*/
package jalview.structure;
+import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.IdentityHashMap;
+import java.util.List;
+import java.util.Locale;
+import java.util.Map;
+import java.util.Vector;
+
import jalview.analysis.AlignSeq;
import jalview.api.StructureSelectionManagerProvider;
+import jalview.bin.Cache;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
import jalview.commands.OrderCommand;
import jalview.io.StructureFile;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import jalview.ws.sifts.SiftsClient;
import jalview.ws.sifts.SiftsException;
import jalview.ws.sifts.SiftsSettings;
-
-import java.io.PrintStream;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.IdentityHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Vector;
-
-import MCview.Atom;
-import MCview.PDBChain;
-import MCview.PDBfile;
+import mc_view.Atom;
+import mc_view.PDBChain;
+import mc_view.PDBfile;
public class StructureSelectionManager
{
private boolean addTempFacAnnot = false;
- private SiftsClient siftsClient = null;
-
/*
* Set of any registered mappings between (dataset) sequences.
*/
}
/**
- * Returns the file name for a mapped PDB id (or null if not mapped).
+ * Returns the filename the PDB id is already mapped to if known, or null if
+ * it is not mapped
*
* @param pdbid
* @return
{
for (StructureMapping sm : mappings)
{
- if (sm.getPdbId().equals(pdbid))
+ if (sm.getPdbId().equalsIgnoreCase(pdbid))
{
return sm.pdbfile;
}
}
/**
- * create sequence structure mappings between each sequence and the given
- * pdbFile (retrieved via the given protocol).
+ * Import a single structure file and register sequence structure mappings for
+ * broadcasting colouring, mouseovers and selection events (convenience
+ * wrapper).
*
* @param forStructureView
* when true, record the mapping for use in mouseOvers
- *
- * @param sequenceArray
+ * @param sequence
* - one or more sequences to be mapped to pdbFile
- * @param targetChainIds
+ * @param targetChains
* - optional chain specification for mapping each sequence to pdb
- * (may be nill, individual elements may be nill) - JBPNote: JAL-2693
- * - this should be List<List<String>>, empty lists indicate no
- * predefined mappings
+ * (may be nill, individual elements may be nill)
* @param pdbFile
* - structure data resource
- * @param sourceType
+ * @param protocol
* - how to resolve data from resource
* @return null or the structure data parsed as a pdb file
*/
pdbFile, sourceType, null);
}
+ /**
+ * create sequence structure mappings between each sequence and the given
+ * pdbFile (retrieved via the given protocol). Either constructs a mapping
+ * using NW alignment or derives one from any available SIFTS mapping data.
+ *
+ * @param forStructureView
+ * when true, record the mapping for use in mouseOvers
+ *
+ * @param sequenceArray
+ * - 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) - JBPNote: JAL-2693
+ * - this should be List<List<String>>, empty lists indicate no
+ * predefined mappings
+ * @param pdbFile
+ * - structure data resource
+ * @param sourceType
+ * - how to resolve data from resource
+ * @param IProgressIndicator
+ * reference to UI component that maintains a progress bar for the
+ * mapping operation
+ * @return null or the structure data parsed as a pdb file
+ */
synchronized public StructureFile computeMapping(
boolean forStructureView, SequenceI[] sequenceArray,
String[] targetChainIds, String pdbFile, DataSourceType sourceType,
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
+
+ /**
+ * do we extract and transfer annotation from 3D data ?
