X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fsifts%2FSiftsClient.java;h=e08b8cbfe59b94513880406db9d7301c7170806b;hb=49321390421afef1f818b3b1ec10badd83e95cc2;hp=7d5ae2e528ce74fae7426868df8b1e3954882583;hpb=6971cef43ca33a794aef8e8493ba7301d921444e;p=jalview.git diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java index 7d5ae2e..e08b8cb 100644 --- a/src/jalview/ws/sifts/SiftsClient.java +++ b/src/jalview/ws/sifts/SiftsClient.java @@ -26,8 +26,10 @@ import jalview.api.SiftsClientI; import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; import jalview.datamodel.SequenceI; +import jalview.io.StructureFile; import jalview.schemes.ResidueProperties; import jalview.structure.StructureMapping; +import jalview.util.DBRefUtils; import jalview.util.Format; import jalview.xml.binding.sifts.Entry; import jalview.xml.binding.sifts.Entry.Entity; @@ -36,11 +38,9 @@ import jalview.xml.binding.sifts.Entry.Entity.Segment.ListMapRegion.MapRegion; import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue; import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue.CrossRefDb; import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue.ResidueDetail; -import jalview.xml.binding.sifts.Entry.ListDB.Db; import java.io.File; import java.io.FileInputStream; -import java.io.FileNotFoundException; import java.io.FileOutputStream; import java.io.IOException; import java.io.InputStream; @@ -58,33 +58,29 @@ import java.util.Date; import java.util.HashMap; import java.util.HashSet; import java.util.List; +import java.util.Map; +import java.util.Set; import java.util.TreeMap; import java.util.zip.GZIPInputStream; import javax.xml.bind.JAXBContext; -import javax.xml.bind.JAXBException; import javax.xml.bind.Unmarshaller; -import javax.xml.stream.FactoryConfigurationError; import javax.xml.stream.XMLInputFactory; -import javax.xml.stream.XMLStreamException; import javax.xml.stream.XMLStreamReader; import MCview.Atom; import MCview.PDBChain; -import MCview.PDBfile; public class SiftsClient implements SiftsClientI { private Entry siftsEntry; - private PDBfile pdb; + private StructureFile pdb; private String pdbId; private String structId; - private String segStartEnd; - private CoordinateSys seqCoordSys = CoordinateSys.UNIPROT; private static final int BUFFER_SIZE = 4096; @@ -95,21 +91,17 @@ public class SiftsClient implements SiftsClientI private static final int PDB_ATOM_POS = 1; - private static final String NOT_FOUND = "Not_Found"; - private static final String NOT_OBSERVED = "Not_Observed"; - private static final String SIFTS_FTP_BASE_URL = "ftp://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/"; + private static final String SIFTS_FTP_BASE_URL = "http://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/"; private final static String NEWLINE = System.lineSeparator(); - private final static int THRESHOLD_IN_DAYS = 2; - private String curSourceDBRef; private HashSet curDBRefAccessionIdsString; - public enum CoordinateSys + private enum CoordinateSys { UNIPROT("UniProt"), PDB("PDBresnum"), PDBe("PDBe"); private String name; @@ -125,7 +117,7 @@ public class SiftsClient implements SiftsClientI } }; - public enum ResidueDetailType + private enum ResidueDetailType { NAME_SEC_STRUCTURE("nameSecondaryStructure"), CODE_SEC_STRUCTURE( "codeSecondaryStructure"), ANNOTATION("Annotation"); @@ -149,29 +141,14 @@ public class SiftsClient implements SiftsClientI * @param pdbId * @throws SiftsException */ - public SiftsClient(PDBfile pdb) throws SiftsException + public SiftsClient(StructureFile pdb) throws SiftsException { this.pdb = pdb; - this.pdbId = pdb.id; + this.pdbId = pdb.getId(); File