X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fsifts%2FSiftsClient.java;h=92cb7af43a656462d41bd578d2ad0bf539c45dcf;hb=7f09e6ac5717bc78373c5d77f309831403e6ebf8;hp=b5f9653274344e97bad532411c21c7db43b45009;hpb=842713f26c299ec867320918a721ff5be9df7dbb;p=jalview.git diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java index b5f9653..92cb7af 100644 --- a/src/jalview/ws/sifts/SiftsClient.java +++ b/src/jalview/ws/sifts/SiftsClient.java @@ -20,27 +20,7 @@ */ package jalview.ws.sifts; -import jalview.analysis.AlignSeq; -import jalview.analysis.scoremodels.ScoreMatrix; -import jalview.analysis.scoremodels.ScoreModels; -import jalview.api.DBRefEntryI; -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.Comparison; -import jalview.util.DBRefUtils; -import jalview.util.Format; -import jalview.xml.binding.sifts.Entry; -import jalview.xml.binding.sifts.Entry.Entity; -import jalview.xml.binding.sifts.Entry.Entity.Segment; -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 java.util.Locale; import java.io.File; import java.io.FileInputStream; @@ -67,12 +47,37 @@ import java.util.TreeMap; import java.util.zip.GZIPInputStream; import javax.xml.bind.JAXBContext; +import javax.xml.bind.JAXBElement; import javax.xml.bind.Unmarshaller; import javax.xml.stream.XMLInputFactory; import javax.xml.stream.XMLStreamReader; -import MCview.Atom; -import MCview.PDBChain; +import jalview.analysis.AlignSeq; +import jalview.analysis.scoremodels.ScoreMatrix; +import jalview.analysis.scoremodels.ScoreModels; +import jalview.api.DBRefEntryI; +import jalview.api.SiftsClientI; +import jalview.bin.Console; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.DBRefSource; +import jalview.datamodel.SequenceI; +import jalview.io.BackupFiles; +import jalview.io.StructureFile; +import jalview.schemes.ResidueProperties; +import jalview.structure.StructureMapping; +import jalview.util.Comparison; +import jalview.util.DBRefUtils; +import jalview.util.Format; +import jalview.util.Platform; +import jalview.xml.binding.sifts.Entry; +import jalview.xml.binding.sifts.Entry.Entity; +import jalview.xml.binding.sifts.Entry.Entity.Segment; +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 mc_view.Atom; +import mc_view.PDBChain; public class SiftsClient implements SiftsClientI { @@ -112,7 +117,7 @@ public class SiftsClient implements SiftsClientI private static final String NOT_OBSERVED = "Not_Observed"; - private static final String SIFTS_FTP_BASE_URL = "http://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/"; + private static final String SIFTS_SPLIT_FTP_BASE_URL = "https://ftp.ebi.ac.uk/pub/databases/msd/sifts/split_xml/"; private final static String NEWLINE = System.lineSeparator(); @@ -123,6 +128,7 @@ public class SiftsClient implements SiftsClientI private enum CoordinateSys { UNIPROT("UniProt"), PDB("PDBresnum"), PDBe("PDBe"); + private String name; private CoordinateSys(String name) @@ -140,6 +146,7 @@ public class SiftsClient implements SiftsClientI { NAME_SEC_STRUCTURE("nameSecondaryStructure"), CODE_SEC_STRUCTURE("codeSecondaryStructure"), ANNOTATION("Annotation"); + private String code; private ResidueDetailType(String code) @@ -182,12 +189,13 @@ public class SiftsClient implements SiftsClientI try (InputStream in = new FileInputStream(siftFile); GZIPInputStream gzis = new GZIPInputStream(in);) { - // System.out.println("File : " + siftFile.getAbsolutePath()); + // jalview.bin.Console.outPrintln("File : " + siftFile.getAbsolutePath()); JAXBContext jc = JAXBContext.newInstance("jalview.xml.binding.sifts"); XMLStreamReader streamReader = XMLInputFactory.newInstance() .createXMLStreamReader(gzis); Unmarshaller um = jc.createUnmarshaller(); - return (Entry) um.unmarshal(streamReader); + JAXBElement jbe = um.unmarshal(streamReader, Entry.class); + return jbe.getValue(); } catch (Exception e) { e.printStackTrace(); @@ -214,27 +222,27 @@ public class SiftsClient implements SiftsClientI } String siftsFileName = SiftsSettings.getSiftDownloadDirectory() - + pdbId.toLowerCase() + ".xml.gz"; + + pdbId.toLowerCase(Locale.ROOT) + ".