public AppletPDBCanvas(PDBEntry pdbentry,
SequenceI[] seq,
+ String [] chains,
AlignmentPanel ap,
String protocol)
ssm = StructureSelectionManager.getStructureSelectionManager();
try{
- pdb = ssm.setMapping(seq, pdbentry.getFile(), protocol);
- //if (fr!=null)
- // fr.featuresAdded();
+ pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
+
+ 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;
int pdbend = 0;
int seqstart = 0;
int seqend = 0;
- AlignSeq maxAlignseq = null;
//JUST DEAL WITH ONE SEQUENCE FOR NOW
SequenceI sequence = seq[0];
pdbend = as.seq2end;
seqstart = as.seq1start + sequence.getStart() - 1;
seqend = as.seq1end + sequence.getEnd() - 1;
- maxAlignseq = as;
- }
+ }
mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend);
mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend);
}
}
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 = new SequenceRenderer(ap.av);
+
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;
}
///StructureListener
public String getPdbFile()
{
- return "???";
+ return pdbentry.getFile();
}
public void updateColours(Object source)
{
- AlignmentPanel ap = (AlignmentPanel) source;
- colourBySequence(ap.getSequenceRenderer(),
- ap.av.getShowSequenceFeatures() ?
- ap.getFeatureRenderer() : null);
+ colourBySequence();
redrawneeded = true;
repaint();
}