DataSetAnnotations dsa = (DataSetAnnotations) vobj;
if (dsa.getSeqRefCount() != 1)
{
- Cache.log
- .warn("Not binding "
- + dsa.getVorbaId()
- + " to Sequence Feature - has multiple dataset sequence references.");
+ Cache.log.warn("Not binding " + dsa.getVorbaId()
+ + " to Sequence Feature - has multiple dataset sequence references.");
return;
}
jalview.datamodel.SequenceFeature sf = (jalview.datamodel.SequenceFeature) jvobj;
if (dsa.getSeqRefCount() != 1)
{
replaceJvObjMapping(feature, null);
- Cache.log
- .warn("Binding of annotation to jalview feature has changed. Removing binding and recreating.");
+ Cache.log.warn(
+ "Binding of annotation to jalview feature has changed. Removing binding and recreating.");
doSync(); // re-verify bindings.
}
else
{
// conflicting update from document - we cannot map this feature anymore.
replaceJvObjMapping(feature, null);
- Cache.log
- .warn("annotation ("
- + dsa.getVorbaId()
- + " bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");
+ Cache.log.warn("annotation (" + dsa.getVorbaId()
+ + " bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");
// - consider deleting the feature ?
dsSeq.deleteFeature(feature);
// doSync();
vSeg.setInclusive(true);
if (dsa.getSegCount() > 1)
{
- Cache.log
- .debug("About to destroy complex annotation in vamsas document mapped to sequence feature ("
+ Cache.log.debug(
+ "About to destroy complex annotation in vamsas document mapped to sequence feature ("
+ dsa.getVorbaId() + ")");
}
dsa.setSeg(new Seg[] { vSeg });
else if (vlu instanceof Integer)
{
valid = true;
- nprop.setType(uk.ac.vamsas.objects.utils.Properties.INTEGERTYPE);
+ nprop.setType(
+ uk.ac.vamsas.objects.utils.Properties.INTEGERTYPE);
}
else if (vlu instanceof Float)
{
private SequenceFeature getJalviewSeqFeature(RangeAnnotation dseta)
{
int[] se = getBounds(dseta);
- SequenceFeature sf = new jalview.datamodel.SequenceFeature(
- dseta.getType(), dseta.getDescription(), dseta.getStatus(),
- se[0], se[1], dseta.getGroup());
+
+ /*
+ * try to identify feature score
+ */
+ boolean scoreFound = false;
+ float theScore = 0f;
+ String featureType = dseta.getType();
+ if (dseta.getScoreCount() > 0)
+ {
+ Enumeration scr = dseta.enumerateScore();
+ while (scr.hasMoreElements())
+ {
+ Score score = (Score) scr.nextElement();
+ if (score.getName().equals(featureType))
+ {
+ theScore = score.getContent();
+ scoreFound = true;
+ }
+ }
+ }
+
+ SequenceFeature sf = null;
+ if (scoreFound)
+ {
+ sf = new SequenceFeature(featureType, dseta.getDescription(), se[0],
+ se[1], theScore, dseta.getGroup());
+ }
+ else
+ {
+ sf = new SequenceFeature(featureType, dseta.getDescription(), se[0],
+ se[1], dseta.getGroup());
+ }
+ sf.setStatus(dseta.getStatus());
if (dseta.getLinkCount() > 0)
{
Link[] links = dseta.getLink();
while (scr.hasMoreElements())
{
Score score = (Score) scr.nextElement();
- if (score.getName().equals(sf.getType()))
- {
- sf.setScore(score.getContent());
- }
- else
+ if (!score.getName().equals(sf.getType()))
{
sf.setValue(score.getName(), "" + score.getContent());
}