From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Tue, 21 Aug 2007 16:03:27 +0000 (+0000)
Subject: beginning of 'simple' interface for newick string based tree representation
X-Git-Tag: Release_0.2~80
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=eb584e50596aa1345d7fd5e609c94d990980b692;p=vamsas.git

beginning of 'simple' interface for newick string based tree representation

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@440 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
index 45d4e99..718d8fa 100644
--- a/src/uk/ac/vamsas/objects/utils/Trees.java
+++ b/src/uk/ac/vamsas/objects/utils/Trees.java
@@ -1,5 +1,19 @@
 package uk.ac.vamsas.objects.utils;
 
+import java.io.IOException;
+
+import uk.ac.vamsas.objects.core.Tree;
+import uk.ac.vamsas.objects.utils.trees.NewickFile;
+
 public class Trees {
 
+  /**
+   * TODO: implement
+   * helper functions based on NewickFile tree parser
+   * 
+   * 1. create a newickfile object from a newick string.
+   * 2. let user map a vamsas object to each node by setting that node's ((SequenceNode)node).setElement(VorbaId) 
+   * 3. generate Tree object with newickString as a newick string, and added treenodes to  record mapping to vorba ids
+   */
+  
 }