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); + jalview.bin.Console.outPrintln(">>> SIFTS File already downloaded for " + pdbId); if (isFileOlderThanThreshold(siftsFile, SiftsSettings.getCacheThresholdInDays())) { File oldSiftsFile = new File(siftsFileName + "_old"); - siftsFile.renameTo(oldSiftsFile); + BackupFiles.moveFileToFile(siftsFile, oldSiftsFile); try { - siftsFile = downloadSiftsFile(pdbId.toLowerCase()); + siftsFile = downloadSiftsFile(pdbId.toLowerCase(Locale.ROOT)); oldSiftsFile.delete(); return siftsFile; } catch (IOException e) { e.printStackTrace(); - oldSiftsFile.renameTo(siftsFile); + BackupFiles.moveFileToFile(oldSiftsFile, siftsFile); return new File(siftsFileName); } } @@ -245,7 +253,7 @@ public class SiftsClient implements SiftsClientI } try { - siftsFile = downloadSiftsFile(pdbId.toLowerCase()); + siftsFile = downloadSiftsFile(pdbId.toLowerCase(Locale.ROOT)); } catch (IOException e) { throw new SiftsException(e.getMessage()); @@ -274,7 +282,7 @@ public class SiftsClient implements SiftsClientI diffInDays = (int) ((new Date().getTime() - attr.lastModifiedTime().toMillis()) / (1000 * 60 * 60 * 24)); - // System.out.println("Diff in days : " + diffInDays); + // jalview.bin.Console.outPrintln("Diff in days : " + diffInDays); } catch (IOException e) { e.printStackTrace(); @@ -298,22 +306,36 @@ public class SiftsClient implements SiftsClientI pdbId = pdbId.replace(".cif", ""); } String siftFile = pdbId + ".xml.gz"; - String siftsFileFTPURL = SIFTS_FTP_BASE_URL + siftFile; - String downloadedSiftsFile = SiftsSettings.getSiftDownloadDirectory() - + siftFile; - File siftsDownloadDir = new File( - SiftsSettings.getSiftDownloadDirectory()); - if (!siftsDownloadDir.exists()) + String siftsFileFTPURL = getDownloadUrlFor(siftFile); + + /* + * Download the file from URL to either + * Java: directory of cached downloaded SIFTS files + * Javascript: temporary 'file' (in-memory cache) + */ + File downloadTo = null; + if (Platform.isJS()) + { + downloadTo = File.createTempFile(siftFile, ".xml.gz"); + } + else { - siftsDownloadDir.mkdirs(); + downloadTo = new File( + SiftsSettings.getSiftDownloadDirectory() + siftFile); + File siftsDownloadDir = new File( + SiftsSettings.getSiftDownloadDirectory()); + if (!siftsDownloadDir.exists()) + { + siftsDownloadDir.mkdirs(); + } } - // System.out.println(">> Download ftp url : " + siftsFileFTPURL); + + // jalview.bin.Console.outPrintln(">> Download ftp url : " + siftsFileFTPURL); // long now = System.currentTimeMillis(); URL url = new URL(siftsFileFTPURL); URLConnection conn = url.openConnection(); InputStream inputStream = conn.getInputStream(); - FileOutputStream outputStream = new FileOutputStream( - downloadedSiftsFile); + FileOutputStream outputStream = new FileOutputStream(downloadTo); byte[] buffer = new byte[BUFFER_SIZE]; int bytesRead = -1; while ((bytesRead = inputStream.read(buffer)) != -1) @@ -322,9 +344,17 @@ public class SiftsClient implements SiftsClientI } outputStream.close(); inputStream.close(); - // System.out.println(">>> File downloaded : " + downloadedSiftsFile + // jalview.bin.Console.outPrintln(">>> File downloaded : " + downloadedSiftsFile // + " took " + (System.currentTimeMillis() - now) + "ms"); - return new File(downloadedSiftsFile); + return downloadTo; + } + + public static String getDownloadUrlFor(String siftFile) + { + String durl = SIFTS_SPLIT_FTP_BASE_URL+siftFile.substring(1, 3)+"/"+siftFile; + Console.trace("SIFTS URL for "+siftFile+" is "+durl); + return durl; + } /** @@ -337,7 +367,7 @@ public class SiftsClient implements SiftsClientI public static boolean deleteSiftsFileByPDBId(String pdbId) { File siftsFile = new File(SiftsSettings.getSiftDownloadDirectory() - + pdbId.toLowerCase() + ".xml.gz"); + + pdbId.toLowerCase(Locale.ROOT) + ".xml.gz"); if (siftsFile.exists()) { return siftsFile.delete(); @@ -411,8 +441,8 @@ public class SiftsClient implements SiftsClientI .getMapRegion(); for (MapRegion mapRegion : mapRegions) { - accessions - .add(mapRegion.getDb().getDbAccessionId().toLowerCase()); + accessions.add(mapRegion.getDb().getDbAccessionId() + .toLowerCase(Locale.ROOT)); } } } @@ -429,7 +459,7 @@ public class SiftsClient implements SiftsClientI seq = seq.getDatasetSequence(); } structId = (chain == null) ? pdbId : pdbId + "|" + chain; - System.out.println("Getting SIFTS mapping for " + structId + ": seq " + jalview.bin.Console.outPrintln("Getting SIFTS mapping for " + structId + ": seq " + seq.getName()); final StringBuilder mappingDetails = new StringBuilder(128); @@ -461,8 +491,8 @@ public class SiftsClient implements SiftsClientI SequenceI seq, java.io.PrintStream os) throws SiftsException { List omitNonObserved = new ArrayList<>(); - int nonObservedShiftIndex = 0,pdbeNonObserved=0; - // System.out.println("Generating mappings for : " + entityId); + int nonObservedShiftIndex = 0, pdbeNonObserved = 0; + // jalview.bin.Console.outPrintln("Generating mappings for : " + entityId); Entity entity = null; entity = getEntityById(entityId); String originalSeq = AlignSeq.extractGaps( @@ -482,9 +512,11 @@ public class SiftsClient implements SiftsClientI HashSet dbRefAccessionIdsString = new HashSet(); for (DBRefEntry dbref : seq.getDBRefs()) { - dbRefAccessionIdsString.add(dbref.getAccessionId().toLowerCase()); + dbRefAccessionIdsString + .add(dbref.getAccessionId().toLowerCase(Locale.ROOT)); } - dbRefAccessionIdsString.add(sourceDBRef.getAccessionId().toLowerCase()); + dbRefAccessionIdsString + .add(sourceDBRef.getAccessionId().toLowerCase(Locale.ROOT)); curDBRefAccessionIdsString = dbRefAccessionIdsString; curSourceDBRef = sourceDBRef.getAccessionId(); @@ -492,7 +524,7 @@ public class SiftsClient implements SiftsClientI TreeMap resNumMap = new TreeMap(); List segments = entity.getSegment(); SegmentHelperPojo shp = new SegmentHelperPojo(seq, mapping, resNumMap, - omitNonObserved, nonObservedShiftIndex,pdbeNonObserved); + omitNonObserved, nonObservedShiftIndex, pdbeNonObserved); processSegments(segments, shp); try { @@ -512,20 +544,22 @@ public class SiftsClient implements SiftsClientI if (mapping.isEmpty()) { - throw new SiftsException("SIFTS mapping failed"); + throw new SiftsException("SIFTS mapping failed for "+entityId+" and "+seq.getName()); } - // also construct a mapping object between the seq-coord sys and the PDB seq's coord sys + // 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 from=new ArrayList<>(),to=new ArrayList<>(); - int[]_cfrom=null,_cto=null; + List from = new ArrayList<>(), to = new ArrayList<>(); + int[] _cfrom = null, _cto = null; String matchedSeq = originalSeq; - if (seqStart != UNASSIGNED) // fixme! seqStart can map to -1 for a pdb sequence that starts <-1 + if (seqStart != UNASSIGNED) // fixme! seqStart can map to -1 for a pdb + // sequence that starts <-1 { - for (int seqps:keys) + for (int seqps : keys) { int pdbpos = mapping.get(seqps)[PDBE_POS]; if (pdbpos == UNASSIGNED) @@ -533,19 +567,23 @@ public class SiftsClient implements SiftsClientI // not correct - pdbpos might be -1, but leave it for now continue; } - if (_cfrom==null || seqps!