JAL-2795 Added get and set values to the converted matrix

[jalview.git] / src / jalview / ext / archaeopteryx / ArchaeopteryxInit.java

diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java b/src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java
index 8302140..3bd9d19 100644 (file)
--- a/src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java
+++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java
@@ -13,7 +13,7 @@ public final class ArchaeopteryxInit
 {
   public static MainFrame createInstance(Phylogeny[] aptxTrees)
   {
-    return createAptxFrame(aptxTrees);
+    return createBoundAptxFrame(aptxTrees);
 
   }
 
@@ -21,24 +21,25 @@ public final class ArchaeopteryxInit
   {
     Phylogeny[] aptxTrees = { aptxTree }; // future possibility to load in
     // several trees simultaneously
-    return createAptxFrame(aptxTrees);
+    return createBoundAptxFrame(aptxTrees);
 
   }
 
   public static MainFrame createInstance(
           TreeBuilder calculatedTree)
   {
-    ArchaeopteryxTreeBuilder aptxTreeBuilder = new ArchaeopteryxTreeBuilder();
-    Phylogeny aptxTree = aptxTreeBuilder.buildAptxTree(calculatedTree);
+    ArchaeopteryxTreeConverter aptxTreeBuilder = new ArchaeopteryxTreeConverter(
+            calculatedTree);
+    Phylogeny aptxTree = aptxTreeBuilder.buildAptxTree();
     Phylogeny[] aptxTrees = { aptxTree }; // future possibility to load in
                                           // several trees simultaneously
 
-    return createAptxFrame(aptxTrees);
+    return createBoundAptxFrame(aptxTrees);
 
   }
 
 
-  private static MainFrame createAptxFrame(Phylogeny[] aptxTrees)
+  private static MainFrame createBoundAptxFrame(Phylogeny[] aptxTrees)
   {
     MainFrame aptxApp = Archaeopteryx.createApplication(aptxTrees,
             "_aptx_jalview_configuration_file", null);