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());
}
{
try
{
- val = new Boolean(p.getContent());
+ val = Boolean.valueOf(p.getContent());
} catch (Exception e)
{
}
{
try
{
- val = new Float(p.getContent());
+ val = Float.valueOf(p.getContent());
} catch (Exception e)
{
{
try
{
- val = new Integer(p.getContent());
+ val = Integer.valueOf(p.getContent());
} catch (Exception e)
{
}