From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 27 Jun 2017 13:27:36 +0000 (+0100)
Subject: Merge branch 'develop' into features/JAL-2446NCList
X-Git-Tag: Release_2_10_3b1~185
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d065bc916cb63af83cdab7319f5177a855724aba;p=jalview.git

Merge branch 'develop' into features/JAL-2446NCList

Conflicts:
	src/jalview/appletgui/SeqPanel.java
	src/jalview/renderer/seqfeatures/FeatureRenderer.java
---

d065bc916cb63af83cdab7319f5177a855724aba
diff --cc src/jalview/appletgui/SeqPanel.java
index 9e31efe,a72bbaa..f854e03
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@@ -1175,7 -1227,7 +1175,7 @@@ public class SeqPanel extends Panel imp
          // Find the next gap before the end
          // of the visible region boundary
          boolean blank = false;
--        for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--)
++        for (; fixedRight > lastres; fixedRight--)
          {
            blank = true;
  
diff --cc src/jalview/gui/SeqCanvas.java
index ed3d298,1625c52..c05c172
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@@ -656,11 -663,7 +657,8 @@@ public class SeqCanvas extends JCompone
      }
      else
      {
-       List<int[]> regions = av.getAlignment().getHiddenColumns()
-               .getHiddenRegions();
- 
        int screenY = 0;
 +      final int screenYMax = endRes - startRes;
        int blockStart = startRes;
        int blockEnd = endRes;
  
diff --cc src/jalview/io/JSONFile.java
index 14574d0,c293cd4..36fe35a
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@@ -319,11 -309,11 +309,11 @@@ public class JSONFile extends AlignFil
      return hiddenSections;
    }
  
 -  public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
 -          SequenceI[] sqs, FeatureRenderer fr)
 +  protected List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
 +          SequenceI[] sqs)
    {
      displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
-     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
+     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<>();
      if (sqs == null)
      {
        return sequenceFeaturesPojo;