=_cfrom[1]+1) + if (_cfrom == null || seqps != _cfrom[1] + 1) { - _cfrom = new int[] { seqps,seqps}; + _cfrom = new int[] { seqps, seqps }; from.add(_cfrom); _cto = null; // discontinuity - } else { - _cfrom[1]= seqps; } - if (_cto==null || pdbpos!=1+_cto[1]) + else + { + _cfrom[1] = seqps; + } + if (_cto == null || pdbpos != 1 + _cto[1]) { - _cto = new int[] { pdbpos,pdbpos}; + _cto = new int[] { pdbpos, pdbpos }; to.add(_cto); - } else { + } + else + { _cto[1] = pdbpos; } } @@ -567,8 +605,7 @@ public class SiftsClient implements SiftsClientI ; seqFromPdbMapping = new jalview.datamodel.Mapping(null, _cto, _cfrom, - 1, - 1); + 1, 1); pdbStart = mapping.get(seqStart)[PDB_RES_POS]; pdbEnd = mapping.get(seqEnd)[PDB_RES_POS]; int orignalSeqStart = seq.getStart(); @@ -625,7 +662,7 @@ public class SiftsClient implements SiftsClientI int firstPDBResNum = UNASSIGNED; for (Segment segment : segments) { - // System.out.println("Mapping segments : " + segment.getSegId() + "\\"s + // jalview.bin.Console.outPrintln("Mapping segments : " + segment.getSegId() + "\\"s // + segStartEnd); List residues = segment.getListResidue().getResidue(); for (Residue residue : residues) @@ -699,12 +736,12 @@ public class SiftsClient implements SiftsClientI } // if (currSeqIndex >= seq.getStart() && currSeqIndex <= seqlength) // // true - // numbering - // is - // not - // up - // to - // seq.getEnd() + // numbering + // is + // not + // up + // to + // seq.getEnd() { int resNum = (pdbRefDb == null) @@ -867,14 +904,15 @@ public class SiftsClient implements SiftsClientI { boolean isStrictMatch = true; return isStrictMatch ? curSourceDBRef.equalsIgnoreCase(accession) - : curDBRefAccessionIdsString.contains(accession.toLowerCase()); + : curDBRefAccessionIdsString + .contains(accession.toLowerCase(Locale.ROOT)); } private boolean isFoundInSiftsEntry(String accessionId) { Set siftsDBRefs = getAllMappingAccession(); return accessionId != null - && siftsDBRefs.contains(accessionId.toLowerCase()); + && siftsDBRefs.contains(accessionId.toLowerCase(Locale.ROOT)); } /** @@ -893,8 +931,8 @@ 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); + // jalview.bin.Console.outPrintln("Min value " + firstIndex); + // jalview.bin.Console.outPrintln("Max value " + lastIndex); for (int x = firstIndex; x <= lastIndex; x++) { if (!resNumMap.containsKey(x) && !omitNonObserved.contains(x)) @@ -927,7 +965,7 @@ public class SiftsClient implements SiftsClientI */ public Entity getEntityByMostOptimalMatchedId(String chainId) { - // System.out.println("---> advanced greedy entityId matching block + // jalview.bin.Console.outPrintln("---> advanced greedy entityId matching block // entered.."); List entities = siftsEntry.getEntity(); SiftsEntitySortPojo[] sPojo = new SiftsEntitySortPojo[entities.size()]; @@ -963,8 +1001,8 @@ 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); + // jalview.bin.Console.outPrintln("highest matched entity : " + sPojo[0].entityId); + // jalview.bin.Console.outPrintln("highest matched pid : " + sPojo[0].pid); if (sPojo[0].entityId != null) { @@ -1044,6 +1082,7 @@ public class SiftsClient implements SiftsClientI { return pdbeNonObserved; } + public SequenceI getSeq() { return seq;