From 3a7e301b545949dc3e5906c0e4343b4f6db56b0c Mon Sep 17 00:00:00 2001
From: TZVanaalten <TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Date: Tue, 15 Aug 2017 10:45:55 +0100
Subject: [PATCH] JAL-2599 fix HMMER scheme not colouring inserts and made red
 darker

---
 src/jalview/schemes/HMMERColourScheme.java |   48 +++++++++++++++-------------
 1 file changed, 26 insertions(+), 22 deletions(-)

diff --git a/src/jalview/schemes/HMMERColourScheme.java b/src/jalview/schemes/HMMERColourScheme.java
index 3c25ec2..113afd1 100644
--- a/src/jalview/schemes/HMMERColourScheme.java
+++ b/src/jalview/schemes/HMMERColourScheme.java
@@ -49,6 +49,10 @@ public class HMMERColourScheme extends ResidueColourScheme
     {
       return Color.white;
     }
+    if (Character.isLowerCase(symbol))
+    {
+      return new Color(230, 0, 0);
+    }
     Double prob;
     prob = hmm.getMatchEmissionProbability(position, symbol);
     double freq = 0;
@@ -78,7 +82,7 @@ public class HMMERColourScheme extends ResidueColourScheme
     }
     if (prob == 0)
     {
-      return Color.red;
+      return new Color(230, 0, 0);
     }
     Double value = Math.log(prob / freq);
     Color colour = null;
@@ -106,15 +110,15 @@ public class HMMERColourScheme extends ResidueColourScheme
   public void alignmentChanged(AnnotatedCollectionI collection,
           Map<SequenceI, SequenceCollectionI> hiddenReps)
   {
-    List<SequenceI> seqs = collection.getSequences();
-    for (SequenceI seq : seqs)
-    {
-      if (seq.getHMM() != null)
-      {
-        hmm = seq.getHMM();
-        break;
-      }
-    }
+	  List<SequenceI> seqs = collection.getSequences();
+	    for (SequenceI seq : seqs)
+	    {
+	      if (seq.getHMM() != null)
+	      {
+	        hmm = seq.getHMM();
+	        break;
+	      }
+	    }
 
   }
 
@@ -124,18 +128,18 @@ public class HMMERColourScheme extends ResidueColourScheme
   public ColourSchemeI getInstance(AnnotatedCollectionI sg,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
-    HiddenMarkovModel markov = null;
-    List<SequenceI> seqs = sg.getSequences();
-    for (SequenceI seq : seqs)
-    {
-      if (seq.getHMM() != null)
-      {
-        markov = seq.getHMM();
-        break;
-      }
-    }
-    HMMERColourScheme colour = new HMMERColourScheme(markov);
-    return colour;
+	  HiddenMarkovModel markov = null;
+	    List<SequenceI> seqs = sg.getSequences();
+	    for (SequenceI seq : seqs)
+	    {
+	      if (seq.getHMM() != null)
+	      {
+	        markov = seq.getHMM();
+	        break;
+	      }
+	    }
+	    HMMERColourScheme colour = new HMMERColourScheme(markov);
+	    return colour;
 
   }
 
-- 
1.7.10.2