JAL-2629 add multiple options for running hmmbuild on alignment/groups

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

diff --git a/src/jalview/schemes/HMMERColourScheme.java b/src/jalview/schemes/HMMERColourScheme.java
index f3691f0..61eb693 100644 (file)
--- a/src/jalview/schemes/HMMERColourScheme.java
+++ b/src/jalview/schemes/HMMERColourScheme.java
@@ -61,7 +61,7 @@ public class HMMERColourScheme extends ResidueColourScheme
     }
     if (Character.isLowerCase(symbol))
     {
-      return new Color(230, 0, 0);
+      symbol = Character.toUpperCase(symbol);
     }
     Double prob;
     prob = hmm.getMatchEmissionProbability(position, symbol);
@@ -108,7 +108,7 @@ public class HMMERColourScheme extends ResidueColourScheme
          List<SequenceI> seqs = collection.getSequences();
            for (SequenceI seq : seqs)
            {
-             if (seq.getHMM() != null)
+      if (seq.isHMMConsensusSequence())
              {
                hmm = seq.getHMM();
                break;