import javax.xml.stream.XMLInputFactory;
import javax.xml.stream.XMLStreamReader;
-import MCview.Atom;
-import MCview.PDBChain;
+import mc_view.Atom;
+import mc_view.PDBChain;
public class SiftsClient implements SiftsClientI
{
*/
private static File mockSiftsFile;
- private Entry siftsEntry;
+ private static final int BUFFER_SIZE = 4096;
- private StructureFile pdb;
+ public static final int UNASSIGNED = Integer.MIN_VALUE;
- private String pdbId;
+ private static final int PDB_RES_POS = 0;
- private String structId;
+ private static final int PDB_ATOM_POS = 1;
- private CoordinateSys seqCoordSys = CoordinateSys.UNIPROT;
+ private static final int PDBE_POS = 2;
- private static final int BUFFER_SIZE = 4096;
+ private static final String NOT_OBSERVED = "Not_Observed";
- public static final int UNASSIGNED = -1;
+ protected static final String SIFTS_FTP_BASE_URL = "http://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
- private static final int PDB_RES_POS = 0;
+ protected final static String NEWLINE = System.lineSeparator();
- private static final int PDB_ATOM_POS = 1;
+ private Entry siftsEntry;
- private static final String NOT_OBSERVED = "Not_Observed";
+ private StructureFile pdb;
+
+ private String pdbId;
+
+ private String structId;
- private static final String SIFTS_FTP_BASE_URL = "https://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
+ private CoordinateSys seqCoordSys = CoordinateSys.UNIPROT;
- private final static String NEWLINE = System.lineSeparator();
+ /**
+ * PDB sequence position to sequence coordinate mapping as derived from SIFTS
+ * record for the identified SeqCoordSys Used for lift-over from sequence
+ * derived from PDB (with first extracted PDBRESNUM as 'start' to the sequence
+ * being annotated with PDB data
+ */
+ private jalview.datamodel.Mapping seqFromPdbMapping;
private String curSourceDBRef;
@Override
public HashSet<String> getAllMappingAccession()
{
- HashSet<String> accessions = new HashSet<String>();
+ HashSet<String> accessions = new HashSet<>();
List<Entity> entities = siftsEntry.getEntity();
for (Entity entity : entities)
{
public StructureMapping getSiftsStructureMapping(SequenceI seq,
String pdbFile, String chain) throws SiftsException
{
+ SequenceI aseq = seq;
+ while (seq.getDatasetSequence() != null)
+ {
+ seq = seq.getDatasetSequence();
+ }
structId = (chain == null) ? pdbId : pdbId + "|" + chain;
System.out.println("Getting SIFTS mapping for " + structId + ": seq "
+ seq.getName());
HashMap<Integer, int[]> mapping = getGreedyMapping(chain, seq, ps);
String mappingOutput = mappingDetails.toString();
- StructureMapping siftsMapping = new StructureMapping(seq, pdbFile,
- pdbId, chain, mapping, mappingOutput);
+ StructureMapping siftsMapping = new StructureMapping(aseq, pdbFile,
+ pdbId, chain, mapping, mappingOutput, seqFromPdbMapping);
+
return siftsMapping;
}
public HashMap<Integer, int[]> getGreedyMapping(String entityId,
SequenceI seq, java.io.PrintStream os) throws SiftsException
{
- List<Integer> omitNonObserved = new ArrayList<Integer>();
- int nonObservedShiftIndex = 0;
+ List<Integer> omitNonObserved = new ArrayList<>();
+ int nonObservedShiftIndex = 0,pdbeNonObserved=0;
// System.out.println("Generating mappings for : " + entityId);
Entity entity = null;
entity = getEntityById(entityId);
String originalSeq = AlignSeq.extractGaps(
jalview.util.Comparison.GapChars, seq.getSequenceAsString());
- HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>();
+ HashMap<Integer, int[]> mapping = new HashMap<>();
DBRefEntryI sourceDBRef;
sourceDBRef = getValidSourceDBRef(seq);
