JAL-2629 add hmmalign command

[jalview.git] / src / jalview / schemes / HMMERColourScheme.java

diff --git a/src/jalview/schemes/HMMERColourScheme.java b/src/jalview/schemes/HMMERColourScheme.java
index c9e081f..3c25ec2 100644 (file)
--- a/src/jalview/schemes/HMMERColourScheme.java
+++ b/src/jalview/schemes/HMMERColourScheme.java
@@ -8,6 +8,7 @@ import jalview.util.ColorUtils;
 import jalview.util.Comparison;
 
 import java.awt.Color;
+import java.util.List;
 import java.util.Map;
 
 public class HMMERColourScheme extends ResidueColourScheme
@@ -85,7 +86,7 @@ public class HMMERColourScheme extends ResidueColourScheme
     {
 
       colour = ColorUtils.getGraduatedColour(value.floatValue(), 0,
-              Color.WHITE, 3f, Color.blue);
+              Color.WHITE, 4.52f, Color.blue);
     }
     else if (value < 0)
     {
@@ -105,8 +106,16 @@ public class HMMERColourScheme extends ResidueColourScheme
   public void alignmentChanged(AnnotatedCollectionI collection,
           Map<SequenceI, SequenceCollectionI> hiddenReps)
   {
-    SequenceI seq = collection.getSequences().get(0);
-    hmm = seq.getHMM();
+    List<SequenceI> seqs = collection.getSequences();
+    for (SequenceI seq : seqs)
+    {
+      if (seq.getHMM() != null)
+      {
+        hmm = seq.getHMM();
+        break;
+      }
+    }
+
   }
 
 
@@ -116,8 +125,15 @@ public class HMMERColourScheme extends ResidueColourScheme
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
     HiddenMarkovModel markov = null;
-    SequenceI seq = sg.getSequences().get(0);
-    markov = seq.getHMM();
+    List<SequenceI> seqs = sg.getSequences();
+    for (SequenceI seq : seqs)
+    {
+      if (seq.getHMM() != null)
+      {
+        markov = seq.getHMM();
+        break;
+      }
+    }
     HMMERColourScheme colour = new HMMERColourScheme(markov);
     return colour;