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;
import java.util.Collections;
import java.util.Enumeration;
import java.util.HashMap;
+import java.util.Hashtable;
import java.util.IdentityHashMap;
import java.util.List;
import java.util.Map;
private long progressSessionId;
+
/*
* Set of any registered mappings between (dataset) sequences.
*/
private List<SelectionListener> sel_listeners = new ArrayList<SelectionListener>();
+ private Map<String, String> phyre2ModelTemplates = new Hashtable<String, String>();
+
/**
* @return true if will try to use external services for processing secondary
* structure
* - how to resolve data from resource
* @return null or the structure data parsed as a pdb file
*/
- synchronized public PDBfile setMapping(SequenceI[] sequence,
- String[] targetChains, String pdbFile, String protocol)
+ synchronized public StructureFile setMapping(SequenceI[] sequence,
+ String[] targetChains, String pdbFile, DataSourceType protocol,
+ IProgressIndicator progress)
{
- return setMapping(true, sequence, targetChains, pdbFile, protocol);
+ return computeMapping(true, sequence, targetChains, pdbFile, protocol,
+ progress);
}
+
/**
* create sequence structure mappings between each sequence and the given
* pdbFile (retrieved via the given protocol).
* - one or more sequences to be mapped to pdbFile
* @param targetChainIds
* - optional chain specification for mapping each sequence to pdb
- * (may be nill, individual elements may be nill)
+ * (may be null, individual elements may be null)
* @param pdbFile
* - structure data resource
* @param 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)
+ String pdbFile, DataSourceType protocol)
+ {
+ return computeMapping(forStructureView, sequenceArray, targetChainIds,
+ pdbFile, protocol, null);
+ }
+
+ synchronized public StructureFile computeMapping(
+ boolean forStructureView, SequenceI[] sequenceArray,
+ String[] targetChainIds, String pdbFile, DataSourceType protocol,
+ IProgressIndicator progress)
{
+ long progressSessionId = System.currentTimeMillis() * 3;
/*
* There will be better ways of doing this in the future, for now we'll use
* the tried and tested MCview pdb mapping
}
}
}
- PDBfile pdb = null;
+ StructureFile pdb = null;
boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
try
{
- 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)
+ boolean phyre2Template = isPhyre2Template(pdbFile);
+ List<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
+ if (!phyre2Template && isMapUsingSIFTs && seq.isProtein())
{
- setProgressBar(null);
- setProgressBar("Obtaining mapping with SIFTS");
+ if (progress!=null) {
+ progress.setProgressBar(MessageManager
+ .getString("status.obtaining_mapping_with_sifts"),
+ progressSessionId);
+ }
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);// FIXME: is this
+ // "IEA:SIFTS" ?
+ maxChain.transferResidueAnnotation(siftsMapping, sqmpping);
+ ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+
+ } 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);
+ 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
{
+ List<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());
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+ if (!foundSiftsMappings.isEmpty())
+ {
+ seqToStrucMapping.addAll(foundSiftsMappings);
+ maxChain.makeExactMapping(maxAlignseq, seq);
+ 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
+ else if (phyre2Template)
{
setProgressBar(null);
- setProgressBar("Obtaining mapping with NW alignment");
- seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId,
- maxChain, pdb, maxAlignseq));
+ setProgressBar(MessageManager
+ .getString("status.obtaining_mapping_with_phyre2_template_alignment"));
+ String fastaFile = getPhyre2FastaFileFor(pdbFile);
+ StructureMapping phyre2ModelMapping = new Phyre2Client(pdb)
+ .getStructureMapping(seq, pdbFile, fastaFile, " ");
+ seqToStrucMapping.add(phyre2ModelMapping);
+ maxChain.makeExactMapping(maxAlignseq, seq);
+ maxChain.transferRESNUMFeatures(seq, null);
+ jalview.datamodel.Mapping sqmpping = maxAlignseq
+ .getMappingFromS1(false);
+ maxChain.transferResidueAnnotation(phyre2ModelMapping, sqmpping);
+ ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+ }
+ else
+ {
+ if (progress != null)
+ {
+ progress.setProgressBar(MessageManager
+ .getString("status.obtaining_mapping_with_nw_alignment"),
+ progressSessionId);
+ }
+ StructureMapping nwMapping = getNWMappings(seq, pdbFile,
+ maxChainId, maxChain, pdb, maxAlignseq);
+ seqToStrucMapping.add(nwMapping);
+ ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+
}
if (forStructureView)
return pdb;
}
+ public void registerPhyre2Template(String phyre2Template,
+ String fastaMappingFile)
+ {
+ phyre2ModelTemplates.put(phyre2Template, fastaMappingFile);
+ }
+
+ /**
+ * 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, PDBfile pdb,
+ String pdbFile, String targetChainId, StructureFile pdb,
PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
- AlignSeq maxAlignseq)
+ AlignSeq maxAlignseq) throws Exception
{
- String maxChainId = targetChainId;
+ StructureMapping curChainMapping = siftsClient
+ .getStructureMapping(seq, pdbFile, targetChainId);
try
{
- StructureMapping curChainMapping = siftsClient
- .getSiftsStructureMapping(seq, pdbFile, targetChainId);
- try
- {
PDBChain chain = pdb.findChain(targetChainId);
if (chain != null)
{
chain.transferResidueAnnotation(curChainMapping, sqmpping);
}
- } catch (Exception e)
- {
- e.printStackTrace();
- }
- return curChainMapping;
- } catch (SiftsException e)
+ } catch (Exception 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);
+ e.printStackTrace();
}
+ return curChainMapping;
}
- private StructureMapping getNWMappings(SequenceI seq,
- String pdbFile,
- String maxChainId, PDBChain maxChain, PDBfile pdb,
+ private StructureMapping getNWMappings(SequenceI seq, String pdbFile,
+ String maxChainId, PDBChain maxChain, StructureFile pdb,
AlignSeq maxAlignseq)
{
final StringBuilder mappingDetails = new StringBuilder(128);
if (listeners.elementAt(i) instanceof StructureListener)
{
sl = (StructureListener) listeners.elementAt(i);
- for (String pdbfile : sl.getPdbFile())
+ for (String pdbfile : sl.getStructureFiles())
{
pdbs.remove(pdbfile);
}
return;
}
- SearchResults results = new SearchResults();
+ SearchResultsI results = findAlignmentPositionsForStructurePositions(atoms);
+ for (Object li : listeners)
+ {
+ if (li instanceof SequenceListener)
+ {
+ ((SequenceListener) li).highlightSequence(results);
+ }
+ }
+ }
+
+ /**
+ * Constructs a SearchResults object holding regions (if any) in the Jalview
+ * alignment which have a mapping to the structure viewer positions in the
+ * supplied list
+ *
+ * @param atoms
+ * @return
+ */
+ public SearchResultsI findAlignmentPositionsForStructurePositions(
+ List<AtomSpec> atoms)
+ {
+ SearchResultsI results = new SearchResults();
for (AtomSpec atom : atoms)
{
SequenceI lastseq = null;
}
}
}
- for (Object li : listeners)
- {
- if (li instanceof SequenceListener)
- {
- ((SequenceListener) li).highlightSequence(results);
- }
- }
+ return results;
}
/**
{
boolean hasSequenceListeners = handlingVamsasMo
|| !seqmappings.isEmpty();
- SearchResults results = null;
+ SearchResultsI results = null;
if (seqPos == -1)
{
seqPos = seq.findPosition(indexpos);
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);
}
return seqmappings;
}
+ public boolean isPhyre2Template(String structureFile)
+ {
+ if (structureFile == null || phyre2ModelTemplates == null
+ || phyre2ModelTemplates.isEmpty())
+ {
+ return false;
+ }
+ return phyre2ModelTemplates.get(structureFile) != null
+ && !phyre2ModelTemplates.get(structureFile).isEmpty();
+ }
+
+ public String getPhyre2FastaFileFor(String structureFile)
+ {
+ return phyre2ModelTemplates.get(structureFile);
+ }
+
+
+ public static StructureSelectionManager getStructureSelectionManager()
+ {
+ return instances.values().iterator().next();
+ }
+
+ public void addStructureMapping(StructureMapping smapping)
+ {
+ mappings.add(smapping);
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff