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develop merge
[jalview.git]
/
src
/
jalview
/
analysis
/
SeqsetUtils.java
diff --git
a/src/jalview/analysis/SeqsetUtils.java
b/src/jalview/analysis/SeqsetUtils.java
index
40bedad
..
b0ecfde
100755
(executable)
--- a/
src/jalview/analysis/SeqsetUtils.java
+++ b/
src/jalview/analysis/SeqsetUtils.java
@@
-59,13
+59,19
@@
public class SeqsetUtils
sfeat.addElement(sfarray[i]);
}
}
sfeat.addElement(sfarray[i]);
}
}
- sqinfo.put("SeqFeatures", sfeat);
- sqinfo.put("PdbId",
+ if (seq.getDatasetSequence() == null)
+ {
+ sqinfo.put("SeqFeatures", sfeat);
+ sqinfo.put("PdbId",
(seq.getAllPDBEntries() != null) ? seq.getAllPDBEntries()
: new Vector<PDBEntry>());
(seq.getAllPDBEntries() != null) ? seq.getAllPDBEntries()
: new Vector<PDBEntry>());
- sqinfo.put("datasetSequence",
+ }
+ else
+ {
+ sqinfo.put("datasetSequence",
(seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
: new Sequence("THISISAPLACEHOLDER", ""));
(seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
: new Sequence("THISISAPLACEHOLDER", ""));
+ }
return sqinfo;
}
return sqinfo;
}
@@
-129,6
+135,11
@@
public class SeqsetUtils
&& !(seqds.getName().equals("THISISAPLACEHOLDER") && seqds
.getLength() == 0))
{
&& !(seqds.getName().equals("THISISAPLACEHOLDER") && seqds
.getLength() == 0))
{
+ if (sfeatures!=null)
+ {
+ System.err
+ .println("Implementation error: setting dataset sequence for a sequence which has sequence features.\n\tDataset sequence features will not be visible.");
+ }
sq.setDatasetSequence(seqds);
}
sq.setDatasetSequence(seqds);
}