X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fsifts%2FSiftsClient.java;h=f25c1cf7d551363c58f4f9198fad065f38c433ff;hb=77ac7f545e96bd4bde47991f77291a71eb5b90e6;hp=bde215da2a187639c968ad1946da67e1333c5905;hpb=89f62b210bafac2a3341ce3fa9a360d5ea6c1c3c;p=jalview.git
diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index bde215d..f25c1cf 100644
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -18,12 +18,13 @@
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-package jalview.io;
+package jalview.ws.sifts;
import jalview.analysis.AlignSeq;
import jalview.api.DBRefEntryI;
import jalview.api.SiftsClientI;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureMapping;
@@ -34,7 +35,7 @@ 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.EntryDetail;
+import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue.ResidueDetail;
import jalview.xml.binding.sifts.Entry.ListDB.Db;
import java.io.File;
@@ -46,9 +47,18 @@ 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.TreeMap;
import java.util.zip.GZIPInputStream;
import javax.xml.bind.JAXBContext;
@@ -59,63 +69,106 @@ 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 String pdbId;
+ private String structId;
+
+ private String segStartEnd;
+
+ private CoordinateSys seqCoordSys = CoordinateSys.UNIPROT;
+
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 = -1;
+
+ private static final int PDB_RES_POS = 0;
+
+ private static final int PDB_ATOM_POS = 1;
+
+ 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 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(String pdbId)
+ public SiftsClient(PDBfile pdb) throws SiftsException
{
- this.pdbId = pdbId;
- try
- {
- File siftsFile = getSiftsFile(pdbId);
- siftsEntry = parseSIFTs(siftsFile);
- } catch (Exception e)
- {
- e.printStackTrace();
- }
+ this.pdb = pdb;
+ this.pdbId = pdb.id;
+ 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(String pdbId, File siftsFile)
+ public SiftsClient(PDBfile pdb, File siftsFile) throws SiftsException
{
- this.pdbId = pdbId;
- try
- {
- siftsEntry = parseSIFTs(siftsFile);
- } catch (Exception e)
- {
- e.printStackTrace();
- }
-
+ this.pdb = pdb;
+ this.pdbId = pdb.id;
+ siftsEntry = parseSIFTs(siftsFile);
}
/**
@@ -127,14 +180,13 @@ public class SiftsClient implements SiftsClientI
* @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();
@@ -142,38 +194,49 @@ public class SiftsClient implements SiftsClientI
} 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()
- + ".xml.gz");
+ File siftsFile = new File(SiftsSettings.getSiftDownloadDirectory()
+ + pdbId.toLowerCase() + ".xml.gz");
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);
+
+ if (isFileOlderThanThreshold(siftsFile,
+ SiftsSettings.getCacheThresholdInDays()))
+ {
+ // System.out.println("Downloaded file is out of date, hence re-downloading...");
+ siftsFile = downloadSiftsFile(pdbId.toLowerCase());
+ }
return siftsFile;
}
siftsFile = downloadSiftsFile(pdbId.toLowerCase());
@@ -181,24 +244,59 @@ public class SiftsClient implements SiftsClientI
}
/**
- * 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
*/
- public static File downloadSiftsFile(String pdbId)
+ public static File downloadSiftsFile(String pdbId) throws SiftsException
{
+ 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);
+ // System.out.println(">> Download ftp url : " + siftsFileFTPURL);
URL url = new URL(siftsFileFTPURL);
URLConnection conn = url.openConnection();
InputStream inputStream = conn.getInputStream();
@@ -212,10 +310,10 @@ public class SiftsClient implements SiftsClientI
}
outputStream.close();
inputStream.close();
- System.out.println(">>> File downloaded : " + downloadedSiftsFile);
+ // System.out.println(">>> File downloaded : " + downloadedSiftsFile);
} catch (IOException ex)
{
- ex.printStackTrace();
+ throw new SiftsException(ex.getMessage());
}
return new File(downloadedSiftsFile);
}
@@ -229,8 +327,8 @@ public class SiftsClient implements SiftsClientI
*/
