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 (file)
--- 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;\r
 \r
+import java.io.IOException;\r
+\r
+import uk.ac.vamsas.objects.core.Tree;\r
+import uk.ac.vamsas.objects.utils.trees.NewickFile;\r
+\r
 public class Trees {\r
 \r
+  /**\r
+   * TODO: implement\r
+   * helper functions based on NewickFile tree parser\r
+   * \r
+   * 1. create a newickfile object from a newick string.\r
+   * 2. let user map a vamsas object to each node by setting that node's ((SequenceNode)node).setElement(VorbaId) \r
+   * 3. generate Tree object with newickString as a newick string, and added treenodes to  record mapping to vorba ids\r
+   */\r
+  \r
 }\r