From: Jim Procter 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/?a=commitdiff_plain;h=55fe3787a3eda4a3fec091c3b6435012ad7e6bf3;p=jalview.git 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);