@Override
public void setConservation(Conservation cons)
{
+ alignment.setConservation(cons);
hconservation = cons;
}
@Override
public void setSequenceConsensusHash(ProfilesI hconsensus)
{
+ alignment.setSequenceConsensusHash(hconsensus);
this.hconsensus = hconsensus;
}
public void setComplementConsensusHash(
Hashtable<String, Object>[] hconsensus)
{
+ alignment.setComplementConsensusHash(hconsensus);
this.hcomplementConsensus = hconsensus;
}
public void setRnaStructureConsensusHash(
Hashtable<String, Object>[] hStrucConsensus)
{
+ alignment.setRnaStructureConsensusHash(hStrucConsensus);
this.hStrucConsensus = hStrucConsensus;
}
ranges = null;
currentTree = null;
selectionGroup = null;
+ colSel = null;
setAlignment(null);
}
codingComplement.setUpdateStructures(needToUpdateStructureViews);
}
}
+
+ @Override
+ public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
+ {
+ int start = 0;
+ int end = 0;
+ if (selectedRegionOnly && selectionGroup != null)
+ {
+ start = selectionGroup.getStartRes();
+ end = selectionGroup.getEndRes() + 1;
+ }
+ else
+ {
+ end = alignment.getWidth();
+ }
+ return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
+ false));
+ }
}