X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fsifts%2FSiftsClient.java;h=9f7bc525335d335aaa1ca6923c20ee7997ab5e01;hb=6dacd9d2805d0899a59329fdc4e43dfacdf93044;hp=106a66effa2e9fedcb2d30c26e065d577ef3a165;hpb=4ff572f7cf17f5ca9c23f82bbe41005af8af55cc;p=jalview.git diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java index 106a66e..9f7bc52 100644 --- a/src/jalview/ws/sifts/SiftsClient.java +++ b/src/jalview/ws/sifts/SiftsClient.java @@ -47,9 +47,14 @@ import java.io.InputStream; import java.io.PrintStream; import java.net.URL; import java.net.URLConnection; +import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.attribute.BasicFileAttributes; import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; +import java.util.Collections; +import java.util.Date; import java.util.HashMap; import java.util.HashSet; import java.util.List; @@ -96,16 +101,10 @@ public class SiftsClient implements SiftsClientI private static final String SIFTS_FTP_BASE_URL = "ftp://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/"; - public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System - .getProperty("user.home") - + File.separatorChar - + ".sifts_downloads" + File.separatorChar; - - public static final String SIFTS_DOWNLOAD_DIR = jalview.bin.Cache - .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR); - private final static String NEWLINE = System.lineSeparator(); + private final static int THRESHOLD_IN_DAYS = 2; + private String curSourceDBRef; private HashSet curDBRefAccessionIdsString; @@ -185,12 +184,11 @@ public class SiftsClient implements SiftsClientI */ private Entry parseSIFTs(File siftFile) throws SiftsException { - try + try (InputStream in = new FileInputStream(siftFile); + GZIPInputStream gzis = new GZIPInputStream(in);) { - System.out.println("File : " + siftFile.getAbsolutePath()); + // System.out.println("File : " + siftFile.getAbsolutePath()); JAXBContext jc = JAXBContext.newInstance("jalview.xml.binding.sifts"); - InputStream in = new FileInputStream(siftFile); - GZIPInputStream gzis = new GZIPInputStream(in); XMLStreamReader streamReader = XMLInputFactory.newInstance() .createXMLStreamReader(gzis); Unmarshaller um = jc.createUnmarshaller(); @@ -228,14 +226,18 @@ public class SiftsClient implements SiftsClientI */ public static File getSiftsFile(String pdbId) throws SiftsException { - File siftsFile = new File(SIFTS_DOWNLOAD_DIR + pdbId.toLowerCase() - + ".xml.gz"); + File siftsFile = new File(SiftsSettings.getSiftDownloadDirectory() + + pdbId.toLowerCase() + ".xml.gz"); if (siftsFile.exists()) { - // TODO it may be worth performing an age check to determine if a - // new SIFTs file should be re-downloaded as SIFTs entries are usually - // updated weekly + // 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)) + { + // System.out.println("Downloaded file is out of date, hence re-downloading..."); + siftsFile = downloadSiftsFile(pdbId.toLowerCase()); + } return siftsFile; } siftsFile = downloadSiftsFile(pdbId.toLowerCase()); @@ -243,6 +245,34 @@ public class SiftsClient implements SiftsClientI } /** + * This method enables checking if a cached file has exceeded a certain + * threshold(in days) + * + * @param file + * the cached file + * @param noOfDays + * the threshold in days + * @return + */ + public static boolean isFileOlderThanThreshold(File file, int noOfDays) + { + Path filePath = file.toPath(); + BasicFileAttributes attr; + int diffInDays = 0; + try + { + attr = Files.readAttributes(filePath, BasicFileAttributes.class); + diffInDays = (int) ((new Date().getTime() - attr.lastModifiedTime() + .toMillis()) / (1000 * 60 * 60 * 24)); + // System.out.println("Diff in days : " + diffInDays); + } catch (IOException e) + { + e.printStackTrace(); + } + return noOfDays <= diffInDays; + } + + /** * Download a SIFTs XML file for a given PDB Id from an FTP repository * * @param pdbId @@ -253,15 +283,17 @@ public class SiftsClient implements SiftsClientI { String siftFile = pdbId + ".xml.gz"; String siftsFileFTPURL = SIFTS_FTP_BASE_URL + siftFile; - String downloadedSiftsFile = SIFTS_DOWNLOAD_DIR + siftFile; - File siftsDownloadDir = new File(SIFTS_DOWNLOAD_DIR); + String downloadedSiftsFile = SiftsSettings.getSiftDownloadDirectory() + + siftFile; + File siftsDownloadDir = new