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.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;
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 final static int THRESHOLD_IN_DAYS = 2;
+
private String curSourceDBRef;
private HashSet<String> curDBRefAccessionIdsString;
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
}
/**
- * 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
*/
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();
} 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 SiftsException("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 an age check to determine if a
- // new SIFTs file should be re-downloaded as SIFTs entries are usually
- // updated weekly
+ // The line below is required for unit testing... don't comment it out!!!
System.out.println(">>> SIFTS File already downloaded for " + pdbId);
+
+ if (isFileOlderThanThreshold(siftsFile, THRESHOLD_IN_DAYS))
+ {
+ // System.out.println("Downloaded file is out of date, hence re-downloading...");
+ siftsFile = downloadSiftsFile(pdbId.toLowerCase());
+ }
return siftsFile;
}
siftsFile = downloadSiftsFile(pdbId.toLowerCase());
}
/**
- * 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
{
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();
}
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);
}
*/
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
*
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");
}
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
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,
- pdbId, chain, mapping,
- mappingOutput);
+ pdbId, chain, mapping, mappingOutput);
return siftsMapping;
}
@Override
- public int[][] getGreedyMapping(String entityId, SequenceI seq,
- java.io.PrintStream os)
- throws SiftsException
+ public HashMap<Integer, int[]> getGreedyMapping(String entityId,
+ SequenceI seq, java.io.PrintStream os) throws SiftsException
{
-
+ ArrayList<Integer> omitNonObserved = new ArrayList<Integer>();
+ 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];
+ jalview.util.Comparison.GapChars, seq.getSequenceAsString());
+ HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>();
DBRefEntryI sourceDBRef = seq.getSourceDBRef();
if (sourceDBRef == null)
{
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)
}
if (cRefDb.getDbCoordSys()
.equalsIgnoreCase(seqCoordSys.getName())
- && hasAccessionId(cRefDb.getDbAccessionId()))
+ && isAccessionMatched(cRefDb.getDbAccessionId()))
{
String resNumIndexString = cRefDb.getDbResNum()
.equalsIgnoreCase("None") ? String.valueOf(UNASSIGNED)
: cRefDb.getDbResNum();
- currSeqIndex = Integer.valueOf(resNumIndexString);
+ try
+ {
+ currSeqIndex = Integer.valueOf(resNumIndexString);
+ } catch (NumberFormatException nfe)
+ {
+ currSeqIndex = Integer.valueOf(resNumIndexString
+ .split("[a-zA-Z]")[0]);
+ }
if (pdbRefDb != null)
{
break;// exit loop if pdb and uniprot are already found
try
{
resNum = (pdbRefDb == null) ? Integer.valueOf(residue
- .getDbResNum()) : Integer.valueOf(pdbRefDb.getDbResNum());
+ .getDbResNum()) : Integer.valueOf(pdbRefDb
+ .getDbResNum());
} catch (NumberFormatException nfe)
{
resNum = (pdbRefDb == null) ? Integer.valueOf(residue
.getDbResNum()) : Integer.valueOf(pdbRefDb
.getDbResNum().split("[a-zA-Z]")[0]);
}
- try
+
+ if (isResidueObserved(residue)
+ || seqCoordSys == CoordinateSys.UNIPROT)
{
- mapping[currSeqIndex][PDB_RES_POS] = Integer.valueOf(resNum);
- } catch (ArrayIndexOutOfBoundsException e)
+ char resCharCode = ResidueProperties
+ .getSingleCharacterCode(ResidueProperties
+ .getCanonicalAminoAcid(residue.getDbResName()));
+ resNumMap.put(currSeqIndex, String.valueOf(resCharCode));
+ }
+ else
{
- // do nothing..
+ omitNonObserved.add(currSeqIndex);
+ ++nonObservedShiftIndex;
}
- char resCharCode = ResidueProperties
- .getSingleCharacterCode(residue.getDbResName());
- resNumMap.put(currSeqIndex, String.valueOf(resCharCode));
+ mapping.put(currSeqIndex - nonObservedShiftIndex, new int[] {
+ Integer.valueOf(resNum), UNASSIGNED });
}
}
}
{
e.printStackTrace();
}
- padWithGaps(resNumMap);
- int counter = 0;
+ if (seqCoordSys == CoordinateSys.UNIPROT)
+ {
+ padWithGaps(resNumMap, omitNonObserved);
+ }
int seqStart = UNASSIGNED;
int seqEnd = UNASSIGNED;
int pdbStart = UNASSIGNED;
int pdbEnd = UNASSIGNED;
- boolean startDetected = false;
- for (int[] x : mapping)
- {
- if (!startDetected && x[PDB_RES_POS] != UNASSIGNED)
- {
- seqStart = counter;
- startDetected = true;
- // System.out.println("Seq start: "+ seqStart);
- }
- 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);
}
}
return mapping;
}
- private boolean hasAccessionId(String accession)
+ /**
+ * 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)
+ {
+ 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()))
+ {
+ return resDetail.getContent();
+ }
+ }
+ return NOT_FOUND;
+ }
+
+ @Override
+ public boolean isAccessionMatched(String accession)
{
boolean isStrictMatch = true;
return isStrictMatch ? curSourceDBRef.equalsIgnoreCase(accession)
: curDBRefAccessionIdsString.contains(accession.toLowerCase());
}
- @Override
- public boolean isFoundInSiftsEntry(String accessionId)
+ 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())
{
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, "-");
}
* @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)
{
}
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<Entity> entities = siftsEntry.getEntity();
+ SiftsEntitySortPojo[] sPojo = new SiftsEntitySortPojo[entities.size()];
+ int count = 0;
+ for (Entity entity : entities)
+ {
+ sPojo[count] = new SiftsEntitySortPojo();
+ sPojo[count].entityId = entity.getEntityId();
+
+ List<Segment> segments = entity.getSegment();
+ for (Segment segment : segments)
+ {
+ List<Residue> residues = segment.getListResidue().getResidue();
+ for (Residue residue : residues)
+ {
+ List<CrossRefDb> cRefDbs = residue.getCrossRefDb();
+ for (CrossRefDb cRefDb : cRefDbs)
+ {
+ if (!cRefDb.getDbSource().equalsIgnoreCase("PDB"))
+ {
+ continue;
+ }
+ ++sPojo[count].resCount;
+ if (cRefDb.getDbChainId().equalsIgnoreCase(chainId))
+ {
+ ++sPojo[count].chainIdFreq;
+ }
+ }
+ }
+ }
+ sPojo[count].pid = 100 * (sPojo[count].chainIdFreq / sPojo[count].resCount);
+ ++count;
+ }
+ 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)
+ {
+ if (!entity.getEntityId().equalsIgnoreCase(sPojo[0].entityId))
+ {
+ continue;
+ }
+ return entity;
+ }
+ }
+ return null;
+ }
+
+ public 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;
+ }
+ }
+
@Override
public String[] getEntryDBs()
{
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;
output.append(" - ");
output.append(String.valueOf(pdbEnd));
output.append(NEWLINE).append(NEWLINE);
-
+
int matchedSeqCount = 0;
for (int j = 0; j < nochunks; j++)
{
{
try
{
- if ((i + (j * len)) < seqRes.length())
- {
- if (seqRes.charAt(i + (j * len)) == strRes.charAt(i + (j * len))
- && !jalview.util.Comparison.isGap(seqRes.charAt(i
- + (j * len))))
+ if ((i + (j * len)) < seqRes.length())
{
+ 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"))
- {
- if (ResidueProperties.getPAM250(seqRes.charAt(i + (j * len)),
- strRes.charAt(i + (j * len))) > 0)
+ 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;
{
throw new SiftsException("Low PID detected for SIFTs mapping...");
}
- output.append("Length of alignment = " + seqRes.length())
- .append(NEWLINE);
+ output.append("Length of alignment = " + seqRes.length()).append(
+ NEWLINE);
output.append(new Format("Percentage ID = %2.2f").form(pid));
output.append(NEWLINE);
return output;
}
-
+
@Override
public int getEntityCount()
{
{
return siftsEntry.getDbVersion();
}
+
}
git://source.jalview.org / jalview.git / blobdiff