Merge branch 'kjvdh/features/PhylogenyViewer' of

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

diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java b/src/jalview/ext/archaeopteryx/AptxInit.java
similarity index 89%
rename from src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java
rename to src/jalview/ext/archaeopteryx/AptxInit.java
index 364260e..ce34573 100644 (file)
--- a/src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java
+++ b/src/jalview/ext/archaeopteryx/AptxInit.java
@@ -2,6 +2,8 @@ package jalview.ext.archaeopteryx;
 
 import jalview.analysis.TreeBuilder;
 import jalview.datamodel.SequenceI;
+import jalview.ext.treeviewer.ExternalTreeBuilderI;
+import jalview.ext.treeviewer.ExternalTreeViewerBindingI;
 import jalview.gui.Desktop;
 import jalview.viewmodel.AlignmentViewport;
 
@@ -20,7 +22,7 @@ import org.forester.phylogeny.PhylogenyNode;
  * @author kjvanderheide
  *
  */
-public final class ArchaeopteryxInit
+public final class AptxInit
 {
   /**
    * Test method, should generally not be used as it does not bind the tree to
@@ -54,7 +56,7 @@ public final class ArchaeopteryxInit
   public static MainFrame createInstance(
           final TreeBuilder calculatedTree) // very dense method, to be split up
   {
-    ExternalTreeBuilderI<Phylogeny, PhylogenyNode> aptxTreeBuilder = new ArchaeopteryxTreeBuilder(
+    ExternalTreeBuilderI<Phylogeny, PhylogenyNode> aptxTreeBuilder = new AptxTreeBuilder(
             calculatedTree);
 
     Phylogeny aptxTree = aptxTreeBuilder.buildTree();
@@ -87,7 +89,7 @@ public final class ArchaeopteryxInit
           final Map<SequenceI, PhylogenyNode> alignMappedToNodes,
           final Map<PhylogenyNode, SequenceI> nodesMappedToAlign)
   {
-    return new AptxBinding(aptxApp, jalviewAlignViewport,
+    return new JalviewBinding(aptxApp, jalviewAlignViewport,
             alignMappedToNodes, nodesMappedToAlign);
   }
 
@@ -97,6 +99,8 @@ public final class ArchaeopteryxInit
     int width = 400;
     int height = 550;
     aptxApp.setMinimumSize(new Dimension(width, height));
+    // aptxApp.setFont(Desktop.instance.getFont());
+    // aptxApp.getMainPanel().setFont(Desktop.instance.getFont());
 
     Desktop.addInternalFrame(aptxApp, "Archaeopteryx Tree View", true,
             width, height, true, true);