From 55fe3787a3eda4a3fec091c3b6435012ad7e6bf3 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Sun, 4 Dec 2016 12:36:39 +0000 Subject: [PATCH 1/1] JAL-1933 switch from gap count to occupancy --- src/jalview/analysis/AAFrequency.java | 2 +- src/jalview/viewmodel/AlignmentViewport.java | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) 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); -- 1.7.10.2