refactored and new methods for making and processing treenode vector for parsed...

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@439 be28352e-c001-0410-b1a7-c7978e42abec

diff --git a/src/uk/ac/vamsas/objects/utils/trees/NewickFile.java b/src/uk/ac/vamsas/objects/utils/trees/NewickFile.java
index db62ef9..2e1e893 100644 (file)
--- a/src/uk/ac/vamsas/objects/utils/trees/NewickFile.java
+++ b/src/uk/ac/vamsas/objects/utils/trees/NewickFile.java
@@ -1,4 +1,6 @@
 /*\r
+ * originally from \r
+ * \r
  * Jalview - A Sequence Alignment Editor and Viewer\r
  * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
@@ -25,6 +27,7 @@
 // TODO: Extended SequenceNodeI to hold parsed NHX strings\r
 package uk.ac.vamsas.objects.utils.trees;\r
 \r
+\r
 import java.io.*;\r
 import java.util.Enumeration;\r
 import java.util.Hashtable;\r
@@ -33,8 +36,6 @@ import java.util.regex.Matcher;
 import java.util.regex.Pattern;\r
 \r
 import uk.ac.vamsas.client.Vobject;\r
-import uk.ac.vamsas.client.VorbaId;\r
-import uk.ac.vamsas.objects.core.SequenceType;\r
 import uk.ac.vamsas.objects.core.Treenode;\r
 import uk.ac.vamsas.objects.core.Vref;\r
 \r
@@ -45,395 +46,6 @@ import uk.ac.vamsas.objects.core.Vref;
  * @version $Revision: 1.12 $\r
  */\r
 public class NewickFile {\r
-  public class BinaryNode {\r
-    VorbaId element;\r
-\r
-    String name;\r
-\r
-    BinaryNode left;\r
-\r
-    BinaryNode right;\r
-\r
-    BinaryNode parent;\r
-\r
-    /** DOCUMENT ME!! */\r
-    public int bootstrap;\r
-\r
-    /**\r
-     * Creates a new BinaryNode object.\r
-     */\r
-    public BinaryNode() {\r
-      left = right = parent = null;\r
-      bootstrap = 0;\r
-    }\r
-\r
-    /**\r
-     * Creates a new BinaryNode object.\r
-     * \r
-     * @param element\r
-     *          DOCUMENT ME!\r
-     * @param parent\r
-     *          DOCUMENT ME!\r
-     * @param name\r
-     *          DOCUMENT ME!\r
-     */\r
-    public BinaryNode(VorbaId element, BinaryNode parent, String name) {\r
-      this.element = element;\r
-      this.parent = parent;\r
-      this.name = name;\r
-\r
-      left = right = null;\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     * \r
-     * @return DOCUMENT ME!\r
-     */\r
-    public VorbaId element() {\r
-      return element;\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     * \r
-     * @param v\r
-     *          DOCUMENT ME!\r
-     * \r
-     * @return DOCUMENT ME!\r
-     */\r
-    public VorbaId setElement(VorbaId v) {\r
-      return element = v;\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     * \r
-     * @return DOCUMENT ME!\r
-     */\r
-    public BinaryNode left() {\r
-      return left;\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     * \r
-     * @param n\r
-     *          DOCUMENT ME!\r
-     * \r
-     * @return DOCUMENT ME!\r
-     */\r
-    public BinaryNode setLeft(BinaryNode n) {\r
-      return left = n;\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     * \r
-     * @return DOCUMENT ME!\r
-     */\r
-    public BinaryNode right() {\r
-      return right;\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     * \r
-     * @param n\r
-     *          DOCUMENT ME!\r
-     * \r
-     * @return DOCUMENT ME!\r
-     */\r
-    public BinaryNode setRight(BinaryNode n) {\r
-      return right = n;\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     * \r
-     * @return DOCUMENT ME!\r
-     */\r
-    public BinaryNode parent() {\r
-      return parent;\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     * \r
-     * @param n\r
-     *          DOCUMENT ME!\r
-     * \r
-     * @return DOCUMENT ME!\r
-     */\r
-    public BinaryNode setParent(BinaryNode n) {\r
-      return parent = n;\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     * \r
-     * @return DOCUMENT ME!\r
-     */\r
-    public boolean isLeaf() {\r
-      return (left == null) && (right == null);\r
-    }\r
-\r
-    /**\r
-     * attaches FIRST and SECOND node arguments as the LEFT and RIGHT children\r
-     * of this node (removing any old references) a null parameter DOES NOT mean\r
-     * that the pointer to the corresponding child node is set to NULL - you\r
-     * should use setChild(null), or detach() for this.\r
-     * \r
-     */\r
-    public void SetChildren(BinaryNode leftchild, BinaryNode rightchild) {\r
-      if (leftchild != null) {\r
-        this.setLeft(leftchild);\r
-        leftchild.detach();\r
-        leftchild.setParent(this);\r