// TODO ensure sequence start/end is in the same coordinate system and
seqCoordSys = CoordinateSys.PDB;
}
- HashSet<String> dbRefAccessionIdsString = new HashSet<String>();
+ HashSet<String> dbRefAccessionIdsString = new HashSet<>();
for (DBRefEntry dbref : seq.getDBRefs())
{
dbRefAccessionIdsString.add(dbref.getAccessionId().toLowerCase());
curDBRefAccessionIdsString = dbRefAccessionIdsString;
curSourceDBRef = sourceDBRef.getAccessionId();
- TreeMap<Integer, String> resNumMap = new TreeMap<Integer, String>();
+ TreeMap<Integer, String> resNumMap = new TreeMap<>();
List<Segment> segments = entity.getSegment();
SegmentHelperPojo shp = new SegmentHelperPojo(seq, mapping, resNumMap,
- omitNonObserved, nonObservedShiftIndex);
+ omitNonObserved, nonObservedShiftIndex,pdbeNonObserved);
processSegments(segments, shp);
try
{
{
throw new SiftsException("SIFTS mapping failed");
}
+ // also construct a mapping object between the seq-coord sys and the PDB seq's coord sys
Integer[] keys = mapping.keySet().toArray(new Integer[0]);
Arrays.sort(keys);
seqStart = keys[0];
seqEnd = keys[keys.length - 1];
-
+ List<int[]> from=new ArrayList<>(),to=new ArrayList<>();
+ int[]_cfrom=null,_cto=null;
String matchedSeq = originalSeq;
- if (seqStart != UNASSIGNED)
+ if (seqStart != UNASSIGNED) // fixme! seqStart can map to -1 for a pdb sequence that starts <-1
{
+ for (int seqps:keys)
+ {
+ int pdbpos = mapping.get(seqps)[PDBE_POS];
+ if (pdbpos == UNASSIGNED)
+ {
+ // not correct - pdbpos might be -1, but leave it for now
+ continue;
+ }
+ if (_cfrom==null || seqps!=_cfrom[1]+1)
+ {
+ _cfrom = new int[] { seqps,seqps};
+ from.add(_cfrom);
+ _cto = null; // discontinuity
+ } else {
+ _cfrom[1]= seqps;
+ }
+ if (_cto==null || pdbpos!=1+_cto[1])
+ {
+ _cto = new int[] { pdbpos,pdbpos};
+ to.add(_cto);
+ } else {
+ _cto[1] = pdbpos;
+ }
+ }
+ _cfrom = new int[from.size() * 2];
+ _cto = new int[to.size() * 2];
+ int p = 0;
+ for (int[] range : from)
+ {
+ _cfrom[p++] = range[0];
+ _cfrom[p++] = range[1];
+ }
+ ;
+ p = 0;
+ for (int[] range : to)
+ {
+ _cto[p++] = range[0];
+ _cto[p++] = range[1];
+ }
+ ;
+
+ seqFromPdbMapping = new jalview.datamodel.Mapping(null, _cto, _cfrom,
+ 1,
+ 1);
pdbStart = mapping.get(seqStart)[PDB_RES_POS];
pdbEnd = mapping.get(seqEnd)[PDB_RES_POS];
int orignalSeqStart = seq.getStart();
TreeMap<Integer, String> resNumMap = shp.getResNumMap();
List<Integer> omitNonObserved = shp.getOmitNonObserved();
int nonObservedShiftIndex = shp.getNonObservedShiftIndex();
+ int pdbeNonObservedCount = shp.getPdbeNonObserved();
+ int firstPDBResNum = UNASSIGNED;
for (Segment segment : segments)
{
// System.out.println("Mapping segments : " + segment.getSegId() + "\\"s
List<Residue> residues = segment.getListResidue().getResidue();
for (Residue residue : residues)
{
+ boolean isObserved = isResidueObserved(residue);
+ int pdbeIndex = getLeadingIntegerValue(residue.getDbResNum(),
+ UNASSIGNED);
int currSeqIndex = UNASSIGNED;
List<CrossRefDb> cRefDbs = residue.getCrossRefDb();
CrossRefDb pdbRefDb = null;
if (cRefDb.getDbSource().equalsIgnoreCase(DBRefSource.PDB))
{
pdbRefDb = cRefDb;
+ if (firstPDBResNum == UNASSIGNED)
+ {
+ firstPDBResNum = getLeadingIntegerValue(cRefDb.getDbResNum(),
+ UNASSIGNED);
+ }
+ else
+ {
+ if (isObserved)
+ {
+ // after we find the first observed residue we just increment
+ firstPDBResNum++;
+ }
+ }
}
if (cRefDb.getDbCoordSys().equalsIgnoreCase(seqCoordSys.getName())
&& isAccessionMatched(cRefDb.getDbAccessionId()))
}
}
}
+ if (!isObserved)
+ {
+ ++pdbeNonObservedCount; // TODO this value is never used
+ }
+ if (seqCoordSys == CoordinateSys.PDB) // FIXME: is seqCoordSys ever PDBe
+ // ???