File( + SiftsSettings.getSiftDownloadDirectory()); if (!siftsDownloadDir.exists()) { siftsDownloadDir.mkdirs(); } try { - System.out.println(">> Download ftp url : " + siftsFileFTPURL); + // System.out.println(">> Download ftp url : " + siftsFileFTPURL); URL url = new URL(siftsFileFTPURL); URLConnection conn = url.openConnection(); InputStream inputStream = conn.getInputStream(); @@ -275,7 +307,7 @@ public class SiftsClient implements SiftsClientI } outputStream.close(); inputStream.close(); - System.out.println(">>> File downloaded : " + downloadedSiftsFile); + // System.out.println(">>> File downloaded : " + downloadedSiftsFile); } catch (IOException ex) { throw new SiftsException(ex.getMessage()); @@ -292,8 +324,8 @@ public class SiftsClient implements SiftsClientI */ public static boolean deleteSiftsFileByPDBId(String pdbId) { - File siftsFile = new File(SIFTS_DOWNLOAD_DIR + pdbId.toLowerCase() - + ".xml.gz"); + File siftsFile = new File(SiftsSettings.getSiftDownloadDirectory() + + pdbId.toLowerCase() + ".xml.gz"); if (siftsFile.exists()) { return siftsFile.delete(); @@ -301,7 +333,6 @@ public class SiftsClient implements SiftsClientI return true; } - /** * Get a valid SIFTs DBRef for the given sequence current SIFTs entry * @@ -325,14 +356,6 @@ public class SiftsClient implements SiftsClientI DBRefEntry[] dbRefs = seq.getDBRefs(); if (dbRefs == null || dbRefs.length < 1) { - final SequenceI[] seqs = new SequenceI[] { seq }; - new jalview.ws.DBRefFetcher(seqs, null, null, null, false) - .fetchDBRefs(true); - dbRefs = seq.getDBRefs(); - } - - if (dbRefs == null || dbRefs.length < 1) - { throw new SiftsException("Could not get source DB Ref"); } @@ -358,7 +381,6 @@ public class SiftsClient implements SiftsClientI throw new SiftsException("Could not get source DB Ref"); } - /** * Check that the DBRef Entry is properly populated and is available in this * SiftClient instance @@ -421,15 +443,13 @@ public class SiftsClient implements SiftsClientI String mappingOutput = mappingDetails.toString(); StructureMapping siftsMapping = new StructureMapping(seq, pdbFile, - pdbId, chain, mapping, - mappingOutput); + pdbId, chain, mapping, mappingOutput); return siftsMapping; } @Override - public HashMap getGreedyMapping(String entityId, SequenceI seq, - java.io.PrintStream os) - throws SiftsException + public HashMap getGreedyMapping(String entityId, + SequenceI seq, java.io.PrintStream os) throws SiftsException { ArrayList omitNonObserved = new ArrayList(); int nonObservedShiftIndex = 0; @@ -437,8 +457,7 @@ public class SiftsClient implements SiftsClientI Entity entity = null; entity = getEntityById(entityId); String originalSeq = AlignSeq.extractGaps( - jalview.util.Comparison.GapChars, - seq.getSequenceAsString()); + jalview.util.Comparison.GapChars, seq.getSequenceAsString()); HashMap mapping = new HashMap(); DBRefEntryI sourceDBRef = seq.getSourceDBRef(); if (sourceDBRef == null) @@ -490,7 +509,14 @@ public class SiftsClient implements SiftsClientI String resNumIndexString = cRefDb.getDbResNum() .equalsIgnoreCase("None") ? String.valueOf(UNASSIGNED) : cRefDb.getDbResNum(); - currSeqIndex = Integer.valueOf(resNumIndexString); + try + { + currSeqIndex = Integer.valueOf(resNumIndexString); + } catch (NumberFormatException nfe) + { + currSeqIndex = Integer.valueOf(resNumIndexString + .split("[a-zA-Z]")[0]); + } if (pdbRefDb != null) { break;// exit loop if pdb and uniprot are already found @@ -507,7 +533,8 @@ public class SiftsClient implements SiftsClientI try { resNum = (pdbRefDb == null) ? Integer.valueOf(residue - .getDbResNum()) : Integer.valueOf(pdbRefDb.getDbResNum()); + .getDbResNum()) : Integer.valueOf(pdbRefDb + .getDbResNum()); } catch (NumberFormatException nfe) { resNum = (pdbRefDb == null) ? Integer.valueOf(residue @@ -519,7 +546,8 @@ public class SiftsClient implements SiftsClientI || seqCoordSys == CoordinateSys.UNIPROT) { char resCharCode = ResidueProperties - .getSingleCharacterCode(residue.getDbResName()); + .getSingleCharacterCode(ResidueProperties + .getCanonicalAminoAcid(residue.getDbResName())); resNumMap.put(currSeqIndex, String.valueOf(resCharCode)); } else @@ -539,7 +567,10 @@ public class SiftsClient implements SiftsClientI { e.printStackTrace(); } - padWithGaps(resNumMap, omitNonObserved); + if (seqCoordSys == CoordinateSys.UNIPROT) + { + padWithGaps(resNumMap, omitNonObserved); + } int seqStart = UNASSIGNED; int seqEnd = UNASSIGNED; int pdbStart = UNASSIGNED; @@ -675,7 +706,6 @@ public class SiftsClient implements SiftsClientI } } - /** * * @param chainId @@ -740,9 +770,94 @@ public class SiftsClient implements SiftsClientI } return entity; } + Entity entity = getEntityByMostOptimalMatchedId(id); + if (entity != null) + { + return entity; + } throw new SiftsException("Entity " + id + " not found"); } + /** + * This method was added because EntityId is NOT always equal to ChainId. + * Hence, it provides the logic to greedily detect the "true" Entity for a + * given chainId where discrepancies exist. + * + * @param chainId + * @return + */ + public Entity getEntityByMostOptimalMatchedId(String chainId) + { + System.out + .println("--------------> advanced greedy entityId matching block entered.."); + List entities = siftsEntry.getEntity(); + SiftsEntitySortPojo[] sPojo = new SiftsEntitySortPojo[entities.size()]; + int count = 0; + for (Entity entity : entities) + { + sPojo[count] = new SiftsEntitySortPojo(); + sPojo[count].entityId = entity.getEntityId(); + + List segments = entity.getSegment(); + for (Segment segment : segments) + { + List residues = segment.getListResidue().getResidue(); + for (Residue residue : residues) + { + List cRefDbs = residue.getCrossRefDb(); + for (CrossRefDb cRefDb : cRefDbs) + { + if (!cRefDb.getDbSource().equalsIgnoreCase("PDB")) + { + continue; + } + ++sPojo[count].resCount; + if (cRefDb.getDbChainId().equalsIgnoreCase(chainId)) + { + ++sPojo[count].chainIdFreq; + } + } + } + } + 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); + + if (sPojo[0].entityId != null) + { + for (Entity entity : entities) + { + if (!entity.getEntityId().equalsIgnoreCase(sPojo[0].entityId)) + { + continue; + } + return entity; + } + } + return null; + } + + public class SiftsEntitySortPojo implements + Comparable + { + public String entityId; + + public int chainIdFreq; + + public int pid; + + public int resCount; + + @Override + public int compareTo(SiftsEntitySortPojo o) + { + return this.pid - o.pid; + } + } + @Override public String[] getEntryDBs() { @@ -770,9 +885,9 @@ public class SiftsClient implements SiftsClientI String strName = mp.getStrName(); int pdbStart = mp.getStrStart(); int pdbEnd = mp.getStrEnd(); - + String type = mp.getType(); - + int maxid = (seqName.length() >= strName.length()) ? seqName.length() : strName.length(); int len = 72 - maxid - 1; @@ -799,7 +914,7 @@ public class SiftsClient implements SiftsClientI output.append(" - "); output.append(String.valueOf(pdbEnd)); output.append(NEWLINE).append(NEWLINE); - + int matchedSeqCount = 0; for (int j = 0; j < nochunks; j++) { @@ -823,32 +938,33 @@ public class SiftsClient implements SiftsClientI { try { - if ((i + (j * len)) < seqRes.length()) - { - if (seqRes.charAt(i + (j * len)) == strRes.charAt(i + (j * len)) - && !jalview.util.Comparison.isGap(seqRes.charAt(i - + (j * len)))) + if ((i + (j * len)) < seqRes.length()) { + if (seqRes.charAt(i + (j * len)) == strRes + .charAt(i + (j * len)) + && !jalview.util.Comparison.isGap(seqRes.charAt(i + + (j * len)))) + { matchedSeqCount++; - output.append("|"); - } - else if (type.equals("pep")) - { - if (ResidueProperties.getPAM250(seqRes.charAt(i + (j * len)), - strRes.charAt(i + (j * len))) > 0) + output.append("|"); + } + else if (type.equals("pep")) { - output.append("."); + if (ResidueProperties.getPAM250(seqRes.charAt(i + (j * len)), + strRes.charAt(i + (j * len))) > 0) + { + output.append("."); + } + else + { + output.append(" "); + } } else { output.append(" "); } } - else - { - output.append(" "); - } - } } catch (IndexOutOfBoundsException e) { continue; @@ -872,13 +988,13 @@ public class SiftsClient implements SiftsClientI { throw new SiftsException("Low PID detected for SIFTs mapping..."); } - output.append("Length of alignment = " + seqRes.length()) - .append(NEWLINE); + output.append("Length of alignment = " + seqRes.length()).append( + NEWLINE); output.append(new Format("Percentage ID = %2.2f").form(pid)); output.append(NEWLINE); return output; } - + @Override public int getEntityCount() { @@ -914,4 +1030,5 @@ public class SiftsClient implements SiftsClientI { return siftsEntry.getDbVersion(); } + }