siftsFile = getSiftsFile(pdbId); siftsEntry = parseSIFTs(siftsFile); } - /** - * Construct an instance of SiftsClient using the supplied SIFTs file. Note: - * The SIFTs file should correspond to the PDB Id in PDBfile instance - * - * @param pdbId - * @param siftsFile - * @throws SiftsException - * @throws Exception - */ - public SiftsClient(PDBfile pdb, File siftsFile) throws SiftsException - { - this.pdb = pdb; - this.pdbId = pdb.id; - siftsEntry = parseSIFTs(siftsFile); - } /** * Parse the given SIFTs File and return a JAXB POJO of parsed data @@ -193,23 +170,7 @@ public class SiftsClient implements SiftsClientI .createXMLStreamReader(gzis); Unmarshaller um = jc.createUnmarshaller(); return (Entry) um.unmarshal(streamReader); - } catch (JAXBException e) - { - e.printStackTrace(); - throw new SiftsException(e.getMessage()); - } catch (FileNotFoundException e) - { - e.printStackTrace(); - throw new SiftsException(e.getMessage()); - } catch (XMLStreamException e) - { - e.printStackTrace(); - throw new SiftsException(e.getMessage()); - } catch (FactoryConfigurationError e) - { - e.printStackTrace(); - throw new SiftsException(e.getMessage()); - } catch (IOException e) + } catch (Exception e) { e.printStackTrace(); throw new SiftsException(e.getMessage()); @@ -226,21 +187,39 @@ public class SiftsClient implements SiftsClientI */ public static File getSiftsFile(String pdbId) throws SiftsException { - File siftsFile = new File(SiftsSettings.getSiftDownloadDirectory() - + pdbId.toLowerCase() + ".xml.gz"); + String siftsFileName = SiftsSettings.getSiftDownloadDirectory() + + pdbId.toLowerCase() + ".xml.gz"; + File siftsFile = new File(siftsFileName); if (siftsFile.exists()) { // The line below is required for unit testing... don't comment it out!!! System.out.println(">>> SIFTS File already downloaded for " + pdbId); - if (isFileOlderThanThreshold(siftsFile, THRESHOLD_IN_DAYS)) + if (isFileOlderThanThreshold(siftsFile, + SiftsSettings.getCacheThresholdInDays())) { - // System.out.println("Downloaded file is out of date, hence re-downloading..."); - siftsFile = downloadSiftsFile(pdbId.toLowerCase()); + File oldSiftsFile = new File(siftsFileName + "_old"); + siftsFile.renameTo(oldSiftsFile); + try + { + siftsFile = downloadSiftsFile(pdbId.toLowerCase()); + oldSiftsFile.delete(); + return siftsFile; + } catch (IOException e) + { + e.printStackTrace(); + oldSiftsFile.renameTo(siftsFile); + return new File(siftsFileName); + } } - return siftsFile; } - siftsFile = downloadSiftsFile(pdbId.toLowerCase()); + try + { + siftsFile = downloadSiftsFile(pdbId.toLowerCase()); + } catch (IOException e) + { + throw new SiftsException(e.getMessage()); + } return siftsFile; } @@ -278,9 +257,15 @@ public class SiftsClient implements SiftsClientI * @param pdbId * @return downloaded SIFTs XML file * @throws SiftsException + * @throws IOException */ - public static File downloadSiftsFile(String pdbId) throws SiftsException + public static File downloadSiftsFile(String pdbId) throws SiftsException, + IOException { + if (pdbId.contains(".cif")) + { + pdbId = pdbId.replace(".cif", ""); + } String siftFile = pdbId + ".xml.gz"; String siftsFileFTPURL = SIFTS_FTP_BASE_URL + siftFile; String downloadedSiftsFile = SiftsSettings.getSiftDownloadDirectory() @@ -291,8 +276,6 @@ public class SiftsClient implements SiftsClientI { siftsDownloadDir.mkdirs(); } - try - { // System.out.println(">> Download ftp url : " + siftsFileFTPURL); URL url = new URL(siftsFileFTPURL); URLConnection conn = url.openConnection(); @@ -308,10 +291,6 @@ public class SiftsClient implements SiftsClientI outputStream.close(); inputStream.close(); // System.out.println(">>> File