X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Farchaeopteryx%2FArchaeopteryxTreeConverter.java;h=689d5cd3cc57f167ef7675875c783135f6114704;hb=ed6eee466c185fbc257e9228da41678c6d527b02;hp=e159763ab95f979f7bcffe8f9a2ebbe0a8b513e0;hpb=430b086b6520849b18f4f58347dceb974564fb74;p=jalview.git

diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeConverter.java b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeConverter.java
index e159763..689d5cd 100644
--- a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeConverter.java
+++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeConverter.java
@@ -3,15 +3,12 @@ package jalview.ext.archaeopteryx;
 import jalview.analysis.TreeBuilder;
 import jalview.datamodel.SequenceI;
 import jalview.math.MatrixI;
+import jalview.util.MessageManager;
 
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyNode;
 
-public class ArchaeopteryxTreeBuilder // cannot inherit
-                                                        // TreeBuilder as that
-                                                        // demands the use of
-                                                        // SequenceNode (instead
-                                                        // of PhylogenyNode)
+public class ArchaeopteryxTreeConverter
 {
   protected SequenceI[] sequences;
 
@@ -20,34 +17,38 @@ public class ArchaeopteryxTreeBuilder // cannot inherit
   private PhylogenyNode rootNode;
 
   protected MatrixI distances;
+  
+  protected TreeBuilder jalviewTree;
+  
+  public String treeTitle;
 
-  {
-    this.aptxTree = new Phylogeny();
-  }
 
 
-  public ArchaeopteryxTreeBuilder()
+  public ArchaeopteryxTreeConverter(TreeBuilder calculatedTree)
   {
-
-    this.rootNode = new PhylogenyNode();
-    this.rootNode.setName("root");
+    this.jalviewTree = calculatedTree;
+    this.sequences = jalviewTree.getSequences();
+    this.distances = jalviewTree.getDistances();
 
   }
 
-  public ArchaeopteryxTreeBuilder(PhylogenyNode treeRoot)
+  public Phylogeny buildAptxTree()
   {
+    this.rootNode = new PhylogenyNode();
 
-    this.rootNode = treeRoot;
+    return buildAptxTree(rootNode);
 
   }
 
-  public Phylogeny buildAptxTree(TreeBuilder tree)
+  public Phylogeny buildAptxTree(PhylogenyNode treeRoot)
   {
-    this.sequences = tree.getSequences();
-    this.distances = tree.getDistances();
 
-    aptxTree.setName(
-            "PLEASE FIX ME reheaheth35yheqhb3q5hyq3bt3q5u4jwqjwuh6");
+    this.rootNode = treeRoot;
+
+    this.aptxTree = new Phylogeny();
+
+    this.treeTitle = generateTreeName();
+    this.aptxTree.setName(treeTitle);
 
     // final NeighborJoiningF nj = NeighborJoiningF.createInstance(false, 5);
 
@@ -85,31 +86,32 @@ public class ArchaeopteryxTreeBuilder // cannot inherit
    * 
    * @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;
-  // }
-  // }
+  public String generateTreeName()
+  {
+    if (treeTitle != null) // will currently never happen, loaded tree file will
+                           // take a different path
+    {
+      return treeTitle;
+    }
+    else
+    {
+      /*
+      * i18n description of Neighbour Joining or Average Distance method
+      */
+      String treecalcnm = MessageManager
+              .getString("label.tree_calc_" + jalviewTree.getClass()
+                      .getSimpleName().substring(0, 2).toLowerCase());
+      /*
+      * short score model name (long description can be too long)
+      */
+      String smn = jalviewTree.getScoreModel().getName();
+
+      /*
+      * put them together as <method> Using <model>
+      */
+      final String ttl = MessageManager
+              .formatMessage("label.treecalc_title", treecalcnm, smn);
+      return ttl;
+    }
+  }
 }