X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FJalviewModelSequence.java;h=4ac40d516600f7e75865249d5528b963f48fc175;hb=d19f6b27ef8ee7350763cfaa511270bf128e76a9;hp=7f1789363e4eab365c1cc40101fac60a06fc8e38;hpb=124589ea0c58cbb7b3788bbf13b687a0ece3c9e0;p=jalview.git

diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java
index 7f17893..4ac40d5 100755
--- a/src/jalview/binding/JalviewModelSequence.java
+++ b/src/jalview/binding/JalviewModelSequence.java
@@ -50,6 +50,16 @@ public class JalviewModelSequence implements java.io.Serializable {
      */
     private java.util.Vector _viewportList;
 
+    /**
+     * Field _userColoursList
+     */
+    private java.util.Vector _userColoursList;
+
+    /**
+     * Field _treeList
+     */
+    private java.util.Vector _treeList;
+
 
       //----------------/
      //- Constructors -/
@@ -60,6 +70,8 @@ public class JalviewModelSequence implements java.io.Serializable {
         _JSeqList = new Vector();
         _JGroupList = new Vector();
         _viewportList = new Vector();
+        _userColoursList = new Vector();
+        _treeList = new Vector();
     } //-- jalview.binding.JalviewModelSequence()
 
 
@@ -122,6 +134,60 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- void addJSeq(int, jalview.binding.JSeq) 
 
     /**
+     * Method addTree
+     * 
+     * 
+     * 
+     * @param vTree
+     */
+    public void addTree(jalview.binding.Tree vTree)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _treeList.addElement(vTree);
+    } //-- void addTree(jalview.binding.Tree) 
+
+    /**
+     * Method addTree
+     * 
+     * 
+     * 
+     * @param index
+     * @param vTree
+     */
+    public void addTree(int index, jalview.binding.Tree vTree)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _treeList.insertElementAt(vTree, index);
+    } //-- void addTree(int, jalview.binding.Tree) 
+
+    /**
+     * 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 +239,30 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- java.util.Enumeration enumerateJSeq() 
 
     /**
+     * Method enumerateTree
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateTree()
+    {
+        return _treeList.elements();
+    } //-- java.util.Enumeration enumerateTree() 
+
+    /**
+     * Method enumerateUserColours
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateUserColours()
+    {
+        return _userColoursList.elements();
+    } //-- java.util.Enumeration enumerateUserColours() 
+
+    /**
      * Method enumerateViewport
      * 
      * 
@@ -281,6 +371,102 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- int getJSeqCount() 
 
     /**
+     * Method getTree
+     * 
+     * 
+     * 
+     * @param index
+     * @return Tree
+     */
+    public jalview.binding.Tree getTree(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _treeList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.binding.Tree) _treeList.elementAt(index);
+    } //-- jalview.binding.Tree getTree(int) 
+
+    /**
+     * Method getTree
+     * 
+     * 
+     * 
+     * @return Tree
+     */
+    public jalview.binding.Tree[] getTree()
+    {
+        int size = _treeList.size();
+        jalview.binding.Tree[] mArray = new jalview.binding.Tree[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.binding.Tree) _treeList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.binding.Tree[] getTree() 
+
+    /**
+     * Method getTreeCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getTreeCount()
+    {
+        return _treeList.size();
+    } //-- int getTreeCount() 
+
+    /**
+     * 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 +579,24 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- void removeAllJSeq() 
 
     /**
+     * Method removeAllTree
+     * 
+     */
+    public void removeAllTree()
+    {
+        _treeList.removeAllElements();
+    } //-- void removeAllTree() 
+
+    /**
+     * Method removeAllUserColours
+     * 
+     */
+    public void removeAllUserColours()
+    {
+        _userColoursList.removeAllElements();
+    } //-- void removeAllUserColours() 
+
+    /**
      * Method removeAllViewport
      * 
      */
@@ -432,6 +636,36 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- jalview.binding.JSeq removeJSeq(int) 
 
     /**
+     * Method removeTree
+     * 
+     * 
+     * 
+     * @param index
+     * @return Tree
+     */
+    public jalview.binding.Tree removeTree(int index)
+    {
+        java.lang.Object obj = _treeList.elementAt(index);
+        _treeList.removeElementAt(index);
+        return (jalview.binding.Tree) obj;
+    } //-- jalview.binding.Tree removeTree(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 +749,74 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- void setJSeq(jalview.binding.JSeq) 
 
     /**
+     * Method setTree
+     * 
+     * 
+     * 
+     * @param index
+     * @param vTree
+     */
+    public void setTree(int index, jalview.binding.Tree vTree)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _treeList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _treeList.setElementAt(vTree, index);
+    } //-- void setTree(int, jalview.binding.Tree) 
+
+    /**
+     * Method setTree
+     * 
+     * 
+     * 
+     * @param treeArray
+     */
+    public void setTree(jalview.binding.Tree[] treeArray)
+    {
+        //-- copy array
+        _treeList.removeAllElements();
+        for (int i = 0; i < treeArray.length; i++) {
+            _treeList.addElement(treeArray[i]);
+        }
+    } //-- void setTree(jalview.binding.Tree) 
+
+    /**
+     * 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
      * 
      *