downloaded : " + downloadedSiftsFile); - } catch (IOException ex) - { - throw new SiftsException(ex.getMessage()); - } return new File(downloadedSiftsFile); } @@ -345,39 +324,30 @@ public class SiftsClient implements SiftsClientI public DBRefEntryI getValidSourceDBRef(SequenceI seq) throws SiftsException { - DBRefEntryI sourceDBRef = null; - sourceDBRef = seq.getSourceDBRef(); - if (sourceDBRef != null && isValidDBRefEntry(sourceDBRef)) + List dbRefs = seq.getPrimaryDBRefs(); + if (dbRefs == null || dbRefs.size() < 1) { - return sourceDBRef; + throw new SiftsException( + "Source DBRef could not be determined. DBRefs might not have been retrieved."); } - else + + for (DBRefEntry dbRef : dbRefs) { - DBRefEntry[] dbRefs = seq.getDBRefs(); - if (dbRefs == null || dbRefs.length < 1) + if (dbRef == null || dbRef.getAccessionId() == null + || dbRef.getSource() == null) { - throw new SiftsException("Could not get source DB Ref"); + continue; } - - for (DBRefEntryI dbRef : dbRefs) + if (isValidDBRefEntry(dbRef) + && dbRef.isPrimary() + && (DBRefUtils.getCanonicalName(dbRef.getSource()) + .equalsIgnoreCase(DBRefSource.UNIPROT) || DBRefUtils + .getCanonicalName(dbRef.getSource()) + .equalsIgnoreCase(DBRefSource.PDB))) { - if (dbRef == null || dbRef.getAccessionId() == null - || dbRef.getSource() == null) - { - continue; - } - if (isFoundInSiftsEntry(dbRef.getAccessionId()) - && (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT) || dbRef - .getSource().equalsIgnoreCase(DBRefSource.PDB))) - { - return dbRef; - } + return dbRef; } } - if (sourceDBRef != null && isValidDBRefEntry(sourceDBRef)) - { - return sourceDBRef; - } throw new SiftsException("Could not get source DB Ref"); } @@ -389,7 +359,7 @@ public class SiftsClient implements SiftsClientI * - DBRefEntry to validate * @return true validation is successful otherwise false is returned. */ - private boolean isValidDBRefEntry(DBRefEntryI entry) + boolean isValidDBRefEntry(DBRefEntryI entry) { return entry != null && entry.getAccessionId() != null && isFoundInSiftsEntry(entry.getAccessionId()); @@ -409,7 +379,8 @@ public class SiftsClient implements SiftsClientI .getMapRegion(); for (MapRegion mapRegion : mapRegions) { - accessions.add(mapRegion.getDb().getDbAccessionId()); + accessions + .add(mapRegion.getDb().getDbAccessionId().toLowerCase()); } } } @@ -451,21 +422,18 @@ public class SiftsClient implements SiftsClientI public HashMap getGreedyMapping(String entityId, SequenceI seq, java.io.PrintStream os) throws SiftsException { - ArrayList omitNonObserved = new ArrayList(); + List omitNonObserved = new ArrayList(); int nonObservedShiftIndex = 0; - System.out.println("Generating mappings for : " + entityId); + // System.out.println("Generating mappings for : " + entityId); Entity entity = null; entity = getEntityById(entityId); String originalSeq = AlignSeq.extractGaps( jalview.util.Comparison.GapChars, seq.getSequenceAsString()); HashMap mapping = new HashMap(); - DBRefEntryI sourceDBRef = seq.getSourceDBRef(); - if (sourceDBRef == null) - { - sourceDBRef = getValidSourceDBRef(seq); - // TODO ensure sequence start/end is in the same coordinate system and - // consistent with the choosen sourceDBRef - } + DBRefEntryI sourceDBRef; + sourceDBRef = getValidSourceDBRef(seq); + // TODO ensure sequence start/end is in the same coordinate system and + // consistent with the choosen sourceDBRef // set sequence coordinate system - default value is UniProt if (sourceDBRef.getSource().equalsIgnoreCase(DBRefSource.PDB)) @@ -485,11 +453,92 @@ public class SiftsClient implements SiftsClientI TreeMap resNumMap = new