import jalview.datamodel.Annotation;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JmolParser;
import jalview.gui.IProgressIndicator;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
+import jalview.ws.phyre2.Phyre2Client;
import jalview.ws.sifts.SiftsClient;
import jalview.ws.sifts.SiftsException;
import jalview.ws.sifts.SiftsSettings;
private boolean addTempFacAnnot = false;
+ private IProgressIndicator progressIndicator;
+
private SiftsClient siftsClient = null;
+ private long progressSessionId;
+
+ private boolean mappingForPhyre2Model;
+
/*
* Set of any registered mappings between (dataset) sequences.
*/
* @return null or the structure data parsed as a pdb file
*/
synchronized public StructureFile setMapping(SequenceI[] sequence,
- String[] targetChains, String pdbFile, String protocol,
+ String[] targetChains, String pdbFile, DataSourceType protocol,
IProgressIndicator progress)
{
return computeMapping(true, sequence, targetChains, pdbFile, protocol,
*/
synchronized public StructureFile setMapping(boolean forStructureView,
SequenceI[] sequenceArray, String[] targetChainIds,
- String pdbFile,
- String protocol)
+ String pdbFile, DataSourceType protocol)
{
return computeMapping(forStructureView, sequenceArray, targetChainIds,
pdbFile, protocol, null);
synchronized public StructureFile computeMapping(
boolean forStructureView, SequenceI[] sequenceArray,
- String[] targetChainIds, String pdbFile, String protocol,
+ String[] targetChainIds, String pdbFile, DataSourceType protocol,
IProgressIndicator progress)
{
long progressSessionId = System.currentTimeMillis() * 3;
boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
try
{
-
- 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);
- }
+ pdb = new JmolParser(pdbFile, protocol);
if (pdb.getId() != null && pdb.getId().trim().length() > 0
- && AppletFormatAdapter.FILE.equals(protocol))
+ && DataSourceType.FILE == protocol)
{
registerPDBFile(pdb.getId().trim(), pdbFile);
}
+ // if PDBId is unavailable then skip SIFTS mapping execution path
+ isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable();
+
} catch (Exception ex)
{
ex.printStackTrace();
{
boolean infChain = true;
final SequenceI seq = sequenceArray[s];
+ SequenceI ds = seq;
+ while (ds.getDatasetSequence() != null)
+ {
+ ds = ds.getDatasetSequence();
+ }
+
if (targetChainIds != null && targetChainIds[s] != null)
{
infChain = false;
continue;
}
- if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+ if (protocol.equals(DataSourceType.PASTE))
{
pdbFile = "INLINE" + pdb.getId();
}
- ArrayList<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
- if (isMapUsingSIFTs)
+
+ List<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
+ if (!isMappingForPhyre2Model() && isMapUsingSIFTs && seq.isProtein())
{
if (progress!=null) {
progress.setProgressBar(MessageManager
pdb, maxChain, sqmpping, maxAlignseq);
seqToStrucMapping.add(siftsMapping);
maxChain.makeExactMapping(maxAlignseq, seq);
- maxChain.transferRESNUMFeatures(seq, null);
+ maxChain.transferRESNUMFeatures(seq, null);// FIXME: is this
+ // "IEA:SIFTS" ?
maxChain.transferResidueAnnotation(siftsMapping, sqmpping);
+ ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+
} catch (SiftsException e)
{
// fall back to NW alignment
StructureMapping nwMapping = getNWMappings(seq, pdbFile,
targetChainId, maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
+ maxChain.makeExactMapping(maxAlignseq, seq);
+ maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this
+ // "IEA:Jalview" ?
+ maxChain.transferResidueAnnotation(nwMapping, sqmpping);
+ ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+ } catch (Exception e)
+ {
+ e.printStackTrace();
}
}
else
{
- ArrayList<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
+ List<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
for (PDBChain chain : pdb.getChains())
{
try
{
StructureMapping siftsMapping = getStructureMapping(seq,
- pdbFile,
- chain.id, pdb, chain, sqmpping, maxAlignseq);
+ pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq);
foundSiftsMappings.add(siftsMapping);
} catch (SiftsException e)
{
System.err.println(e.getMessage());
+ } catch (Exception e)
+ {
+ e.printStackTrace();
}
}
if (!foundSiftsMappings.isEmpty())
{
seqToStrucMapping.addAll(foundSiftsMappings);
maxChain.makeExactMapping(maxAlignseq, seq);
- maxChain.transferRESNUMFeatures(seq, null);
+ maxChain.transferRESNUMFeatures(seq, null);// FIXME: is this
+ // "IEA:SIFTS" ?
maxChain.transferResidueAnnotation(foundSiftsMappings.get(0),
sqmpping);
+ ds.addPDBId(sqmpping.getTo().getAllPDBEntries().get(0));
}
else
{
StructureMapping nwMapping = getNWMappings(seq, pdbFile,
maxChainId, maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
+ maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this
+ // "IEA:Jalview" ?
