import java.util.Collections;
import java.util.Enumeration;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.IdentityHashMap;
import java.util.List;
import java.util.Locale;
import java.util.Map;
+import java.util.Set;
import java.util.Vector;
import jalview.analysis.AlignSeq;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.ContiguousI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
import jalview.io.StructureFile;
+import jalview.structure.StructureImportSettings.TFType;
+import jalview.util.MapList;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
{
if (mappings.isEmpty())
{
- System.err.println("reportMapping: No PDB/Sequence mappings.");
+ jalview.bin.Console
+ .errPrintln("reportMapping: No PDB/Sequence mappings.");
}
else
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"reportMapping: There are " + mappings.size() + " mappings.");
int i = 0;
for (StructureMapping sm : mappings)
{
- System.err.println("mapping " + i++ + " : " + sm.pdbfile);
+ jalview.bin.Console
+ .errPrintln("mapping " + i++ + " : " + sm.pdbfile);
}
}
}
IProgressIndicator progress)
{
return computeMapping(true, sequence, targetChains, pdbFile, protocol,
- progress);
+ progress, null, null, true);
}
/**
*/
synchronized public StructureFile setMapping(boolean forStructureView,
SequenceI[] sequenceArray, String[] targetChainIds,
- String pdbFile, DataSourceType sourceType)
+ String pdbFile, DataSourceType sourceType, TFType tft,
+ String paeFilename)
+ {
+ return setMapping(forStructureView, sequenceArray, targetChainIds,
+ pdbFile, sourceType, tft, paeFilename, true);
+ }
+
+ /**
+ * 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 tft
+ * - specify how to interpret the temperature factor column in the
+ * atom data
+ * @param paeFilename
+ * - when not null, specifies a filename containing a matrix
+ * formatted in JSON using one of the known PAE formats
+ * @param doXferSettings
+ * - when true, transfer annotation to mapped sequences in
+ * sequenceArray
+ * @return null or the structure data parsed as a pdb file
+ */
+ synchronized public StructureFile setMapping(boolean forStructureView,
+ SequenceI[] sequenceArray, String[] targetChainIds,
+ String pdbFile, DataSourceType sourceType, TFType tft,
+ String paeFilename, boolean doXferSettings)
{
return computeMapping(forStructureView, sequenceArray, targetChainIds,
- pdbFile, sourceType, null);
+ pdbFile, sourceType, null, tft, paeFilename, doXferSettings);
}
/**
* @param IProgressIndicator
* reference to UI component that maintains a progress bar for the
* mapping operation
+ * @param tft
+ * - specify how to interpret the temperature factor column in the
+ * atom data
+ * @param paeFilename
+ * - when not null, specifies a filename containing a matrix
+ * formatted in JSON using one of the known PAE formats
+ * @param doXferSettings
+ * - when true, transfer annotation to mapped sequences in
+ * sequenceArray
* @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)
+ IProgressIndicator progress, TFType tft, String paeFilename,
+ boolean doXferSettings)
{
long progressSessionId = System.currentTimeMillis() * 3;
// FIXME: possibly should just delete
boolean parseSecStr = processSecondaryStructure
- ? isStructureFileProcessed(pdbFile, sequenceArray)
- : false;
+ && !isStructureFileProcessed(pdbFile, sequenceArray);
StructureFile pdb = null;
boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
// FIXME if sourceType is not null, we've lost data here
sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
pdb = new JmolParser(false, pdbFile, sourceType);
+ if (paeFilename != null)
+ {
+ pdb.setPAEMatrix(paeFilename);
+ }
+ pdb.setTemperatureFactorType(tft);
pdb.addSettings(parseSecStr && processSecondaryStructure,
parseSecStr && addTempFacAnnot,
parseSecStr && secStructServices);
+ // save doXferSettings and reset after doParse()
+ boolean temp = pdb.getDoXferSettings();
+ pdb.setDoXferSettings(doXferSettings);
pdb.doParse();
+ pdb.setDoXferSettings(temp);
if (pdb.getId() != null && pdb.getId().trim().length() > 0
&& DataSourceType.FILE == sourceType)
{
{
ds = ds.getDatasetSequence();
}
-
+ List <PDBEntry> putativePDBe = PDBEntryUtils.selectPutativePDBe(seq,ds, pdb);
+
if (targetChainIds != null && targetChainIds[s] != null)
{
infChain = false;
targetChainId = targetChainIds[s];
}
- else if (seq.getName().indexOf("|") > -1)
- {
- targetChainId = seq.getName()
- .substring(seq.getName().lastIndexOf("|") + 1);
- if (targetChainId.length() > 1)
- {
- if (targetChainId.trim().length() == 0)
- {
- targetChainId = " ";
- }
- else
- {
- // not a valid chain identifier
- targetChainId = "";
- }
- }
- }
- else
- {
- targetChainId = "";
+ else {
+ targetChainId = PDBEntryUtils.inferChainId(seq);
}
/*
String maxChainId = " ";
PDBChain maxChain = null;
boolean first = true;
+ PDBChain idLengthChain = null;
for (PDBChain chain : pdb.getChains())
{
if (targetChainId.length() > 0 && !targetChainId.equals(chain.id)
{
continue; // don't try to map chains don't match.
}
+ PDBEntry putativeChain = null;
+ if (!putativePDBe.isEmpty() && (putativeChain = PDBEntryUtils
+ .selectPutativePDBEntry(putativePDBe, chain)) == null)
+ {
+ continue;
+ }
// TODO: correctly determine sequence type for mixed na/peptide
// structures
final String type = chain.isNa ? AlignSeq.DNA : AlignSeq.PEP;
AlignSeq as = AlignSeq.doGlobalNWAlignment(seq, chain.sequence,
type);
- // equivalent to:
- // AlignSeq as = new AlignSeq(sequence[s], chain.sequence, type);
- // as.calcScoreMatrix();
- // as.traceAlignment();
+ // TODO: JAL-4366 determinine of a crummy alignment but exact match should make this chain the one to be mapped to a 3di sequence
+ if (as.s1str.length() == as.s2str.length())
+ {
+ idLengthChain = chain;
+ }
if (first || as.maxscore > max
|| (as.maxscore == max && chain.id.equals(targetChainId)))
{
continue;
}
-
if (sourceType == DataSourceType.PASTE)
{
pdbFile = "INLINE" + pdb.getId();
}
-
List<StructureMapping> seqToStrucMapping = new ArrayList<>();
+
+ List<StructureMapping> foundSiftsMappings = new ArrayList<>();
if (isMapUsingSIFTs && seq.isProtein())
{
if (progress != null)
pdb.getId().toLowerCase(Locale.ROOT));
maxChain.transferResidueAnnotation(siftsMapping, null);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+ foundSiftsMappings.add(siftsMapping);
} catch (SiftsException e)
{
- // fall back to NW alignment
Console.error(e.getMessage());
- StructureMapping nwMapping = getNWMappings(seq, pdbFile,
- targetChainId, maxChain, pdb, maxAlignseq);
- seqToStrucMapping.add(nwMapping);
- maxChain.makeExactMapping(maxAlignseq, seq);
- maxChain.transferRESNUMFeatures(seq, "IEA:Jalview",
- pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is
- // this
- // "IEA:Jalview" ?
- maxChain.transferResidueAnnotation(nwMapping, sqmpping);
- ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
}
}
else
{
- List<StructureMapping> foundSiftsMappings = new ArrayList<>();
for (PDBChain chain : pdb.getChains())
{
StructureMapping siftsMapping = null;
chain.transferResidueAnnotation(siftsMapping, null);
} catch (SiftsException e)
{
- System.err.println(e.getMessage());
+ jalview.bin.Console.errPrintln(e.getMessage());
} catch (Exception e)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Unexpected exception during SIFTS mapping - falling back to NW for this sequence/structure pair");
- System.err.println(e.getMessage());
+ jalview.bin.Console.errPrintln(e.getMessage());
}
}
+ // If sifts was successful, add mappings and return
if (!foundSiftsMappings.isEmpty())
{
- seqToStrucMapping.addAll(foundSiftsMappings);
ds.addPDBId(sqmpping.getTo().getAllPDBEntries().get(0));
}
- else
- {
- StructureMapping nwMapping = getNWMappings(seq, pdbFile,
- maxChainId, maxChain, pdb, maxAlignseq);
- seqToStrucMapping.add(nwMapping);
- 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 sifts was successful, add mappings and return
+ if (!foundSiftsMappings.isEmpty())
+ {
+ seqToStrucMapping.addAll(foundSiftsMappings);
}
}
- else
+ if (foundSiftsMappings.isEmpty())
{
- if (progress != null)
+ // Not doing SIFTS, or SIFTS failed for some reason.
+
+ // first check if we should use an identity mapping
+ if (idLengthChain != null && maxAlignseq.getS2Coverage() < 0.75)
{
- progress.setProgressBar(
- MessageManager.getString(
- "status.obtaining_mapping_with_nw_alignment"),
- progressSessionId);
+ Console.info(
+ "Assuming 3Dsi identity mapping between structure and sequence");
+ StructureMapping matchMapping = getIdMappings(seq, pdbFile,
+ idLengthChain.id, idLengthChain, pdb);
+ seqToStrucMapping.add(matchMapping);
+ ds.addPDBId(idLengthChain.sequence.getAllPDBEntries().get(0));
+ Console.info("Mapping added.");
+ }
+ else
+ {
+ if (maxAlignseq.getS1Coverage()<0.15 && maxAlignseq.getS2Coverage()<0.15)
+ {
+ // skip this - the NW alignment is spurious
+ continue;
+ }
+ // Construct a needleman wunsch mapping instead.
+ 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));
}
- StructureMapping nwMapping = getNWMappings(seq, pdbFile, maxChainId,
- maxChain, pdb, maxAlignseq);
- seqToStrucMapping.add(nwMapping);
- ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
}
if (forStructureView)
{
private boolean isStructureFileProcessed(String pdbFile,
SequenceI[] sequenceArray)
{
- boolean parseSecStr = true;
+ boolean processed = false;
if (isPDBFileRegistered(pdbFile))
{
for (SequenceI sq : sequenceArray)
// passed, not the structure data ID -
if (PDBfile.isCalcIdForFile(ala, findIdForPDBFile(pdbFile)))
{
- parseSecStr = false;
+ processed = true;
}
}
}
}
}
- return parseSecStr;
+ return processed;
}
public void addStructureMapping(StructureMapping sm)
}
return curChainMapping;
}
+
+ /**
+ * construct a mapping based on a pairwise alignment of the sequence and chain
+ * @param seq
+ * @param pdbFile
+ * @param maxChainId
+ * @param maxChain
+ * @param pdb
+ * @param maxAlignseq
+ * @return
+ */
private StructureMapping getNWMappings(SequenceI seq, String pdbFile,
String maxChainId, PDBChain maxChain, StructureFile pdb,
maxChain.transferResidueAnnotation(nwMapping, sqmpping);
return nwMapping;
}
+
+ /**
+ * construct a 1:1 mapping using given residue and sequence numbering
+ * @param seq
+ * @param pdbFile
+ * @param identityChainId
+ * @param identityChain
+ * @param pdb
+ * @return
+ */
+
+ private StructureMapping getIdMappings(SequenceI seq, String pdbFile,
+ String identityChainId, PDBChain identityChain, StructureFile pdb)
+ {
+ final StringBuilder mappingDetails = new StringBuilder(128);
+ mappingDetails.append(NEWLINE)
+ .append("Sequence \u27f7 Structure mapping details");
+ mappingDetails.append(NEWLINE);
+ mappingDetails.append("Method: Matching length 1:1");
+ mappingDetails.append(NEWLINE).append("PDB Sequence is :")
+ .append(NEWLINE).append("Sequence = ")
+ .append(identityChain.sequence.getSequenceAsString());
+ mappingDetails.append(NEWLINE).append("No of residues = ")
+ .append(identityChain.residues.size()).append(NEWLINE)
+ .append(NEWLINE);
+
+ mappingDetails.append(NEWLINE)
+ .append("Aligned Sequence is: " + seq.getDisplayId(true));
+ mappingDetails.append(NEWLINE)
+ .append("Sequence = " + seq.getSequenceAsString());
+
+ int from = Math.max(seq.getStart(),identityChain.sequence.getStart());
+ int to = Math.min(seq.getEnd(), identityChain.sequence.getEnd());
+ jalview.datamodel.Mapping sqmpping = new jalview.datamodel.Mapping(seq,
+ new MapList(new int[]
+ { from,to },
+ new int[]
+ { from,to },
+ 1, 1));
+ identityChain.mapChainWith(sqmpping, seq);
+
+ identityChain.transferRESNUMFeatures(seq, null,
+ pdb.getId().toLowerCase(Locale.ROOT));
+
+ // Construct mapping
+ // TODO REFACTOR TO PDBChain as a builder
+ HashMap<Integer, int[]> mapping = new HashMap<>();
+ int resNum = -10000;
+ int index = 0;
+ char insCode = ' ';
+
+ do
+ {
+ Atom tmp = identityChain.atoms.elementAt(index);
