JAL-1953 2.11.2 with Archeopteryx!

[jalview.git] / src / jalview / io / FileLoader.java

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index fec0b3a..4cf77de 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -37,6 +37,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.ext.archaeopteryx.AptxInit;
 import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
 import jalview.gui.Desktop;
@@ -111,7 +112,7 @@ public class FileLoader implements Runnable
     this.protocol = protocol;
     this.format = format;
 
-    final Thread loader = new Thread(this, "LoadFileThread");
+    final Thread loader = new Thread(this, "LoadFile");
 
     SwingUtilities.invokeLater(new Runnable()
     {
@@ -212,6 +213,7 @@ public class FileLoader implements Runnable
     return alignFrame;
   }
 
+  // add support for recently opened Aptx trees
   public void updateRecentlyOpened()
   {
     Vector<String> recent = new Vector<>();
@@ -470,6 +472,13 @@ public class FileLoader implements Runnable
               alignFrame.getViewport()
                       .applyFeaturesStyle(proxyColourScheme);
             }
+            if (format.isTreeFile())
+            {
+              // make generic instead of Aptx specific?
+              AptxInit.createInstancesFromFile(file,
+                      alignFrame.getViewport());
+
+            }
             alignFrame.setStatus(MessageManager.formatMessage(
                     "label.successfully_loaded_file", new String[]
                     { title }));
@@ -485,6 +494,7 @@ public class FileLoader implements Runnable
                       AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
             }
 
+
             try
             {
               alignFrame.setMaximum(