+ maxChain.transferResidueAnnotation(nwMapping, sqmpping);
+ ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
}
}
}
+ else if (isMappingForPhyre2Model())
+ {
+ setProgressBar(null);
+ setProgressBar(MessageManager
+ .getString("status.obtaining_mapping_with_phyre2_template_alignment"));
+ StructureMapping phyre2ModelMapping = new Phyre2Client(pdb)
+ .getStructureMapping(seq, pdbFile, " ");
+
+ seqToStrucMapping.add(phyre2ModelMapping);
+ ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+ }
else
{
if (progress != null)
{
progress.setProgressBar(MessageManager
- .getString("status.obtaining_mapping_with_nw_alignment"),
+ .getString("status.obtaining_mapping_with_nw_alignment"),
progressSessionId);
}
- seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId,
- maxChain, pdb, maxAlignseq));
+ StructureMapping nwMapping = getNWMappings(seq, pdbFile,
+ maxChainId, maxChain, pdb, maxAlignseq);
+ seqToStrucMapping.add(nwMapping);
+ ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+
}
+
if (forStructureView)
{
mappings.addAll(seqToStrucMapping);
}
- if (progress != null)
- {
- progress.setProgressBar(null, progressSessionId);
- }
}
return pdb;
}
return "cif".equalsIgnoreCase(fileExt);
}
+ /**
+ * retrieve a mapping for seq from SIFTs using associated DBRefEntry for
+ * uniprot or PDB
+ *
+ * @param seq
+ * @param pdbFile
+ * @param targetChainId
+ * @param pdb
+ * @param maxChain
+ * @param sqmpping
+ * @param maxAlignseq
+ * @return
+ * @throws SiftsException
+ */
private StructureMapping getStructureMapping(SequenceI seq,
String pdbFile, String targetChainId, StructureFile pdb,
PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
- AlignSeq maxAlignseq) throws SiftsException
+ AlignSeq maxAlignseq) throws Exception
{
- StructureMapping curChainMapping = siftsClient
- .getSiftsStructureMapping(seq, pdbFile, targetChainId);
- try
- {
+ StructureMapping curChainMapping = siftsClient
+ .getStructureMapping(seq, pdbFile, targetChainId);
+ try
+ {
PDBChain chain = pdb.findChain(targetChainId);
if (chain != null)
{
chain.transferResidueAnnotation(curChainMapping, sqmpping);
}
- } catch (Exception e)
- {
- e.printStackTrace();
- }
- return curChainMapping;
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ return curChainMapping;
}
- private StructureMapping getNWMappings(SequenceI seq,
- String pdbFile,
+ private StructureMapping getNWMappings(SequenceI seq, String pdbFile,
String maxChainId, PDBChain maxChain, StructureFile pdb,
AlignSeq maxAlignseq)
{
return;
}
- SearchResults results = new SearchResults();
+ SearchResultsI results = new SearchResults();
for (AtomSpec atom : atoms)
{
SequenceI lastseq = null;
{
boolean hasSequenceListeners = handlingVamsasMo
|| !seqmappings.isEmpty();
- SearchResults results = null;
+ SearchResultsI results = null;
if (seqPos == -1)
{
seqPos = seq.findPosition(indexpos);
return null;
}
+ public IProgressIndicator getProgressIndicator()
+ {
+ return progressIndicator;
+ }
+
+ public void setProgressIndicator(IProgressIndicator progressIndicator)
+ {
+ this.progressIndicator = progressIndicator;
+ }
+
+ public long getProgressSessionId()
+ {
+ return progressSessionId;
+ }
+
+ public void setProgressSessionId(long progressSessionId)
+ {
+ this.progressSessionId = progressSessionId;
+ }
+
+ public void setProgressBar(String message)
+ {
+ if (progressIndicator == null)
+ {
+ return;
+ }
+ progressIndicator.setProgressBar(message, progressSessionId);
+ }
+
public List<AlignedCodonFrame> getSequenceMappings()
{
return seqmappings;
}
+ public boolean isMappingForPhyre2Model()
+ {
+ return mappingForPhyre2Model;
+ }
+
+ public void setMappingForPhyre2Model(boolean mappingForPhyre2Model)
+ {
+ this.mappingForPhyre2Model = mappingForPhyre2Model;
+ }
+
+ public static StructureSelectionManager getStructureSelectionManager()
+ {
+ return instances.values().iterator().next();
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff