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.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
+import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.TreeMap;
private String segStartEnd;
- private static final String UNIPROT_COORDINATE_SYS = "UniProt";
-
- private static final String PDB_COORDINATE_SYS = "PDBresnum";
-
- private String seqCoordSys = UNIPROT_COORDINATE_SYS;
+ private CoordinateSys seqCoordSys = CoordinateSys.UNIPROT;
private static final int BUFFER_SIZE = 4096;
private static final int PDB_ATOM_POS = 1;
- private static final String SIFTS_FTP_BASE_URL = "ftp://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
+ private static final String NOT_FOUND = "Not_Found";
- 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 = "ftp://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
private final static String NEWLINE = System.lineSeparator();
+ private String curSourceDBRef;
+
+ private HashSet<String> curDBRefAccessionIdsString;
+
+ public enum CoordinateSys
+ {
+ UNIPROT("UniProt"), PDB("PDBresnum"), PDBe("PDBe");
+ private String name;
+
+ private CoordinateSys(String name)
+ {
+ this.name = name;
+ }
+
+ public String getName()
+ {
+ return name;
+ }
+ };
+
+ public enum ResidueDetailType
+ {
+ NAME_SEC_STRUCTURE("nameSecondaryStructure"), CODE_SEC_STRUCTURE(
+ "codeSecondaryStructure"), ANNOTATION("Annotation");
+ private String code;
+
+ private ResidueDetailType(String code)
+ {
+ this.code = code;
+ }
+
+ public String getCode()
+ {
+ return code;
+ }
+ };
+
/**
- * Fetch SIFTs file for the given PDB Id and construct an instance of
+ * Fetch SIFTs file for the given PDBfile and construct an instance of
* SiftsClient
*
* @param pdbId
+ * @throws SiftsException
*/
- public SiftsClient(PDBfile pdb)
+ public SiftsClient(PDBfile pdb) throws SiftsException
{
this.pdb = pdb;
this.pdbId = pdb.id;
- try
- {
- File siftsFile = getSiftsFile(pdbId);
- siftsEntry = parseSIFTs(siftsFile);
- } catch (Exception e)
- {
- e.printStackTrace();
- }
+ File siftsFile = getSiftsFile(pdbId);
+ siftsEntry = parseSIFTs(siftsFile);
}
/**
- * Construct an instance of SiftsClient using the supplied SIFTs file -
- * the SIFTs file should correspond to the given PDB Id
+ * 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)
+ public SiftsClient(PDBfile pdb, File siftsFile) throws SiftsException
{
this.pdb = pdb;
this.pdbId = pdb.id;
- try
- {
- siftsEntry = parseSIFTs(siftsFile);
- } catch (Exception e)
- {
- e.printStackTrace();
- }
-
+ 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());
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();
} 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)
{
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()
+ File siftsFile = new File(SiftsSettings.getSiftDownloadDirectory()
+ + pdbId.toLowerCase()
+ ".xml.gz");
if (siftsFile.exists())
{
}
/**
- * Download a SIFTs XML file for a given PDB Id
+ * Download a SIFTs XML file for a given PDB Id from an FTP repository
*
* @param pdbId
* @return downloaded SIFTs XML file
+ * @throws SiftsException
*/
- public static File downloadSiftsFile(String pdbId)
+ public static File downloadSiftsFile(String pdbId) throws SiftsException
{
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();
System.out.println(">>> File downloaded : " + downloadedSiftsFile);
} catch (IOException ex)
{
- ex.printStackTrace();
+ throw new SiftsException(ex.getMessage());
}
return new File(downloadedSiftsFile);
}
*/
public static boolean deleteSiftsFileByPDBId(String pdbId)
{
- File siftsFile = new File(SIFTS_DOWNLOAD_DIR + pdbId.toLowerCase()
+ File siftsFile = new File(SiftsSettings.getSiftDownloadDirectory()
+ + pdbId.toLowerCase()
+ ".xml.gz");
if (siftsFile.exists())
{
DBRefEntry[] dbRefs = seq.getDBRefs();
if (dbRefs == null || dbRefs.length < 1)
{
- final SequenceI[] seqs = new SequenceI[] { seq };
- new jalview.ws.DBRefFetcher(seqs, null, null, null, false)
- .fetchDBRefs(true);
- dbRefs = seq.getDBRefs();
- }
-
- if (dbRefs == null || dbRefs.length < 1)
- {
throw new SiftsException("Could not get source DB Ref");
}
continue;
}
if (isFoundInSiftsEntry(dbRef.getAccessionId())
- && (dbRef.getSource().equalsIgnoreCase("uniprot") || dbRef
- .getSource().equalsIgnoreCase("pdb")))
+ && (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT) || dbRef
+ .getSource().equalsIgnoreCase(DBRefSource.PDB)))
{
return dbRef;
}
/**
- * 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
mappingDetails.append(NEWLINE);
}
};
- int[][] mapping = getGreedyMapping(chain, seq, ps);
+ HashMap<Integer, int[]> mapping = getGreedyMapping(chain, seq, ps);
String mappingOutput = mappingDetails.toString();
StructureMapping siftsMapping = new StructureMapping(seq, pdbFile,
}
@Override
- public int[][] getGreedyMapping(String entityId, SequenceI seq,
+ public HashMap<Integer, int[]> getGreedyMapping(String entityId, SequenceI seq,
java.io.PrintStream os)
throws SiftsException
{
-
+ ArrayList<Integer> omitNonObserved = new ArrayList<Integer>();
+ int nonObservedShiftIndex = 0;
System.out.println("Generating mappings for : " + entityId);
Entity entity = null;
entity = getEntityById(entityId);
String originalSeq = AlignSeq.extractGaps(
jalview.util.Comparison.GapChars,
seq.getSequenceAsString());
- int mapping[][] = new int[originalSeq.length() + seq.getStart()][2];
+ HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>();
DBRefEntryI sourceDBRef = seq.getSourceDBRef();
if (sourceDBRef == null)
{
// set sequence coordinate system - default value is UniProt
if (sourceDBRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
{
- seqCoordSys = PDB_COORDINATE_SYS;
+ seqCoordSys = CoordinateSys.PDB;
}
- ArrayList<String> dbRefAccessionIdsString = new ArrayList<String>();
+ HashSet<String> dbRefAccessionIdsString = new HashSet<String>();
for (DBRefEntry dbref : seq.getDBRefs())
{
- dbRefAccessionIdsString.add(dbref.getAccessionId());
+ dbRefAccessionIdsString.add(dbref.getAccessionId().toLowerCase());
}
+ dbRefAccessionIdsString.add(sourceDBRef.getAccessionId().toLowerCase());
+
+ curDBRefAccessionIdsString = dbRefAccessionIdsString;
+ curSourceDBRef = sourceDBRef.getAccessionId();
- // initialise all mapping positions to unassigned
- for (int residuePos[] : mapping)
- {
- residuePos[PDB_RES_POS] = UNASSIGNED;
- residuePos[PDB_ATOM_POS] = UNASSIGNED;
- }
-
TreeMap<Integer, String> resNumMap = new TreeMap<Integer, String>();
List<Segment> segments = entity.getSegment();
for (Segment segment : segments)
{
int currSeqIndex = UNASSIGNED;
List<CrossRefDb> cRefDbs = residue.getCrossRefDb();
+ CrossRefDb pdbRefDb = null;
for (CrossRefDb cRefDb : cRefDbs)
{
- if (cRefDb.getDbCoordSys().equalsIgnoreCase(seqCoordSys)
- && dbRefAccessionIdsString.contains(cRefDb
- .getDbAccessionId()))
+ if (cRefDb.getDbSource().equalsIgnoreCase(DBRefSource.PDB))
+ {
+ pdbRefDb = cRefDb;
+ }
+ if (cRefDb.getDbCoordSys()
+ .equalsIgnoreCase(seqCoordSys.getName())
+ && isAccessionMatched(cRefDb.getDbAccessionId()))
{
String resNumIndexString = cRefDb.getDbResNum()
.equalsIgnoreCase("None") ? String.valueOf(UNASSIGNED)
: cRefDb.getDbResNum();
currSeqIndex = Integer.valueOf(resNumIndexString);
- break;
+ if (pdbRefDb != null)
+ {
+ break;// exit loop if pdb and uniprot are already found
+ }
}
}
if (currSeqIndex == UNASSIGNED)
}
if (currSeqIndex > seq.getStart() && currSeqIndex <= seq.getEnd())
{
- int resNum = Integer.valueOf(residue.getDbResNum());
- mapping[currSeqIndex][PDB_RES_POS] = Integer.valueOf(resNum);
- char resCharCode = ResidueProperties
- .getSingleCharacterCode(residue.getDbResName());
- resNumMap.put(currSeqIndex, String.valueOf(resCharCode));
+ int resNum;
+ try
+ {
+ resNum = (pdbRefDb == null) ? Integer.valueOf(residue
+ .getDbResNum()) : Integer.valueOf(pdbRefDb.getDbResNum());
+ } catch (NumberFormatException nfe)
+ {
+ resNum = (pdbRefDb == null) ? Integer.valueOf(residue
+ .getDbResNum()) : Integer.valueOf(pdbRefDb
+ .getDbResNum().split("[a-zA-Z]")[0]);
+ }
+
+ if (isResidueObserved(residue)
+ || seqCoordSys == CoordinateSys.UNIPROT)
+ {
+ char resCharCode = ResidueProperties
+ .getSingleCharacterCode(residue.getDbResName());
+ resNumMap.put(currSeqIndex, String.valueOf(resCharCode));
+ }
+ else
+ {
+ omitNonObserved.add(currSeqIndex);
+ ++nonObservedShiftIndex;
+ }
+ mapping.put(currSeqIndex - nonObservedShiftIndex, new int[] {
+ Integer.valueOf(resNum), UNASSIGNED });
}
}
}
{
e.printStackTrace();
}
- padWithGaps(resNumMap);
- int counter = 0;
- int seqStart = 0;
- int seqEnd = 0;
- int pdbStart = 0;
- int pdbEnd = 0;
- boolean startDetected = false;
- for (int[] x : mapping)
- {
- if (!startDetected && x[PDB_RES_POS] != UNASSIGNED)
- {
- seqStart = counter;
- startDetected = true;
- // System.out.println("Seq start: "+ seqStart);
- }
+ padWithGaps(resNumMap, omitNonObserved);
+ int seqStart = UNASSIGNED;
+ int seqEnd = UNASSIGNED;
+ int pdbStart = UNASSIGNED;
+ int pdbEnd = UNASSIGNED;
- if (startDetected && x[PDB_RES_POS] != UNASSIGNED)
- {
- seqEnd = counter;
- }
- ++counter;
- }
+ 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)
{
- seqEnd = (seqEnd == UNASSIGNED) ? counter : seqEnd;
- pdbStart = mapping[seqStart][PDB_RES_POS];
- pdbEnd = mapping[seqEnd][PDB_RES_POS];
+ 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);
}
}
targetStrucSeqs.append(res);
}
- try
+ 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;
+ }
+
+ /**
+ * Checks if the residue instance is marked 'Not_observed' or not
+ *
+ * @param residue
+ * @return
+ */
+ private boolean isResidueObserved(Residue residue)
+ {
+ String annotation = getResidueAnnotaiton(residue,
+ ResidueDetailType.ANNOTATION);
+ if (annotation == null)
{
- if (os != null)
+ return true;
+ }
+ if (!annotation.equalsIgnoreCase(NOT_FOUND)
+ && annotation.equalsIgnoreCase(NOT_OBSERVED))
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * Get annotation String for a given residue and annotation type
+ *
+ * @param residue
+ * @param type
+ * @return
+ */
+ private String getResidueAnnotaiton(Residue residue,
+ ResidueDetailType type)
+ {
+ List<ResidueDetail> resDetails = residue.getResidueDetail();
+ for (ResidueDetail resDetail : resDetails)
+ {
+ if (resDetail.getProperty().equalsIgnoreCase(type.getCode()))
{
- 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 resDetail.getContent();
}
- } catch (Exception ex)
- {
- ex.printStackTrace();
}
- return mapping;
+ return NOT_FOUND;
}
@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)
{
return accessionId != null
&& getAllMappingAccession().contains(accessionId);
}
/**
- * Pads missing positions with gaps
+ * Pad omitted residue positions in PDB sequence with gaps
*
* @param resNumMap
*/
- void padWithGaps(TreeMap<Integer, String> resNumMap)
+ void padWithGaps(TreeMap<Integer, String> resNumMap,
+ ArrayList<Integer> omitNonObserved)
{
+ if (resNumMap == null || resNumMap.isEmpty())
+ {
+ return;
+ }
Integer[] keys = resNumMap.keySet().toArray(new Integer[0]);
Arrays.sort(keys);
int firstIndex = keys[0];
System.out.println("Max value " + lastIndex);
for (int x = firstIndex; x <= lastIndex; x++)
{
- if (!resNumMap.containsKey(x))
+ if (!resNumMap.containsKey(x) && !omitNonObserved.contains(x))
{
resNumMap.put(x, "-");
}
}
}
+
/**
*
* @param chainId
* @throws IllegalArgumentException
* Thrown if chainId or mapping is null
*/
- void populateAtomPositions(String chainId, int[][] mapping)
+ void populateAtomPositions(String chainId, HashMap<Integer, int[]> mapping)
throws IllegalArgumentException
{
PDBChain chain = pdb.findChain(chainId);
throw new IllegalArgumentException(
"Chain id or mapping must not be null.");
}
- for (int[] map : mapping)
+ for (int[] map : mapping.values())
{
if (map[PDB_RES_POS] != UNASSIGNED)
{
output.append(NEWLINE).append(NEWLINE);
}
float pid = (float) matchedSeqCount / seqRes.length() * 100;
+ if (pid < 2)
+ {
+ 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));
git://source.jalview.org / jalview.git / blobdiff