git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Merge branch 'develop' into patch/JAL-3921_jmol_session_save
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceGroup.java
diff --git
a/src/jalview/datamodel/SequenceGroup.java
b/src/jalview/datamodel/SequenceGroup.java
index
b356894
..
9837104
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
+303,11
@@
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
+644,7
@@
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;
}