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;
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.net.URL;
import java.net.URLConnection;
import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
import java.util.HashSet;
-import java.util.LinkedHashMap;
import java.util.List;
+import java.util.TreeMap;
import java.util.zip.GZIPInputStream;
import javax.xml.bind.JAXBContext;
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;
+ 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 SIFTS_FTP_BASE_URL = "ftp://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
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
* 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 - the
+ * SIFTs file should correspond to the given PDB Id
*
* @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);
}
/**
* @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
{
} 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");
}
/**
*
* @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");
if (siftsFile.exists())
{
- // TODO it may be worth performing a timestamp age check to determine if a
+ // 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
System.out.println(">>> SIFTS File already downloaded for " + pdbId);
*
* @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;
System.out.println(">>> File downloaded : " + downloadedSiftsFile);
} catch (IOException ex)
{
- ex.printStackTrace();
+ throw new SiftsException(ex.getMessage());
}
return new File(downloadedSiftsFile);
}
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;
}
{
return entry != null && entry.getAccessionId() != null
&& isFoundInSiftsEntry(entry.getAccessionId());
- // & entry.getStartRes() > 0;
}
@Override
int[][] mapping = getGreedyMapping(chain, seq, ps);
String mappingOutput = mappingDetails.toString();
- return new StructureMapping(seq, pdbFile, pdbId, chain, mapping,
+ StructureMapping siftsMapping = new StructureMapping(seq, pdbFile,
+ pdbId, chain, mapping,
mappingOutput);
+ return siftsMapping;
}
@Override
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);
Entity entity = null;
entity = getEntityById(entityId);
- String seqStr = AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
+ String originalSeq = AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars,
seq.getSequenceAsString());
- int mapping[][] = new int[seqStr.length() + seq.getStart()][2];
+ int mapping[][] = new int[originalSeq.length() + seq.getStart()][2];
DBRefEntryI sourceDBRef = seq.getSourceDBRef();
if (sourceDBRef == null)
{
sourceDBRef = getValidSourceDBRef(seq);
- // TODO update sequence start/end with sourceDBRef start/end
- // seq.setStart(sourceDBRef.getStartRes());
- // seq.setEnd(sourceDBRef.getEndRes());
+ // TODO ensure sequence start/end is in the same coordinate system and
+ // consistent with the choosen sourceDBRef
}
- String crossRefAccessionId = sourceDBRef.getAccessionId();
- int count = 0;
- for (int residue[] : mapping)
+ // set sequence coordinate system - default value is UniProt
+ if (sourceDBRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
{
- residue[1] = count++;
- residue[0] = -1;
+ seqCoordSys = CoordinateSys.PDB;
}
-
- LinkedHashMap<Integer, String> resNumMap = new LinkedHashMap<Integer, String>();
+
+ HashSet<String> dbRefAccessionIdsString = new HashSet<String>();
+ for (DBRefEntry dbref : seq.getDBRefs())
+ {
+ 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)
{
List<Residue> residues = segment.getListResidue().getResidue();
for (Residue residue : residues)
{
- int refDbResNum = -1;
+ 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))
{
- refDbResNum = Integer.valueOf(cRefDb.getDbResNum());
+ pdbRefDb = cRefDb;
+ }
+ if (cRefDb.getDbCoordSys()
+ .equalsIgnoreCase(seqCoordSys.getName())
+ && hasAccessionId(cRefDb.getDbAccessionId()))
+ {
+ String resNumIndexString = cRefDb.getDbResNum()
+ .equalsIgnoreCase("None") ? String.valueOf(UNASSIGNED)
+ : cRefDb.getDbResNum();
+ currSeqIndex = Integer.valueOf(resNumIndexString);
+ if (pdbRefDb != null)
+ {
+ break;// exit loop if pdb and uniprot are already found
+ }
}
}
- if (refDbResNum == -1)
+ if (currSeqIndex == UNASSIGNED)
{
continue;
}
- int loopCount = 0;
- for (int[] x : mapping)
+ if (currSeqIndex > seq.getStart() && currSeqIndex <= seq.getEnd())
{
- if (loopCount > seq.getStart() && x[1] == refDbResNum)
+ 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]);
+ }
+ try
+ {
+ mapping[currSeqIndex][PDB_RES_POS] = Integer
+ .valueOf(resNum);
+ } catch (ArrayIndexOutOfBoundsException e)
{
- int resNum = Integer.valueOf(residue.getDbResNum());
- x[0] = resNum;
- char resCharCode = ResidueProperties
- .getSingleCharacterCode(residue.getDbResName());
- resNumMap.put(resNum, String.valueOf(resCharCode));
+ // do nothing..
