JAL-2805 First try at loading tree through Forester by calling Aptx main

[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 744bf04..dc887fb 100644 (file)
--- a/src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java
+++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java
@@ -32,24 +32,24 @@ public final class ArchaeopteryxInit
   public static MainFrame createUnboundInstance(final Phylogeny aptxTree)
   {
     Phylogeny[] aptxTrees = { aptxTree };
-    return createBoundAptxFrame(aptxTrees, null);
+    return createAptxFrameInJalview(aptxTrees);
   }
 
-  public static MainFrame createInstance(final Phylogeny[] aptxTrees,
-          AlignmentViewport jalviewAlignmentView)
-  {
-    return createBoundAptxFrame(aptxTrees, jalviewAlignmentView);
-
-  }
-
-  public static MainFrame createInstance(final Phylogeny aptxTree,
-          final AlignmentViewport jalviewAlignmentView)
-  {
-    Phylogeny[] aptxTrees = { aptxTree }; // future possibility to load in
-    // several trees simultaneously
-    return createBoundAptxFrame(aptxTrees, jalviewAlignmentView);
-
-  }
+  // public static MainFrame createInstance(final Phylogeny[] aptxTrees,
+  // AlignmentViewport jalviewAlignmentView)
+  // {
+  // return createAptxFrameInJalview(aptxTrees);
+  //
+  // }
+  //
+  // public static MainFrame createInstance(final Phylogeny aptxTree,
+  // final AlignmentViewport jalviewAlignmentView)
+  // {
+  // Phylogeny[] aptxTrees = { aptxTree }; // future possibility to load in
+  // // several trees simultaneously
+  // return createAptxFrameInJalview(aptxTrees);
+  //
+  // }
 
   public static MainFrame createInstance(
           final TreeBuilder calculatedTree) // very dense method, to be split up
@@ -61,8 +61,8 @@ public final class ArchaeopteryxInit
     Phylogeny[] aptxTrees = { aptxTree }; // future possibility to load in
                                           // several trees simultaneously
 
-    MainFrame aptxApp = createBoundAptxFrame(aptxTrees,
-            calculatedTree.getAvport());
+    MainFrame aptxApp = createAptxFrameInJalview(aptxTrees);
+            
     bindNodesToJalviewSequences(aptxApp, calculatedTree.getAvport(),
             aptxTreeBuilder.getAlignmentBoundNodes(),
             aptxTreeBuilder.getNodesBoundAlignment());
@@ -73,16 +73,16 @@ public final class ArchaeopteryxInit
 
 
 
-  private static MainFrame createBoundAptxFrame(final Phylogeny[] aptxTrees,
-          final AlignmentViewport jalviewAlignmentView)
+  public static MainFrame createAptxFrameInJalview(
+          final Phylogeny[] aptxTrees)
   {
     MainFrame aptxApp = Archaeopteryx.createApplication(aptxTrees,
             "_aptx_jalview_configuration_file", null);
-
+    bindFrameToJalview(aptxApp);
     return aptxApp;
   }
 
-  private static void bindNodesToJalviewSequences(final MainFrame aptxApp,
+  public static void bindNodesToJalviewSequences(final MainFrame aptxApp,
           final AlignmentViewport jalviewAlignViewport,
           final Map<SequenceI, PhylogenyNode> alignMappedToNodes,
           final Map<PhylogenyNode, SequenceI> nodesMappedToAlign)
@@ -92,7 +92,7 @@ public final class ArchaeopteryxInit
   }
 
 
-  private static MainFrame bindFrameToJalview(final MainFrame aptxApp)
+  public static MainFrame bindFrameToJalview(final MainFrame aptxApp)
   {
     int width = 400;
     int height = 550;