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JAL-3111 JAL-3280 hide the version check preference option in ‘Connections’ tab
[jalview.git]
/
src
/
jalview
/
io
/
AnnotationFile.java
diff --git
a/src/jalview/io/AnnotationFile.java
b/src/jalview/io/AnnotationFile.java
index
00476d6
..
86b4402
100755
(executable)
--- a/
src/jalview/io/AnnotationFile.java
+++ b/
src/jalview/io/AnnotationFile.java
@@
-274,7
+274,7
@@
public class AnnotationFile
if (row.graphGroup > -1)
{
graphGroupSeen.set(row.graphGroup);
if (row.graphGroup > -1)
{
graphGroupSeen.set(row.graphGroup);
- Integer key = new Integer(row.graphGroup);
+ Integer key = Integer.valueOf(row.graphGroup);
if (graphGroup.containsKey(key))
{
graphGroup.put(key, graphGroup.get(key) + "\t" + row.label);
if (graphGroup.containsKey(key))
{
graphGroup.put(key, graphGroup.get(key) + "\t" + row.label);
@@
-762,7
+762,7
@@
public class AnnotationFile
autoAnnotsKey(aa[aai], aa[aai].sequenceRef,
(aa[aai].groupRef == null ? null
: aa[aai].groupRef.getName())),
autoAnnotsKey(aa[aai], aa[aai].sequenceRef,
(aa[aai].groupRef == null ? null
: aa[aai].groupRef.getName())),
- new Integer(1));
+ Integer.valueOf(1));
}
}
}
}
}
}
@@
-968,7
+968,7
@@
public class AnnotationFile
else
{
// consider deferring this till after the file has been parsed ?
else
{
// consider deferring this till after the file has been parsed ?
- hidden.hideInsertionsFor(sr);
+ hidden.hideList(sr.getInsertions());
}
}
modified = true;
}
}
modified = true;
@@
-1271,7
+1271,7
@@
public class AnnotationFile
{
displayChar = token;
// foo
{
displayChar = token;
// foo
- value = new Float(token).floatValue();
+ value = Float.valueOf(token).floatValue();
parsedValue = true;
continue;
} catch (NumberFormatException ex)
parsedValue = true;
continue;
} catch (NumberFormatException ex)
@@
-1617,8
+1617,10
@@
public class AnnotationFile
}
else if (key.equalsIgnoreCase("colour"))
{
}
else if (key.equalsIgnoreCase("colour"))
{
+ // TODO need to notify colourscheme of view reference once it is
+ // available
sg.cs.setColourScheme(
sg.cs.setColourScheme(
- ColourSchemeProperty.getColourScheme(al, value));
+ ColourSchemeProperty.getColourScheme(null, al, value));
}
else if (key.equalsIgnoreCase("pidThreshold"))
{
}
else if (key.equalsIgnoreCase("pidThreshold"))
{