import jalview.appletgui.SequenceRenderer;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
import jalview.io.StructureFile;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.structure.AtomSpec;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
StructureSelectionManager ssm;
public AppletPDBCanvas(PDBEntry pdbentry, SequenceI[] seq,
- String[] chains, AlignmentPanel ap, String protocol)
+ String[] chains, AlignmentPanel ap, DataSourceType protocol)
{
this.ap = ap;
{
pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
- if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+ if (protocol == DataSourceType.PASTE)
{
pdbentry.setFile("INLINE" + pdb.getId());
}
showFeatures = true;
}
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
+
PDBChain chain;
if (bysequence && pdb != null)
{
tmp.startCol = sr.getResidueBoxColour(sequence[s], pos);
if (showFeatures)
{
- tmp.startCol = fr.findFeatureColour(tmp.startCol,
+ tmp.startCol = finder.findFeatureColour(tmp.startCol,
sequence[s], pos);
}
}
tmp.endCol = sr.getResidueBoxColour(sequence[s], pos);
if (showFeatures)
{
- tmp.endCol = fr.findFeatureColour(tmp.endCol,
+ tmp.endCol = finder.findFeatureColour(tmp.endCol,
sequence[s], pos);
}
}
-
}
}
}