import jalview.io.AppletFormatAdapter;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
+import jalview.ws.sifts.SiftsClient;
+import jalview.ws.sifts.SiftsException;
import java.io.PrintStream;
import java.util.ArrayList;
* @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
* - optional chain specification for mapping each sequence to pdb
* @return null or the structure data parsed as a pdb file
*/
synchronized public PDBfile setMapping(boolean forStructureView,
- SequenceI[] sequence, String[] targetChains, String pdbFile,
+ SequenceI[] sequenceArray, String[] targetChains, String pdbFile,
String protocol)
{
/*
boolean parseSecStr = processSecondaryStructure;
if (isPDBFileRegistered(pdbFile))
{
- for (SequenceI sq : sequence)
+ for (SequenceI sq : sequenceArray)
{
SequenceI ds = sq;
while (ds.getDatasetSequence() != null)
}
}
PDBfile pdb = null;
+ boolean isMapUsingSIFTs = Boolean.valueOf(jalview.bin.Cache.getDefault(
+ "MAP_WITH_SIFTS", "false"));
+ SiftsClient siftsClient = null;
try
{
pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
pdbFile, protocol);
+ if (isMapUsingSIFTs)
+ {
+ siftsClient = new SiftsClient(pdb);
+ }
if (pdb.id != null && pdb.id.trim().length() > 0
&& AppletFormatAdapter.FILE.equals(protocol))
{
registerPDBFile(pdb.id.trim(), pdbFile);
}
+ } catch (SiftsException e)
+ {
+ e.printStackTrace();
} catch (Exception ex)
{
ex.printStackTrace();
}
String targetChain;
- for (int s = 0; s < sequence.length; s++)
+ for (int s = 0; s < sequenceArray.length; s++)
{
boolean infChain = true;
- final SequenceI seq = sequence[s];
+ final SequenceI seq = sequenceArray[s];
if (targetChains != null && targetChains[s] != null)
{
infChain = false;
{
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 (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
{
- @Override
- public void print(String x)
- {
- mappingDetails.append(x);
- }
+ pdbFile = "INLINE" + pdb.id;
+ }
- @Override
- public void println()
- {
- mappingDetails.append(NEWLINE);
- }
- };
-
- 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 ");
- 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
+ ArrayList<StructureMapping> seqToStrucMapping = null;
+ if (isMapUsingSIFTs)
{
- Atom tmp = maxChain.atoms.elementAt(index);
- if (resNum != tmp.resNumber && tmp.alignmentMapping != -1)
+ try
{
- resNum = tmp.resNumber;
- if (tmp.alignmentMapping >= -1)
+ seqToStrucMapping = new ArrayList<StructureMapping>();
+ if (targetChain != null && !targetChain.trim().isEmpty())
{
- // 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;
+ maxChainId = targetChain;
+ StructureMapping curChainMapping = siftsClient
+ .getSiftsStructureMapping(seq, pdbFile, targetChain);
+ seqToStrucMapping.add(curChainMapping);
}
+ else
+ {
+ for (PDBChain chain : pdb.chains)
+ {
+ maxChainId = chain.id;
+ StructureMapping curChainMapping = siftsClient
+ .getSiftsStructureMapping(seq, pdbFile, chain.id);
+ seqToStrucMapping.add(curChainMapping);
+ }
+ }
+ } catch (SiftsException e)
+ {
+ System.err
+ .println(">>>>>>> SIFTs mapping could not be obtained... Now mapping with NW alignment");
+ seqToStrucMapping = getNWMappings(seq, pdbFile, maxChainId,
+ maxChain, pdb, maxAlignseq);
}
-
- index++;
- } while (index < maxChain.atoms.size());
-
- if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+ }
+ else
{
- pdbFile = "INLINE" + pdb.id;
+ seqToStrucMapping = getNWMappings(seq, pdbFile,
+ maxChainId, maxChain, pdb,
+ maxAlignseq);
}
- StructureMapping newMapping = new StructureMapping(seq, pdbFile,
- pdb.id, maxChainId, mapping, mappingDetails.toString());
+
if (forStructureView)
{
- mappings.add(newMapping);
+ // mappings.add(seqToStrucMapping);
+ mappings.addAll(seqToStrucMapping);
}
- maxChain.transferResidueAnnotation(newMapping, sqmpping);
}
- // ///////
-
return pdb;
}
+ private ArrayList<StructureMapping> getNWMappings(SequenceI seq,
+ String pdbFile,
+ String maxChainId, PDBChain maxChain, PDBfile 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 ");
+ mappingDetails.append(String.valueOf(maxAlignseq.seq2start))
+ .append(" ");
+ mappingDetails.append(String.valueOf(maxAlignseq.seq2end));
+ mappingDetails.append(NEWLINE).append("SEQ start/end ");
+ mappingDetails.append(
+ String.valueOf(maxAlignseq.seq1start + (seq.getStart() - 1)))
+ .append(" ");
+ mappingDetails.append(String.valueOf(maxAlignseq.seq1end
+ + (seq.getStart() - 1)));
+ mappingDetails.append(NEWLINE);
+ maxChain.makeExactMapping(maxAlignseq, seq);
+ jalview.datamodel.Mapping sqmpping = maxAlignseq
+ .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];
+ int resNum = -10000;
+ int index = 0;
+
+ do
+ {
+ Atom tmp = maxChain.atoms.elementAt(index);
+ if (resNum != tmp.resNumber && tmp.alignmentMapping != -1)
+ {
+ resNum = tmp.resNumber;
+ 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;
+ }
+ }
+
+ index++;
+ } while (index < maxChain.atoms.size());
+
+ StructureMapping nwMapping = new StructureMapping(seq, pdbFile,
+ pdb.id, maxChainId, mapping, mappingDetails.toString());
+ maxChain.transferResidueAnnotation(nwMapping, sqmpping);
+ ArrayList<StructureMapping> mappings = new ArrayList<StructureMapping>();
+ mappings.add(nwMapping);
+ return mappings;
+ }
+
public void removeStructureViewerListener(Object svl, String[] pdbfiles)
{
listeners.removeElement(svl);
git://source.jalview.org / jalview.git / blobdiff