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JAL-1239 cancelled flag should be checked and counted
[jalview.git]
/
src
/
jalview
/
schemes
/
TCoffeeColourScheme.java
diff --git
a/src/jalview/schemes/TCoffeeColourScheme.java
b/src/jalview/schemes/TCoffeeColourScheme.java
index
6eb48c2
..
1c8e469
100644
(file)
--- a/
src/jalview/schemes/TCoffeeColourScheme.java
+++ b/
src/jalview/schemes/TCoffeeColourScheme.java
@@
-85,8
+85,9
@@
public class TCoffeeColourScheme extends ResidueColourScheme
// Search alignment to get all tcoffee annotation and pick one set of
// annotation to use to colour seqs.
seqMap = new IdentityHashMap<SequenceI, Color[]>();
// Search alignment to get all tcoffee annotation and pick one set of
// annotation to use to colour seqs.
seqMap = new IdentityHashMap<SequenceI, Color[]>();
+ AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment : alignment.getContext();
int w = 0;
int w = 0;
- for (AlignmentAnnotation al : alignment
+ for (AlignmentAnnotation al : alcontext
.findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
{
if (al.sequenceRef != null && !al.belowAlignment)
.findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
{
if (al.sequenceRef != null && !al.belowAlignment)
@@
-129,4
+130,11
@@
public class TCoffeeColourScheme extends ResidueColourScheme
}
return cols[j];
}
}
return cols[j];
}
+
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ return new TCoffeeColourScheme(sg);
+ }
}
}