+ {
+ // if the sequence has a primary reference to the PDB, then we are
+ // dealing with a sequence extracted directly from the PDB. In that
+ // case, numbering is PDBe - non-observed residues
+ currSeqIndex = seq.getStart() - 1 + pdbeIndex;
+ }
+ if (!isObserved)
+ {
+ if (seqCoordSys != CoordinateSys.UNIPROT) // FIXME: PDB or PDBe only
+ // here
+ {
+ // mapping to PDB or PDBe so we need to bookkeep for the
+ // non-observed
+ // SEQRES positions
+ omitNonObserved.add(currSeqIndex);
+ ++nonObservedShiftIndex;
+ }
+ }
if (currSeqIndex == UNASSIGNED)
{
+ // change in logic - unobserved residues with no currSeqIndex
+ // corresponding are still counted in both nonObservedShiftIndex and
+ // pdbeIndex...
continue;
}
- if (currSeqIndex >= seq.getStart() && currSeqIndex <= seq.getEnd())
+ // if (currSeqIndex >= seq.getStart() && currSeqIndex <= seqlength) //
+ // true
+ // numbering
+ // is
+ // not
+ // up
+ // to
+ // seq.getEnd()
{
int resNum = (pdbRefDb == null)
: getLeadingIntegerValue(pdbRefDb.getDbResNum(),
UNASSIGNED);
- if (isResidueObserved(residue)
- || seqCoordSys == CoordinateSys.UNIPROT)
+ if (isObserved)
{
char resCharCode = ResidueProperties
.getSingleCharacterCode(ResidueProperties
.getCanonicalAminoAcid(residue.getDbResName()));
resNumMap.put(currSeqIndex, String.valueOf(resCharCode));
+
+ int[] mappingcols = new int[] { Integer.valueOf(resNum),
+ UNASSIGNED, isObserved ? firstPDBResNum : UNASSIGNED };
+
+ mapping.put(currSeqIndex - nonObservedShiftIndex, mappingcols);
}
- else
- {
- omitNonObserved.add(currSeqIndex);
- ++nonObservedShiftIndex;
- }
- mapping.put(currSeqIndex - nonObservedShiftIndex,
- new int[]
- { Integer.valueOf(resNum), UNASSIGNED });
}
}
}
*/
private boolean isResidueObserved(Residue residue)
{
- Set<String> annotations = getResidueAnnotaitons(residue,
+ Set<String> annotations = getResidueAnnotations(residue,
ResidueDetailType.ANNOTATION);
if (annotations == null || annotations.isEmpty())
{
* @param type
* @return
*/
- private Set<String> getResidueAnnotaitons(Residue residue,
+ private Set<String> getResidueAnnotations(Residue residue,
ResidueDetailType type)
{
- HashSet<String> foundAnnotations = new HashSet<String>();
+ HashSet<String> foundAnnotations = new HashSet<>();
List<ResidueDetail> resDetails = residue.getResidueDetail();
for (ResidueDetail resDetail : resDetails)
{
public int resCount;
+ protected SiftsEntitySortPojo()
+ {
+ }
+
@Override
public int compareTo(SiftsEntitySortPojo o)
{
private int nonObservedShiftIndex;
+ /**
+ * count of number of 'not observed' positions in the PDB record's SEQRES
+ * (total number of residues with coordinates == length(SEQRES) -
+ * pdbeNonObserved
+ */
+ private int pdbeNonObserved;
+
public SegmentHelperPojo(SequenceI seq, HashMap<Integer, int[]> mapping,
TreeMap<Integer, String> resNumMap,
- List<Integer> omitNonObserved, int nonObservedShiftIndex)
+ List<Integer> omitNonObserved, int nonObservedShiftIndex,
+ int pdbeNonObserved)
{
setSeq(seq);
setMapping(mapping);
setResNumMap(resNumMap);
setOmitNonObserved(omitNonObserved);
setNonObservedShiftIndex(nonObservedShiftIndex);
+ setPdbeNonObserved(pdbeNonObserved);
+
+ }
+
+ public void setPdbeNonObserved(int pdbeNonObserved2)
+ {
+ this.pdbeNonObserved = pdbeNonObserved2;
+ }
+
+ public int getPdbeNonObserved()
+ {
+ return pdbeNonObserved;
}
public SequenceI getSeq()
{
this.nonObservedShiftIndex = nonObservedShiftIndex;
}
+
}
@Override
git://source.jalview.org / jalview.git / blobdiff