method removeDBRef
+     * 
+     * 
+     * 
+     * @param index
+     * @return DBRef
+     */
+    public jalview.schemabinding.version2.DBRef removeDBRef(int index)
+    {
+        java.lang.Object obj = _DBRefList.elementAt(index);
+        _DBRefList.removeElementAt(index);
+        return (jalview.schemabinding.version2.DBRef) obj;
+    } //-- jalview.schemabinding.version2.DBRef removeDBRef(int) 
+
+    /**
+     * Method setDBRef
+     * 
+     * 
+     * 
+     * @param index
+     * @param vDBRef
+     */
+    public void setDBRef(int index, jalview.schemabinding.version2.DBRef vDBRef)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _DBRefList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _DBRefList.setElementAt(vDBRef, index);
+    } //-- void setDBRef(int, jalview.schemabinding.version2.DBRef) 
+
+    /**
+     * Method setDBRef
+     * 
+     * 
+     * 
+     * @param DBRefArray
+     */
+    public void setDBRef(jalview.schemabinding.version2.DBRef[] DBRefArray)
+    {
+        //-- copy array
+        _DBRefList.removeAllElements();
+        for (int i = 0; i < DBRefArray.length; i++) {
+            _DBRefList.addElement(DBRefArray[i]);
+        }
+    } //-- void setDBRef(jalview.schemabinding.version2.DBRef) 
+
+    /**
      * Method unmarshal
      * 
      *