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.SiftsClient;
+import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
+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.Enumeration;
import java.util.HashMap;
import java.util.IdentityHashMap;
-import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
-import java.util.Set;
import java.util.Vector;
import MCview.Atom;
private boolean addTempFacAnnot = false;
+ private IProgressIndicator progressIndicator;
+
+ private SiftsClient siftsClient = null;
+
+ private long progressSessionId;
+
/*
* Set of any registered mappings between (dataset) sequences.
*/
- public Set<AlignedCodonFrame> seqmappings = new LinkedHashSet<AlignedCodonFrame>();
+ private List<AlignedCodonFrame> seqmappings = new ArrayList<AlignedCodonFrame>();
private List<CommandListener> commandListeners = new ArrayList<CommandListener>();
* - 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)
{
return setMapping(true, sequence, targetChains, pdbFile, protocol);
}
* @param forStructureView
* when true, record the mapping for use in mouseOvers
*
- * @param sequence
+ * @param sequenceArray
* - one or more sequences to be mapped to pdbFile
- * @param targetChains
+ * @param targetChainIds
* - optional chain specification for mapping each sequence to pdb
* (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 PDBfile setMapping(boolean forStructureView,
- SequenceI[] sequence, String[] targetChains, String pdbFile,
- String protocol)
+ synchronized public StructureFile setMapping(boolean forStructureView,
+ SequenceI[] sequenceArray, String[] targetChainIds,
+ String pdbFile, DataSourceType sourceType)
{
/*
* There will be better ways of doing this in the future, for now we'll use
boolean parseSecStr = processSecondaryStructure;
if (isPDBFileRegistered(pdbFile))
{
- for (SequenceI sq : sequence)
+ for (SequenceI sq : sequenceArray)
{
SequenceI ds = sq;
while (ds.getDatasetSequence() != null)
}
}
}
- PDBfile pdb = null;
+ StructureFile pdb = null;
+ boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
try
{
- pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
- pdbFile, protocol);
- if (pdb.id != null && pdb.id.trim().length() > 0
- && AppletFormatAdapter.FILE.equals(protocol))
+ sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
+ pdb = new JmolParser(pdbFile, sourceType);
+
+ if (pdb.getId() != null && pdb.getId().trim().length() > 0
+ && DataSourceType.FILE == sourceType)
{
- registerPDBFile(pdb.id.trim(), pdbFile);
+ registerPDBFile(pdb.getId().trim(), pdbFile);
}
+ // if PDBId is unavailable then skip SIFTS mapping execution path
+ isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable();
+
} catch (Exception ex)
{
ex.printStackTrace();
return null;
}
- String targetChain;
- for (int s = 0; s < sequence.length; s++)
+ try
+ {
+ if (isMapUsingSIFTs)
+ {
+ siftsClient = new SiftsClient(pdb);
+ }
+ } catch (SiftsException e)
+ {
+ isMapUsingSIFTs = false;
+ e.printStackTrace();
+ }
+
+ String targetChainId;
+ for (int s = 0; s < sequenceArray.length; s++)
{
boolean infChain = true;
- final SequenceI seq = sequence[s];
- if (targetChains != null && targetChains[s] != null)
+ final SequenceI seq = sequenceArray[s];
+ SequenceI ds = seq;
+ while (ds.getDatasetSequence() != null)
+ {
+ ds = ds.getDatasetSequence();
+ }
+
+ if (targetChainIds != null && targetChainIds[s] != null)
{
infChain = false;
- targetChain = targetChains[s];
+ targetChainId = targetChainIds[s];
}
else if (seq.getName().indexOf("|") > -1)
{
- targetChain = seq.getName().substring(
+ targetChainId = seq.getName().substring(
seq.getName().lastIndexOf("|") + 1);
- if (targetChain.length() > 1)
+ if (targetChainId.length() > 1)
{
- if (targetChain.trim().length() == 0)
+ if (targetChainId.trim().length() == 0)
{
- targetChain = " ";
+ targetChainId = " ";
}
else
{
// not a valid chain identifier
- targetChain = "";
+ targetChainId = "";
}
}
}
else
{
- targetChain = "";
+ targetChainId = "";
}
/*
* 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;
boolean first = true;
- for (PDBChain chain : pdb.chains)
+ for (PDBChain chain : pdb.getChains())
{
- if (targetChain.length() > 0 && !targetChain.equals(chain.id)
+ if (targetChainId.length() > 0 && !targetChainId.equals(chain.id)
&& !infChain)
{
continue; // don't try to map chains don't match.
