newickfile class moved into its own package ready for refactoring public methods...

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@437 be28352e-c001-0410-b1a7-c7978e42abec

diff --git a/src/uk/ac/vamsas/objects/utils/Trees.java b/src/uk/ac/vamsas/objects/utils/Trees.java
new file mode 100644 (file)
index 0000000..45d4e99
--- /dev/null
+++ b/src/uk/ac/vamsas/objects/utils/Trees.java
@@ -0,0 +1,5 @@
+package uk.ac.vamsas.objects.utils;\r
+\r
+public class Trees {\r
+\r
+}\r

diff --git a/src/uk/ac/vamsas/objects/utils/NewickFile.java b/src/uk/ac/vamsas/objects/utils/trees/NewickFile.java
similarity index 84%
rename from src/uk/ac/vamsas/objects/utils/NewickFile.java
rename to src/uk/ac/vamsas/objects/utils/trees/NewickFile.java
index 058bca9..db62ef9 100644 (file)
--- a/src/uk/ac/vamsas/objects/utils/NewickFile.java
+++ b/src/uk/ac/vamsas/objects/utils/trees/NewickFile.java
@@ -23,15 +23,20 @@
 // TODO: Implement Basic NHX tag parsing and preservation\r
 // TODO: http://evolution.genetics.wustl.edu/eddy/forester/NHX.html\r
 // TODO: Extended SequenceNodeI to hold parsed NHX strings\r
-package uk.ac.vamsas.objects.utils;\r
+package uk.ac.vamsas.objects.utils.trees;\r
 \r
 import java.io.*;\r
+import java.util.Enumeration;\r
+import java.util.Hashtable;\r
+import java.util.Vector;\r
 import java.util.regex.Matcher;\r
 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
 /**\r
  * DOCUMENT ME!\r
@@ -1131,4 +1136,136 @@ public class NewickFile {
       e.printStackTrace();\r
     }\r
   }\r
+  /**\r
+   * Search for leaf nodes.\r
+   *\r
+   * @param node root node to search from\r
+   * @param leaves Vector of leaves to add leaf node objects too.\r
+   *\r
+   * @return Vector of leaf nodes on binary tree\r
+   */\r
+  public Vector findLeaves(SequenceNode node, Vector leaves)\r
+  { \r
+    if (node == null)\r
+    {\r
+      return leaves;\r
+    }\r
+\r
+    if ( (node.left() == null) && (node.right() == null)) // Interior node detection\r
+    {\r
+      leaves.addElement(node);\r
+\r
+      return leaves;\r
+    }\r
+    else\r
+    {\r
+/*  TODO: Identify internal nodes...    if (node.isSequenceLabel())\r
+      {\r
+        leaves.addElement(node);\r
+      }*/\r
+      findLeaves( (SequenceNode) node.left(), leaves);\r
+      findLeaves( (SequenceNode) node.right(), leaves);\r
+    }\r
+\r
+    return leaves;\r
+  }\r
+\r
+  /**\r
+   * make tree node vector from a newick tree structure with associated vamsas objects\r
+   * @param ntree\r
+   * @return\r
+   */\r
+  public Treenode[] makeTreeNodes() { // NJTree ntree) {\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
+      BinaryNode tnode = (BinaryNode) l.nextElement();\r
+      if (tnode instanceof SequenceNode)\r
+      {\r
+        if (!((SequenceNode) tnode).isPlaceholder())\r
+        {\r
+          Object assocseq = ((SequenceNode) tnode).element();\r
+          if (assocseq instanceof Vobject)\r
+          {\r
+            Vobject vobj = (Vobject) assocseq;\r
+            if (vobj!=null)\r
+            {\r
+              Treenode node = new Treenode();\r
+              node.setNodespec(makeNodeSpec(nodespecs, tnode));\r
+              node.setName(tnode.getName());\r
+              Vref vr = new Vref();\r
+              vr.addRefs(vobj);\r
+              node.addVref(vr);\r
+              tnv.addElement(node);\r
+            }\r
+            else\r
+            {\r
+              System.err.println("WARNING: Unassociated treeNode "+tnode.element().toString()+" "\r
+                      +((tnode.getName()!=null) ? " label "+tnode.getName() : ""));\r
+            }\r
+          }\r
+        }\r
+      }\r
+    }\r
+    if (tnv.size()>0)\r
+    {\r
+      Treenode[] tn = new Treenode[tnv.size()];\r
+      tnv.copyInto(tn);  \r
+      return tn;\r
+    }\r
+    return new Treenode[] {};\r
+  }\r
+  private String makeNodeSpec(Hashtable nodespecs, BinaryNode tnode)\r
+  { \r
+    String nname = new String(tnode.getName());\r
+    Integer nindx = (Integer) nodespecs.get(nname);\r
+    if (nindx==null)\r
+    {\r
+      nindx = new Integer(1);\r
+    }\r
+    nname = nindx.toString()+" "+nname;\r
+    return nname;\r
+  }\r
+  /**\r
+   * call to match up Treenode specs to NJTree parsed from document object.\r
+   * \r
+   * @param nodespec\r
+   * @param leaves\r
+   *          as returned from NJTree.findLeaves( .., ..) ..\r
+   * @return\r
+   */\r
+  private BinaryNode findNodeSpec(String nodespec, Vector leaves)\r
+  {\r
+    int occurence=-1;\r
+    String nspec = nodespec.substring(nodespec.indexOf(' ')+1);\r
+    String oval = nodespec.substring(0, nodespec.indexOf(' '));\r
+    try {\r
+      occurence = new Integer(oval).intValue();\r
+    }\r
+    catch (Exception e)\r
+    {\r
+      System.err.println("Invalid nodespec '"+nodespec+"'");\r
+      return null;\r
+    }\r
+    BinaryNode bn = null;\r
+    \r
+    int nocc = 0;\r
+    Enumeration en = leaves.elements();\r
+    while (en.hasMoreElements() && nocc<occurence)\r
+    {\r
+      bn = (BinaryNode) en.nextElement();\r
+      if (bn instanceof SequenceNode && bn.getName().equals(nspec))\r
+      {\r
+         --occurence;\r
+      } else \r
+        bn=null;\r
+    }\r
+    return bn;\r
+  }\r
+\r
 }\r