String description;
int start;
int end;
- Color color = Color.white;
Vector pdbIds;
String vamsasId;
DBRefEntry[] dbrefs;
sequenceFeatures = temp;
}
+ public void deleteFeature(SequenceFeature sf)
+ {
+ if(sequenceFeatures==null)
+ return;
+
+ int index=0;
+ for (index = 0; index < sequenceFeatures.length; index++)
+ {
+ if (sequenceFeatures[index].equals(sf))
+ {
+ break;
+ }
+ }
+
+
+ if(index==sequenceFeatures.length)
+ return;
+
+ int sfLength = sequenceFeatures.length;
+ if(sfLength<2)
+ {
+ sequenceFeatures = null;
+ }
+ else
+ {
+ SequenceFeature[] temp = new SequenceFeature[sfLength-1];
+ System.arraycopy(sequenceFeatures, 0, temp, 0, index);
+
+ if(index<sfLength)
+ System.arraycopy(sequenceFeatures,
+ index + 1,
+ temp,
+ index, sequenceFeatures.length - index -1);
+
+ sequenceFeatures = temp;
+ }
+ }
+
/**
* DOCUMENT ME!
*
int nend = findPosition(end) - 1;
// JBPNote - this is an incomplete copy.
SequenceI nseq = new Sequence(this.getName(), seq, nstart, nend);
+ nseq.setDescription(description);
nseq.setDatasetSequence(getDatasetSequence());
return nseq;
}
if (i >= sequence.length())
{
- length = i - sequence.length() + 1;
tmp = new StringBuffer(sequence);
}
else
insertCharAt(i, 1, c);
}
- /**
- * DOCUMENT ME!
- *
- * @param c DOCUMENT ME!
- */
- public void setColor(Color c)
- {
- this.color = c;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Color getColor()
- {
- return color;
- }
-
public String getVamsasId()
{
return vamsasId;
if (dbrefs == null)
dbrefs = new DBRefEntry[0];
- DBRefEntry[] temp = new DBRefEntry[dbrefs.length + 1];
- System.arraycopy(dbrefs, 0, temp, 0, dbrefs.length);
+ int i, iSize = dbrefs.length;
+
+ for(i=0; i<iSize; i++)
+ if(dbrefs[i].getAccessionId().equals(entry.getAccessionId())
+ && dbrefs[i].getSource().equals(entry.getSource())
+ && dbrefs[i].getVersion().equals(entry.getVersion()))
+ {
+ return;
+ }
+ DBRefEntry[] temp = new DBRefEntry[iSize + 1];
+ System.arraycopy(dbrefs, 0, temp, 0, iSize);
temp[temp.length - 1] = entry;
dbrefs = temp;