-      }\r
-\r
-      if (rightchild != null) {\r
-        this.setRight(rightchild);\r
-        rightchild.detach();\r
-        rightchild.setParent(this);\r
-      }\r
-    }\r
-\r
-    /**\r
-     * Detaches the node from the binary tree, along with all its child nodes.\r
-     * \r
-     * @return BinaryNode The detached node.\r
-     */\r
-    public BinaryNode detach() {\r
-      if (this.parent != null) {\r
-        if (this.parent.left == this) {\r
-          this.parent.left = null;\r
-        } else {\r
-          if (this.parent.right == this) {\r
-            this.parent.right = null;\r
-          }\r
-        }\r
-      }\r
-\r
-      this.parent = null;\r
-\r
-      return this;\r
-    }\r
-\r
-    /**\r
-     * Traverses up through the tree until a node with a free leftchild is\r
-     * discovered.\r
-     * \r
-     * @return BinaryNode\r
-     */\r
-    public BinaryNode ascendLeft() {\r
-      BinaryNode c = this;\r
-\r
-      do {\r
-        c = c.parent();\r
-      } while ((c != null) && (c.left() != null) && !c.left().isLeaf());\r
-\r
-      return c;\r
-    }\r
-\r
-    /**\r
-     * Traverses up through the tree until a node with a free rightchild is\r
-     * discovered. Jalview builds trees by descent on the left, so this may be\r
-     * unused.\r
-     * \r
-     * @return BinaryNode\r
-     */\r
-    public BinaryNode ascendRight() {\r
-      BinaryNode c = this;\r
-\r
-      do {\r
-        c = c.parent();\r
-      } while ((c != null) && (c.right() != null) && !c.right().isLeaf());\r
-\r
-      return c;\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     * \r
-     * @param name\r
-     *          DOCUMENT ME!\r
-     */\r
-    public void setName(String name) {\r
-      this.name = name;\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     * \r
-     * @return DOCUMENT ME!\r
-     */\r
-    public String getName() {\r
-      return this.name;\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     * \r
-     * @param boot\r
-     *          DOCUMENT ME!\r
-     */\r
-    public void setBootstrap(int boot) {\r
-      this.bootstrap = boot;\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     * \r
-     * @return DOCUMENT ME!\r
-     */\r
-    public int getBootstrap() {\r
-      return bootstrap;\r
-    }\r
-    /**\r
-     * \r
-     * @return unquoted string of form VorbaId|v|node name string\r
-     */\r
-    public String getNewickNodeName() {\r
-      if (element!=null || name!=null)\r
-        {\r
-        return ((element!=null) ? element.getId()+"|v|" : "")\r
-          + ((name == null) ? "" : name);\r
-        }\r
-      return "";\r
-    }\r
-    public boolean parseNodeNameString(uk.ac.vamsas.client.ClientDocument binder)\r
-    {\r
-      \r
-      if (element==null && name!=null && name.indexOf("|v|")>-1)\r
-      {\r
-        element = binder.getObject(null).getVorbaId(); // TODO: fix THIS ! name.substring(0, name.indexOf("|v")));\r
-        \r
-      }\r
-      return false;\r
-    }\r
-  }\r
-\r
-  public class SequenceNode extends BinaryNode {\r
-    /** DOCUMENT ME!! */\r
-    public float dist;\r
-\r
-    /** DOCUMENT ME!! */\r
-    public boolean dummy = false;\r
-\r
-    private boolean placeholder = false;\r
-\r
-    /**\r
-     * Creates a new SequenceNode object.\r
-     */\r
-    public SequenceNode() {\r
-      super();\r
-    }\r
-\r
-    /**\r
-     * Creates a new SequenceNode object.\r
-     * \r
-     * @param val\r
-     *          DOCUMENT ME!\r
-     * @param parent\r
-     *          DOCUMENT ME!\r
-     * @param dist\r
-     *          DOCUMENT ME!\r
-     * @param name\r
-     *          DOCUMENT ME!\r
-     */\r
-    public SequenceNode(VorbaId val, SequenceNode parent, float dist, String name) {\r
-      super(val, parent, name);\r
-      this.dist = dist;\r
-    }\r
-    public SequenceNode(Vobject val, SequenceNode parent, float dist, String name) {\r
-      super(val.getVorbaId(), parent, name);\r
-      this.dist = dist;\r
-    }\r
-\r
-    /**\r
-     * Creates a new SequenceNode object.\r
-     * \r
-     * @param val\r
-     *          DOCUMENT ME!\r
-     * @param parent\r
-     *          DOCUMENT ME!\r
-     * @param name\r
-     *          DOCUMENT ME!\r
-     * @param dist\r
-     *          DOCUMENT ME!\r
-     * @param bootstrap\r
-     *          DOCUMENT ME!\r
-     * @param dummy\r
-     *          DOCUMENT ME!\r
-     */\r
-    public SequenceNode(Vobject val, SequenceNode parent, String name,\r
