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.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;
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;
+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
{
+ /*
+ * for use in mocking out file fetch for tests only
+ * - reset to null after testing!
+ */
+ private static File mockSiftsFile;
+
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;
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/";
-
- 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 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 HashSet<String> curDBRefAccessionIdsString;
- public enum CoordinateSys
+ private enum CoordinateSys
{
UNIPROT("UniProt"), PDB("PDBresnum"), PDBe("PDBe");
private String name;
}
};
- public enum ResidueDetailType
+ private enum ResidueDetailType
{
NAME_SEC_STRUCTURE("nameSecondaryStructure"), CODE_SEC_STRUCTURE(
"codeSecondaryStructure"), ANNOTATION("Annotation");
* @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
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");
XMLStreamReader streamReader = XMLInputFactory.newInstance()
.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());
*/
public static File getSiftsFile(String pdbId) throws SiftsException
{
- File siftsFile = new File(SIFTS_DOWNLOAD_DIR + pdbId.toLowerCase()
- + ".xml.gz");
+ /*
+ * return mocked file if it has been set
+ */
+ if (mockSiftsFile != null)
+ {
+ return mockSiftsFile;
+ }
+
+ String siftsFileName = SiftsSettings.getSiftDownloadDirectory()
+ + pdbId.toLowerCase() + ".xml.gz";
+ File siftsFile = new File(siftsFileName);
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);
- return siftsFile;
+
+ if (isFileOlderThanThreshold(siftsFile,
+ SiftsSettings.getCacheThresholdInDays()))
+ {
+ 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);
+ }
+ }
+ else
+ {
+ return siftsFile;
+ }
+ }
+ try
+ {
+ siftsFile = downloadSiftsFile(pdbId.toLowerCase());
+ } catch (IOException e)
+ {
+ throw new SiftsException(e.getMessage());
}
- siftsFile = downloadSiftsFile(pdbId.toLowerCase());
return siftsFile;
}
/**
+ * 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
* @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 = 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);
+ // long now = System.currentTimeMillis();
+ 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)
{
- 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)
- {
- throw new SiftsException(ex.getMessage());
+ outputStream.write(buffer, 0, bytesRead);
}
+ outputStream.close();
+ inputStream.close();
+// System.out.println(">>> File downloaded : " + downloadedSiftsFile
+// + " took " + (System.currentTimeMillis() - now) + "ms");
return new File(downloadedSiftsFile);
}
*/
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();
return true;
}
-
/**
* Get a valid SIFTs DBRef for the given sequence current SIFTs entry
*
public DBRefEntryI getValidSourceDBRef(SequenceI seq)
throws SiftsException
{
- DBRefEntryI sourceDBRef = null;
- sourceDBRef = seq.getSourceDBRef();
- if (sourceDBRef != null && isValidDBRefEntry(sourceDBRef))
+ List<DBRefEntry> 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
- {
- 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)
+ for (DBRefEntry dbRef : dbRefs)
+ {
+ 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");
}
-
/**
* Check that the DBRef Entry is properly populated and is available in this
* SiftClient instance
* - 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());
.getMapRegion();
for (MapRegion mapRegion : mapRegions)
{
- accessions.add(mapRegion.getDb().getDbAccessionId());
+ accessions
+ .add(mapRegion.getDb().getDbAccessionId().toLowerCase());
}
}
}
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)
String mappingOutput = mappingDetails.toString();
StructureMapping siftsMapping = new StructureMapping(seq, pdbFile,
- pdbId, chain, mapping,
- mappingOutput);
+ pdbId, chain, mapping, mappingOutput);
return siftsMapping;
}
@Override
- public HashMap<Integer, int[]> getGreedyMapping(String entityId, SequenceI seq,
- java.io.PrintStream os)
- throws SiftsException
+ public HashMap<Integer, int[]> getGreedyMapping(String entityId,
+ SequenceI seq, java.io.PrintStream os) throws SiftsException
{
- ArrayList<Integer> omitNonObserved = new ArrayList<Integer>();
+ List<Integer> omitNonObserved = new ArrayList<Integer>();
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());
