From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Sat, 24 Jun 2017 10:31:51 +0000 (+0100)
Subject: Merge branch 'features/JAL-2446NCList' into spikes/mungo
X-Git-Tag: Release_2_11_0~62^2~30
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=05e90fa615d589a46a9f29a9909d70709e7188d8;p=jalview.git

Merge branch 'features/JAL-2446NCList' into spikes/mungo

Conflicts:
	help/html/releases.html
	src/jalview/datamodel/BinarySequence.java
	src/jalview/datamodel/Sequence.java
	src/jalview/datamodel/SequenceI.java
	src/jalview/datamodel/features/FeatureStore.java
	src/jalview/datamodel/features/NCList.java
	src/jalview/datamodel/features/NCNode.java
	src/jalview/datamodel/features/SequenceFeatures.java
	src/jalview/gui/SeqCanvas.java
	src/jalview/renderer/seqfeatures/FeatureRenderer.java
	src/jalview/schemes/ClustalxColourScheme.java
	src/jalview/urls/UrlLinkDisplay.java
	test/jalview/datamodel/AlignmentTest.java
	test/jalview/datamodel/SequenceTest.java
	test/jalview/datamodel/features/FeatureStoreTest.java
	test/jalview/datamodel/features/SequenceFeaturesTest.java
	test/jalview/urls/UrlLinkDisplayTest.java
---

05e90fa615d589a46a9f29a9909d70709e7188d8
diff --cc src/jalview/datamodel/BinarySequence.java
index b7e15a6,477f4a7..5789b2b
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@@ -69,8 -69,8 +69,7 @@@ public class BinarySequence extends Seq
    {
      int nores = (isNa) ? ResidueProperties.maxNucleotideIndex
              : ResidueProperties.maxProteinIndex;
--
-     dbinary = new double[getSequence().length * nores];
+     dbinary = new double[getLength() * nores];
  
      return nores;
    }