JAL-3664 hmm related TODOs

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

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 66b51cd..1126de6 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -33,9 +33,9 @@ import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
 import jalview.gui.Desktop;
-import jalview.gui.Jalview2XML;
 import jalview.gui.JvOptionPane;
 import jalview.json.binding.biojson.v1.ColourSchemeMapper;
+import jalview.project.Jalview2XML;
 import jalview.schemes.ColourSchemeI;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
@@ -196,6 +196,9 @@ public class FileLoader implements Runnable
         Thread.sleep(500);
       } catch (Exception ex)
       {
+        System.out.println(
+                "Exception caught while waiting for FileLoader thread");
+        ex.printStackTrace();
       }
     }
 
@@ -438,9 +441,10 @@ public class FileLoader implements Runnable
             viewport.addAlignment(al, title);
             if (source instanceof HMMFile)
             {
+              // TODO: absorb into viewport.addAlignment above ?
               AlignmentI alignment = viewport.getAlignment();
               SequenceI seq = alignment
-                      .getSequenceAt(alignment.getAbsoluteHeight() - 1);
+                      .getSequenceAt(alignment.getHeight() - 1);
               if (seq.hasHMMProfile())
               {
                 /* 
@@ -451,6 +455,11 @@ public class FileLoader implements Runnable
               }
               viewport.getAlignPanel().adjustAnnotationHeight();
               viewport.updateSequenceIdColours();
+              // update HMM colour options 
+              if (alignFrame != null)
+              {
+                alignFrame.buildColourMenu();
+              }
             }
           }
           else
@@ -498,7 +507,7 @@ public class FileLoader implements Runnable
               alignFrame.getViewport()
                       .applyFeaturesStyle(proxyColourScheme);
             }
-            alignFrame.statusBar.setText(MessageManager.formatMessage(
+            alignFrame.setStatus(MessageManager.formatMessage(
                     "label.successfully_loaded_file", new String[]
                     { title }));