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 6ac0869..1126de6 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -441,9 +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())
               {
                 /* 
@@ -454,6 +455,11 @@ public class FileLoader implements Runnable
               }
               viewport.getAlignPanel().adjustAnnotationHeight();
               viewport.updateSequenceIdColours();
+              // update HMM colour options 
+              if (alignFrame != null)
+              {
+                alignFrame.buildColourMenu();
+              }
             }
           }
           else