*/
package jalview.datamodel;
-import jalview.analysis.AlignSeq;
-import jalview.datamodel.features.SequenceFeatures;
-import jalview.datamodel.features.SequenceFeaturesI;
-import jalview.util.Comparison;
-import jalview.util.DBRefUtils;
-import jalview.util.MapList;
-import jalview.util.StringUtils;
-
import java.util.ArrayList;
import java.util.Arrays;
import java.util.BitSet;
import java.util.Vector;
import fr.orsay.lri.varna.models.rna.RNA;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.features.SequenceFeatures;
+import jalview.datamodel.features.SequenceFeaturesI;
+import jalview.util.Comparison;
+import jalview.util.DBRefUtils;
+import jalview.util.MapList;
+import jalview.util.StringUtils;
/**
*
@Override
public void addDBRef(DBRefEntry entry)
{
+ // TODO JAL-3980 maintain as sorted list
if (datasetSequence != null)
{
datasetSequence.addDBRef(entry);
{
dbrefs = new DBModList<>();
}
+ // TODO JAL-3979 LOOK UP RATHER THAN SWEEP FOR EFFICIENCY
for (int ib = 0, nb = dbrefs.size(); ib < nb; ib++)
{
getStart(), getEnd());
datasetSequence = dsseq;
+ updateDatasetFrom(dsseq, this);
+ }
+ return datasetSequence;
+ }
- dsseq.setDescription(description);
- // move features and database references onto dataset sequence
- dsseq.sequenceFeatureStore = sequenceFeatureStore;
- sequenceFeatureStore = null;
- dsseq.dbrefs = dbrefs;
- dbrefs = null;
- // TODO: search and replace any references to this sequence with
- // references to the dataset sequence in Mappings on dbref
- dsseq.pdbIds = pdbIds;
- pdbIds = null;
- datasetSequence.updatePDBIds();
- if (annotation != null)
+ /**
+ * used by createDatasetSequence - transfers dataset-only properties to dsseq
+ * from sequence2
+ *
+ * @param dsseq
+ * - newly created dataset sequenceI for sequence
+ * @param sequence2
+ * - sequence object that needs a dataset
+ */
+ protected void updateDatasetFrom(Sequence dsseq, Sequence sequence2)
+ {
+ dsseq.setDescription(description);
+ // move features and database references onto dataset sequence
+ dsseq.sequenceFeatureStore = sequenceFeatureStore;
+ sequenceFeatureStore = null;
+ dsseq.dbrefs = dbrefs;
+ dbrefs = null;
+ // TODO: search and replace any references to this sequence with
+ // references to the dataset sequence in Mappings on dbref
+ dsseq.pdbIds = pdbIds;
+ pdbIds = null;
+ datasetSequence.updatePDBIds();
+ if (annotation != null)
+ {
+ // annotation is cloned rather than moved, to preserve what's currently
+ // on the alignment
+ for (AlignmentAnnotation aa : annotation)
{
- // annotation is cloned rather than moved, to preserve what's currently
- // on the alignment
- for (AlignmentAnnotation aa : annotation)
- {
- AlignmentAnnotation _aa = new AlignmentAnnotation(aa);
- _aa.sequenceRef = datasetSequence;
- _aa.adjustForAlignment(); // uses annotation's own record of
- // sequence-column mapping
- datasetSequence.addAlignmentAnnotation(_aa);
- }
+ AlignmentAnnotation _aa = new AlignmentAnnotation(aa);
+ _aa.sequenceRef = datasetSequence;
+ _aa.adjustForAlignment(); // uses annotation's own record of
+ // sequence-column mapping
+ datasetSequence.addAlignmentAnnotation(_aa);
}
}
- return datasetSequence;
}
/*