X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fsifts%2FSiftsClient.java;h=acca50f861973ce4a593a3193efc89d0644c9429;hb=d5ada7fd50053719348ac1301f45b54970616a87;hp=cd132df0ad989e8af9b565b51d9ab7e4e0cb17f8;hpb=85fe40df41ed696ed5ca8128221a3a51c1047f2d;p=jalview.git diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java index cd132df..acca50f 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; @@ -95,23 +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 CACHE_THRESHOLD_IN_DAYS = 2; - // - // private final static int FAIL_SAFE_PID_THRESHOLD = 30; - private String curSourceDBRef; private HashSet curDBRefAccessionIdsString; - public enum CoordinateSys + private enum CoordinateSys { UNIPROT("UniProt"), PDB("PDBresnum"), PDBe("PDBe"); private String name; @@ -127,7 +117,7 @@ public class SiftsClient implements SiftsClientI } }; - public enum ResidueDetailType + private enum ResidueDetailType { NAME_SEC_STRUCTURE("nameSecondaryStructure"), CODE_SEC_STRUCTURE( "codeSecondaryStructure"), ANNOTATION("Annotation"); @@ -151,31 +141,15 @@ 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 * * @param siftFile @@ -195,23 +169,7 @@ 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()); @@ -228,8 +186,9 @@ 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!!! @@ -238,12 +197,28 @@ 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; } @@ -281,8 +256,10 @@ 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")) { @@ -298,27 +275,21 @@ public class SiftsClient implements SiftsClientI { siftsDownloadDir.mkdirs(); } - try - { - // System.out.println(">> Download ftp url : " + siftsFileFTPURL); - URL url = new URL(siftsFileFTPURL); - URLConnection conn = url.openConnection(); - InputStream inputStream = conn.getInputStream(); - FileOutputStream outputStream = new FileOutputStream( - downloadedSiftsFile); - byte[] buffer = new byte[BUFFER_SIZE]; - int bytesRead = -1; - while ((bytesRead = inputStream.read(buffer)) != -1) - { - outputStream.write(buffer, 0, bytesRead); - } - outputStream.close(); - inputStream.close(); - // System.out.println(">>> File downloaded : " + downloadedSiftsFile); - } catch (IOException ex) + // System.out.println(">> Download ftp url : " + siftsFileFTPURL); + URL url = new URL(siftsFileFTPURL); + URLConnection conn = url.openConnection(); + InputStream inputStream = conn.getInputStream(); + FileOutputStream outputStream = new FileOutputStream( + downloadedSiftsFile); + byte[] buffer = new byte[BUFFER_SIZE]; + int bytesRead = -1; + while ((bytesRead = inputStream.read(buffer)) != -1) { - throw new SiftsException(ex.getMessage()); + outputStream.write(buffer, 0, bytesRead); } + outputStream.close(); + inputStream.close(); + // System.out.println(">>> File downloaded : " + downloadedSiftsFile); return new File(downloadedSiftsFile); } @@ -352,39 +323,29 @@ 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) + String canonicalSource = DBRefUtils.getCanonicalName(dbRef + .getSource()); + if (isValidDBRefEntry(dbRef) + && (canonicalSource.equalsIgnoreCase(DBRefSource.UNIPROT) || canonicalSource + .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"); } @@ -396,7 +357,7 @@ 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()); @@ -416,7 +377,8 @@ public class SiftsClient implements SiftsClientI .getMapRegion(); for (MapRegion mapRegion : mapRegions) { - accessions.add(mapRegion.getDb().getDbAccessionId()); + accessions + .add(mapRegion.getDb().getDbAccessionId().toLowerCase()); } } } @@ -428,8 +390,8 @@ public class SiftsClient implements SiftsClientI String pdbFile, String chain) throws SiftsException { structId = (chain == null) ? pdbId : pdbId + "|" + chain; - System.out.println("Getting mapping for: " + pdbId + "|" + chain - + " : seq- " + seq.getName()); + System.out.println("Getting SIFTS mapping for " + structId + ": seq " + + seq.getName()); final StringBuilder mappingDetails = new StringBuilder(128); PrintStream ps = new PrintStream(System.out) @@ -458,21 +420,18 @@ 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)) @@ -492,11 +451,93 @@ 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; + + if (mapping.isEmpty()) + { + throw new SiftsException("SIFTS mapping failed"); + } + + Integer[] keys = mapping.keySet().toArray(new Integer[0]); + Arrays.sort(keys); + 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) { @@ -523,6 +564,7 @@ public class SiftsClient implements SiftsClientI { currSeqIndex = Integer.valueOf(resNumIndexString .split("[a-zA-Z]")[0]); + continue; } if (pdbRefDb != null) { @@ -534,7 +576,7 @@ public class SiftsClient implements SiftsClientI { continue; } - if (currSeqIndex > seq.getStart() && currSeqIndex <= seq.getEnd()) + if (currSeqIndex >= seq.getStart() && currSeqIndex <= seq.getEnd()) { int resNum; try @@ -547,6 +589,7 @@ 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) @@ -567,70 +610,6 @@ public class SiftsClient implements SiftsClientI } } } - 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; - int subSeqEnd = seqEnd - (orignalSeqStart - 1); - subSeqEnd = originalSeq.length() < subSeqEnd ? originalSeq.length() - : subSeqEnd; - matchedSeq = originalSeq.substring(subSeqStart, subSeqEnd); - } - } - - StringBuilder targetStrucSeqs = new StringBuilder(); - for (String res : resNumMap.values()) - { - targetStrucSeqs.append(res); - } - - if (os != null) - { - 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()); - } - return mapping; } /** @@ -641,22 +620,33 @@ 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 { - 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()) + try { - if (map[PDB_RES_POS] != UNASSIGNED) + PDBChain chain = pdb.findChain(chainId); + + if (chain == null || mapping == null) { - map[PDB_ATOM_POS] = getAtomIndex(map[PDB_RES_POS], chain.atoms); + 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()); } } @@ -693,7 +683,7 @@ 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()) { @@ -716,7 +706,7 @@ public class SiftsClient implements SiftsClientI * @param type * @return */ - private HashSet getResidueAnnotaitons(Residue residue, + private Set getResidueAnnotaitons(Residue residue, ResidueDetailType type) { HashSet foundAnnotations = new HashSet(); @@ -741,8 +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()); } /** @@ -750,19 +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)) @@ -772,20 +763,11 @@ public class SiftsClient implements SiftsClientI } } - - @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) { @@ -804,8 +786,7 @@ 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; @@ -835,12 +816,13 @@ 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) { @@ -856,7 +838,7 @@ public class SiftsClient implements SiftsClientI return null; } - public class SiftsEntitySortPojo implements + private class SiftsEntitySortPojo implements Comparable { public String entityId; @@ -874,18 +856,79 @@ 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) { - availDbs.add(db.getDbSource()); - System.out.println(db.getDbSource() + " | " + db.getDbCoordSys()); + 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) + { + 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 @@ -913,7 +956,8 @@ 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); @@ -1002,13 +1046,11 @@ public class SiftsClient implements SiftsClientI float pid = (float) matchedSeqCount / seqRes.length() * 100; 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; } @@ -1031,12 +1073,6 @@ public class SiftsClient implements SiftsClientI } @Override - public String getDbEvidence() - { - return siftsEntry.getDbEvidence(); - } - - @Override public String getDbSource() { return siftsEntry.getDbSource();