try{
pdb = ssm.setMapping(seq, pdbentry.getFile(), protocol);
- //if (fr!=null)
- // fr.featuresAdded();
+
+ if(protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+ pdbentry.setFile("INLINE"+pdb.id);
+
}catch(Exception ex)
{
ex.printStackTrace();
ssm.addStructureViewerListener(this);
- colourBySequence(ap.getSequenceRenderer(),
- ap.av.getShowSequenceFeatures() ?
- ap.getFeatureRenderer() : null);
+ colourBySequence();
int max = -10;
int maxchain = -1;
}
}
seqColoursReady = true;
- colourBySequence(ap.getSequenceRenderer(),
- ap.av.getShowSequenceFeatures() ?
- ap.getFeatureRenderer() : null);
+ colourBySequence();
redrawneeded = true;
repaint();
}
// This method has been taken out of PDBChain to allow
// Applet and Application specific sequence renderers to be used
- void colourBySequence(SequenceRenderer sr, FeatureRenderer fr)
+ void colourBySequence()
{
+ SequenceRenderer sr = ap.getSequenceRenderer();
+
StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
boolean showFeatures = false;
- if (fr!=null)
+ if (ap.av.getShowSequenceFeatures())
{
if (fr == null)
{
fr = new jalview.appletgui.FeatureRenderer(ap.av);
}
- fr.transferSettings(fr);
+
+ fr.transferSettings(ap.getFeatureRenderer());
+
showFeatures = true;
}
repaint();
}
+
+ public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
+ {
+ return Color.white;
+ // if (!pdbfile.equals(pdbentry.getFile()))
+ // return null;
+
+ //return new Color(viewer.getAtomArgb(atomIndex));
+ }
+
public void updateColours(Object source)
{
AlignmentPanel ap = (AlignmentPanel) source;
- colourBySequence(ap.getSequenceRenderer(),
- ap.av.getShowSequenceFeatures() ?
- ap.getFeatureRenderer() : null);
+ colourBySequence();
redrawneeded = true;
repaint();
}