import jalview.datamodel.SequenceI;
import jalview.gui.IProgressIndicator;
import jalview.io.AppletFormatAdapter;
+import jalview.io.StructureFile;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
import jalview.ws.sifts.SiftsClient;
* - how to resolve data from resource
* @return null or the structure data parsed as a pdb file
*/
- synchronized public PDBfile setMapping(SequenceI[] sequence,
+ synchronized public StructureFile setMapping(SequenceI[] sequence,
String[] targetChains, String pdbFile, String protocol)
{
return setMapping(true, sequence, targetChains, pdbFile, protocol);
}
+
/**
* create sequence structure mappings between each sequence and the given
* pdbFile (retrieved via the given protocol).
* - how to resolve data from resource
* @return null or the structure data parsed as a pdb file
*/
- synchronized public PDBfile setMapping(boolean forStructureView,
+ synchronized public StructureFile setMapping(boolean forStructureView,
SequenceI[] sequenceArray, String[] targetChainIds,
String pdbFile,
String protocol)
}
}
}
- PDBfile pdb = null;
+ StructureFile pdb = null;
boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
try
{
- pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
- pdbFile, protocol);
+
+ if (pdbFile != null && isCIFFile(pdbFile))
+ {
+ pdb = new jalview.ext.jmol.JmolParser(addTempFacAnnot, parseSecStr,
+ secStructServices, pdbFile, protocol);
+ }
+ else
+ {
+ pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
+ pdbFile, protocol);
+ }
if (pdb.getId() != null && pdb.getId().trim().length() > 0
&& AppletFormatAdapter.FILE.equals(protocol))
if (isMapUsingSIFTs)
{
setProgressBar(null);
- setProgressBar("Obtaining mapping with SIFTS");
+ setProgressBar(MessageManager
+ .getString("status.obtaining_mapping_with_sifts"));
jalview.datamodel.Mapping sqmpping = maxAlignseq
.getMappingFromS1(false);
if (targetChainId != null && !targetChainId.trim().isEmpty())
{
- StructureMapping mapping = getStructureMapping(seq, pdbFile,
- targetChainId, pdb, maxChain, sqmpping, maxAlignseq);
- seqToStrucMapping.add(mapping);
+ StructureMapping siftsMapping;
+ try
+ {
+ siftsMapping = getStructureMapping(seq, pdbFile, targetChainId,
+ pdb, maxChain, sqmpping, maxAlignseq);
+ seqToStrucMapping.add(siftsMapping);
+ maxChain.makeExactMapping(maxAlignseq, seq);
+ maxChain.transferRESNUMFeatures(seq, null);
+ maxChain.transferResidueAnnotation(siftsMapping, sqmpping);
+ } catch (SiftsException e)
+ {
+ // fall back to NW alignment
+ System.err.println(e.getMessage());
+ StructureMapping nwMapping = getNWMappings(seq, pdbFile,
+ targetChainId, maxChain, pdb, maxAlignseq);
+ seqToStrucMapping.add(nwMapping);
+ }
}
else
{
+ ArrayList<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
for (PDBChain chain : pdb.getChains())
{
- StructureMapping mapping = getStructureMapping(seq, pdbFile,
- chain.id, pdb, chain, sqmpping, maxAlignseq);
- seqToStrucMapping.add(mapping);
+ try
+ {
+ StructureMapping siftsMapping = getStructureMapping(seq,
+ pdbFile,
+ chain.id, pdb, chain, sqmpping, maxAlignseq);
+ foundSiftsMappings.add(siftsMapping);
+ } catch (SiftsException e)
+ {
+ System.err.println(e.getMessage());
+ }
+ }
+ if (!foundSiftsMappings.isEmpty())
+ {
+ seqToStrucMapping.addAll(foundSiftsMappings);
+ maxChain.makeExactMapping(maxAlignseq, seq);
+ maxChain.transferRESNUMFeatures(seq, null);
+ maxChain.transferResidueAnnotation(foundSiftsMappings.get(0),
+ sqmpping);
+ }
+ else
+ {
+ StructureMapping nwMapping = getNWMappings(seq, pdbFile,
+ maxChainId, maxChain, pdb, maxAlignseq);
+ seqToStrucMapping.add(nwMapping);
}
}
}
else
{
setProgressBar(null);
- setProgressBar("Obtaining mapping with NW alignment");
+ setProgressBar(MessageManager
+ .getString("status.obtaining_mapping_with_nw_alignment"));
seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId,
maxChain, pdb, maxAlignseq));
}
return pdb;
}
+ private boolean isCIFFile(String filename)
+ {
+ String fileExt = filename.substring(filename.lastIndexOf(".") + 1,
+ filename.length());
+ return "cif".equalsIgnoreCase(fileExt);
+ }
+
private StructureMapping getStructureMapping(SequenceI seq,
- String pdbFile, String targetChainId, PDBfile pdb,
+ String pdbFile, String targetChainId, StructureFile pdb,
PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
- AlignSeq maxAlignseq)
+ AlignSeq maxAlignseq) throws SiftsException
{
- String maxChainId = targetChainId;
- try
- {
StructureMapping curChainMapping = siftsClient
.getSiftsStructureMapping(seq, pdbFile, targetChainId);
try
e.printStackTrace();
}
return curChainMapping;
- } catch (SiftsException e)
- {
- System.err.println(e.getMessage());
- System.err.println(">>> Now switching mapping with NW alignment...");
- setProgressBar(null);
- setProgressBar(">>> Now switching mapping with NW alignment...");
- return getNWMappings(seq, pdbFile, maxChainId, maxChain, pdb,
- maxAlignseq);
- }
}
private StructureMapping getNWMappings(SequenceI seq,
String pdbFile,
- String maxChainId, PDBChain maxChain, PDBfile pdb,
+ String maxChainId, PDBChain maxChain, StructureFile pdb,
AlignSeq maxAlignseq)
{
final StringBuilder mappingDetails = new StringBuilder(128);
List<AtomSpec> atoms = new ArrayList<AtomSpec>();
for (StructureMapping sm : mappings)
{
- if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence())
+ if (sm.sequence == seq
+ || sm.sequence == seq.getDatasetSequence()
+ || (sm.sequence.getDatasetSequence() != null && sm.sequence
+ .getDatasetSequence() == seq.getDatasetSequence()))
{
for (int index : positions)
{
public void setProgressBar(String message)
{
+ if (progressIndicator == null)
+ {
+ return;
+ }
progressIndicator.setProgressBar(message, progressSessionId);
}