// as.traceAlignment();
if (first || as.maxscore > max
- || (as.maxscore == max && chain.id.equals(targetChain)))
+ || (as.maxscore == max && chain.id.equals(targetChainId)))
{
first = false;
maxChain = chain;
{
continue;
}
- final StringBuilder mappingDetails = new StringBuilder(128);
- mappingDetails.append(NEWLINE).append("PDB Sequence is :")
- .append(NEWLINE).append("Sequence = ")
- .append(maxChain.sequence.getSequenceAsString());
- mappingDetails.append(NEWLINE).append("No of residues = ")
- .append(maxChain.residues.size()).append(NEWLINE)
- .append(NEWLINE);
- PrintStream ps = new PrintStream(System.out)
+
+ if (sourceType == DataSourceType.PASTE)
{
- @Override
- public void print(String x)
- {
- mappingDetails.append(x);
- }
+ pdbFile = "INLINE" + pdb.getId();
+ }
- @Override
- public void println()
+ List<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
+ if (isMapUsingSIFTs && seq.isProtein())
+ {
+ setProgressBar(null);
+ setProgressBar(MessageManager
+ .getString("status.obtaining_mapping_with_sifts"));
+ jalview.datamodel.Mapping sqmpping = maxAlignseq
+ .getMappingFromS1(false);
+ if (targetChainId != null && !targetChainId.trim().isEmpty())
{
- mappingDetails.append(NEWLINE);
+ 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));
+ }
}
- };
-
- // mapWithNWAlignment();
- // mapWithSIFTS();
- maxAlignseq.printAlignment(ps);
-
- mappingDetails.append(NEWLINE).append("PDB start/end ");
- mappingDetails.append(String.valueOf(maxAlignseq.seq2start)).append(
- " ");
- mappingDetails.append(String.valueOf(maxAlignseq.seq2end));
- mappingDetails.append(NEWLINE).append("SEQ start/end ");
- // TODO JAL-1887 should be fixed from here
- mappingDetails.append(
- String.valueOf(maxAlignseq.seq1start + seq.getStart() - 1))
- .append(" ");
- mappingDetails.append(String.valueOf(maxAlignseq.seq1end
- + seq.getEnd() - 1));
-
- maxChain.makeExactMapping(maxAlignseq, seq);
- jalview.datamodel.Mapping sqmpping = maxAlignseq
- .getMappingFromS1(false);
- jalview.datamodel.Mapping omap = new jalview.datamodel.Mapping(
- sqmpping.getMap().getInverse());
- maxChain.transferRESNUMFeatures(seq, null);
-
- // allocate enough slots to store the mapping from positions in
- // sequence[s] to the associated chain
- int[][] mapping = new int[seq.findPosition(seq.getLength()) + 2][2];
- int resNum = -10000;
- int index = 0;
-
- do
- {
- Atom tmp = maxChain.atoms.elementAt(index);
- if (resNum != tmp.resNumber && tmp.alignmentMapping != -1)
+ else
{
- resNum = tmp.resNumber;
- if (tmp.alignmentMapping >= -1)
+ List<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
+ for (PDBChain chain : pdb.getChains())
+ {
+ try
+ {
+ StructureMapping siftsMapping = getStructureMapping(seq,
+ pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq);
+ foundSiftsMappings.add(siftsMapping);
+ } catch (SiftsException e)
+ {
+ System.err.println(e.getMessage());
+ }
+ }
+ 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
{
- // TODO (JAL-1836) address root cause: negative residue no in PDB
- // file
- mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber;
- mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex;
+ 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));
}
}
-
- index++;
- } while (index < maxChain.atoms.size());
-
- if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+ }
+ else
{
- pdbFile = "INLINE" + pdb.id;
+ setProgressBar(null);
+ 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));