*/
- boolean parseSecStr = processSecondaryStructure;
- if (isPDBFileRegistered(pdbFile))
- {
- for (SequenceI sq : sequenceArray)
- {
- SequenceI ds = sq;
- while (ds.getDatasetSequence() != null)
- {
- ds = ds.getDatasetSequence();
- }
- ;
- if (ds.getAnnotation() != null)
- {
- for (AlignmentAnnotation ala : ds.getAnnotation())
- {
- // false if any annotation present from this structure
- // JBPNote this fails for jmol/chimera view because the *file* is
- // passed, not the structure data ID -
- if (PDBfile.isCalcIdForFile(ala, findIdForPDBFile(pdbFile)))
- {
- parseSecStr = false;
- }
- }
- }
- }
- }
+ // FIXME: possibly should just delete
+
+ boolean parseSecStr = processSecondaryStructure
+ ? isStructureFileProcessed(pdbFile, sequenceArray)
+ : false;
+
StructureFile pdb = null;
boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
try
{
+ // FIXME if sourceType is not null, we've lost data here
sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
- pdb = new JmolParser(pdbFile, sourceType);
-
+ pdb = new JmolParser(false, pdbFile, sourceType);
+ pdb.addSettings(parseSecStr && processSecondaryStructure,
+ parseSecStr && addTempFacAnnot,
+ parseSecStr && secStructServices);
+ pdb.doParse();
if (pdb.getId() != null && pdb.getId().trim().length() > 0
&& DataSourceType.FILE == sourceType)
{
registerPDBFile(pdb.getId().trim(), pdbFile);
}
// if PDBId is unavailable then skip SIFTS mapping execution path
- isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable();
+ // TODO: JAL-3868 need to know if structure is actually from
+ // PDB (has valid PDB ID and has provenance suggesting it
+ // actually came from PDB)
+ boolean isProtein = false;
+ for (SequenceI s:sequenceArray) {
+ if (s.isProtein()) {
+ isProtein = true;
+ break;
+ }
+ }
+ isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable() && !pdb.getId().startsWith("AF-") && isProtein;
} catch (Exception ex)
{
ex.printStackTrace();
return null;
}
-
+ /*
+ * sifts client - non null if SIFTS mappings are to be used
+ */
+ SiftsClient siftsClient = null;
try
{
if (isMapUsingSIFTs)
} catch (SiftsException e)
{
isMapUsingSIFTs = false;
- e.printStackTrace();
+ Cache.error("SIFTS mapping failed", e);
+ Cache.error("Falling back on Needleman & Wunsch alignment");
+ siftsClient = null;
}
String targetChainId;
try
{
siftsMapping = getStructureMapping(seq, pdbFile, targetChainId,
- pdb, maxChain, sqmpping, maxAlignseq);
+ pdb, maxChain, sqmpping, maxAlignseq, siftsClient);
seqToStrucMapping.add(siftsMapping);
maxChain.makeExactMapping(siftsMapping, seq);
- maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this
- // "IEA:SIFTS" ?
+ maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS",pdb.getId().toLowerCase(Locale.ROOT));
maxChain.transferResidueAnnotation(siftsMapping, null);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
} catch (SiftsException e)
{
// fall back to NW alignment
- System.err.println(e.getMessage());
+ Cache.error(e.getMessage());
StructureMapping nwMapping = getNWMappings(seq, pdbFile,
targetChainId, maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
maxChain.makeExactMapping(maxAlignseq, seq);
- maxChain.transferRESNUMFeatures(seq, "IEA:Jalview"); // FIXME: is
+ maxChain.transferRESNUMFeatures(seq, "IEA:Jalview",pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is
// this
// "IEA:Jalview" ?
maxChain.transferResidueAnnotation(nwMapping, sqmpping);
try
{
siftsMapping = getStructureMapping(seq,
- pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq);
+ pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq,
+ siftsClient);
foundSiftsMappings.add(siftsMapping);
chain.makeExactMapping(siftsMapping, seq);
- chain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this
+ chain.transferRESNUMFeatures(seq, "IEA: SIFTS",pdb.getId().toLowerCase(Locale.ROOT));// FIXME: is this
// "IEA:SIFTS" ?
chain.transferResidueAnnotation(siftsMapping, null);
} catch (SiftsException e)
{
System.err.println(e.getMessage());
}
+ catch (Exception e)
+ {
+ System.err
+ .println(
+ "Unexpected exception during SIFTS mapping - falling back to NW for this sequence/structure pair");
+ System.err.println(e.getMessage());
+ }
}
if (!foundSiftsMappings.isEmpty())
{
StructureMapping nwMapping = getNWMappings(seq, pdbFile,
maxChainId, maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
- maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this
+ maxChain.transferRESNUMFeatures(seq, null,pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is this
// "IEA:Jalview" ?
maxChain.transferResidueAnnotation(nwMapping, sqmpping);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
}
if (forStructureView)
{
- mappings.addAll(seqToStrucMapping);
+ for (StructureMapping sm : seqToStrucMapping)
+ {
+ addStructureMapping(sm); // not addAll!
