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JAL-1912 efficiency: look up sequenceMapping once per position and only when sequence...
[jalview.git]
/
src
/
jalview
/
datamodel
/
AlignmentAnnotation.java
diff --git
a/src/jalview/datamodel/AlignmentAnnotation.java
b/src/jalview/datamodel/AlignmentAnnotation.java
index
01926dc
..
b00f27d
100755
(executable)
--- a/
src/jalview/datamodel/AlignmentAnnotation.java
+++ b/
src/jalview/datamodel/AlignmentAnnotation.java
@@
-980,18
+980,20
@@
public class AlignmentAnnotation
int position;
Annotation[] temp = new Annotation[aSize];
Integer index;
int position;
Annotation[] temp = new Annotation[aSize];
Integer index;
-
- for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
+ if (sequenceMapping != null)
{
{
- index = new Integer(a);
- if (sequenceMapping != null && sequenceMapping.containsKey(index))
+ for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
{
{
- position = sequenceRef.findIndex(a) - 1;
+ index = new Integer(a);
+ Annotation annot = sequenceMapping.get(index);
+ if (annot != null)
+ {
+ position = sequenceRef.findIndex(a) - 1;
- temp[position] = sequenceMapping.get(index);
+ temp[position] = annot;
+ }
}
}
}
}
-
annotations = temp;
}
annotations = temp;
}