+
}
- // StructureMapping newMapping = new StructureMapping(seq, pdbFile,
- // pdb.id, maxChainId, mapping, mappingDetails.toString());
- StructureMapping newMapping = new SiftsClient(pdb.id)
- .getSiftsMappingsFor(seq, pdbFile, maxChainId);
+
if (forStructureView)
{
- mappings.add(newMapping);
+ mappings.addAll(seqToStrucMapping);
}
- maxChain.transferResidueAnnotation(newMapping, sqmpping);
}
- // ///////
-
return pdb;
}
- private StructureMapping mapWithNWAlignment(StringBuilder mappingDetails,
- PDBChain maxChain, AlignSeq maxAlignseq, SequenceI seq,
- PrintStream ps)
+ public void addStructureMapping(StructureMapping sm)
+ {
+ 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
+ {
+ PDBChain chain = pdb.findChain(targetChainId);
+ if (chain != null)
+ {
+ chain.transferResidueAnnotation(curChainMapping, sqmpping);
+ }
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ return curChainMapping;
+ }
+
+ private StructureMapping getNWMappings(SequenceI seq, String pdbFile,
+ String maxChainId, PDBChain maxChain, StructureFile pdb,
+ AlignSeq maxAlignseq)
+ {
+ final StringBuilder mappingDetails = new StringBuilder(128);
+ mappingDetails.append(NEWLINE).append(
+ "Sequence \u27f7 Structure mapping details");
+ mappingDetails.append(NEWLINE);
+ mappingDetails
+ .append("Method: inferred with Needleman & Wunsch alignment");
+ mappingDetails.append(NEWLINE).append("PDB Sequence is :")
+ .append(NEWLINE).append("Sequence = ")
+ .append(maxChain.sequence.getSequenceAsString());
+ mappingDetails.append(NEWLINE).append("No of residues = ")
+ .append(maxChain.residues.size()).append(NEWLINE)
+ .append(NEWLINE);
+ PrintStream ps = new PrintStream(System.out)
+ {
+ @Override
+ public void print(String x)
+ {
+ mappingDetails.append(x);
+ }
+
+ @Override
+ public void println()
+ {
+ mappingDetails.append(NEWLINE);
+ }
+ };
+
maxAlignseq.printAlignment(ps);
mappingDetails.append(NEWLINE).append("PDB start/end ");
.append(" ");
mappingDetails.append(String.valueOf(maxAlignseq.seq2end));
mappingDetails.append(NEWLINE).append("SEQ start/end ");
- // TODO JAL-1887 should be fixed from here
mappingDetails.append(
- String.valueOf(maxAlignseq.seq1start + seq.getStart() - 1))
+ String.valueOf(maxAlignseq.seq1start + (seq.getStart() - 1)))
.append(" ");
- mappingDetails.append(String.valueOf(maxAlignseq.seq1end + seq.getEnd()
- - 1));
-
+ mappingDetails.append(String.valueOf(maxAlignseq.seq1end
+ + (seq.getStart() - 1)));
+ mappingDetails.append(NEWLINE);
maxChain.makeExactMapping(maxAlignseq, seq);
jalview.datamodel.Mapping sqmpping = maxAlignseq
.getMappingFromS1(false);
- jalview.datamodel.Mapping omap = new jalview.datamodel.Mapping(sqmpping
- .getMap().getInverse());
maxChain.transferRESNUMFeatures(seq, null);
- // allocate enough slots to store the mapping from positions in
- // sequence[s] to the associated chain
- int[][] mapping = new int[seq.findPosition(seq.getLength()) + 2][2];
+ HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>();
int resNum = -10000;
int index = 0;
+ char insCode = ' ';
do
{
Atom tmp = maxChain.atoms.elementAt(index);
- if (resNum != tmp.resNumber && tmp.alignmentMapping != -1)
+ if ((resNum != tmp.resNumber || insCode != tmp.insCode)
+ && tmp.alignmentMapping != -1)
{
resNum = tmp.resNumber;
+ insCode = tmp.insCode;
if (tmp.alignmentMapping >= -1)
{
- // TODO (JAL-1836) address root cause: negative residue no in PDB
