From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Tue, 29 Sep 2015 10:46:54 +0000 (+0100)
Subject: JAL-1896 fixed NPE for RNA Helice without equivalent annotation
X-Git-Tag: Release_2_10_0~382
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0fd1986d18c3093cc5386697ed49301599b74379;p=jalview.git

JAL-1896 fixed NPE for RNA Helice without equivalent annotation
---

diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index 1ee8393..70a7319 100644
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -268,7 +268,10 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
           af.getAlignViewport().setShowSequenceFeatures(showSeqFeatures);
           ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
                   colourSchemeName, al);
-          af.changeColour(cs);
+          if (cs != null)
+          {
+            af.changeColour(cs);
+          }
         }
         else
         {
diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index acc71f3..4541fc2 100644
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -273,7 +273,10 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
           af.getViewport().setFeaturesDisplayed(fd);
           ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
                   colourSchemeName, al);
-          af.changeColour(cs);
+          if (cs != null)
+          {
+            af.changeColour(cs);
+          }
         }
         else
         {
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 9931f32..11c40c3 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -388,7 +388,10 @@ public class FileLoader implements Runnable
               alignFrame.getViewport().setFeaturesDisplayed(fd);
               ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
                       colourSchemeName, al);
-              alignFrame.changeColour(cs);
+              if (cs != null)
+              {
+                alignFrame.changeColour(cs);
+              }
             }
             else
             {
diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 8725556..3ac4aa7 100644
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -209,6 +209,13 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         jsonAlignmentPojo
                 .setAlignAnnotation(annotationToJsonPojo(annotations));
       }
+      else
+      {
+        if (globalColourScheme.equalsIgnoreCase("RNA Helices"))
+        {
+          jsonAlignmentPojo.setGlobalColorScheme("None");
+        }
+      }
 
       if (exportSettings.isExportFeatures())
       {