From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 2 Jun 2017 13:11:30 +0000 (+0100)
Subject: JAL-2228 always set minimum for count to zero for annotation row
X-Git-Tag: Release_2_10_2~3^2~43^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7ff8c3bd7a91e45a889765d7e2985bab04ff21a8;p=jalview.git

JAL-2228 always set minimum for count to zero for annotation row
---

diff --git a/src/jalview/workers/ColumnCounterSetWorker.java b/src/jalview/workers/ColumnCounterSetWorker.java
index 6c5707d..8a1c8ec 100644
--- a/src/jalview/workers/ColumnCounterSetWorker.java
+++ b/src/jalview/workers/ColumnCounterSetWorker.java
@@ -182,8 +182,9 @@ class ColumnCounterSetWorker extends AlignCalcWorker
     for (int anrow = 0; anrow < rows; anrow++)
     {
       Annotation[] anns = new Annotation[width];
+      long rmax = 0;
       /*
-       * add non-zero counts as annotations
+       * add counts as annotations. zeros are needed since select-by-annotation ignores empty annotation positions
        */
       for (int i = 0; i < counts.length; i++)
       {
@@ -195,6 +196,7 @@ class ColumnCounterSetWorker extends AlignCalcWorker
           String str = String.valueOf(count);
           anns[i] = new Annotation(str, str, '0', count, color);
         }
+          rmax = Long.max(count, rmax);
       }
 
       /*
@@ -212,7 +214,8 @@ class ColumnCounterSetWorker extends AlignCalcWorker
       ann.scaleColLabel = true;
       ann.graph = AlignmentAnnotation.BAR_GRAPH;
       ann.annotations = anns;
-      setGraphMinMax(ann, anns);
+      ann.graphMin = 0f; // minimum always zero count
+      ann.graphMax = rmax; // maximum count from loop over feature columns
       ann.validateRangeAndDisplay();
       if (!ourAnnots.contains(ann))
       {