}
- ++loopCount;
+ char resCharCode = ResidueProperties
+ .getSingleCharacterCode(residue.getDbResName());
+ resNumMap.put(currSeqIndex, String.valueOf(resCharCode));
}
}
}
-
+ try
+ {
+ populateAtomPositions(entityId, mapping);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ padWithGaps(resNumMap);
+ int counter = 0;
+ int seqStart = UNASSIGNED;
+ int seqEnd = UNASSIGNED;
+ int pdbStart = UNASSIGNED;
+ int pdbEnd = UNASSIGNED;
+ boolean startDetected = false;
for (int[] x : mapping)
{
- if (!startDetected && x[0] > -1)
+ if (!startDetected && x[PDB_RES_POS] != UNASSIGNED)
{
- matchedResStart = counter;
- // System.out.println(matchedResStart);
+ seqStart = counter;
startDetected = true;
+ // System.out.println("Seq start: "+ seqStart);
}
- if (startDetected && x[0] == -1)
+ if (startDetected && x[PDB_RES_POS] != UNASSIGNED)
{
- matchedResEnd = counter;
+ seqEnd = counter;
}
++counter;
}
- String matchedSeqStr = seqStr;
- if (matchedResStart != -1)
+ String matchedSeq = originalSeq;
+ if (seqStart != UNASSIGNED)
{
- 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
+ seqEnd = (seqEnd == UNASSIGNED) ? counter : seqEnd;
+ pdbStart = mapping[seqStart][PDB_RES_POS];
+ pdbEnd = mapping[seqEnd][PDB_RES_POS];
+ int orignalSeqStart = seq.getStart();
+ if (orignalSeqStart >= 1)
{
- --matchedResStart;
- --matchedResEnd;
+ int subSeqStart = seqStart - orignalSeqStart;
+ int subSeqEnd = seqEnd - (orignalSeqStart - 1);
+ matchedSeq = originalSeq.substring(subSeqStart, subSeqEnd);
}
- matchedSeqStr = seqStr.substring(matchedResStart, matchedResEnd);
}
StringBuilder targetStrucSeqs = new StringBuilder();
targetStrucSeqs.append(res);
}
- try
+ if (os != null)
{
- 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;
+ }
+
+ private boolean isResidueObserved(Residue residue)
+ {
+ String annotation = getResidueAnnotaiton(residue,
+ ResidueDetailType.ANNOTATION);
+ if (annotation == null)
+ {
+ return true;
+ }
+ if (!annotation.equalsIgnoreCase("Not_Found")
+ && annotation.equalsIgnoreCase("Not_Observed"))
+ {
+ return false;
+ }
+ return true;
+ }
+
+ 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(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 resDetail.getContent();
}
- } catch (Exception ex)
- {
- ex.printStackTrace();
}
- return mapping;
+ return "Not_Found";
+ }
+
+ private boolean hasAccessionId(String accession)
+ {
+ boolean isStrictMatch = true;
+ return isStrictMatch ? curSourceDBRef.equalsIgnoreCase(accession)
+ : curDBRefAccessionIdsString.contains(accession.toLowerCase());
}
@Override
&& getAllMappingAccession().contains(accessionId);
}
+ /**
+ * Pads missing positions with gaps
+ *
+ * @param resNumMap
+ */
+ void padWithGaps(TreeMap<Integer, String> resNumMap)
+ {
+ 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))
+ {
+ resNumMap.put(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, int[][] mapping)
+ throws IllegalArgumentException
+ {
+ 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)
+ {
+ if (map[PDB_RES_POS] != UNASSIGNED)
+ {
+ map[PDB_ATOM_POS] = getAtomIndex(map[PDB_RES_POS], chain.atoms);
+ }
+ }
+ }
+
+ /**
+ *
+ * @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)
+ {
+ throw new IllegalArgumentException(
+ "atoms collection must not be null!");
+ }
+ for (Atom atom : atoms)
+ {
+ if (atom.resNumber == residueIndex)
+ {
+ return atom.atomIndex;
+ }
+ }
+ return UNASSIGNED;
+ }
@Override
public Entity getEntityById(String id) throws SiftsException
@Override
public StringBuffer getMappingOutput(MappingOutputPojo mp)
+ throws SiftsException
{
String seqRes = mp.getSeqResidue();
String seqName = mp.getSeqName();
: 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();
output.append(NEWLINE);
- output.append("Sequence ⟷ Structure mapping details:");
+ output.append("Sequence ⟷ Structure mapping details").append(NEWLINE);
+ output.append("Method: SIFTS");
output.append(NEWLINE).append(NEWLINE);
output.append(new Format("%" + maxid + "s").form(seqName));
output.append(String.valueOf(pdbEnd));
output.append(NEWLINE).append(NEWLINE);
- float pid = 0;
+ int matchedSeqCount = 0;
for (int j = 0; j < nochunks; j++)
{
// Print the first aligned sequence
// Print out the matching chars
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))))
{
- pid++;
+ matchedSeqCount++;
output.append("|");
}
else if (type.equals("pep"))
output.append(" ");
}
}
+ } catch (IndexOutOfBoundsException e)
+ {
+ continue;
+ }
}
// Now print the second aligned sequence
output = output.append(NEWLINE);
}
output.append(NEWLINE).append(NEWLINE);
}
- pid = pid / (seqRes.length()) * 100;
+ 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));
output.append(NEWLINE);
- output.append("Mapping method: SIFTS").append(NEWLINE);
return output;
}
git://source.jalview.org / jalview.git / blobdiff