From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 29 Sep 2016 11:49:56 +0000 (+0100)
Subject: Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
X-Git-Tag: Release_2_10_0~30
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=78c650c30d56b625a110e2cf5fdec93b9ff55e88;hp=0d099414b4c6d0014630589ea4218de07ccf3db9;p=jalview.git

Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
---

diff --git a/help/html/na/index.html b/help/html/na/index.html
index 22ea27e..1d17058 100644
--- a/help/html/na/index.html
+++ b/help/html/na/index.html
@@ -79,7 +79,7 @@ td {
     the alignment will have a secondary structure line shown below it,
     and a number of additional options become available:
   <ul>
-    <li><a href="../colourschemes/rnahelicesColouring.html">RNA
+    <li><a href="../colourSchemes/rnahelicesColouring.html">RNA
         Helix colouring</a> - highlights columns of alignment involved in
       particular RNA helices, Uses the first displayed secondary
       structure annotation.</li>
diff --git a/src/jalview/appletgui/AnnotationRowFilter.java b/src/jalview/appletgui/AnnotationRowFilter.java
index fc49de5..cd00fcf 100644
--- a/src/jalview/appletgui/AnnotationRowFilter.java
+++ b/src/jalview/appletgui/AnnotationRowFilter.java
@@ -104,6 +104,16 @@ public abstract class AnnotationRowFilter extends Panel
         enableSeqAss = true;
       }
       String label = av.getAlignment().getAlignmentAnnotation()[i].label;
+      // add associated sequence ID if available
+      if (!isSeqAssociated
+              && av.getAlignment().getAlignmentAnnotation()[i].sequenceRef != null)
+      {
+        label = label
+                + "_"
+                + av.getAlignment().getAlignmentAnnotation()[i].sequenceRef
+                        .getName();
+      }
+      // make label unique
       if (!list.contains(label))
       {
         anmap[list.size()] = i;
diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java
index f0bea60..0a5e96c 100644
--- a/src/jalview/gui/AnnotationRowFilter.java
+++ b/src/jalview/gui/AnnotationRowFilter.java
@@ -161,6 +161,16 @@ public abstract class AnnotationRowFilter extends JPanel
         enableSeqAss = true;
       }
       String label = av.getAlignment().getAlignmentAnnotation()[i].label;
+      // add associated sequence ID if available
+      if (!isSeqAssociated
+              && av.getAlignment().getAlignmentAnnotation()[i].sequenceRef != null)
+      {
+        label = label
+                + "_"
+                + av.getAlignment().getAlignmentAnnotation()[i].sequenceRef
+                        .getName();
+      }
+      // make label unique
       if (!list.contains(label))
       {
         anmap[list.size()] = i;
diff --git a/src/jalview/schemes/TCoffeeColourScheme.java b/src/jalview/schemes/TCoffeeColourScheme.java
index 62f3a2e..2be51c2 100644
--- a/src/jalview/schemes/TCoffeeColourScheme.java
+++ b/src/jalview/schemes/TCoffeeColourScheme.java
@@ -86,6 +86,10 @@ public class TCoffeeColourScheme extends ResidueColourScheme
     seqMap = new IdentityHashMap<SequenceI, Color[]>();
     AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
             : alignment.getContext();
+    if (alcontext == null)
+    {
+      return;
+    }
     int w = 0;
     for (AlignmentAnnotation al : alcontext
             .findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))