JAL-2805 Jalview sequence binding interface expanded

[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 dc887fb..bd7de87 100644 (file)
--- a/src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java
+++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java
@@ -32,7 +32,7 @@ public final class ArchaeopteryxInit
   public static MainFrame createUnboundInstance(final Phylogeny aptxTree)
   {
     Phylogeny[] aptxTrees = { aptxTree };
-    return createAptxFrameInJalview(aptxTrees);
+    return createAptxFrame(aptxTrees);
   }
 
   // public static MainFrame createInstance(final Phylogeny[] aptxTrees,
@@ -54,14 +54,14 @@ public final class ArchaeopteryxInit
   public static MainFrame createInstance(
           final TreeBuilder calculatedTree) // very dense method, to be split up
   {
-    ArchaeopteryxTreeConverter aptxTreeBuilder = new ArchaeopteryxTreeConverter(
+    ExternalTreeBuilderI<Phylogeny, PhylogenyNode> aptxTreeBuilder = new ArchaeopteryxTreeBuilder(
             calculatedTree);
 
-    Phylogeny aptxTree = aptxTreeBuilder.buildAptxTree();
+    Phylogeny aptxTree = aptxTreeBuilder.buildTree();
     Phylogeny[] aptxTrees = { aptxTree }; // future possibility to load in
                                           // several trees simultaneously
 
-    MainFrame aptxApp = createAptxFrameInJalview(aptxTrees);
+    MainFrame aptxApp = createAptxFrame(aptxTrees);
             
     bindNodesToJalviewSequences(aptxApp, calculatedTree.getAvport(),
             aptxTreeBuilder.getAlignmentBoundNodes(),
@@ -73,21 +73,21 @@ public final class ArchaeopteryxInit
 
 
 
-  public static MainFrame createAptxFrameInJalview(
+  public static MainFrame createAptxFrame(
           final Phylogeny[] aptxTrees)
   {
     MainFrame aptxApp = Archaeopteryx.createApplication(aptxTrees,
             "_aptx_jalview_configuration_file", null);
-    bindFrameToJalview(aptxApp);
     return aptxApp;
   }
 
-  public static void bindNodesToJalviewSequences(final MainFrame aptxApp,
+  public static JalviewTreeViewerBindingI<?> bindNodesToJalviewSequences(
+          final MainFrame aptxApp,
           final AlignmentViewport jalviewAlignViewport,
           final Map<SequenceI, PhylogenyNode> alignMappedToNodes,
           final Map<PhylogenyNode, SequenceI> nodesMappedToAlign)
   {
-    new JalviewAptxBinding(aptxApp, jalviewAlignViewport,
+    return new JalviewAptxBinding(aptxApp, jalviewAlignViewport,
             alignMappedToNodes, nodesMappedToAlign);
   }