public static boolean deleteSiftsFileByPDBId(String pdbId)
{
- File siftsFile = new File(SIFTS_DOWNLOAD_DIR + pdbId.toLowerCase()
- + ".xml.gz");
+ File siftsFile = new File(SiftsSettings.getSiftDownloadDirectory()
+ + pdbId.toLowerCase() + ".xml.gz");
if (siftsFile.exists())
{
return siftsFile.delete();
@@ -238,7 +336,6 @@ public class SiftsClient implements SiftsClientI
return true;
}
-
/**
* Get a valid SIFTs DBRef for the given sequence current SIFTs entry
*
@@ -248,7 +345,8 @@ public class SiftsClient implements SiftsClientI
* @throws Exception
* if no valid source DBRefEntry was found for the given sequences
*/
- public DBRefEntryI getValidSourceDBRef(SequenceI seq) throws Exception
+ public DBRefEntryI getValidSourceDBRef(SequenceI seq)
+ throws SiftsException
{
DBRefEntryI sourceDBRef = null;
sourceDBRef = seq.getSourceDBRef();
@@ -261,15 +359,7 @@ public class SiftsClient implements SiftsClientI
DBRefEntry[] dbRefs = seq.getDBRefs();
if (dbRefs == null || dbRefs.length < 1)
{
- final SequenceI[] seqs = new SequenceI[] { seq };
- new jalview.ws.DBRefFetcher(seqs, null, null, null, false)
- .fetchDBRefs(true);
- dbRefs = seq.getDBRefs();
- }
-
- if (dbRefs == null || dbRefs.length < 1)
- {
- throw new Exception("Could not get source DB Ref");
+ throw new SiftsException("Could not get source DB Ref");
}
for (DBRefEntryI dbRef : dbRefs)
@@ -280,8 +370,8 @@ public class SiftsClient implements SiftsClientI
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;
}
@@ -291,13 +381,12 @@ public class SiftsClient implements SiftsClientI
{
return sourceDBRef;
}
- throw new Exception("Could not get source DB Ref");
+ 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
@@ -307,7 +396,6 @@ public class SiftsClient implements SiftsClientI
{
return entry != null && entry.getAccessionId() != null
&& isFoundInSiftsEntry(entry.getAccessionId());
- // & entry.getStartRes() > 0;
}
@Override
@@ -331,205 +419,544 @@ public class SiftsClient implements SiftsClientI
return accessions;
}
+ @Override
+ public StructureMapping getSiftsStructureMapping(SequenceI seq,
+ String pdbFile, String chain) throws SiftsException
+ {
+ structId = (chain == null) ? pdbId : pdbId + "|" + chain;
+ System.out.println("Getting mapping for: " + pdbId + "|" + chain
+ + " : seq- " + seq.getName());
+
+ final StringBuilder mappingDetails = new StringBuilder(128);
+ PrintStream ps = new PrintStream(System.out)
+ {
+ @Override
+ public void print(String x)
+ {
+ mappingDetails.append(x);
+ }
+
+ @Override
+ public void println()
+ {
+ mappingDetails.append(NEWLINE);
+ }
+ };
+ HashMap mapping = getGreedyMapping(chain, seq, ps);
+
+ String mappingOutput = mappingDetails.toString();
+ StructureMapping siftsMapping = new StructureMapping(seq, pdbFile,
+ pdbId, chain, mapping, mappingOutput);
+ return siftsMapping;
+ }
@Override
- public int[][] getGreedyMapping(String entityId, SequenceI seq,
- java.io.PrintStream os)
- throws Exception
+ public HashMap getGreedyMapping(String entityId,
+ SequenceI seq, java.io.PrintStream os) throws SiftsException
{
+ ArrayList omitNonObserved = new ArrayList();
+ int nonObservedShiftIndex = 0;
System.out.println("Generating mappings for : " + entityId);
Entity entity = null;
entity = getEntityById(entityId);
- String seqStr = AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
- seq.getSequenceAsString());
- // StringBuilder mappedStrucSeq = new StringBuilder(seqStr.length());
- String[] mappedStrucSeq = new String[seqStr.length()];
- int mapping[][] = new int[seqStr.length()][2];
+ 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 if sourceDBRef is null at this point then throw an Exception
+ // TODO ensure sequence start/end is in the same coordinate system and
+ // consistent with the choosen sourceDBRef
+ }
- // TODO update sequence start/end with sourceDBRef start/end
- // seq.setStart(sourceDBRef.getStartRes());
- // seq.setEnd(sourceDBRef.getEndRes());
+ // set sequence coordinate system - default value is UniProt
+ if (sourceDBRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
+ {
+ seqCoordSys = CoordinateSys.PDB;
}
- String crossRefAccessionId = sourceDBRef.getAccessionId();
- int start = seq.getStart() - 1;
- for (int residue[] : mapping)
+ HashSet dbRefAccessionIdsString = new HashSet();
+ for (DBRefEntry dbref : seq.getDBRefs())
{
- residue[1] = start++;
+ dbRefAccessionIdsString.add(dbref.getAccessionId().toLowerCase());
}
-
- HashMap resNumMap = new HashMap();
+ dbRefAccessionIdsString.add(sourceDBRef.getAccessionId().toLowerCase());
+
+ curDBRefAccessionIdsString = dbRefAccessionIdsString;
+ curSourceDBRef = sourceDBRef.getAccessionId();
+
+ TreeMap resNumMap = new TreeMap();
List segments = entity.getSegment();
for (Segment segment : segments)
{
+ segStartEnd = segment.getStart() + " - " + segment.getEnd();
System.out.println("Mappging segments : " + segment.getSegId() + "\\"
- + segment.getStart() + "-" + segment.getEnd());
+ + segStartEnd);
List residues = segment.getListResidue().getResidue();
for (Residue residue : residues)
{
- int refDbResNum = -1;
+ int currSeqIndex = UNASSIGNED;
List cRefDbs = residue.getCrossRefDb();
+ CrossRefDb pdbRefDb = null;
for (CrossRefDb cRefDb : cRefDbs)
{
- if (cRefDb.getDbAccessionId().equalsIgnoreCase(
- crossRefAccessionId))
+ if (cRefDb.getDbSource().equalsIgnoreCase(DBRefSource.PDB))
{
- refDbResNum = Integer.valueOf(cRefDb.getDbResNum());
+ pdbRefDb = cRefDb;
+ }
+ if (cRefDb.getDbCoordSys()
+ .equalsIgnoreCase(seqCoordSys.getName())
+ && isAccessionMatched(cRefDb.getDbAccessionId()))
+ {
+ String resNumIndexString = cRefDb.getDbResNum()
+ .equalsIgnoreCase("None") ? String.valueOf(UNASSIGNED)
+ : cRefDb.getDbResNum();
+ try
+ {
+ currSeqIndex = Integer.valueOf(resNumIndexString);
+ } catch (NumberFormatException nfe)
+ {
+ currSeqIndex = Integer.valueOf(resNumIndexString
+ .split("[a-zA-Z]")[0]);
+ }
+ if (pdbRefDb != null)
+ {
+ break;// exit loop if pdb and uniprot are already found
+ }
}
}
- if (refDbResNum == -1)
+ if (currSeqIndex == UNASSIGNED)
{
continue;
}
- for (int[] x : mapping)
+ if (currSeqIndex >= seq.getStart() && currSeqIndex <= seq.getEnd())
{
- if (x[1] == refDbResNum)
+ int resNum;
+ try
+ {
+ resNum = (pdbRefDb == null) ? Integer.valueOf(residue
+ .getDbResNum()) : Integer.valueOf(pdbRefDb
+ .getDbResNum());
+ } catch (NumberFormatException nfe)
{
- int resNum = Integer.valueOf(residue.getDbResNum());
- x[0] = resNum;
- String value = "x";
- resNumMap.put(resNum, value);
+ resNum = (pdbRefDb == null) ? Integer.valueOf(residue
+ .getDbResNum()) : Integer.valueOf(pdbRefDb
+ .getDbResNum().split("[a-zA-Z]")[0]);
+ continue;
}
+
+ if (isResidueObserved(residue)
+ || seqCoordSys == CoordinateSys.UNIPROT)
+ {
+ char resCharCode = ResidueProperties
+ .getSingleCharacterCode(ResidueProperties
+ .getCanonicalAminoAcid(residue.getDbResName()));
+ resNumMap.put(currSeqIndex, String.valueOf(resCharCode));
+ }
+ else
+ {
+ omitNonObserved.add(currSeqIndex);
+ ++nonObservedShiftIndex;
+ }
+ mapping.put(currSeqIndex - nonObservedShiftIndex, new int[] {
+ Integer.valueOf(resNum), UNASSIGNED });
}
}
}
-
- //Generate visual mapping output
- // StringBuilder strucSeq = new StringBuilder();
- // for(int[] x : mapping){
- // if(mapping[0] == 0){
- // strucSeq.append(b)
- // }
- // }
- mappedStrucSeq[1] = "x";
try
{
- System.out.println(">>>> seq: " + seqStr + "\nlength "
- + seqStr.length());
- System.out.println(">>>> pdb: " + mappedStrucSeq.toString()
- + "\nlength " + mappedStrucSeq.toString().length());
+ 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 printedMapping = getMappingOutput(mappedStrucSeq.toString(),
- seqStr, "seqAccession", "strucAccession", "pep", 3)
- .toString();
- if (os != null)
+ 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
{
- os.print(printedMapping);
+ matchedSeq = originalSeq.substring(1, originalSeq.length());
}
- System.out.println();
- } catch (Exception ex)
+ }
+