TreeMap(); List segments = entity.getSegment(); + SegmentHelperPojo shp = new SegmentHelperPojo(seq, mapping, resNumMap, + omitNonObserved, nonObservedShiftIndex); + processSegments(segments, shp); + try + { + populateAtomPositions(entityId, mapping); + } catch (Exception e) + { + e.printStackTrace(); + } + if (seqCoordSys == CoordinateSys.UNIPROT) + { + padWithGaps(resNumMap, omitNonObserved); + } + int seqStart = UNASSIGNED; + int seqEnd = UNASSIGNED; + int pdbStart = UNASSIGNED; + int pdbEnd = UNASSIGNED; + + Integer[] keys = mapping.keySet().toArray(new Integer[0]); + Arrays.sort(keys); + if (keys.length < 1) + { + throw new SiftsException(">>> Empty SIFTS mapping generated!!"); + } + seqStart = keys[0]; + seqEnd = keys[keys.length - 1]; + + String matchedSeq = originalSeq; + if (seqStart != UNASSIGNED) + { + pdbStart = mapping.get(seqStart)[PDB_RES_POS]; + pdbEnd = mapping.get(seqEnd)[PDB_RES_POS]; + int orignalSeqStart = seq.getStart(); + if (orignalSeqStart >= 1) + { + int subSeqStart = (seqStart >= orignalSeqStart) ? seqStart + - orignalSeqStart : 0; + int subSeqEnd = seqEnd - (orignalSeqStart - 1); + subSeqEnd = originalSeq.length() < subSeqEnd ? originalSeq.length() + : subSeqEnd; + matchedSeq = originalSeq.substring(subSeqStart, subSeqEnd); + } + else + { + matchedSeq = originalSeq.substring(1, originalSeq.length()); + } + } + + StringBuilder targetStrucSeqs = new StringBuilder(); + for (String res : resNumMap.values()) + { + targetStrucSeqs.append(res); + } + + if (os != null) + { + MappingOutputPojo mop = new MappingOutputPojo(); + mop.setSeqStart(pdbStart); + mop.setSeqEnd(pdbEnd); + mop.setSeqName(seq.getName()); + mop.setSeqResidue(matchedSeq); + + mop.setStrStart(seqStart); + mop.setStrEnd(seqEnd); + mop.setStrName(structId); + mop.setStrResidue(targetStrucSeqs.toString()); + + mop.setType("pep"); + os.print(getMappingOutput(mop).toString()); + os.println(); + } + return mapping; + } + + void processSegments(List segments, SegmentHelperPojo shp) + { + SequenceI seq = shp.getSeq(); + HashMap mapping = shp.getMapping(); + TreeMap resNumMap = shp.getResNumMap(); + List omitNonObserved = shp.getOmitNonObserved(); + int nonObservedShiftIndex = shp.getNonObservedShiftIndex(); for (Segment segment : segments) { - segStartEnd = segment.getStart() + " - " + segment.getEnd(); - System.out.println("Mappging segments : " + segment.getSegId() + "\\" - + segStartEnd); + // System.out.println("Mapping segments : " + segment.getSegId() + "\\"s + // + segStartEnd); List residues = segment.getListResidue().getResidue(); for (Residue residue : residues) { @@ -516,6 +565,7 @@ public class SiftsClient implements SiftsClientI { currSeqIndex = Integer.valueOf(resNumIndexString .split("[a-zA-Z]")[0]); + continue; } if (pdbRefDb != null) { @@ -527,7 +577,7 @@ public class SiftsClient implements SiftsClientI { continue; } - if (currSeqIndex > seq.getStart() && currSeqIndex <= seq.getEnd()) + if (currSeqIndex >= seq.getStart() && currSeqIndex <= seq.getEnd()) { int resNum; try @@ -540,13 +590,15 @@ public class SiftsClient implements SiftsClientI resNum = (pdbRefDb == null) ? Integer.valueOf(residue .getDbResNum()) : Integer.valueOf(pdbRefDb .getDbResNum().split("[a-zA-Z]")[0]); + continue; } if (isResidueObserved(residue) || seqCoordSys == CoordinateSys.UNIPROT) { char resCharCode = ResidueProperties - .getSingleCharacterCode(residue.getDbResName()); + .getSingleCharacterCode(ResidueProperties + .getCanonicalAminoAcid(residue.getDbResName())); resNumMap.put(currSeqIndex, String.valueOf(resCharCode)); } else @@ -559,66 +611,68 @@ public class SiftsClient implements SiftsClientI } } } + } + /** + * + * @param chainId + * Target chain to populate mapping of its atom positions. + * @param mapping + * Two dimension array of residue index versus atom position + * @throws IllegalArgumentException + * Thrown if chainId or mapping is null + * @throws SiftsException + */ + void populateAtomPositions(String chainId, Map mapping) + throws IllegalArgumentException, SiftsException + { try { - populateAtomPositions(entityId, mapping); - } catch (Exception e) - { - e.printStackTrace(); - } - if (seqCoordSys == CoordinateSys.UNIPROT) - { - padWithGaps(resNumMap, omitNonObserved); - } - int seqStart = UNASSIGNED; - int seqEnd = UNASSIGNED; - int pdbStart = UNASSIGNED; - int pdbEnd = UNASSIGNED; - - Integer[] keys = mapping.keySet().toArray(new Integer[0]); - Arrays.sort(keys); - seqStart = keys[0]; - seqEnd = keys[keys.length - 1]; + PDBChain chain = pdb.findChain(chainId); - String matchedSeq = originalSeq; - if (seqStart != UNASSIGNED) - { - pdbStart = mapping.get(seqStart)[PDB_RES_POS]; - pdbEnd = mapping.get(seqEnd)[PDB_RES_POS]; - int orignalSeqStart = seq.getStart(); - if (orignalSeqStart >= 1) + if (chain == null || mapping == null) { - int subSeqStart = seqStart - orignalSeqStart; - int subSeqEnd = seqEnd - (orignalSeqStart - 1); - subSeqEnd = originalSeq.length() < subSeqEnd ? originalSeq.length() - : subSeqEnd; - matchedSeq = originalSeq.substring(subSeqStart, subSeqEnd); + throw new IllegalArgumentException( + "Chain id or mapping must not be null."); + } + for (int[] map : mapping.values()) + { + if (map[PDB_RES_POS] != UNASSIGNED) + { + map[PDB_ATOM_POS] = getAtomIndex(map[PDB_RES_POS], chain.atoms); + } } + } catch (NullPointerException e) + { + throw new SiftsException(e.getMessage()); + } catch (Exception e) + { + throw new SiftsException(e.getMessage()); } + } - StringBuilder targetStrucSeqs = new StringBuilder(); - for (String res : resNumMap.values()) + /** + * + * @param residueIndex + * The residue index used for the search + * @param atoms + * A collection of Atom to search + * @return atom position for the given residue index + */ + int getAtomIndex(int residueIndex, Collection atoms) + { + if (atoms == null) { - targetStrucSeqs.append(res); + throw new IllegalArgumentException( + "atoms collection must not be null!"); } - - if (os != null) + for (Atom atom : atoms) { - MappingOutputPojo mop = new MappingOutputPojo(); - mop.setSeqStart(seqStart); - mop.setSeqEnd(seqEnd); - mop.setSeqName(seq.getName()); - mop.setSeqResidue(matchedSeq); - - mop.setStrStart(pdbStart); - mop.setStrEnd(pdbEnd); - mop.setStrName(structId); - mop.setStrResidue(targetStrucSeqs.toString()); - - mop.setType("pep"); - os.print(getMappingOutput(mop).toString()); + if (atom.resNumber == residueIndex) + { + return atom.atomIndex; + } } - return mapping; + return UNASSIGNED; } /** @@ -629,16 +683,18 @@ public class SiftsClient implements SiftsClientI */ private boolean isResidueObserved(Residue residue) { - String annotation = getResidueAnnotaiton(residue, + Set annotations = getResidueAnnotaitons(residue, ResidueDetailType.ANNOTATION); - if (annotation == null) + if (annotations == null || annotations.isEmpty()) { return true; } - if (!annotation.equalsIgnoreCase(NOT_FOUND) - && annotation.equalsIgnoreCase(NOT_OBSERVED)) + for (String annotation : annotations) { - return false; + if (annotation.equalsIgnoreCase(NOT_OBSERVED)) + { + return false; + } } return true; } @@ -650,18 +706,19 @@ public class SiftsClient implements SiftsClientI * @param type * @return */ - private String getResidueAnnotaiton(Residue residue, + private Set getResidueAnnotaitons(Residue residue, ResidueDetailType