Slight Aptx colour change

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

diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxFrame.java b/src/jalview/ext/archaeopteryx/ArchaeopteryxFrame.java
index d0728c4..3c9e175 100644 (file)
--- a/src/jalview/ext/archaeopteryx/ArchaeopteryxFrame.java
+++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxFrame.java
@@ -12,16 +12,16 @@ import org.forester.phylogeny.Phylogeny;
 public class ArchaeopteryxFrame
 {
 
-  public static void createInstance(Phylogeny aptxTree)
+  public static ArchaeopteryxFrame createInstance(Phylogeny aptxTree)
   {
-    new ArchaeopteryxFrame(aptxTree);
+    return new ArchaeopteryxFrame(aptxTree);
 
   }
 
-  public static void createInstance(
+  public static ArchaeopteryxFrame createInstance(
           TreeBuilder calculatedTree)
   {
-    new ArchaeopteryxFrame(calculatedTree);
+    return new ArchaeopteryxFrame(calculatedTree);
 
   }
 
@@ -36,7 +36,12 @@ public class ArchaeopteryxFrame
   {
     ArchaeopteryxTreeBuilder aptxTreeBuilder = new ArchaeopteryxTreeBuilder();
     Phylogeny aptxTree = aptxTreeBuilder.buildAptxTree(calculatedTree);
-    MainFrame aptxApp = Archaeopteryx.createApplication(aptxTree);
+
+    Phylogeny[] aptxTrees = { aptxTree }; // future possibility to load in
+                                          // several trees simultaneously
+
+    MainFrame aptxApp = Archaeopteryx.createApplication(aptxTrees,
+            "_aptx_jalview_configuration_file", null);
     start(aptxApp);
   }
 
@@ -46,16 +51,10 @@ public class ArchaeopteryxFrame
   {
     int width = 400;
     int height = 550;
-    aptxApp.setMinimumSize(new Dimension(width - 30, height - 50)); // doesn't
-                                                                    // work
-                                                                    // as it
-                                                                    // gets
-                                                                    // overridden
-                                                                    // during
-                                                                    // addInternalFrame?
-
-    Desktop.addInternalFrame(aptxApp, "Archaeopteryx Tree View", width,
-            height, true);
+    aptxApp.setMinimumSize(new Dimension(width, height));
+
+    Desktop.addInternalFrame(aptxApp, "Archaeopteryx Tree View", true,
+            width, height, true, true);
 
   }