+ StringBuilder targetStrucSeqs = new StringBuilder();
+ for (String res : resNumMap.values())
{
- ex.printStackTrace();
+ 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());
}
return mapping;
}
- @Override
- public boolean isFoundInSiftsEntry(String accessionId)
+ /**
+ *
+ * @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 mapping) throws IllegalArgumentException
{
- return accessionId != null
- && getAllMappingAccession().contains(accessionId);
+ 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())
+ {
+ if (map[PDB_RES_POS] != UNASSIGNED)
+ {
+ map[PDB_ATOM_POS] = getAtomIndex(map[PDB_RES_POS], chain.atoms);
+ }
+ }
}
- @Override
- public StructureMapping getSiftsStructureMapping(SequenceI seq,
- String pdbFile, String chain)
+ /**
+ *
+ * @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 atoms)
{
- System.out.println("Getting mapping for: " + pdbId + "|" + chain
- + " : seq- " + seq.getName());
+ if (atoms == null)
+ {
+ throw new IllegalArgumentException(
+ "atoms collection must not be null!");
+ }
+ for (Atom atom : atoms)
+ {
+ if (atom.resNumber == residueIndex)
+ {
+ return atom.atomIndex;
+ }
+ }
+ return UNASSIGNED;
+ }
- final StringBuilder mappingDetails = new StringBuilder(128);
- PrintStream ps = new PrintStream(System.out)
+ /**
+ * Checks if the residue instance is marked 'Not_observed' or not
+ *
+ * @param residue
+ * @return
+ */
+ private boolean isResidueObserved(Residue residue)
+ {
+ HashSet annotations = getResidueAnnotaitons(residue,
+ ResidueDetailType.ANNOTATION);
+ if (annotations == null || annotations.isEmpty())
{
- @Override
- public void print(String x)
+ return true;
+ }
+ for (String annotation : annotations)
+ {
+ if (annotation.equalsIgnoreCase(NOT_OBSERVED))
{
- mappingDetails.append(x);
+ return false;
}
+ }
+ return true;
+ }
- @Override
- public void println()
+ /**
+ * Get annotation String for a given residue and annotation type
+ *
+ * @param residue
+ * @param type
+ * @return
+ */
+ private HashSet getResidueAnnotaitons(Residue residue,
+ ResidueDetailType type)
+ {
+ HashSet foundAnnotations = new HashSet();
+ List resDetails = residue.getResidueDetail();
+ for (ResidueDetail resDetail : resDetails)
+ {
+ if (resDetail.getProperty().equalsIgnoreCase(type.getCode()))
{
- mappingDetails.append(NEWLINE);
+ foundAnnotations.add(resDetail.getContent());
}
- };
- int[][] mapping = null;
- try
+ }
+ return foundAnnotations;
+ }
+
+ @Override
+ 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);
+ }
+
+ /**
+ * Pad omitted residue positions in PDB sequence with gaps
+ *
+ * @param resNumMap
+ */
+ void padWithGaps(TreeMap resNumMap,
+ ArrayList omitNonObserved)
+ {
+ if (resNumMap == null || resNumMap.isEmpty())
{
- mapping = getGreedyMapping(chain, seq, ps);
- } catch (Exception e)
+ 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++)
{
- e.printStackTrace();
+ if (!resNumMap.containsKey(x) && !omitNonObserved.contains(x))
+ {
+ resNumMap.put(x, "-");
+ }
}
- // String mappingOutput = mappingDetails.toString();
- String mappingOutput = null;
- return new StructureMapping(seq, pdbFile, pdbId, chain, mapping,
- mappingOutput);
}
+
+
@Override
- public Entity getEntityById(String id) throws Exception
+ public Entity getEntityById(String id) throws SiftsException
{
+ // Sometimes SIFTS mappings are wrongly swapped between different chains of
+ // a PDB entry. This results to wrong mappings being generated. The boolean
+ // flag 'isGetEntityIdDirectly, determines whether an entity to process is
+ // determined by a greedy heuristic search or by just matching the Chain Id
+ // directly against the entity Id tag. Setting the default value to 'false'
+ // utilise the heuristic search which always produces correct mappings but
+ // less optimised processing, where as changing the value to 'true'
+ // optimises performance but might result to incorrect mapping in some cases
+ // where SIFTS mappings are wrongly swapped between different chains.
+ boolean isGetEntityIdDirectly = false;
+ if (isGetEntityIdDirectly)
+ {
+ List entities = siftsEntry.getEntity();
+ for (Entity entity : entities)
+ {
+ if (!entity.getEntityId().equalsIgnoreCase(id))
+ {
+ continue;
+ }
+ return entity;
+ }
+ }
+ Entity entity = getEntityByMostOptimalMatchedId(id);
+ if (entity != null)
+ {
+ return entity;
+ }
+ throw new SiftsException("Entity " + id + " not found");
+ }
+
+ /**
+ * This method was added because EntityId is NOT always equal to ChainId.
+ * Hence, it provides the logic to greedily detect the "true" Entity for a
+ * given chainId where discrepancies exist.
+ *
+ * @param chainId
+ * @return
+ */
+ public Entity getEntityByMostOptimalMatchedId(String chainId)
+ {
+ // System.out.println("---> advanced greedy entityId matching block entered..");
List entities = siftsEntry.getEntity();
+ SiftsEntitySortPojo[] sPojo = new SiftsEntitySortPojo[entities.size()];
+ int count = 0;
for (Entity entity : entities)
{
- if (!entity.getEntityId().equalsIgnoreCase(id))
+ sPojo[count] = new SiftsEntitySortPojo();
+ sPojo[count].entityId = entity.getEntityId();
+
+ List segments = entity.getSegment();
+ for (Segment segment : segments)
+ {
+ List residues = segment.getListResidue().getResidue();
+ for (Residue residue : residues)
+ {
+ List cRefDbs = residue.getCrossRefDb();
+ for (CrossRefDb cRefDb : cRefDbs)
+ {
+ if (!cRefDb.getDbSource().equalsIgnoreCase("PDB"))
+ {
+ continue;
+ }
+ ++sPojo[count].resCount;
+ if (cRefDb.getDbChainId().equalsIgnoreCase(chainId))
+ {
+ ++sPojo[count].chainIdFreq;
+ }
+ }
+ }
+ }
+ sPojo[count].pid = 100 * (sPojo[count].chainIdFreq / sPojo[count].resCount);
+ ++count;
+ }
+ Arrays.sort(sPojo, Collections.reverseOrder());
+ System.out.println("highest matched entity : " + sPojo[0].entityId);
+ System.out.println("highest matched pid : " + sPojo[0].pid);
+
+ if (sPojo[0].entityId != null)
+ {
+ for (Entity entity : entities)
{
- continue;
+ if (!entity.getEntityId().equalsIgnoreCase(sPojo[0].entityId))
+ {
+ continue;
+ }
+ return entity;
}
- return entity;
}
- throw new Exception("Entity " + id + " not found");
+ return null;
+ }
+
+ public class SiftsEntitySortPojo implements
+ Comparable
+ {
+ public String entityId;
+
+ public int chainIdFreq;
+
+ public int pid;
+
+ public int resCount;
+
+ @Override
+ public int compareTo(SiftsEntitySortPojo o)
+ {
+ return this.pid - o.pid;
+ }
}
@Override
public String[] getEntryDBs()
{
System.out.println("\nListing DB entries...");
+ List availDbs = new ArrayList();
List dbs = siftsEntry.getListDB().getDb();
for (Db db : dbs)
{
+ availDbs.add(db.getDbSource());
System.out.println(db.getDbSource() + " | " + db.getDbCoordSys());
}
- return null;
+ return availDbs.toArray(new String[0]);
}
@Override
- public void getEntryDetails()
+ public StringBuffer getMappingOutput(MappingOutputPojo mp)
+ throws SiftsException
{
- List eds = siftsEntry.getEntryDetail();
- for (EntryDetail ed : eds)
- {
- System.out.println("Entry Details: " + ed.getContent() + " "
- + ed.getDbSource() + " " + ed.getProperty() + " "
- + ed.toString());
- }
- }
+ String seqRes = mp.getSeqResidue();
+ String seqName = mp.getSeqName();
+ int sStart = mp.getSeqStart();
+ int sEnd = mp.getSeqEnd();
- @Override
- public StringBuffer getMappingOutput(String astr1, String astr2, String s1id,
- String s2id, String type, int nochunks)
- {
- int maxid = s1id.length();
+ String strRes = mp.getStrResidue();
+ 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;
- StringBuffer output = new StringBuffer();
+
+ int nochunks = ((seqRes.length()) / len)
+ + ((seqRes.length()) % len > 0 ? 1 : 0);
// output mappings
- float pid = 0;
+ StringBuffer output = new StringBuffer();
+ output.append(NEWLINE);
+ output.append("Sequence â· 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(sStart));
+ output.append(" - ");
+ output.append(String.valueOf(sEnd));
+ output.append(" Maps to ");
+ output.append(NEWLINE);
+ output.append(new Format("%" + maxid + "s").form(structId));
+ output.append(" : ");
+ output.append(String.valueOf(pdbStart));
+ output.append(" - ");
+ output.append(String.valueOf(pdbEnd));
+ output.append(NEWLINE).append(NEWLINE);
+
+ int matchedSeqCount = 0;
for (int j = 0; j < nochunks; j++)
{
// Print the first aligned sequence
- output.append(new Format("%" + (maxid) + "s").form(s1id)).append(" ");
+ output.append(new Format("%" + (maxid) + "s").form(seqName)).append(
+ " ");
for (int i = 0; i < len; i++)
{
- if ((i + (j * len)) < astr1.length())
+ if ((i + (j * len)) < seqRes.length())
{
- output.append(astr1.charAt(i + (j * len)));
+ output.append(seqRes.charAt(i + (j * len)));
}
}
@@ -539,53 +966,65 @@ public class SiftsClient implements SiftsClientI
// Print out the matching chars
for (int i = 0; i < len; i++)
{
- if ((i + (j * len)) < astr1.length())
+ try
{
- if (astr1.charAt(i + (j * len)) == astr2.charAt(i + (j * len))
- && !jalview.util.Comparison.isGap(astr1.charAt(i
- + (j * len))))
+ if ((i + (j * len)) < seqRes.length())
{
- pid++;
- output.append("|");
- }
- else if (type.equals("pep"))
- {
- if (ResidueProperties.getPAM250(astr1.charAt(i + (j * len)),
- astr2.charAt(i + (j * len))) > 0)
+ if (seqRes.charAt(i + (j * len)) == strRes
+ .charAt(i + (j * len))
+ && !jalview.util.Comparison.isGap(seqRes.charAt(i
+ + (j * len))))
+ {
+ matchedSeqCount++;
+ output.append("|");
+ }
+ else if (type.equals("pep"))
{
- output.append(".");
+ if (ResidueProperties.getPAM250(seqRes.charAt(i + (j * len)),
+ strRes.charAt(i + (j * len))) > 0)
+ {
+ output.append(".");
+ }
+ else
+ {
+ output.append(" ");
+ }
}
else
{
output.append(" ");
}
}
- else
- {
- output.append(" ");
- }
+ } catch (IndexOutOfBoundsException e)
+ {
+ continue;
}
}
// Now print the second aligned sequence
output = output.append(NEWLINE);
- output = output.append(new Format("%" + (maxid) + "s").form(s2id))
+ output = output.append(new Format("%" + (maxid) + "s").form(strName))
.append(" ");
for (int i = 0; i < len; i++)
{
- if ((i + (j * len)) < astr2.length())
+ if ((i + (j * len)) < strRes.length())
{
- output.append(astr2.charAt(i + (j * len)));
+ output.append(strRes.charAt(i + (j * len)));
}
}
output.append(NEWLINE).append(NEWLINE);
}
- pid = pid / (astr1.length()) * 100;
- System.out.println(output);
- System.out.println(pid);
- // TODO return output & pid
+ 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);
return output;
}
-
+
@Override
public int getEntityCount()
{
@@ -621,4 +1060,5 @@ public class SiftsClient implements SiftsClientI
{
return siftsEntry.getDbVersion();
}
+
}