-        float dist, int bootstrap, boolean dummy) {\r
-      super(val.getVorbaId(), parent, name);\r
-      this.dist = dist;\r
-      this.bootstrap = bootstrap;\r
-      this.dummy = dummy;\r
-    }\r
-\r
-    /**\r
-     * @param dummy\r
-     *          true if node is created for the representation of polytomous\r
-     *          trees\r
-     */\r
-    public boolean isDummy() {\r
-      return dummy;\r
-    }\r
-\r
-    /*\r
-     * @param placeholder is true if the sequence refered to in the element node\r
-     * is not actually present in the associated alignment\r
-     */\r
-    public boolean isPlaceholder() {\r
-      return placeholder;\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     * \r
-     * @param newstate\r
-     *          DOCUMENT ME!\r
-     * \r
-     * @return DOCUMENT ME!\r
-     */\r
-    public boolean setDummy(boolean newstate) {\r
-      boolean oldstate = dummy;\r
-      dummy = newstate;\r
-\r
-      return oldstate;\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     * \r
-     * @param Placeholder\r
-     *          DOCUMENT ME!\r
-     */\r
-    public void setPlaceholder(boolean Placeholder) {\r
-      this.placeholder = Placeholder;\r
-    }\r
-\r
-    /**\r
-     * ascends the tree but doesn't stop until a non-dummy node is discovered.\r
-     * This will probably break if the tree is a mixture of BinaryNodes and\r
-     * SequenceNodes.\r
-     */\r
-    public SequenceNode AscendTree() {\r
-      SequenceNode c = this;\r
-\r
-      do {\r
-        c = (SequenceNode) c.parent();\r
-      } while ((c != null) && c.dummy);\r
-\r
-      return c;\r
-    }\r
-\r
-  }\r
-\r
   SequenceNode root;\r
 \r
   private boolean HasBootstrap = false;\r
@@ -1018,8 +630,9 @@ public class NewickFile {
    * @return DOCUMENT ME!\r
    */\r
   private String printNodeField(SequenceNode c) {\r
-    return c.getNewickNodeName()\r
-        + ((HasBootstrap) ? ((c.getBootstrap() > -1) ? (" " + c.getBootstrap())\r
+    return //c.getNewickNodeName()\r
+    ((c.getName() == null) ? "" : nodeName(c.getName()))\r
+      + ((HasBootstrap) ? ((c.getBootstrap() > -1) ? (" " + c.getBootstrap())\r
             : "") : "") + ((HasDistances) ? (":" + c.dist) : "");\r
   }\r
 \r
@@ -1175,12 +788,11 @@ public class NewickFile {
    * @param ntree\r
    * @return\r
    */\r
-  public Treenode[] makeTreeNodes() { // NJTree ntree) {\r
+  public Treenode[] makeTreeNodes() { \r
     Vector leaves = new Vector();\r
     findLeaves(root, leaves);\r
     Vector tnv = new Vector();\r
     Enumeration l = leaves.elements();\r
-    int i=0;\r
     Hashtable nodespecs = new Hashtable();\r
     while (l.hasMoreElements())\r
     {\r
@@ -1267,5 +879,57 @@ public class NewickFile {
     }\r
     return bn;\r
   }\r
+  /**\r
+   *\r
+   * re-decorate the newick node representation with the VorbaId of an object mapped by its corresponding TreeNode. \r
+   * Note: this only takes the first object in the first set of references.\r
+   * @param tn\r
+   * @return vector of mappings { treenode, SequenceNode, Vobject for VorbaId on sequence node }\r
+   */\r
+  public Vector attachTreeMap(Treenode[] tn)\r
+  {\r
+  if (root!=null || tn==null)\r
+    return null;\r
+  Vector leaves = new Vector();\r
+  Vector nodemap=new Vector();\r
+  findLeaves(root, leaves);\r
+  int sz = tn.length;\r
+  int i = 0;\r
+  \r
+  while (i < sz)\r
+  {\r
+    Treenode node = tn[i++];\r
+    BinaryNode mappednode = findNodeSpec(node.getNodespec(),leaves);\r
+    if (mappednode!=null && mappednode instanceof SequenceNode) {\r
+      SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);\r
+      // check if we can make the specified association\r
+      Vobject noderef = null;\r
+      int vrf=0,refv=0;\r
+      while (noderef==null && vrf<node.getVrefCount())\r
+      {\r
+        if (refv<node.getVref(vrf).getRefsCount())\r
+        {\r
+          Object ref = node.getVref(vrf).getRefs(refv++);\r
+          if (ref instanceof Vobject)\r
+          {\r
+            noderef = (Vobject) ref;\r
+          }\r
+        } else {\r
+          refv=0;\r
+          vrf++;\r
+        }\r
+      }\r
+      if (noderef!=null)\r
+      {\r
+        nodemap.addElement(new Object[] { node, leaf, noderef });\r
+        leaf.setElement(noderef);\r
+        leaf.setPlaceholder(false);\r
+      } else {\r
+        leaf.setPlaceholder(true);\r
+      }\r
+    }\r
+  }\r
+  return nodemap;\r
+}\r
 \r
 }\r