X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FJalviewModelSequence.java;h=61c80aa11b8396e82f26968e453964f5623b12bc;hb=5a35786bf1c4219bfa00603036497a18486c6801;hp=7f1789363e4eab365c1cc40101fac60a06fc8e38;hpb=ed4b153fcf35496ccf42b074bf90d64ab71ed328;p=jalview.git

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