From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Wed, 11 Oct 2017 14:03:33 +0000 (+0100)
Subject: just a comment
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=89f0bcb459ed6acff9f7da0842bf967b8f941dee;p=jalview.git

just a comment
---

diff --git a/src/jalview/analysis/TreeBuilder.java b/src/jalview/analysis/TreeBuilder.java
index b794368..728dd62 100644
--- a/src/jalview/analysis/TreeBuilder.java
+++ b/src/jalview/analysis/TreeBuilder.java
@@ -73,7 +73,7 @@ public abstract class TreeBuilder
 
   Vector<SequenceNode> node;
 
-  private AlignmentView seqStrings;
+  private AlignmentView seqStrings; // redundant? (see seqData)
 
   /**
    * Constructor
diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
index 56f7be9..fb1ebe3 100644
--- a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
+++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
@@ -47,7 +47,8 @@ public class ArchaeopteryxTreeBuilder // cannot inherit
 
   public Phylogeny buildAptxTree(TreeBuilder tree)
   {
-  this.sequences= tree.getSequences();
+    this.sequences = tree.getSequences();
+    aptxTree.setName("word");
     return buildAptxTree(sequences);
 
   }
@@ -62,8 +63,46 @@ public class ArchaeopteryxTreeBuilder // cannot inherit
       rootNode.addAsChild(treeNode);
 
     }
+
     aptxTree.setRoot(rootNode);
     return aptxTree;
 
   }
+
+  /**
+   * Formats a localised title for the tree panel, like
+   * <p>
+   * Neighbour Joining Using BLOSUM62
+   * <p>
+   * For a tree loaded from file, just uses the file name
+   * 
+   * @return
+   */
+  // public String getPanelTitle()
+  // {
+  // if (treeTitle != null)
+  // {
+  // return treeTitle;
+  // }
+  // else
+  // {
+  // /*
+  // * i18n description of Neighbour Joining or Average Distance method
+  // */
+  // String treecalcnm = MessageManager
+  // .getString("label.tree_calc_" + treeType.toLowerCase());
+  //
+  // /*
+  // * short score model name (long description can be too long)
+  // */
+  // String smn = substitutionMatrix;
+  //
+  // /*
+  // * put them together as <method> Using <model>
+  // */
+  // final String ttl = MessageManager
+  // .formatMessage("label.treecalc_title", treecalcnm, smn);
+  // return ttl;
+  // }
+  // }
 }