{
this.seqcanvas = seqcanvas;
this.sequence = seq;
- seqcanvas.setPDBCanvas(this);
}
public void setPDBFile(PDBfile pdb)
mainchain.seqend = seqend;
mainchain.isVisible = true;
mainchain.makeExactMapping(maxAlignseq, sequence);
- mainchain.transferRESNUMFeatures(sequence.getDatasetSequence(), null);
+ mainchain.transferRESNUMFeatures(sequence, null);
seqcanvas.getFeatureRenderer().featuresAdded();
this.pdb = pdb;
this.prefsize = new Dimension(getWidth(), getHeight());
{
// System.out.println("colour by seq");
boolean showFeatures = false;
- if (seqcanvas.getViewport().getShowSequenceFeatures())
+
+ //NO LONGER USED SINCE APPJMOL
+// if (seqcanvas.getViewport().getShowSequenceFeatures())
{
showFeatures = true;
if (fr == null)
{
- fr = new jalview.gui.FeatureRenderer(seqcanvas.getViewport());
+ //NO LONGER USED SINCE APPJMOL
+// fr = new jalview.gui.FeatureRenderer(seqcanvas.getViewport());
}
fr.transferSettings(seqcanvas.getFeatureRenderer());
{
int index = findTrueIndex(tmp.at1.alignmentMapping);
//sequence.findIndex(tmp.at1.alignmentMapping);
- if (index > 0)
+ if (index != -1)
{
tmp.startCol = seqcanvas.getSequenceRenderer().
getResidueBoxColour(sequence, index);
int index = findTrueIndex(tmp.at2.alignmentMapping);
//sequence.findIndex( tmp.at2.alignmentMapping );
- if (index > 0)
+ if (index != -1)
{
tmp.endCol = seqcanvas.getSequenceRenderer().
getResidueBoxColour(sequence, index);