type) { + HashSet foundAnnotations = new HashSet(); List resDetails = residue.getResidueDetail(); for (ResidueDetail resDetail : resDetails) { if (resDetail.getProperty().equalsIgnoreCase(type.getCode())) { - return resDetail.getContent(); + foundAnnotations.add(resDetail.getContent()); } } - return NOT_FOUND; + return foundAnnotations; } @Override @@ -674,8 +731,9 @@ public class SiftsClient implements SiftsClientI private boolean isFoundInSiftsEntry(String accessionId) { + Set siftsDBRefs = getAllMappingAccession(); return accessionId != null - && getAllMappingAccession().contains(accessionId); + && siftsDBRefs.contains(accessionId.toLowerCase()); } /** @@ -683,19 +741,19 @@ public class SiftsClient implements SiftsClientI * * @param resNumMap */ - void padWithGaps(TreeMap resNumMap, - ArrayList omitNonObserved) + void padWithGaps(Map resNumMap, + List omitNonObserved) { if (resNumMap == null || resNumMap.isEmpty()) { return; } Integer[] keys = resNumMap.keySet().toArray(new Integer[0]); - Arrays.sort(keys); + // Arrays.sort(keys); int firstIndex = keys[0]; int lastIndex = keys[keys.length - 1]; - System.out.println("Min value " + firstIndex); - System.out.println("Max value " + lastIndex); + // System.out.println("Min value " + firstIndex); + // System.out.println("Max value " + lastIndex); for (int x = firstIndex; x <= lastIndex; x++) { if (!resNumMap.containsKey(x) && !omitNonObserved.contains(x)) @@ -705,70 +763,13 @@ public class SiftsClient implements SiftsClientI } } - /** - * - * @param chainId - * Target chain to populate mapping of its atom positions. - * @param mapping - * Two dimension array of residue index versus atom position - * @throws IllegalArgumentException - * Thrown if chainId or mapping is null - */ - void populateAtomPositions(String chainId, HashMap mapping) - throws IllegalArgumentException - { - PDBChain chain = pdb.findChain(chainId); - if (chain == null || mapping == null) - { - throw new IllegalArgumentException( - "Chain id or mapping must not be null."); - } - for (int[] map : mapping.values()) - { - if (map[PDB_RES_POS] != UNASSIGNED) - { - map[PDB_ATOM_POS] = getAtomIndex(map[PDB_RES_POS], chain.atoms); - } - } - } - /** - * - * @param residueIndex - * The residue index used for the search - * @param atoms - * A collection of Atom to search - * @return atom position for the given residue index - */ - int getAtomIndex(int residueIndex, Collection atoms) - { - if (atoms == null) - { - throw new IllegalArgumentException( - "atoms collection must not be null!"); - } - for (Atom atom : atoms) - { - if (atom.resNumber == residueIndex) - { - return atom.atomIndex; - } - } - return UNASSIGNED; - } @Override public Entity getEntityById(String id) throws SiftsException { - List entities = siftsEntry.getEntity(); - for (Entity entity : entities) - { - if (!entity.getEntityId().equalsIgnoreCase(id)) - { - continue; - } - return entity; - } + // Determines an entity to process by performing a heuristic matching of all + // Entities with the given chainId and choosing the best matching Entity Entity entity = getEntityByMostOptimalMatchedId(id); if (entity != null) { @@ -787,8 +788,7 @@ public class SiftsClient implements SiftsClientI */ public Entity getEntityByMostOptimalMatchedId(String chainId) { - System.out - .println("--------------> advanced greedy entityId matching block entered.."); + // System.out.println("---> advanced greedy entityId matching block entered.."); List entities = siftsEntry.getEntity(); SiftsEntitySortPojo[] sPojo = new SiftsEntitySortPojo[entities.size()]; int count = 0; @@ -818,12 +818,13 @@ public class SiftsClient implements