import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
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;
* @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)
{
return setMapping(true, sequence, targetChains, pdbFile, protocol);
}
-
/**
* create sequence structure mappings between each sequence and the given
* pdbFile (retrieved via the given protocol).
* (may be nill, individual elements may be nill)
* @param pdbFile
* - structure data resource
- * @param protocol
+ * @param sourceType
* - how to resolve data from resource
* @return null or the structure data parsed as a pdb file
*/
synchronized public StructureFile setMapping(boolean forStructureView,
SequenceI[] sequenceArray, String[] targetChainIds,
- String pdbFile,
- String protocol)
+ String pdbFile, DataSourceType sourceType)
{
/*
* There will be better ways of doing this in the future, for now we'll use
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);
- }
+ sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
+ pdb = new JmolParser(pdbFile, sourceType);
if (pdb.getId() != null && pdb.getId().trim().length() > 0
- && AppletFormatAdapter.FILE.equals(protocol))
+ && DataSourceType.FILE == sourceType)
{
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;
* Attempt pairwise alignment of the sequence with each chain in the PDB,
* and remember the highest scoring chain
*/
- int max = -10;
+ float max = -10;
AlignSeq maxAlignseq = null;
String maxChainId = " ";
PDBChain maxChain = null;
continue;
}
- if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+ if (sourceType == DataSourceType.PASTE)
{
pdbFile = "INLINE" + pdb.getId();
}
- ArrayList<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
- if (isMapUsingSIFTs)
+ List<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
+ if (isMapUsingSIFTs && seq.isProtein())
{
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;
+ StructureMapping siftsMapping;
try
{
- mapping = getStructureMapping(seq, pdbFile, targetChainId, pdb,
- maxChain, sqmpping, maxAlignseq);
- seqToStrucMapping.add(mapping);
+ 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)
{
- // e.printStackTrace();
// fall back to NW alignment
System.err.println(e.getMessage());
- seqToStrucMapping.add(getNWMappings(seq, pdbFile,
- targetChainId,
- maxChain, pdb, maxAlignseq));
+ 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));
}
}
else
{
- try
+ List<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
+ for (PDBChain chain : pdb.getChains())
{
- ArrayList<StructureMapping> tempMapping = new ArrayList<StructureMapping>();
- for (PDBChain chain : pdb.getChains())
+ try
{
- StructureMapping mapping = getStructureMapping(seq, pdbFile,
- chain.id, pdb, chain, sqmpping, maxAlignseq);
- tempMapping.add(mapping);
+ StructureMapping siftsMapping = getStructureMapping(seq,
+ pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq);
+ foundSiftsMappings.add(siftsMapping);
+ } catch (SiftsException e)
+ {
+ System.err.println(e.getMessage());
}
- seqToStrucMapping.addAll(tempMapping);
- } catch (SiftsException e)
+ }
+ if (!foundSiftsMappings.isEmpty())
{
- // e.printStackTrace();
- // fall back to NW alignment
- System.err.println(e.getMessage());
- seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId,
- maxChain, pdb, maxAlignseq));
+ 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
{
setProgressBar(null);
- setProgressBar("Obtaining mapping with NW alignment");
- seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId,
- maxChain, pdb, maxAlignseq));
+ setProgressBar(MessageManager
+ .getString("status.obtaining_mapping_with_nw_alignment"));
+ StructureMapping nwMapping = getNWMappings(seq, pdbFile,
+ maxChainId, maxChain, pdb, maxAlignseq);
+ seqToStrucMapping.add(nwMapping);
+ ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+
}
if (forStructureView)
return pdb;
}
- private boolean isCIFFile(String filename)
+ public void addStructureMapping(StructureMapping sm)
{
- String fileExt = filename.substring(filename.lastIndexOf(".") + 1,
- filename.length());
- return "cif".equalsIgnoreCase(fileExt);
+ mappings.add(sm);
}
+ /**
+ * 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
{
- 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);
}
- } 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)
{
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);
public synchronized void sendSelection(
jalview.datamodel.SequenceGroup selection,
- jalview.datamodel.ColumnSelection colsel, SelectionSource source)
+ jalview.datamodel.ColumnSelection colsel, HiddenColumns hidden,
+ SelectionSource source)
{
for (SelectionListener slis : sel_listeners)
{
if (slis != source)
{
- slis.selection(selection, colsel, source);
+ slis.selection(selection, colsel, hidden, source);
}
}
}
git://source.jalview.org / jalview.git / blobdiff