- // file
- mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber;
- mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex;
+ mapping.put(tmp.alignmentMapping + 1, new int[] { tmp.resNumber,
+ tmp.atomIndex });
}
}
index++;
} while (index < maxChain.atoms.size());
- return null;
+ StructureMapping nwMapping = new StructureMapping(seq, pdbFile,
+ pdb.getId(), maxChainId, mapping, mappingDetails.toString());
+ maxChain.transferResidueAnnotation(nwMapping, sqmpping);
+ return nwMapping;
}
public void removeStructureViewerListener(Object svl, String[] pdbfiles)
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;
}
/**
* the sequence that the mouse over occurred on
* @param indexpos
* the absolute position being mouseovered in seq (0 to seq.length())
- * @param index
+ * @param seqPos
* the sequence position (if -1, seq.findPosition is called to
* resolve the residue number)
*/
- public void mouseOverSequence(SequenceI seq, int indexpos, int index,
+ public void mouseOverSequence(SequenceI seq, int indexpos, int seqPos,
VamsasSource source)
{
boolean hasSequenceListeners = handlingVamsasMo
|| !seqmappings.isEmpty();
- SearchResults results = null;
- if (index == -1)
+ SearchResultsI results = null;
+ if (seqPos == -1)
{
- index = seq.findPosition(indexpos);
+ seqPos = seq.findPosition(indexpos);
}
for (int i = 0; i < listeners.size(); i++)
{
}
if (listener instanceof StructureListener)
{
- highlightStructure((StructureListener) listener, seq, index);
+ highlightStructure((StructureListener) listener, seq, seqPos);
}
else
{
{
if (results == null)
{
- results = MappingUtils.buildSearchResults(seq, index,
+ results = MappingUtils.buildSearchResults(seq, seqPos,
seqmappings);
}
if (handlingVamsasMo)
{
- results.addResult(seq, index, index);
+ results.addResult(seq, seqPos, seqPos);
}
if (!results.isEmpty())
else if (listener instanceof SecondaryStructureListener)
{
((SecondaryStructureListener) listener).mouseOverSequence(seq,
- indexpos, index);
+ indexpos, seqPos);
}
}
}
/**
* Send suitable messages to a StructureListener to highlight atoms
- * corresponding to the given sequence position.
+ * corresponding to the given sequence position(s)
*
* @param sl
* @param seq
- * @param index
+ * @param positions
*/
- protected void highlightStructure(StructureListener sl, SequenceI seq,
- int index)
+ public void highlightStructure(StructureListener sl, SequenceI seq,
+ int... positions)
{
if (!sl.isListeningFor(seq))
{
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()))
{
- atomNo = sm.getAtomNum(index);
-
- if (atomNo > 0)
+ for (int index : positions)
{
- atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, sm
- .getPDBResNum(index), atomNo));
+ atomNo = sm.getAtomNum(index);
+
+ if (atomNo > 0)
+ {
+ atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, sm
+ .getPDBResNum(index), atomNo));
+ }
}
}
}
/**
* Add each of the given codonFrames to the stored set, if not aready present.
*
- * @param set
+ * @param mappings
*/
- public void registerMappings(Set<AlignedCodonFrame> set)
+ public void registerMappings(List<AlignedCodonFrame> mappings)
{
- if (set != null)
+ if (mappings != null)
{
- for (AlignedCodonFrame acf : set)
+ for (AlignedCodonFrame acf : mappings)
{
registerMapping(acf);
}
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);
}
}
}
}
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;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff