*/
package jalview.ws.sifts;
-import jalview.analysis.AlignSeq;
-import jalview.api.DBRefEntryI;
-import jalview.api.SiftsClientI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.SequenceI;
-import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureMapping;
-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.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.LinkedHashMap;
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.JAXBElement;
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 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.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
{
+ /*
+ * for use in mocking out file fetch for tests only
+ * - reset to null after testing!
+ */
+ private static File mockSiftsFile;
+
private Entry siftsEntry;
+ private StructureFile pdb;
+
private String pdbId;
private String structId;
- private String segStartEnd;
+ private CoordinateSys seqCoordSys = CoordinateSys.UNIPROT;
+
+ /**
+ * PDB sequence position to sequence coordinate mapping as derived from SIFTS
+ * record for the identified SeqCoordSys Used for lift-over from sequence
+ * derived from PDB (with first extracted PDBRESNUM as 'start' to the sequence
+ * being annotated with PDB data
+ */
+ private jalview.datamodel.Mapping seqFromPdbMapping;
private static final int BUFFER_SIZE = 4096;
- private static final String SIFTS_FTP_BASE_URL = "ftp://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
+ public static final int UNASSIGNED = Integer.MIN_VALUE;
+
+ private static final int PDB_RES_POS = 0;
+
+ private static final int PDB_ATOM_POS = 1;
+
+ private static final int PDBE_POS = 2;
- public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
- .getProperty("user.home")
- + File.separatorChar
- + ".sifts_downloads" + File.separatorChar;
+ private static final String NOT_OBSERVED = "Not_Observed";
- 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();
- /**
- * Fetch SIFTs file for the given PDB Id and construct an instance of
- * SiftsClient
- *
- * @param pdbId
- */
- public SiftsClient(String pdbId)
+ private String curSourceDBRef;
+
+ private HashSet<String> curDBRefAccessionIdsString;
+
+ private enum CoordinateSys
{
- this.pdbId = pdbId;
- try
+ UNIPROT("UniProt"), PDB("PDBresnum"), PDBe("PDBe");
+ private String name;
+
+ private CoordinateSys(String name)
{
- File siftsFile = getSiftsFile(pdbId);
- siftsEntry = parseSIFTs(siftsFile);
- } catch (Exception e)
+ this.name = name;
+ }
+
+ public String getName()
{
- e.printStackTrace();
+ return name;
}
- }
+ };
- /**
- * Construct an instance of SiftsClient using the supplied SIFTs file -
- * the SIFTs file should correspond to the given PDB Id
- *
- * @param pdbId
- * @param siftsFile
- */
- public SiftsClient(String pdbId, File siftsFile)
+ private enum ResidueDetailType
{
- this.pdbId = pdbId;
- try
+ NAME_SEC_STRUCTURE("nameSecondaryStructure"),
+ CODE_SEC_STRUCTURE("codeSecondaryStructure"), ANNOTATION("Annotation");
+ private String code;
+
+ private ResidueDetailType(String code)
{
- siftsEntry = parseSIFTs(siftsFile);
- } catch (Exception e)
+ this.code = code;
+ }
+
+ public String getCode()
{
- e.printStackTrace();
+ return code;
}
+ };
+ /**
+ * Fetch SIFTs file for the given PDBfile and construct an instance of
+ * SiftsClient
+ *
+ * @param pdbId
+ * @throws SiftsException
+ */
+ public SiftsClient(StructureFile pdb) throws SiftsException
+ {
+ this.pdb = pdb;
+ this.pdbId = pdb.getId();
+ File siftsFile = getSiftsFile(pdbId);
+ siftsEntry = parseSIFTs(siftsFile);
}
/**
* @throws Exception
* if a problem occurs while parsing the SIFTs XML
*/
- private Entry parseSIFTs(File siftFile) throws Exception
+ 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();
- return (Entry) um.unmarshal(streamReader);
- } catch (JAXBException e)
- {
- e.printStackTrace();
- } catch (FileNotFoundException e)
- {
- e.printStackTrace();
- } catch (XMLStreamException e)
- {
- e.printStackTrace();
- } catch (FactoryConfigurationError e)
- {
- e.printStackTrace();
- } catch (IOException e)
+ JAXBElement<Entry> jbe = um.unmarshal(streamReader, Entry.class);
+ return jbe.getValue();
+ } catch (Exception e)
{
e.printStackTrace();
+ throw new SiftsException(e.getMessage());
}
- throw new Exception("Error parsing siftFile");
}
/**
- * Get a SIFTs XML file for a given PDB Id
+ * Get a SIFTs XML file for a given PDB Id from Cache or download from FTP
+ * repository if not found in cache
*
* @param pdbId
* @return SIFTs XML file
+ * @throws SiftsException
*/
- public static File getSiftsFile(String pdbId)
+ 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 a timestamp 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;
}
/**
- * Download a SIFTs XML file for a given PDB Id
+ * 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, 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);
- if (!siftsDownloadDir.exists())
+
+ /*
+ * 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())
{
- siftsDownloadDir.mkdirs();
+ downloadTo = File.createTempFile(siftFile, ".xml.gz");
}
- try
+ else
{
- 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)
+ downloadTo = new File(
+ SiftsSettings.getSiftDownloadDirectory() + siftFile);
+ File siftsDownloadDir = new File(
+ SiftsSettings.getSiftDownloadDirectory());
+ if (!siftsDownloadDir.exists())
{
- outputStream.write(buffer, 0, bytesRead);
+ siftsDownloadDir.mkdirs();
}
- outputStream.close();
- inputStream.close();
- System.out.println(">>> File downloaded : " + downloadedSiftsFile);
- } catch (IOException ex)
+ }
+
+ // 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(
+ downloadTo);
+ byte[] buffer = new byte[BUFFER_SIZE];
+ int bytesRead = -1;
+ while ((bytesRead = inputStream.read(buffer)) != -1)
{
- ex.printStackTrace();
+ outputStream.write(buffer, 0, bytesRead);
}
- return new File(downloadedSiftsFile);
+ outputStream.close();
+ inputStream.close();
+ // System.out.println(">>> File downloaded : " + downloadedSiftsFile
+ // + " took " + (System.currentTimeMillis() - now) + "ms");
+ return downloadTo;
}
/**
*/
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("uniprot") || dbRef
- .getSource().equalsIgnoreCase("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 the
- * instantiated SIFTs Entry
+ * Check that the DBRef Entry is properly populated and is available in this
+ * SiftClient instance
*
* @param entry
* - 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());
- // & entry.getStartRes() > 0;
}
@Override
.getMapRegion();
for (MapRegion mapRegion : mapRegions)
{
- accessions.add(mapRegion.getDb().getDbAccessionId());
+ accessions
+ .add(mapRegion.getDb().getDbAccessionId().toLowerCase());
}
}
}
public StructureMapping getSiftsStructureMapping(SequenceI seq,
String pdbFile, String chain) throws SiftsException
{
+ SequenceI aseq = seq;
+ while (seq.getDatasetSequence() != null)
+ {
+ seq = seq.getDatasetSequence();
+ }
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)
mappingDetails.append(NEWLINE);
}
};
- int[][] mapping = getGreedyMapping(chain, seq, ps);
+ HashMap<Integer, int[]> mapping = getGreedyMapping(chain, seq, ps);
String mappingOutput = mappingDetails.toString();
- return new StructureMapping(seq, pdbFile, pdbId, chain, mapping,
- mappingOutput);
+ StructureMapping siftsMapping = new StructureMapping(aseq, pdbFile,
+ pdbId, chain, mapping, mappingOutput, seqFromPdbMapping);
+
+ return siftsMapping;
}
@Override
- public int[][] getGreedyMapping(String entityId, SequenceI seq,
- java.io.PrintStream os)
- throws SiftsException
- {
- int matchedResStart = -1;
- int matchedResEnd = -1;
- int counter = 0;
- int pdbStart = -1;
- int pdbEnd = -1;
- int sStart = -1;
- int sEnd = -1;
- boolean startDetected = false;
-
- System.out.println("Generating mappings for : " + entityId);
+ public HashMap<Integer, int[]> getGreedyMapping(String entityId,
+ SequenceI seq, java.io.PrintStream os) throws SiftsException
+ {
+ List<Integer> omitNonObserved = new ArrayList<>();
+ int nonObservedShiftIndex = 0,pdbeNonObserved=0;
+ // System.out.println("Generating mappings for : " + entityId);
Entity entity = null;
entity = getEntityById(entityId);
- String seqStr = AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
- seq.getSequenceAsString());
- int mapping[][] = new int[seqStr.length() + seq.getStart()][2];
- DBRefEntryI sourceDBRef = seq.getSourceDBRef();
- if (sourceDBRef == null)
+ String originalSeq = AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars, seq.getSequenceAsString());
+ HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>();
+ 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))
{
- sourceDBRef = getValidSourceDBRef(seq);
- // TODO update sequence start/end with sourceDBRef start/end
- // seq.setStart(sourceDBRef.getStartRes());
- // seq.setEnd(sourceDBRef.getEndRes());
+ seqCoordSys = CoordinateSys.PDB;
}
- String crossRefAccessionId = sourceDBRef.getAccessionId();
- int count = 0;
- for (int residue[] : mapping)
+ HashSet<String> dbRefAccessionIdsString = new HashSet<String>();
+ for (DBRefEntry dbref : seq.getDBRefs())
{
- residue[1] = count++;
- residue[0] = -1;
+ dbRefAccessionIdsString.add(dbref.getAccessionId().toLowerCase());
}
-
- LinkedHashMap<Integer, String> resNumMap = new LinkedHashMap<Integer, String>();
+ dbRefAccessionIdsString.add(sourceDBRef.getAccessionId().toLowerCase());
+
+ curDBRefAccessionIdsString = dbRefAccessionIdsString;
+ curSourceDBRef = sourceDBRef.getAccessionId();
+
+ TreeMap<Integer, String> resNumMap = new TreeMap<Integer, String>();
List<Segment> segments = entity.getSegment();
+ SegmentHelperPojo shp = new SegmentHelperPojo(seq, mapping, resNumMap,
+ omitNonObserved, nonObservedShiftIndex,pdbeNonObserved);
+ 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");
+ }
+ // 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<int[]> 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
+ {
+ for (int seqps:keys)
+ {
+ int pdbpos = mapping.get(seqps)[PDBE_POS];
+ if (pdbpos == UNASSIGNED)
+ {
+ // not correct - pdbpos might be -1, but leave it for now
+ continue;
+ }
+ if (_cfrom==null || seqps!=_cfrom[1]+1)
+ {
+ _cfrom = new int[] { seqps,seqps};
+ from.add(_cfrom);
+ _cto = null; // discontinuity
+ } else {
+ _cfrom[1]= seqps;
+ }
+ if (_cto==null || pdbpos!=1+_cto[1])
+ {
+ _cto = new int[] { pdbpos,pdbpos};
+ to.add(_cto);
+ } else {
+ _cto[1] = pdbpos;
+ }
+ }
+ _cfrom = new int[from.size() * 2];
+ _cto = new int[to.size() * 2];
+ int p = 0;
+ for (int[] range : from)
+ {
+ _cfrom[p++] = range[0];
+ _cfrom[p++] = range[1];
+ }
+ ;
+ p = 0;
+ for (int[] range : to)
+ {
+ _cto[p++] = range[0];
+ _cto[p++] = range[1];
+ }
+ ;
+
+ seqFromPdbMapping = new jalview.datamodel.Mapping(null, _cto, _cfrom,
+ 1,
+ 1);
+ 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();
+ int pdbeNonObservedCount = shp.getPdbeNonObserved();
+ int firstPDBResNum = UNASSIGNED;
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)
{
- int refDbResNum = -1;
+ boolean isObserved = isResidueObserved(residue);
+ int pdbeIndex = getLeadingIntegerValue(residue.getDbResNum(),
+ UNASSIGNED);
+ int currSeqIndex = UNASSIGNED;
List<CrossRefDb> cRefDbs = residue.getCrossRefDb();
+ CrossRefDb pdbRefDb = null;
for (CrossRefDb cRefDb : cRefDbs)
{
- if (cRefDb.getDbAccessionId().equalsIgnoreCase(
- crossRefAccessionId))
+ if (cRefDb.getDbSource().equalsIgnoreCase(DBRefSource.PDB))
+ {
+ pdbRefDb = cRefDb;
+ if (firstPDBResNum == UNASSIGNED)
+ {
+ firstPDBResNum = getLeadingIntegerValue(cRefDb.getDbResNum(),
+ UNASSIGNED);
+ }
+ else
+ {
+ if (isObserved)
+ {
+ // after we find the first observed residue we just increment
+ firstPDBResNum++;
+ }
+ }
+ }
+ if (cRefDb.getDbCoordSys().equalsIgnoreCase(seqCoordSys.getName())
+ && isAccessionMatched(cRefDb.getDbAccessionId()))
{
- refDbResNum = Integer.valueOf(cRefDb.getDbResNum());
+ currSeqIndex = getLeadingIntegerValue(cRefDb.getDbResNum(),
+ UNASSIGNED);
+ if (pdbRefDb != null)
+ {
+ break;// exit loop if pdb and uniprot are already found
+ }
}
}
- if (refDbResNum == -1)
+ if (!isObserved)
+ {
+ ++pdbeNonObservedCount;
+ }
+ if (seqCoordSys == seqCoordSys.PDB) // FIXME: is seqCoordSys ever PDBe
+ // ???
{
+ // if the sequence has a primary reference to the PDB, then we are
+ // dealing with a sequence extracted directly from the PDB. In that
+ // case, numbering is PDBe - non-observed residues
+ currSeqIndex = seq.getStart() - 1 + pdbeIndex;
+ }
+ if (!isObserved)
+ {
+ if (seqCoordSys != CoordinateSys.UNIPROT) // FIXME: PDB or PDBe only
+ // here
+ {
+ // mapping to PDB or PDBe so we need to bookkeep for the
+ // non-observed
+ // SEQRES positions
+ omitNonObserved.add(currSeqIndex);
+ ++nonObservedShiftIndex;
+ }
+ }
+ if (currSeqIndex == UNASSIGNED)
+ {
+ // change in logic - unobserved residues with no currSeqIndex
+ // corresponding are still counted in both nonObservedShiftIndex and
+ // pdbeIndex...
continue;
}
- int loopCount = 0;
- for (int[] x : mapping)
+ // if (currSeqIndex >= seq.getStart() && currSeqIndex <= seqlength) //
+ // true
+ // numbering
+ // is
+ // not
+ // up
+ // to
+ // seq.getEnd()
{
- if (loopCount > seq.getStart() && x[1] == refDbResNum)
+
+ int resNum = (pdbRefDb == null)
+ ? getLeadingIntegerValue(residue.getDbResNum(),
+ UNASSIGNED)
+ : getLeadingIntegerValue(pdbRefDb.getDbResNum(),
+ UNASSIGNED);
+
+ if (isObserved)
{
- int resNum = Integer.valueOf(residue.getDbResNum());
- x[0] = resNum;
char resCharCode = ResidueProperties
- .getSingleCharacterCode(residue.getDbResName());
- resNumMap.put(resNum, String.valueOf(resCharCode));
+ .getSingleCharacterCode(ResidueProperties
+ .getCanonicalAminoAcid(residue.getDbResName()));
+ resNumMap.put(currSeqIndex, String.valueOf(resCharCode));
+
+ int[] mappingcols = new int[] { Integer.valueOf(resNum),
+ UNASSIGNED, isObserved ? firstPDBResNum : UNASSIGNED };
+
+ mapping.put(currSeqIndex - nonObservedShiftIndex, mappingcols);
}
- ++loopCount;
}
}
}
+ }
- for (int[] x : mapping)
+ /**
+ * Get the leading integer part of a string that begins with an integer.
+ *
+ * @param input
+ * - the string input to process
+ * @param failValue
+ * - value returned if unsuccessful
+ * @return
+ */
+ static int getLeadingIntegerValue(String input, int failValue)
+ {
+ if (input == null)
+ {
+ return failValue;
+ }
+ String[] parts = input.split("(?=\\D)(?<=\\d)");
+ if (parts != null && parts.length > 0 && parts[0].matches("[0-9]+"))
+ {
+ return Integer.valueOf(parts[0]);
+ }
+ return failValue;
+ }
+
+ /**
+ *
+ * @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
{
- if (!startDetected && x[0] > -1)
+ PDBChain chain = pdb.findChain(chainId);
+
+ if (chain == null || mapping == null)
{
- matchedResStart = counter;
- // System.out.println(matchedResStart);
- startDetected = true;
+ throw new IllegalArgumentException(
+ "Chain id or mapping must not be null.");
}
-
- if (startDetected && x[0] == -1)
+ for (int[] map : mapping.values())
{
- matchedResEnd = counter;
+ if (map[PDB_RES_POS] != UNASSIGNED)
+ {
+ map[PDB_ATOM_POS] = getAtomIndex(map[PDB_RES_POS], chain.atoms);
+ }
}
- ++counter;
+ } catch (NullPointerException e)
+ {
+ throw new SiftsException(e.getMessage());
+ } catch (Exception e)
+ {
+ throw new SiftsException(e.getMessage());
}
+ }
- String matchedSeqStr = seqStr;
- if (matchedResStart != -1)
+ /**
+ *
+ * @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)
{
- matchedResEnd = (matchedResEnd == -1) ? counter : matchedResEnd;
- pdbStart = mapping[matchedResStart][0];
- pdbEnd = mapping[matchedResEnd - 1][0];
- sStart = mapping[matchedResStart][1];
- sEnd = mapping[matchedResEnd - 1][1];
- int seqStart = seq.getStart();
- if (seqStart > 1)
- {
- matchedResStart = matchedResStart - seqStart;
- matchedResEnd = matchedResEnd - seqStart;
- }
- else
+ throw new IllegalArgumentException(
+ "atoms collection must not be null!");
+ }
+ for (Atom atom : atoms)
+ {
+ if (atom.resNumber == residueIndex)
{
- --matchedResStart;
- --matchedResEnd;
+ return atom.atomIndex;
}
- matchedSeqStr = seqStr.substring(matchedResStart, matchedResEnd);
}
+ return UNASSIGNED;
+ }
- StringBuilder targetStrucSeqs = new StringBuilder();
- for (String res : resNumMap.values())
+ /**
+ * Checks if the residue instance is marked 'Not_observed' or not
+ *
+ * @param residue
+ * @return
+ */
+ private boolean isResidueObserved(Residue residue)
+ {
+ Set<String> annotations = getResidueAnnotaitons(residue,
+ ResidueDetailType.ANNOTATION);
+ if (annotations == null || annotations.isEmpty())
{
- targetStrucSeqs.append(res);
+ return true;
}
-
- try
+ for (String annotation : annotations)
{
- if (os != null)
+ if (annotation.equalsIgnoreCase(NOT_OBSERVED))
{
- MappingOutputPojo mop = new MappingOutputPojo();
- mop.setSeqStart(sStart);
- mop.setSeqEnd(sEnd);
- mop.setSeqName(seq.getName());
- mop.setSeqResidue(matchedSeqStr);
-
- mop.setStrStart(pdbStart);
- mop.setStrEnd(pdbEnd);
- mop.setStrName(structId);
- mop.setStrResidue(targetStrucSeqs.toString());
-
- mop.setType("pep");
- os.print(getMappingOutput(mop).toString());
+ return false;
}
- } catch (Exception ex)
+ }
+ return true;
+ }
+
+ /**
+ * Get annotation String for a given residue and annotation type
+ *
+ * @param residue
+ * @param type
+ * @return
+ */
+ private Set<String> getResidueAnnotaitons(Residue residue,
+ ResidueDetailType type)
+ {
+ HashSet<String> foundAnnotations = new HashSet<String>();
+ List<ResidueDetail> resDetails = residue.getResidueDetail();
+ for (ResidueDetail resDetail : resDetails)
{
- ex.printStackTrace();
+ if (resDetail.getProperty().equalsIgnoreCase(type.getCode()))
+ {
+ foundAnnotations.add(resDetail.getContent());
+ }
}
- return mapping;
+ return foundAnnotations;
}
@Override
- public boolean isFoundInSiftsEntry(String accessionId)
+ public boolean isAccessionMatched(String accession)
+ {
+ boolean isStrictMatch = true;
+ return isStrictMatch ? curSourceDBRef.equalsIgnoreCase(accession)
+ : curDBRefAccessionIdsString.contains(accession.toLowerCase());
+ }
+
+ private boolean isFoundInSiftsEntry(String accessionId)
{
+ Set<String> siftsDBRefs = getAllMappingAccession();
return accessionId != null
- && getAllMappingAccession().contains(accessionId);
+ && siftsDBRefs.contains(accessionId.toLowerCase());
}
+ /**
+ * Pad omitted residue positions in PDB sequence with gaps
+ *
+ * @param resNumMap
+ */
+ 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);
+ int firstIndex = keys[0];
+ int lastIndex = keys[keys.length - 1];
+ // 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))
+ {
+ resNumMap.put(x, "-");
+ }
+ }
+ }
@Override
public Entity getEntityById(String id) throws SiftsException
{
+ // 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)
+ {
+ 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<Entity> entities = siftsEntry.getEntity();
+ SiftsEntitySortPojo[] sPojo = new SiftsEntitySortPojo[entities.size()];
+ int count = 0;
for (Entity entity : entities)
{
- if (!entity.getEntityId().equalsIgnoreCase(id))
+ sPojo[count] = new SiftsEntitySortPojo();
+ sPojo[count].entityId = entity.getEntityId();
+
+ List<Segment> segments = entity.getSegment();
+ for (Segment segment : segments)
{
- continue;
+ 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;
+ }
+ }
+ }
}
- return entity;
+ sPojo[count].pid = (100 * sPojo[count].chainIdFreq)
+ / sPojo[count].resCount;
+ ++count;
}
- throw new SiftsException("Entity " + id + " not found");
+ 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 (sPojo[0].pid < 1)
+ {
+ return null;
+ }
+ for (Entity entity : entities)
+ {
+ if (!entity.getEntityId().equalsIgnoreCase(sPojo[0].entityId))
+ {
+ continue;
+ }
+ return entity;
+ }
+ }
+ return null;
}
- @Override
- public String[] getEntryDBs()
+ private class SiftsEntitySortPojo
+ implements Comparable<SiftsEntitySortPojo>
+ {
+ public String entityId;
+
+ public int chainIdFreq;
+
+ public int pid;
+
+ public int resCount;
+
+ @Override
+ public int compareTo(SiftsEntitySortPojo o)
+ {
+ return this.pid - o.pid;
+ }
+ }
+
+ 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;
+
+ /**
+ * count of number of 'not observed' positions in the PDB record's SEQRES
+ * (total number of residues with coordinates == length(SEQRES) -
+ * pdbeNonObserved
+ */
+ private int pdbeNonObserved;
+
+ public SegmentHelperPojo(SequenceI seq, HashMap<Integer, int[]> mapping,
+ TreeMap<Integer, String> resNumMap,
+ List<Integer> omitNonObserved, int nonObservedShiftIndex,
+ int pdbeNonObserved)
+ {
+ setSeq(seq);
+ setMapping(mapping);
+ setResNumMap(resNumMap);
+ setOmitNonObserved(omitNonObserved);
+ setNonObservedShiftIndex(nonObservedShiftIndex);
+ setPdbeNonObserved(pdbeNonObserved);
+
+ }
+
+ public void setPdbeNonObserved(int pdbeNonObserved2)
+ {
+ this.pdbeNonObserved = pdbeNonObserved2;
+ }
+
+ public int getPdbeNonObserved()
+ {
+ return pdbeNonObserved;
+ }
+ 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)
{
- availDbs.add(db.getDbSource());
- System.out.println(db.getDbSource() + " | " + db.getDbCoordSys());
+ this.omitNonObserved = omitNonObserved;
}
- return availDbs.toArray(new String[0]);
+
+ public int getNonObservedShiftIndex()
+ {
+ return nonObservedShiftIndex;
+ }
+
+ public void setNonObservedShiftIndex(int nonObservedShiftIndex)
+ {
+ this.nonObservedShiftIndex = nonObservedShiftIndex;
+ }
+
}
@Override
- public StringBuffer getMappingOutput(MappingOutputPojo mp)
+ public StringBuilder getMappingOutput(MappingOutputPojo mp)
+ throws SiftsException
{
String seqRes = mp.getSeqResidue();
String seqName = mp.getSeqName();
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 = 2;// mp.getWrapHeight();
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:");
+ output.append("Sequence \u27f7 Structure mapping details")
+ .append(NEWLINE);
+ output.append("Method: SIFTS");
output.append(NEWLINE).append(NEWLINE);
output.append(new Format("%" + maxid + "s").form(seqName));
output.append(" - ");
output.append(String.valueOf(pdbEnd));
output.append(NEWLINE).append(NEWLINE);
-
- float pid = 0;
+
+ ScoreMatrix pam250 = ScoreModels.getInstance().getPam250();
+ int matchedSeqCount = 0;
for (int j = 0; j < nochunks; j++)
{
// Print the first aligned sequence
- output.append(new Format("%" + (maxid) + "s").form(seqName)).append(
- " ");
+ output.append(new Format("%" + (maxid) + "s").form(seqName))
+ .append(" ");
for (int i = 0; i < len; i++)
{
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++)
{
- if ((i + (j * len)) < seqRes.length())
+ try
{
- if (seqRes.charAt(i + (j * len)) == strRes.charAt(i + (j * len))
- && !jalview.util.Comparison.isGap(seqRes.charAt(i
- + (j * len))))
- {
- pid++;
- output.append("|");
- }
- else if (type.equals("pep"))
+ if ((i + (j * len)) < seqRes.length())
{
- if (ResidueProperties.getPAM250(seqRes.charAt(i + (j * len)),
- strRes.charAt(i + (j * len))) > 0)
+ 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))
{
- output.append(".");
+ matchedSeqCount++;
+ output.append("|");
+ }
+ else if (type.equals("pep"))
+ {
+ if (pam250.getPairwiseScore(c1, c2) > 0)
+ {
+ output.append(".");
+ }
+ else
+ {
+ output.append(" ");
+ }
}
else
{
output.append(" ");
}
}
- else
- {
- output.append(" ");
- }
+ } catch (IndexOutOfBoundsException e)
+ {
+ continue;
}
}
// Now print the second aligned sequence
}
output.append(NEWLINE).append(NEWLINE);
}
- pid = pid / (seqRes.length()) * 100;
+ float pid = (float) matchedSeqCount / seqRes.length() * 100;
+ if (pid < SiftsSettings.getFailSafePIDThreshold())
+ {
+ 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);
- output.append("Mapping method: SIFTS").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