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JAL-1896 fixed NPE for RNA Helice without equivalent annotation
author
tcofoegbu
<tcnofoegbu@dundee.ac.uk>
Tue, 29 Sep 2015 10:46:54 +0000
(11:46 +0100)
committer
tcofoegbu
<tcnofoegbu@dundee.ac.uk>
Tue, 29 Sep 2015 10:46:54 +0000
(11:46 +0100)
src/jalview/appletgui/CutAndPasteTransfer.java
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src/jalview/gui/CutAndPasteTransfer.java
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src/jalview/io/FileLoader.java
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src/jalview/io/JSONFile.java
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diff --git
a/src/jalview/appletgui/CutAndPasteTransfer.java
b/src/jalview/appletgui/CutAndPasteTransfer.java
index
1ee8393
..
70a7319
100644
(file)
--- 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.getAlignViewport().setShowSequenceFeatures(showSeqFeatures);
ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
colourSchemeName, al);
- af.changeColour(cs);
+ if (cs != null)
+ {
+ af.changeColour(cs);
+ }
}
else
{
}
else
{
diff --git
a/src/jalview/gui/CutAndPasteTransfer.java
b/src/jalview/gui/CutAndPasteTransfer.java
index
acc71f3
..
4541fc2
100644
(file)
--- 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.getViewport().setFeaturesDisplayed(fd);
ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
colourSchemeName, al);
- af.changeColour(cs);
+ if (cs != null)
+ {
+ af.changeColour(cs);
+ }
}
else
{
}
else
{
diff --git
a/src/jalview/io/FileLoader.java
b/src/jalview/io/FileLoader.java
index
9931f32
..
11c40c3
100755
(executable)
--- 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.getViewport().setFeaturesDisplayed(fd);
ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
colourSchemeName, al);
- alignFrame.changeColour(cs);
+ if (cs != null)
+ {
+ alignFrame.changeColour(cs);
+ }
}
else
{
}
else
{
diff --git
a/src/jalview/io/JSONFile.java
b/src/jalview/io/JSONFile.java
index
8725556
..
3ac4aa7
100644
(file)
--- 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));
}
jsonAlignmentPojo
.setAlignAnnotation(annotationToJsonPojo(annotations));
}
+ else
+ {
+ if (globalColourScheme.equalsIgnoreCase("RNA Helices"))
+ {
+ jsonAlignmentPojo.setGlobalColorScheme("None");
+ }
+ }
if (exportSettings.isExportFeatures())
{
if (exportSettings.isExportFeatures())
{