// the start and end points.
// Align the sequence to the pdb
AlignSeq as = new AlignSeq(sequence,
- ((PDBChain) pdb.chains.elementAt(i)).sequence, "pep");
+ ((PDBChain) pdb.chains.elementAt(i)).sequence, AlignSeq.PEP);
as.calcScoreMatrix();
as.traceAlignment();
PrintStream ps = new PrintStream(System.out)
mainchain.seqend = seqend;
mainchain.isVisible = true;
mainchain.makeExactMapping(maxAlignseq, sequence);
-
+ mainchain.transferRESNUMFeatures(sequence, null);
+ seqcanvas.getFeatureRenderer().featuresAdded();
this.pdb = pdb;
this.prefsize = new Dimension(getWidth(), getHeight());
int findTrueIndex(int pos)
{
// returns the alignment position for a residue
- int j = sequence.getStart();
+ int j = sequence.getStart(); // first position in PDB atom coordinate sequence
int i = 0;
- while ( (i < sequence.getLength()) && (j <= sequence.getEnd()) && (j <= pos+1))
+ while ( (i < sequence.getLength()) && (j <= pos+1))
{
if (!jalview.util.Comparison.isGap(sequence.getCharAt(i)))
{
if(i>1)
i--;
- if ( (j == sequence.getEnd()) && (j < pos))
+ if (j < pos)
{
return sequence.getEnd() + 1;
}
if(chain!=mainchain)
continue;
- if ( (tmp.at1.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&
- (tmp.at1.resNumber <= ( (chain.offset + chain.pdbend) - 1)))
+ //if ( (tmp.at1.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&
+ // (tmp.at1.resNumber <= ( (chain.offset + chain.pdbend) - 1)))
{
int index = findTrueIndex(tmp.at1.alignmentMapping);
//sequence.findIndex(tmp.at1.alignmentMapping);
}
}
- if ( (tmp.at2.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&
- (tmp.at2.resNumber <= ( (chain.pdbend + chain.offset) - 1)))
+ //if ( (tmp.at2.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&
+ // (tmp.at2.resNumber <= ( (chain.pdbend + chain.offset) - 1)))
{
int index = findTrueIndex(tmp.at2.alignmentMapping);