SiftsClientI } } } - sPojo[count].pid = 100 * (sPojo[count].chainIdFreq / sPojo[count].resCount); + sPojo[count].pid = (100 * sPojo[count].chainIdFreq) + / sPojo[count].resCount; ++count; } Arrays.sort(sPojo, Collections.reverseOrder()); - System.out.println("highest matched entity : " + sPojo[0].entityId); - System.out.println("highest matched pid : " + sPojo[0].pid); + // System.out.println("highest matched entity : " + sPojo[0].entityId); + // System.out.println("highest matched pid : " + sPojo[0].pid); if (sPojo[0].entityId != null) { @@ -839,7 +840,7 @@ public class SiftsClient implements SiftsClientI return null; } - public class SiftsEntitySortPojo implements + private class SiftsEntitySortPojo implements Comparable { public String entityId; @@ -857,18 +858,79 @@ public class SiftsClient implements SiftsClientI } } - @Override - public String[] getEntryDBs() + private class SegmentHelperPojo { - System.out.println("\nListing DB entries..."); - List availDbs = new ArrayList(); - List dbs = siftsEntry.getListDB().getDb(); - for (Db db : dbs) + private SequenceI seq; + + private HashMap mapping; + + private TreeMap resNumMap; + + private List omitNonObserved; + + private int nonObservedShiftIndex; + + public SegmentHelperPojo(SequenceI seq, + HashMap mapping, + TreeMap resNumMap, + List omitNonObserved, int nonObservedShiftIndex) + { + setSeq(seq); + setMapping(mapping); + setResNumMap(resNumMap); + setOmitNonObserved(omitNonObserved); + setNonObservedShiftIndex(nonObservedShiftIndex); + } + + public SequenceI getSeq() + { + return seq; + } + + public void setSeq(SequenceI seq) + { + this.seq = seq; + } + + public HashMap getMapping() + { + return mapping; + } + + public void setMapping(HashMap mapping) + { + this.mapping = mapping; + } + + public TreeMap getResNumMap() + { + return resNumMap; + } + + public void setResNumMap(TreeMap resNumMap) { - availDbs.add(db.getDbSource()); - System.out.println(db.getDbSource() + " | " + db.getDbCoordSys()); + this.resNumMap = resNumMap; + } + + public List getOmitNonObserved() + { + return omitNonObserved; + } + + public void setOmitNonObserved(List omitNonObserved) + { + this.omitNonObserved = omitNonObserved; + } + + public int getNonObservedShiftIndex() + { + return nonObservedShiftIndex; + } + + public void setNonObservedShiftIndex(int nonObservedShiftIndex) + { + this.nonObservedShiftIndex = nonObservedShiftIndex; } - return availDbs.toArray(new String[0]); } @Override @@ -896,7 +958,8 @@ public class SiftsClient implements SiftsClientI // output mappings StringBuffer output = new StringBuffer(); output.append(NEWLINE); - output.append("Sequence ⟷ Structure mapping details").append(NEWLINE); + output.append("Sequence \u27f7 Structure mapping details").append( + NEWLINE); output.append("Method: SIFTS"); output.append(NEWLINE).append(NEWLINE); @@ -983,14 +1046,13 @@ public class SiftsClient implements SiftsClientI output.append(NEWLINE).append(NEWLINE); } float pid = (float) matchedSeqCount / seqRes.length() * 100; - if (pid < 2) + if (pid < SiftsSettings.getFailSafePIDThreshold()) { - throw new SiftsException("Low PID detected for SIFTs mapping..."); + throw new SiftsException(">>> Low PID detected for SIFTs mapping..."); } output.append("Length of alignment = " + seqRes.length()).append( NEWLINE); output.append(new Format("Percentage ID = %2.2f").form(pid)); - output.append(NEWLINE); return output; } @@ -1013,12 +1075,6 @@ public class SiftsClient implements SiftsClientI } @Override - public String getDbEvidence() - { - return siftsEntry.getDbEvidence(); - } - - @Override public String getDbSource() { return siftsEntry.getDbSource();