return setMapping(true, sequence, targetChains, pdbFile, protocol);
}
return setMapping(true, sequence, targetChains, pdbFile, protocol);
}
/**
* create sequence structure mappings between each sequence and the given
* pdbFile (retrieved via the given protocol).
/**
* create sequence structure mappings between each sequence and the given
* pdbFile (retrieved via the given protocol).
*/
synchronized public StructureFile setMapping(boolean forStructureView,
SequenceI[] sequenceArray, String[] targetChainIds,
*/
synchronized public StructureFile setMapping(boolean forStructureView,
SequenceI[] sequenceArray, String[] targetChainIds,
- pdbFile,
- chain.id, pdb, chain, sqmpping, maxAlignseq);
+ pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq);
PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
AlignSeq maxAlignseq) throws SiftsException
{
PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
AlignSeq maxAlignseq) throws SiftsException
{
- StructureMapping curChainMapping = siftsClient
- .getSiftsStructureMapping(seq, pdbFile, targetChainId);
- try
- {
+ StructureMapping curChainMapping = siftsClient
+ .getSiftsStructureMapping(seq, pdbFile, targetChainId);
+ try
+ {
PDBChain chain = pdb.findChain(targetChainId);
if (chain != null)
{
chain.transferResidueAnnotation(curChainMapping, sqmpping);
}
PDBChain chain = pdb.findChain(targetChainId);
if (chain != null)
{
chain.transferResidueAnnotation(curChainMapping, sqmpping);
}
String maxChainId, PDBChain maxChain, StructureFile pdb,
AlignSeq maxAlignseq)
{
String maxChainId, PDBChain maxChain, StructureFile pdb,
AlignSeq maxAlignseq)
{