+ jalview.util.Comparison.GapChars, seq.getSequenceAsString());
HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>();
- 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))
TreeMap<Integer, String> resNumMap = new TreeMap<Integer, String>();
List<Segment> 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(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());
+ os.println();
+ }
+ return mapping;
+ }
+
+ void processSegments(List<Segment> segments, SegmentHelperPojo shp)
+ {
+ SequenceI seq = shp.getSeq();
+ HashMap<Integer, int[]> mapping = shp.getMapping();
+ TreeMap<Integer, String> resNumMap = shp.getResNumMap();
+ List<Integer> 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<Residue> residues = segment.getListResidue().getResidue();
for (Residue residue : residues)
{
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]);
+ continue;
+ }
if (pdbRefDb != null)
{
break;// exit loop if pdb and uniprot are already found
{
continue;
}
- if (currSeqIndex > seq.getStart() && currSeqIndex <= seq.getEnd())
+ if (currSeqIndex >= seq.getStart() && currSeqIndex <= seq.getEnd())
{
int resNum;
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
- .getDbResNum()) : Integer.valueOf(pdbRefDb
+ if (pdbRefDb == null || pdbRefDb.getDbResNum().equals("null"))
+ {
+ resNum = UNASSIGNED;
+ continue;
+ }
+ resNum = 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
}
}
}
+ }
+
+ /**
+ *
+ * @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<Integer, int[]> mapping)
+ throws IllegalArgumentException, SiftsException
+ {
try
{
- populateAtomPositions(entityId, mapping);
- } catch (Exception e)
- {
- e.printStackTrace();
- }
- padWithGaps(resNumMap, omitNonObserved);
- int seqStart = UNASSIGNED;
- int seqEnd = UNASSIGNED;
- int pdbStart = UNASSIGNED;
- int pdbEnd = UNASSIGNED;
+ PDBChain chain = pdb.findChain(chainId);
- 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)
+ 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<Atom> 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;
}
/**
*/
private boolean isResidueObserved(Residue residue)
{
- String annotation = getResidueAnnotaiton(residue,
+ Set<String> 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;
}
* @param type
* @return
*/
- private String getResidueAnnotaiton(Residue residue,
+ private Set<String> getResidueAnnotaitons(Residue residue,
ResidueDetailType type)
{
+ HashSet<String> foundAnnotations = new HashSet<String>();
List<ResidueDetail> 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
private boolean isFoundInSiftsEntry(String accessionId)
{
+ Set<String> siftsDBRefs = getAllMappingAccession();
return accessionId != null
- && getAllMappingAccession().contains(accessionId);
+ && siftsDBRefs.contains(accessionId.toLowerCase());
}
/**
*
* @param resNumMap
*/
- void padWithGaps(TreeMap<Integer, String> resNumMap,
- ArrayList<Integer> omitNonObserved)
+ void padWithGaps(Map<Integer, String> resNumMap,
+ List<Integer> 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))
}
}
-
- /**
- *
- * @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<Integer, int[]> mapping)
- throws IllegalArgumentException
+ @Override
+ public Entity getEntityById(String id) throws 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())
+ // 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)
{
- if (map[PDB_RES_POS] != UNASSIGNED)
- {
- map[PDB_ATOM_POS] = getAtomIndex(map[PDB_RES_POS], chain.atoms);
- }
+ 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 residueIndex
- * The residue index used for the search
- * @param atoms
- * A collection of Atom to search
- * @return atom position for the given residue index
+ * @param chainId
+ * @return
*/
- int getAtomIndex(int residueIndex, Collection<Atom> atoms)
+ public Entity getEntityByMostOptimalMatchedId(String chainId)
{
- if (atoms == null)
+ // System.out.println("---> advanced greedy entityId matching block entered..");
+ List<Entity> entities = siftsEntry.getEntity();
+ SiftsEntitySortPojo[] sPojo = new SiftsEntitySortPojo[entities.size()];
+ int count = 0;
+ for (Entity entity : entities)
{
- throw new IllegalArgumentException(
- "atoms collection must not be null!");
+ sPojo[count] = new SiftsEntitySortPojo();
+ sPojo[count].entityId = entity.getEntityId();
+
+ List<Segment> segments = entity.getSegment();
+ for (Segment segment : segments)
+ {
+ List<Residue> residues = segment.getListResidue().getResidue();
+ for (Residue residue : residues)
+ {
+ List<CrossRefDb> 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;
}
- for (Atom atom : atoms)
+ 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)
{
- if (atom.resNumber == residueIndex)
+ if (sPojo[0].pid < 1)
{
- return atom.atomIndex;
+ return null;
+ }
+ for (Entity entity : entities)
+ {
+ if (!entity.getEntityId().equalsIgnoreCase(sPojo[0].entityId))
+ {
+ continue;
+ }
+ return entity;
}
}
- return UNASSIGNED;
+ return null;
}
- @Override
- public Entity getEntityById(String id) throws SiftsException
+ private class SiftsEntitySortPojo implements
+ Comparable<SiftsEntitySortPojo>
{
- List<Entity> entities = siftsEntry.getEntity();
- for (Entity entity : entities)
+ public String entityId;
+
+ public int chainIdFreq;
+
+ public int pid;
+
+ public int resCount;
+
+ @Override
+ public int compareTo(SiftsEntitySortPojo o)
{
- if (!entity.getEntityId().equalsIgnoreCase(id))
- {
- continue;
- }
- return entity;
+ return this.pid - o.pid;
}
- throw new SiftsException("Entity " + id + " not found");
}
- @Override
- public String[] getEntryDBs()
+ private class SegmentHelperPojo
{
- System.out.println("\nListing DB entries...");
- List<String> availDbs = new ArrayList<String>();
- List<Db> dbs = siftsEntry.getListDB().getDb();
- for (Db db : dbs)
+ private SequenceI seq;
+
+ private HashMap<Integer, int[]> mapping;
+
+ private TreeMap<Integer, String> resNumMap;
+
+ private List<Integer> omitNonObserved;
+
+ private int nonObservedShiftIndex;
+
+ public SegmentHelperPojo(SequenceI seq,
+ HashMap<Integer, int[]> mapping,
+ TreeMap<Integer, String> resNumMap,
+ List<Integer> 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<Integer, int[]> getMapping()
+ {
+ return mapping;
+ }
+
+ public void setMapping(HashMap<Integer, int[]> mapping)
+ {
+ this.mapping = mapping;
+ }
+
+ public TreeMap<Integer, String> getResNumMap()
+ {
+ return resNumMap;
+ }
+
+ public void setResNumMap(TreeMap<Integer, String> resNumMap)
+ {
+ this.resNumMap = resNumMap;
+ }
+
+ public List<Integer> getOmitNonObserved()
+ {
+ return omitNonObserved;
+ }
+
+ public void setOmitNonObserved(List<Integer> omitNonObserved)
+ {
+ this.omitNonObserved = omitNonObserved;
+ }
+
+ public int getNonObservedShiftIndex()
+ {
+ return nonObservedShiftIndex;
+ }
+
+ public void setNonObservedShiftIndex(int nonObservedShiftIndex)
+ {
+ this.nonObservedShiftIndex = nonObservedShiftIndex;
}
- return availDbs.toArray(new String[0]);
}
@Override
- public StringBuffer getMappingOutput(MappingOutputPojo mp)
+ public StringBuilder getMappingOutput(MappingOutputPojo mp)
throws SiftsException
{
String seqRes = mp.getSeqResidue();
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;
int nochunks = ((seqRes.length()) / len)
+ ((seqRes.length()) % len > 0 ? 1 : 0);
// output mappings
- StringBuffer output = new StringBuffer();
+ StringBuilder output = new StringBuilder(512);
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);
output.append(" - ");
output.append(String.valueOf(pdbEnd));
output.append(NEWLINE).append(NEWLINE);
-
+
+ ScoreMatrix pam250 = ScoreModels.getInstance().getPam250();
int matchedSeqCount = 0;
for (int j = 0; j < nochunks; j++)
{
output.append(NEWLINE);
output.append(new Format("%" + (maxid) + "s").form(" ")).append(" ");
- // Print out the matching chars
+ /*
+ * Print out the match symbols:
+ * | for exact match (ignoring case)
+ * . if PAM250 score is positive
+ * else a space
+ */
for (int i = 0; i < len; i++)
{
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())
{
+ char c1 = seqRes.charAt(i + (j * len));
+ char c2 = strRes.charAt(i + (j * len));
+ boolean sameChar = Comparison.isSameResidue(c1, c2, false);
+ if (sameChar && !Comparison.isGap(c1))
+ {
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 (pam250.getPairwiseScore(c1, c2) > 0)
+ {
+ output.append(".");
+ }
+ else
+ {
+ output.append(" ");
+ }
}
else
{
output.append(" ");
}
}
- else
- {
- output.append(" ");
- }
- }
} catch (IndexOutOfBoundsException e)
{
continue;
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("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()
{
}
@Override
- public String getDbEvidence()
- {
- return siftsEntry.getDbEvidence();
- }
-
- @Override
public String getDbSource()
{
return siftsEntry.getDbSource();
{
return siftsEntry.getDbVersion();
}
+
+ public static void setMockSiftsFile(File file)
+ {
+ mockSiftsFile = file;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff