X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fsifts%2FSiftsClient.java;h=13e52cdcf92e9eb58f7e847ce5c3daac79eb9a7d;hb=ac8d1df7e4ad0cb6a2e0119b132440c3f439d17c;hp=de8c6a949018cf8c108b8f1dab4c9f5de30b8d13;hpb=6d7ab37f37b09174ec61fee301aed6057ef86605;p=jalview.git diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java index de8c6a9..13e52cd 100644 --- a/src/jalview/ws/sifts/SiftsClient.java +++ b/src/jalview/ws/sifts/SiftsClient.java @@ -26,6 +26,7 @@ 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.Format; @@ -36,11 +37,9 @@ 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; @@ -58,32 +57,30 @@ 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 String segStartEnd; private CoordinateSys seqCoordSys = CoordinateSys.UNIPROT; @@ -95,11 +92,9 @@ 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(); @@ -147,7 +142,7 @@ 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.getId(); @@ -155,21 +150,6 @@ public class SiftsClient implements SiftsClientI 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.getId(); - siftsEntry = parseSIFTs(siftsFile); - } /** * Parse the given SIFTs File and return a JAXB POJO of parsed data @@ -191,23 +171,7 @@ 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()); @@ -224,8 +188,9 @@ 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!!! @@ -234,12 +199,28 @@ public class SiftsClient implements SiftsClientI 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; } @@ -277,8 +258,10 @@ 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")) { @@ -294,8 +277,6 @@ public class SiftsClient implements SiftsClientI { siftsDownloadDir.mkdirs(); } - try - { // System.out.println(">> Download ftp url : " + siftsFileFTPURL); URL url = new URL(siftsFileFTPURL); URLConnection conn = url.openConnection(); @@ -311,10 +292,6 @@ 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); } @@ -359,7 +336,8 @@ public class SiftsClient implements SiftsClientI DBRefEntry[] dbRefs = seq.getDBRefs(); if (dbRefs == null || dbRefs.length < 1) { - throw new SiftsException("Could not get source DB Ref"); + throw new SiftsException( + "Source DBRef could not be determined. DBRefs might not have been retrieved."); } for (DBRefEntryI dbRef : dbRefs) @@ -373,6 +351,7 @@ public class SiftsClient implements SiftsClientI && (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT) || dbRef .getSource().equalsIgnoreCase(DBRefSource.PDB))) { + seq.setSourceDBRef(dbRef); return dbRef; } } @@ -392,7 +371,7 @@ 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()); @@ -412,7 +391,8 @@ public class SiftsClient implements SiftsClientI .getMapRegion(); for (MapRegion mapRegion : mapRegions) { - accessions.add(mapRegion.getDb().getDbAccessionId()); + accessions + .add(mapRegion.getDb().getDbAccessionId().toLowerCase()); } } } @@ -454,21 +434,18 @@ 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 - } + 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)) @@ -490,9 +467,9 @@ public class SiftsClient implements SiftsClientI List segments = entity.getSegment(); for (Segment segment : segments) { - segStartEnd = segment.getStart() + " - " + segment.getEnd(); - System.out.println("Mappging segments : " + segment.getSegId() + "\\" - + segStartEnd); + // segStartEnd = segment.getStart() + " - " + segment.getEnd(); + // System.out.println("Mapping segments : " + segment.getSegId() + "\\" + // + segStartEnd); List residues = segment.getListResidue().getResidue(); for (Residue residue : residues) { @@ -632,6 +609,7 @@ public class SiftsClient implements SiftsClientI mop.setType("pep"); os.print(getMappingOutput(mop).toString()); + os.println(); } return mapping; } @@ -644,9 +622,10 @@ public class SiftsClient implements SiftsClientI * Two dimension array of residue index versus atom position * @throws IllegalArgumentException * Thrown if chainId or mapping is null + * @throws SiftsException */ - void populateAtomPositions(String chainId, - HashMap mapping) throws IllegalArgumentException + void populateAtomPositions(String chainId, Map mapping) + throws IllegalArgumentException, SiftsException { try { @@ -664,9 +643,12 @@ public class SiftsClient implements SiftsClientI map[PDB_ATOM_POS] = getAtomIndex(map[PDB_RES_POS], chain.atoms); } } + } catch (NullPointerException e) + { + throw new SiftsException(e.getMessage()); } catch (Exception e) { - e.printStackTrace(); + throw new SiftsException(e.getMessage()); } } @@ -703,7 +685,7 @@ public class SiftsClient implements SiftsClientI */ private boolean isResidueObserved(Residue residue) { - HashSet annotations = getResidueAnnotaitons(residue, + Set annotations = getResidueAnnotaitons(residue, ResidueDetailType.ANNOTATION); if (annotations == null || annotations.isEmpty()) { @@ -726,7 +708,7 @@ public class SiftsClient implements SiftsClientI * @param type * @return */ - private HashSet getResidueAnnotaitons(Residue residue, + private Set getResidueAnnotaitons(Residue residue, ResidueDetailType type) { HashSet foundAnnotations = new HashSet(); @@ -751,8 +733,9 @@ public class SiftsClient implements SiftsClientI private boolean isFoundInSiftsEntry(String accessionId) { + Set siftsDBRefs = getAllMappingAccession(); return accessionId != null - && getAllMappingAccession().contains(accessionId); + && siftsDBRefs.contains(accessionId.toLowerCase()); } /** @@ -760,8 +743,8 @@ public class SiftsClient implements SiftsClientI * * @param resNumMap */ - void padWithGaps(TreeMap resNumMap, - ArrayList omitNonObserved) + void padWithGaps(Map resNumMap, + List omitNonObserved) { if (resNumMap == null || resNumMap.isEmpty()) { @@ -771,8 +754,8 @@ public class SiftsClient implements SiftsClientI 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)) @@ -796,19 +779,19 @@ public class SiftsClient implements SiftsClientI // less optimised processing, where as changing the value to 'true' // optimises performance but might result to incorrect mapping in some cases // where SIFTS mappings are wrongly swapped between different chains. - boolean isGetEntityIdDirectly = false; - if (isGetEntityIdDirectly) - { - List entities = siftsEntry.getEntity(); - for (Entity entity : entities) - { - if (!entity.getEntityId().equalsIgnoreCase(id)) - { - continue; - } - return entity; - } - } + // boolean isGetEntityIdDirectly = false; + // if (isGetEntityIdDirectly) + // { + // List entities = siftsEntry.getEntity(); + // for (Entity entity : entities) + // { + // if (!entity.getEntityId().equalsIgnoreCase(id)) + // { + // continue; + // } + // return entity; + // } + // } Entity entity = getEntityByMostOptimalMatchedId(id); if (entity != null) { @@ -861,8 +844,8 @@ public class SiftsClient implements SiftsClientI ++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) { @@ -896,19 +879,6 @@ public class SiftsClient implements SiftsClientI } } - @Override - public String[] getEntryDBs() - { - System.out.println("\nListing DB entries..."); - List availDbs = new ArrayList(); - List dbs = siftsEntry.getListDB().getDb(); - for (Db db : dbs) - { - availDbs.add(db.getDbSource()); - System.out.println(db.getDbSource() + " | " + db.getDbCoordSys()); - } - return availDbs.toArray(new String[0]); - } @Override public StringBuffer getMappingOutput(MappingOutputPojo mp) @@ -935,7 +905,8 @@ 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); @@ -1029,7 +1000,6 @@ public class SiftsClient implements SiftsClientI output.append("Length of alignment = " + seqRes.length()).append( NEWLINE); output.append(new Format("Percentage ID = %2.2f").form(pid)); - output.append(NEWLINE); return output; } @@ -1052,12 +1022,6 @@ public class SiftsClient implements SiftsClientI } @Override - public String getDbEvidence() - { - return siftsEntry.getDbEvidence(); - } - - @Override public String getDbSource() { return siftsEntry.getDbSource();