import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JmolParser;
+import jalview.gui.IProgressIndicator;
import jalview.io.AppletFormatAdapter;
+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,
+ synchronized public StructureFile setMapping(SequenceI[] sequence,
String[] targetChains, String pdbFile, String protocol)
{
return setMapping(true, sequence, targetChains, pdbFile, 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, String protocol)
{
/*
* There will be better ways of doing this in the future, for now we'll use
}
}
}
- PDBfile pdb = null;
- boolean isMapUsingSIFTs = Boolean.valueOf(jalview.bin.Cache.getDefault(
- "MAP_WITH_SIFTS", "false"));
- SiftsClient siftsClient = null;
+ StructureFile pdb = null;
+ boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
try
{
- pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
- pdbFile, protocol);
+ pdb = new JmolParser(pdbFile, protocol);
- if (pdb.id != null && pdb.id.trim().length() > 0
+ if (pdb.getId() != null && pdb.getId().trim().length() > 0
&& AppletFormatAdapter.FILE.equals(protocol))
{
- registerPDBFile(pdb.id.trim(), pdbFile);
+ registerPDBFile(pdb.getId().trim(), pdbFile);
}
+ // if PDBId is unavailable then skip SIFTS mapping execution path
+ 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;
String maxChainId = " ";
PDBChain maxChain = null;
boolean first = true;
- for (PDBChain chain : pdb.chains)
+ for (PDBChain chain : pdb.getChains())
{
if (targetChainId.length() > 0 && !targetChainId.equals(chain.id)
&& !infChain)
if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
{
- pdbFile = "INLINE" + pdb.id;
+ pdbFile = "INLINE" + pdb.getId();
}
- ArrayList<StructureMapping> seqToStrucMapping = null;
- if (isMapUsingSIFTs)
+ ArrayList<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
+ if (isMapUsingSIFTs && seq.isProtein())
{
- try
+ setProgressBar(null);
+ setProgressBar(MessageManager
+ .getString("status.obtaining_mapping_with_sifts"));
+ jalview.datamodel.Mapping sqmpping = maxAlignseq
+ .getMappingFromS1(false);
+ if (targetChainId != null && !targetChainId.trim().isEmpty())
{
- jalview.datamodel.Mapping sqmpping = maxAlignseq
- .getMappingFromS1(false);
- seqToStrucMapping = new ArrayList<StructureMapping>();
- if (targetChainId != null && !targetChainId.trim().isEmpty())
+ StructureMapping siftsMapping;
+ try
{
- StructureMapping curChainMapping = siftsClient
- .getSiftsStructureMapping(seq, pdbFile, targetChainId);
- seqToStrucMapping.add(curChainMapping);
- maxChainId = targetChainId;
- PDBChain chain = pdb.findChain(targetChainId);
- if (chain != null)
+ 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));
+ }
+ }
+ else
+ {
+ ArrayList<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
+ for (PDBChain chain : pdb.getChains())
+ {
+ try
{
- chain.transferResidueAnnotation(curChainMapping, sqmpping);
+ 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
{
- for (PDBChain chain : pdb.chains)
- {
- StructureMapping curChainMapping = siftsClient
- .getSiftsStructureMapping(seq, pdbFile, chain.id);
- seqToStrucMapping.add(curChainMapping);
- maxChainId = chain.id;
- chain.transferResidueAnnotation(curChainMapping, sqmpping);
- }
+ 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));
}
- } catch (SiftsException e)
- {
- e.printStackTrace();
- System.err
- .println(">>>>>>> SIFTs mapping could not be obtained... Now mapping with NW alignment");
- seqToStrucMapping = getNWMappings(seq, pdbFile, maxChainId,
- maxChain, pdb, maxAlignseq);
}
}
else
{
- seqToStrucMapping = getNWMappings(seq, pdbFile,
- maxChainId, maxChain, pdb,
- maxAlignseq);
+ 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));
+
}
if (forStructureView)
{
- // mappings.add(seqToStrucMapping);
mappings.addAll(seqToStrucMapping);
}
}
return pdb;
}
- private ArrayList<StructureMapping> getNWMappings(SequenceI seq,
- String pdbFile,
- String maxChainId, PDBChain maxChain, PDBfile pdb,
+ private boolean isCIFFile(String filename)
+ {
+ String fileExt = filename.substring(filename.lastIndexOf(".") + 1,
+ filename.length());
+ return "cif".equalsIgnoreCase(fileExt);
+ }
+
+ /**
+ * 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);
.getMappingFromS1(false);
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 });
}
}
} while (index < maxChain.atoms.size());
StructureMapping nwMapping = new StructureMapping(seq, pdbFile,
- pdb.id, maxChainId, mapping, mappingDetails.toString());
+ pdb.getId(), maxChainId, mapping, mappingDetails.toString());
maxChain.transferResidueAnnotation(nwMapping, sqmpping);
- ArrayList<StructureMapping> mappings = new ArrayList<StructureMapping>();
- mappings.add(nwMapping);
- return mappings;
+ return nwMapping;
}
public void removeStructureViewerListener(Object svl, String[] pdbfiles)
* 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)
+ 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);
}
}
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