better 'main' test and support creation of treenodes for all or just 'associated...

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@441 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 2e1e893..f8e49aa 100644 (file)
--- a/src/uk/ac/vamsas/objects/utils/trees/NewickFile.java
+++ b/src/uk/ac/vamsas/objects/utils/trees/NewickFile.java
@@ -203,13 +203,13 @@ public class NewickFile {
   String errormessage;\r
   java.io.BufferedReader dataIn=null;\r
   public String nextLine() throws IOException {\r
+    if (dataIn==null && newickFile==null)\r
+      throw new IOException("IMPLEMENTATION ERROR: NewickFile has not been initialised for reading a newick string.");\r
     if (dataIn==null)\r
     {\r
       dataIn = new BufferedReader(new StringReader(newickFile));\r
       error=false;\r
     }\r
-    else\r
-      throw new IOException("IMPLEMENTATION ERROR: NewickFile has not been initialised for reading a newick string.");\r
     if (!error)\r
       return dataIn.readLine();\r
     throw new IOException("Invalid Source Stream:" + errormessage);\r
@@ -744,6 +744,18 @@ public class NewickFile {
       System.out.println(trf.print(false, false));\r
       System.out.println("With bootstraps and with distances.\n");\r
       System.out.println(trf.print(true, true));\r
+      System.out.println("leaves.\n");\r
+      Vector lvs = new Vector();\r
+      trf.findLeaves(trf.root, lvs);\r
+      Enumeration lv =lvs.elements();\r
+      while (lv.hasMoreElements())\r
+      {\r
+        BinaryNode leave = (BinaryNode) lv.nextElement();\r
+        if (leave.getName()!=null)\r
+        {\r
+          System.out.println("Node:'"+leave.getName()+"'");\r
+        }\r
+      }      \r
     } catch (java.io.IOException e) {\r
       System.err.println("Exception\n" + e);\r
       e.printStackTrace();\r
@@ -786,9 +798,17 @@ public class NewickFile {
   /**\r
    * make tree node vector from a newick tree structure with associated vamsas objects\r
    * @param ntree\r
-   * @return\r
+   * @return Treenode definitions for nodes with associated objects\r
+   */\r
+  public Treenode[] makeTreeNodes() {\r
+    return makeTreeNodes(true);\r
+  }\r
+  /**\r
+   * make treenode vector for a parsed tree with/out leaf node associations \r
+   * @param ignoreplaceholders if true means only associated nodes are returned\r
+   * @return treenode vector for associated or all leaves\r
    */\r
-  public Treenode[] makeTreeNodes() { \r
+  public Treenode[] makeTreeNodes(boolean ignoreplaceholders) { \r
     Vector leaves = new Vector();\r
     findLeaves(root, leaves);\r
     Vector tnv = new Vector();\r
@@ -799,7 +819,7 @@ public class NewickFile {
       BinaryNode tnode = (BinaryNode) l.nextElement();\r
       if (tnode instanceof SequenceNode)\r
       {\r
-        if (!((SequenceNode) tnode).isPlaceholder())\r
+        if (!(ignoreplaceholders && ((SequenceNode) tnode).isPlaceholder()))\r
         {\r
           Object assocseq = ((SequenceNode) tnode).element();\r
           if (assocseq instanceof Vobject)\r