Start of creating the objects Archaeopteryx needs

diff --git a/src/jalview/ext/archaeopteryx/AlignConvertForArchaeopteryx.java b/src/jalview/ext/archaeopteryx/AlignConvertForArchaeopteryx.java
new file mode 100644 (file)
index 0000000..22aec97
--- /dev/null
+++ b/src/jalview/ext/archaeopteryx/AlignConvertForArchaeopteryx.java
@@ -0,0 +1,6 @@
+package jalview.ext.archaeopteryx;
+
+public class AlignConvertForArchaeopteryx
+{
+
+}

diff --git a/src/jalview/ext/archaeopteryx/AlignmentToTreeViewerI.java b/src/jalview/ext/archaeopteryx/AlignmentToTreeViewerI.java
index 3b3747c..0dddbf1 100644 (file)
--- a/src/jalview/ext/archaeopteryx/AlignmentToTreeViewerI.java
+++ b/src/jalview/ext/archaeopteryx/AlignmentToTreeViewerI.java
@@ -20,8 +20,16 @@
  */
 package jalview.ext.archaeopteryx;
 
+import java.util.Collection;
 
 interface AlignmentToTreeViewerI
 {
+  public void rootNode(Object node);
+
+  public Object makeTreeNode(String nodeName);
+
+  public Object addNodeChild(Object childNode, Object parentNode);
+  
+  public Collection<?> getNodes();
 
 }

diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
new file mode 100644 (file)
index 0000000..e8c5109
--- /dev/null
+++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
@@ -0,0 +1,6 @@
+package jalview.ext.archaeopteryx;
+
+public class ArchaeopteryxTreeBuilder
+{
+  
+}

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index 58a28c0..bd6c5ee 100644 (file)
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -21,7 +21,6 @@
 package jalview.gui;
 
 import jalview.analysis.TreeBuilder;
-import jalview.analysis.TreeCalculator;
 import jalview.analysis.scoremodels.ScoreModels;
 import jalview.analysis.scoremodels.SimilarityParams;
 import jalview.api.analysis.ScoreModelI;
@@ -472,9 +471,8 @@ public class CalculationChooser extends JPanel
     {
 
       String treeAlgo = determineTreeAlgo();
-      TreeCalculator calculateTree = new TreeCalculator(treeAlgo,
-              substitutionMatrix,
-              params);
+      // TreeCalculator calculateTree = new TreeCalculator(treeAlgo,
+      // substitutionMatrix, params);
 
       openTreePanel(treeAlgo, substitutionMatrix, params);
     }