Return accurate RGB for transparent residues

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

diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java
index 61c80aa..4ac40d5 100755 (executable)
--- a/src/jalview/binding/JalviewModelSequence.java
+++ b/src/jalview/binding/JalviewModelSequence.java
@@ -55,6 +55,11 @@ public class JalviewModelSequence implements java.io.Serializable {
      */\r
     private java.util.Vector _userColoursList;\r
 \r
+    /**\r
+     * Field _treeList\r
+     */\r
+    private java.util.Vector _treeList;\r
+\r
 \r
       //----------------/\r
      //- Constructors -/\r
@@ -66,6 +71,7 @@ public class JalviewModelSequence implements java.io.Serializable {
         _JGroupList = new Vector();\r
         _viewportList = new Vector();\r
         _userColoursList = new Vector();\r
+        _treeList = new Vector();\r
     } //-- jalview.binding.JalviewModelSequence()\r
 \r
 \r
@@ -128,6 +134,33 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- void addJSeq(int, jalview.binding.JSeq) \r
 \r
     /**\r
+     * Method addTree\r
+     * \r
+     * \r
+     * \r
+     * @param vTree\r
+     */\r
+    public void addTree(jalview.binding.Tree vTree)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _treeList.addElement(vTree);\r
+    } //-- void addTree(jalview.binding.Tree) \r
+\r
+    /**\r
+     * Method addTree\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vTree\r
+     */\r
+    public void addTree(int index, jalview.binding.Tree vTree)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _treeList.insertElementAt(vTree, index);\r
+    } //-- void addTree(int, jalview.binding.Tree) \r
+\r
+    /**\r
      * Method addUserColours\r
      * \r
      * \r
@@ -206,6 +239,18 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- java.util.Enumeration enumerateJSeq() \r
 \r
     /**\r
+     * Method enumerateTree\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateTree()\r
+    {\r
+        return _treeList.elements();\r
+    } //-- java.util.Enumeration enumerateTree() \r
+\r
+    /**\r
      * Method enumerateUserColours\r
      * \r
      * \r
@@ -326,6 +371,54 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- int getJSeqCount() \r
 \r
     /**\r
+     * Method getTree\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return Tree\r
+     */\r
+    public jalview.binding.Tree getTree(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _treeList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (jalview.binding.Tree) _treeList.elementAt(index);\r
+    } //-- jalview.binding.Tree getTree(int) \r
+\r
+    /**\r
+     * Method getTree\r
+     * \r
+     * \r
+     * \r
+     * @return Tree\r
+     */\r
+    public jalview.binding.Tree[] getTree()\r
+    {\r
+        int size = _treeList.size();\r
+        jalview.binding.Tree[] mArray = new jalview.binding.Tree[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (jalview.binding.Tree) _treeList.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- jalview.binding.Tree[] getTree() \r
+\r
+    /**\r
+     * Method getTreeCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getTreeCount()\r
+    {\r
+        return _treeList.size();\r
+    } //-- int getTreeCount() \r
+\r
+    /**\r
      * Method getUserColours\r
      * \r
      * \r
@@ -486,6 +579,15 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- void removeAllJSeq() \r
 \r
     /**\r
+     * Method removeAllTree\r
+     * \r
+     */\r
+    public void removeAllTree()\r
+    {\r
+        _treeList.removeAllElements();\r
+    } //-- void removeAllTree() \r
+\r
+    /**\r
      * Method removeAllUserColours\r
      * \r
      */\r
@@ -534,6 +636,21 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- jalview.binding.JSeq removeJSeq(int) \r
 \r
     /**\r
+     * Method removeTree\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return Tree\r
+     */\r
+    public jalview.binding.Tree removeTree(int index)\r
+    {\r
+        java.lang.Object obj = _treeList.elementAt(index);\r
+        _treeList.removeElementAt(index);\r
+        return (jalview.binding.Tree) obj;\r
+    } //-- jalview.binding.Tree removeTree(int) \r
+\r
+    /**\r
      * Method removeUserColours\r
      * \r
      * \r
@@ -632,6 +749,40 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- void setJSeq(jalview.binding.JSeq) \r
 \r
     /**\r
+     * Method setTree\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vTree\r
+     */\r
+    public void setTree(int index, jalview.binding.Tree vTree)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _treeList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _treeList.setElementAt(vTree, index);\r
+    } //-- void setTree(int, jalview.binding.Tree) \r
+\r
+    /**\r
+     * Method setTree\r
+     * \r
+     * \r
+     * \r
+     * @param treeArray\r
+     */\r
+    public void setTree(jalview.binding.Tree[] treeArray)\r
+    {\r
+        //-- copy array\r
+        _treeList.removeAllElements();\r
+        for (int i = 0; i < treeArray.length; i++) {\r
+            _treeList.addElement(treeArray[i]);\r
+        }\r
+    } //-- void setTree(jalview.binding.Tree) \r
+\r
+    /**\r
      * Method setUserColours\r
      * \r
      * \r