+ if ((resNum != tmp.resNumber || insCode != tmp.insCode)
+ && tmp.alignmentMapping != -1)
+ {
+ resNum = tmp.resNumber;
+ insCode = tmp.insCode;
+ if (tmp.alignmentMapping >= -1)
+ {
+ mapping.put(tmp.alignmentMapping + 1,
+ new int[]
+ { tmp.resNumber, tmp.atomIndex });
+ }
+ }
+
+ index++;
+ } while (index < identityChain.atoms.size());
+
+ StructureMapping idMapping = new StructureMapping(seq, pdbFile,
+ pdb.getId(), identityChainId, mapping,
+ mappingDetails.toString());
+ identityChain.transferResidueAnnotation(idMapping, sqmpping);
+ return idMapping;
+ }
public void removeStructureViewerListener(Object svl, String[] pdbfiles)
{
int indexpos = sm.getSeqPos(atom.getPdbResNum());
if (lastipos != indexpos || lastseq != sm.sequence)
{
- results.addResult(sm.sequence, indexpos, indexpos);
+ results.appendResult(sm.sequence, indexpos, indexpos);
lastipos = indexpos;
lastseq = sm.sequence;
// construct highlighted sequence list
sl.highlightAtoms(atoms);
}
+ public void highlightStructureRegionsFor(StructureListener sl,
+ SequenceI[] seqs, int... columns)
+ {
+ List<SequenceI> to_highlight = new ArrayList<SequenceI>();
+ for (SequenceI seq : seqs)
+ {
+ if (sl.isListeningFor(seq))
+ {
+ to_highlight.add(seq);
+ }
+ }
+ if (to_highlight.size() == 0)
+ {
+ return;
+ }
+ List<AtomSpec> atoms = new ArrayList<>();
+ for (SequenceI seq : to_highlight)
+ {
+ int atomNo;
+ for (StructureMapping sm : mappings)
+ {
+ if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence()
+ || (sm.sequence.getDatasetSequence() != null && sm.sequence
+ .getDatasetSequence() == seq.getDatasetSequence()))
+ {
+
+ for (int i = 0; i < columns.length; i += 2)
+ {
+ ContiguousI positions = seq.findPositions(columns[i] + 1,
+ columns[i + 1] + 1);
+ if (positions == null)
+ {
+ continue;
+ }
+ for (int index = positions.getBegin(); index <= positions
+ .getEnd(); index++)
+ {
+
+ atomNo = sm.getAtomNum(index);
+
+ if (atomNo > 0)
+ {
+ atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain,
+ sm.getPDBResNum(index), atomNo));
+ }
+ }
+ }
+ }
+ }
+ if (atoms.size() > 0)
+ {
+ sl.highlightAtoms(atoms);
+ }
+ }
+ }
+
/**
* true if a mouse over event from an external (ie Vamsas) source is being
* handled
*
* if (mappings[j].sequence == seq && mappings[j].getPdbId().equals(pdbid)
* && mappings[j].pdbfile.equals(sl.getPdbFile())) {
- * System.out.println(pdbid+" "+mappings[j].getPdbId() +"
+ * jalview.bin.Console.outPrintln(pdbid+" "+mappings[j].getPdbId() +"
* "+mappings[j].pdbfile);
*
* java.awt.Color col; for(int index=0; index<seq.getLength(); index++) {
boolean removed = seqmappings.remove(acf);
if (removed && seqmappings.isEmpty())
{ // debug
- System.out.println("All mappings removed");
+ jalview.bin.Console.outPrintln("All mappings removed");
}
}
}
return seqmappings;
}
+ /**
+ * quick and dirty route to just highlight all structure positions for a range
+ * of columns
+ *
+ * @param sequencesArray
+ * @param is
+ * start-end columns on sequencesArray
+ * @param source
+ * origin parent AlignmentPanel
+ */
+ public void highlightPositionsOnMany(SequenceI[] sequencesArray, int[] is,
+ Object source)
+ {
+ for (int i = 0; i < listeners.size(); i++)
+ {
+ Object listener = listeners.elementAt(i);
+ if (listener == source)
+ {
+ // TODO listener (e.g. SeqPanel) is never == source (AlignViewport)
+ // Temporary fudge with SequenceListener.getVamsasSource()
+ continue;
+ }
+ if (listener instanceof StructureListener)
+ {
+ highlightStructureRegionsFor((StructureListener) listener,
+ sequencesArray, is);
+ }
+ }
+ }
+
+ public Map<String, String> getPdbFileNameIdMap()
+ {
+ return pdbFileNameId;
+ }
+
+ public Map<String, String> getPdbIdFileNameMap()
+ {
+ return pdbIdFileName;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff