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JAL-4343 fix insufficient-caffeine error - add whats new for 2.11.3.1
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceGroup.java
diff --git
a/src/jalview/datamodel/SequenceGroup.java
b/src/jalview/datamodel/SequenceGroup.java
index
6a0e64c
..
7e53c46
100755
(executable)
--- a/
src/jalview/datamodel/SequenceGroup.java
+++ b/
src/jalview/datamodel/SequenceGroup.java
@@
-274,14
+274,6
@@
public class SequenceGroup implements AnnotatedCollectionI
endRes + 1);
if (seqipos != null)
{
endRes + 1);
if (seqipos != null)
{
- seqipos.setDescription(seq.getDescription());
- seqipos.setDBRefs(seq.getDBRefs());
- seqipos.setSequenceFeatures(seq.getSequenceFeatures());
- if (seq.getDatasetSequence() != null)
- {
- seqipos.setDatasetSequence(seq.getDatasetSequence());
- }
-
if (seq.getAnnotation() != null)
{
AlignmentAnnotation[] alann = align.getAlignmentAnnotation();
if (seq.getAnnotation() != null)
{
AlignmentAnnotation[] alann = align.getAlignmentAnnotation();
@@
-311,6
+303,12
@@
public class SequenceGroup implements AnnotatedCollectionI
newannot.restrict(startRes, endRes);
newannot.setSequenceRef(seqs[ipos]);
newannot.adjustForAlignment();
newannot.restrict(startRes, endRes);
newannot.setSequenceRef(seqs[ipos]);
newannot.adjustForAlignment();
+ ContactMatrixI cm = seq
+ .getContactMatrixFor(seq.getAnnotation()[a]);
+ if (cm != null)
+ {
+ seqs[ipos].addContactListFor(newannot, cm);
+ }
seqipos.addAlignmentAnnotation(newannot);
}
}
seqipos.addAlignmentAnnotation(newannot);
}
}
@@
-647,7
+645,8
@@
public class SequenceGroup implements AnnotatedCollectionI
} catch (java.lang.OutOfMemoryError err)
{
// TODO: catch OOM
} catch (java.lang.OutOfMemoryError err)
{
// TODO: catch OOM
- System.out.println("Out of memory loading groups: " + err);
+ jalview.bin.Console
+ .outPrintln("Out of memory loading groups: " + err);
}
return upd;
}
}
return upd;
}
@@
-1499,6
+1498,12
@@
public class SequenceGroup implements AnnotatedCollectionI
}
@Override
}
@Override
+ public ContactMatrixI getContactMatrixFor(AlignmentAnnotation ann)
+ {
+ return cmholder.getContactMatrixFor(ann);
+ }
+
+ @Override
public ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
{
return cmholder.getContactListFor(_aa, column);
public ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
{
return cmholder.getContactListFor(_aa, column);
@@
-1519,4
+1524,12
@@
public class SequenceGroup implements AnnotatedCollectionI
// TODO passing annotations back to context to be added
return aa;
}
// TODO passing annotations back to context to be added
return aa;
}
+
+ @Override
+ public void addContactListFor(AlignmentAnnotation annotation,
+ ContactMatrixI cm)
+ {
+ cmholder.addContactListFor(annotation, cm);
+ }
+
}
}