There will be better ways of doing this in the future, for now we'll use
the tried and tested MCview pdb mapping
*/
- synchronized public MCview.PDBfile setMapping(SequenceI[] sequence,
- String pdbFile,
- String protocol)
+ synchronized public MCview.PDBfile setMapping(
+ SequenceI[] sequence,
+ String[] targetChains,
+ String pdbFile,
+ String protocol)
{
MCview.PDBfile pdb = null;
try
return null;
}
+ String targetChain;
for (int s = 0; s < sequence.length; s++)
{
- String targetChain = "";
-
- if (sequence[s].getName().indexOf("|") > -1)
+ if(targetChains!=null && targetChains[s]!=null)
+ targetChain = targetChains[s];
+ else if (sequence[s].getName().indexOf("|") > -1)
{
targetChain = sequence[s].getName().substring(
sequence[s].getName().lastIndexOf("|") + 1);
}
+ else
+ targetChain = "";
+
int max = -10;
AlignSeq maxAlignseq = null;