+ }
}
if (progress != null)
{
return pdb;
}
+ /**
+ * check if we need to extract secondary structure from given pdbFile and
+ * transfer to sequences
+ *
+ * @param pdbFile
+ * @param sequenceArray
+ * @return
+ */
+ private boolean isStructureFileProcessed(String pdbFile,
+ SequenceI[] sequenceArray)
+ {
+ boolean parseSecStr = true;
+ if (isPDBFileRegistered(pdbFile))
+ {
+ for (SequenceI sq : sequenceArray)
+ {
+ SequenceI ds = sq;
+ while (ds.getDatasetSequence() != null)
+ {
+ ds = ds.getDatasetSequence();
+ }
+ ;
+ if (ds.getAnnotation() != null)
+ {
+ for (AlignmentAnnotation ala : ds.getAnnotation())
+ {
+ // false if any annotation present from this structure
+ // JBPNote this fails for jmol/chimera view because the *file* is
+ // passed, not the structure data ID -
+ if (PDBfile.isCalcIdForFile(ala, findIdForPDBFile(pdbFile)))
+ {
+ parseSecStr = false;
+ }
+ }
+ }
+ }
+ }
+ return parseSecStr;
+ }
+
public void addStructureMapping(StructureMapping sm)
{
- mappings.add(sm);
+ if (!mappings.contains(sm))
+ {
+ mappings.add(sm);
+ }
}
/**
* @param maxChain
* @param sqmpping
* @param maxAlignseq
+ * @param siftsClient
+ * client for retrieval of SIFTS mappings for this structure
* @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, SiftsClient siftsClient) throws SiftsException
{
StructureMapping curChainMapping = siftsClient
.getSiftsStructureMapping(seq, pdbFile, targetChainId);
maxChain.makeExactMapping(maxAlignseq, seq);
jalview.datamodel.Mapping sqmpping = maxAlignseq
.getMappingFromS1(false);
- maxChain.transferRESNUMFeatures(seq, null);
+ maxChain.transferRESNUMFeatures(seq, null, pdb.getId().toLowerCase(Locale.ROOT));
HashMap<Integer, int[]> mapping = new HashMap<>();
int resNum = -10000;
* @param pdbResNum
* @param chain
* @param pdbfile
+ * @return
*/
- public void mouseOverStructure(int pdbResNum, String chain,
+ public String mouseOverStructure(int pdbResNum, String chain,
String pdbfile)
{
AtomSpec atomSpec = new AtomSpec(pdbfile, chain, pdbResNum, 0);
List<AtomSpec> atoms = Collections.singletonList(atomSpec);
- mouseOverStructure(atoms);
+ return mouseOverStructure(atoms);
}
/**
*
* @param atoms
*/
- public void mouseOverStructure(List<AtomSpec> atoms)
+ public String mouseOverStructure(List<AtomSpec> atoms)
{
if (listeners == null)
{
// old or prematurely sent event
- return;
+ return null;
}
boolean hasSequenceListener = false;
for (int i = 0; i < listeners.size(); i++)
}
if (!hasSequenceListener)
{
- return;
+ return null;
}
SearchResultsI results = findAlignmentPositionsForStructurePositions(
atoms);
+ String result = null;
for (Object li : listeners)
{
if (li instanceof SequenceListener)
{
- ((SequenceListener) li).highlightSequence(results);
+ String s = ((SequenceListener) li).highlightSequence(results);
+ if (s != null)
+ {
+ result = s;
+ }
}
}
+ return result;
}
/**
StringBuilder sb = new StringBuilder(64);
for (StructureMapping sm : mappings)
{
- if (sm.pdbfile.equals(pdbfile) && seqs.contains(sm.sequence))
+ if (Platform.pathEquals(sm.pdbfile, pdbfile)
+ && seqs.contains(sm.sequence))
{
sb.append(sm.mappingDetails);
sb.append(NEWLINE);
instances.remove(jalviewLite);
try
{
- mnger.finalize();
+ /* bsoares 2019-03-20 finalize deprecated, no apparent external
+ * resources to close
+ */
+ // mnger.finalize();
} catch (Throwable x)
{
}
git://source.jalview.org / jalview.git / blobdiff