XML schema changes

[jalview.git] / src / jalview / binding / JalviewModelSequence.java

diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java
index 7f17893..61c80aa 100755 (executable)
--- a/src/jalview/binding/JalviewModelSequence.java
+++ b/src/jalview/binding/JalviewModelSequence.java
@@ -50,6 +50,11 @@ public class JalviewModelSequence implements java.io.Serializable {
      */\r
     private java.util.Vector _viewportList;\r
 \r
+    /**\r
+     * Field _userColoursList\r
+     */\r
+    private java.util.Vector _userColoursList;\r
+\r
 \r
       //----------------/\r
      //- Constructors -/\r
@@ -60,6 +65,7 @@ public class JalviewModelSequence implements java.io.Serializable {
         _JSeqList = new Vector();\r
         _JGroupList = new Vector();\r
         _viewportList = new Vector();\r
+        _userColoursList = new Vector();\r
     } //-- jalview.binding.JalviewModelSequence()\r
 \r
 \r
@@ -122,6 +128,33 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- void addJSeq(int, jalview.binding.JSeq) \r
 \r
     /**\r
+     * Method addUserColours\r
+     * \r
+     * \r
+     * \r
+     * @param vUserColours\r
+     */\r
+    public void addUserColours(jalview.binding.UserColours vUserColours)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _userColoursList.addElement(vUserColours);\r
+    } //-- void addUserColours(jalview.binding.UserColours) \r
+\r
+    /**\r
+     * Method addUserColours\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vUserColours\r
+     */\r
+    public void addUserColours(int index, jalview.binding.UserColours vUserColours)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _userColoursList.insertElementAt(vUserColours, index);\r
+    } //-- void addUserColours(int, jalview.binding.UserColours) \r
+\r
+    /**\r
      * Method addViewport\r
      * \r
      * \r
@@ -173,6 +206,18 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- java.util.Enumeration enumerateJSeq() \r
 \r
     /**\r
+     * Method enumerateUserColours\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateUserColours()\r
+    {\r
+        return _userColoursList.elements();\r
+    } //-- java.util.Enumeration enumerateUserColours() \r
+\r
+    /**\r
      * Method enumerateViewport\r
      * \r
      * \r
@@ -281,6 +326,54 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- int getJSeqCount() \r
 \r
     /**\r
+     * Method getUserColours\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return UserColours\r
+     */\r
+    public jalview.binding.UserColours getUserColours(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _userColoursList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (jalview.binding.UserColours) _userColoursList.elementAt(index);\r
+    } //-- jalview.binding.UserColours getUserColours(int) \r
+\r
+    /**\r
+     * Method getUserColours\r
+     * \r
+     * \r
+     * \r
+     * @return UserColours\r
+     */\r
+    public jalview.binding.UserColours[] getUserColours()\r
+    {\r
+        int size = _userColoursList.size();\r
+        jalview.binding.UserColours[] mArray = new jalview.binding.UserColours[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (jalview.binding.UserColours) _userColoursList.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- jalview.binding.UserColours[] getUserColours() \r
+\r
+    /**\r
+     * Method getUserColoursCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getUserColoursCount()\r
+    {\r
+        return _userColoursList.size();\r
+    } //-- int getUserColoursCount() \r
+\r
+    /**\r
      * Method getViewport\r
      * \r
      * \r
@@ -393,6 +486,15 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- void removeAllJSeq() \r
 \r
     /**\r
+     * Method removeAllUserColours\r
+     * \r
+     */\r
+    public void removeAllUserColours()\r
+    {\r
+        _userColoursList.removeAllElements();\r
+    } //-- void removeAllUserColours() \r
+\r
+    /**\r
      * Method removeAllViewport\r
      * \r
      */\r
@@ -432,6 +534,21 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- jalview.binding.JSeq removeJSeq(int) \r
 \r
     /**\r
+     * Method removeUserColours\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return UserColours\r
+     */\r
+    public jalview.binding.UserColours removeUserColours(int index)\r
+    {\r
+        java.lang.Object obj = _userColoursList.elementAt(index);\r
+        _userColoursList.removeElementAt(index);\r
+        return (jalview.binding.UserColours) obj;\r
+    } //-- jalview.binding.UserColours removeUserColours(int) \r
+\r
+    /**\r
      * Method removeViewport\r
      * \r
      * \r
@@ -515,6 +632,40 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- void setJSeq(jalview.binding.JSeq) \r
 \r
     /**\r
+     * Method setUserColours\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vUserColours\r
+     */\r
+    public void setUserColours(int index, jalview.binding.UserColours vUserColours)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _userColoursList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _userColoursList.setElementAt(vUserColours, index);\r
+    } //-- void setUserColours(int, jalview.binding.UserColours) \r
+\r
+    /**\r
+     * Method setUserColours\r
+     * \r
+     * \r
+     * \r
+     * @param userColoursArray\r
+     */\r
+    public void setUserColours(jalview.binding.UserColours[] userColoursArray)\r
+    {\r
+        //-- copy array\r
+        _userColoursList.removeAllElements();\r
+        for (int i = 0; i < userColoursArray.length; i++) {\r
+            _userColoursList.addElement(userColoursArray[i]);\r
+        }\r
+    } //-- void setUserColours(jalview.binding.UserColours) \r
+\r
+    /**\r
      * Method setViewport\r
      * \r
      * \r