HiddenSequences hiddenSequences = new HiddenSequences(this);
+ public Hashtable alignmentProperties;
+
private void initAlignment(SequenceI[] seqs)
{
int i = 0;
// derive new sequence
SequenceI adding = snew.deriveSequence();
getDataset().addSequence(adding.getDatasetSequence());
- snew = adding;
+ snew = adding;
}
}
if (sequences==null) {
*/
public void deleteAnnotation(AlignmentAnnotation aa)
{
+ if(aa.sequenceRef!=null)
+ aa.sequenceRef.removeAlignmentAnnotation(aa);
+
int aSize = 1;
if (annotations != null)
return cal;
}
+ public void setProperty(Object key, Object value)
+ {
+ if(alignmentProperties==null)
+ alignmentProperties = new Hashtable();
+
+ alignmentProperties.put(key,value);
+ }
+
+ public Object getProperty(Object key)
+ {
+ if(alignmentProperties!=null)
+ return alignmentProperties.get(key);
+ else
+ return null;
+ }
+
+
}