From: Jim Procter <jprocter@issues.jalview.org>
Date: Sun, 4 Dec 2016 12:36:39 +0000 (+0000)
Subject: JAL-1933 switch from gap count to occupancy
X-Git-Tag: Release_2_11_0~62^2~36^2~1
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=55fe3787a3eda4a3fec091c3b6435012ad7e6bf3

JAL-1933 switch from gap count to occupancy
---

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 0e055e4..132abc0 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -328,7 +328,7 @@ public class AAFrequency
         return;
       }
 
-      final int gapped = profile.getGapped();
+      final int gapped = profile.getNonGapped();
 
       String description = String.valueOf(gapped);
 
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index da05a09..0cca5b4 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1911,7 +1911,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
       consensus = new AlignmentAnnotation("Consensus", "PID",
               new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
       initConsensus(consensus);
-      gapcounts = new AlignmentAnnotation("Gaps", "Number of Gaps",
+      gapcounts = new AlignmentAnnotation("Occupancy",
+              "Number of aligned positions",
               new Annotation[1], 0f, alignment.getHeight(),
               AlignmentAnnotation.BAR_GRAPH);
       initGapCounts(gapcounts);