total annotation score is a double for maximum precision.

[jalview.git] / src / jalview / schemabinding / version2 / Sequence.java

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