showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
-
+ centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false);
autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
padGaps = Cache.getDefault("PAD_GAPS", true);
boolean updatingConsensus = false;
boolean updatingConservation = false;
+ /**
+ * centre columnar annotation labels in displayed alignment annotation
+ * TODO: add to jalviewXML and annotation display settings
+ */
+ boolean centreColumnLabels=false;
/**
- * DOCUMENT ME!
+ * trigger update of conservation annotation
*/
public void updateConservation(final AlignmentPanel ap)
{
}
/**
- * DOCUMENT ME!
+ * trigger update of consensus annotation
*/
public void updateConsensus(final AlignmentPanel ap)
{
}
return false;
}
+
+ public boolean getCentreColumnLabels()
+ {
+ return centreColumnLabels;
+ }
+ public void setCentreColumnLabels(boolean centrecolumnlabels)
+ {
+ centreColumnLabels = centrecolumnlabels;
+ }
+ public void updateSequenceIdColours()
+ {
+ Vector groups = alignment.getGroups();
+ if (sequenceColours==null)
+ {
+ sequenceColours = new Hashtable();
+ }
+ for (int ig=0,igSize=groups.size(); ig<igSize; ig++)
+ {
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(ig);
+ if (sg.idColour!=null)
+ {
+ Vector sqs = sg.getSequences(hiddenRepSequences);
+ for (int s=0,sSize=sqs.size();s<sSize;s++)
+ {
+ sequenceColours.put(sqs.elementAt(s), sg.idColour);
+ }
+ }
+ }
+ }
}