X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FJalviewModelSequence.java;h=cbb50d51d53666f8e3fc80a9c4672c4cf7c39ca4;hb=23d3cb8d0e4c227224587135f41132d436dc1178;hp=61c80aa11b8396e82f26968e453964f5623b12bc;hpb=5a35786bf1c4219bfa00603036497a18486c6801;p=jalview.git

diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java
index 61c80aa..cbb50d5 100755
--- a/src/jalview/binding/JalviewModelSequence.java
+++ b/src/jalview/binding/JalviewModelSequence.java
@@ -55,6 +55,16 @@ public class JalviewModelSequence implements java.io.Serializable {
      */
     private java.util.Vector _userColoursList;
 
+    /**
+     * Field _treeList
+     */
+    private java.util.Vector _treeList;
+
+    /**
+     * Field _featureSettings
+     */
+    private jalview.binding.FeatureSettings _featureSettings;
+
 
       //----------------/
      //- Constructors -/
@@ -66,6 +76,7 @@ public class JalviewModelSequence implements java.io.Serializable {
         _JGroupList = new Vector();
         _viewportList = new Vector();
         _userColoursList = new Vector();
+        _treeList = new Vector();
     } //-- jalview.binding.JalviewModelSequence()
 
 
@@ -128,6 +139,33 @@ 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
      * 
      * 
@@ -206,6 +244,18 @@ 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
      * 
      * 
@@ -230,6 +280,17 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- java.util.Enumeration enumerateViewport() 
 
     /**
+     * Returns the value of field 'featureSettings'.
+     * 
+     * @return FeatureSettings
+     * @return the value of field 'featureSettings'.
+     */
+    public jalview.binding.FeatureSettings getFeatureSettings()
+    {
+        return this._featureSettings;
+    } //-- jalview.binding.FeatureSettings getFeatureSettings() 
+
+    /**
      * Method getJGroup
      * 
      * 
@@ -326,6 +387,54 @@ 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
      * 
      * 
@@ -486,6 +595,15 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- void removeAllJSeq() 
 
     /**
+     * Method removeAllTree
+     * 
+     */
+    public void removeAllTree()
+    {
+        _treeList.removeAllElements();
+    } //-- void removeAllTree() 
+
+    /**
      * Method removeAllUserColours
      * 
      */
@@ -534,6 +652,21 @@ 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
      * 
      * 
@@ -564,6 +697,16 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- jalview.binding.Viewport removeViewport(int) 
 
     /**
+     * Sets the value of field 'featureSettings'.
+     * 
+     * @param featureSettings the value of field 'featureSettings'.
+     */
+    public void setFeatureSettings(jalview.binding.FeatureSettings featureSettings)
+    {
+        this._featureSettings = featureSettings;
+    } //-- void setFeatureSettings(jalview.binding.FeatureSettings) 
+
+    /**
      * Method setJGroup
      * 
      * 
@@ -632,6 +775,40 @@ 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
      * 
      *