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.Format;
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.FileInputStream;
-import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.HashMap;
import java.util.HashSet;
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.Unmarshaller;
-import javax.xml.stream.FactoryConfigurationError;
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 StructureFile pdb;
private String pdbId;
private String structId;
- private String segStartEnd;
+ // private String segStartEnd;
private CoordinateSys seqCoordSys = CoordinateSys.UNIPROT;
private static final int PDB_ATOM_POS = 1;
- private static final String NOT_FOUND = "Not_Found";
-
private static final String NOT_OBSERVED = "Not_Observed";
- private static final String SIFTS_FTP_BASE_URL = "ftp://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
+ 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();
* @param pdbId
* @throws SiftsException
*/
- public SiftsClient(PDBfile pdb) throws SiftsException
+ public SiftsClient(StructureFile pdb) throws SiftsException
{
this.pdb = pdb;
- this.pdbId = pdb.id;
+ this.pdbId = pdb.getId();
File siftsFile = getSiftsFile(pdbId);
siftsEntry = parseSIFTs(siftsFile);
}
- /**
- * 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) throws SiftsException
- {
- this.pdb = pdb;
- this.pdbId = pdb.id;
- siftsEntry = parseSIFTs(siftsFile);
- }
/**
* Parse the given SIFTs File and return a JAXB POJO of parsed data
.createXMLStreamReader(gzis);
Unmarshaller um = jc.createUnmarshaller();
return (Entry) um.unmarshal(streamReader);
- } 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)
+ } catch (Exception e)
{
e.printStackTrace();
throw new SiftsException(e.getMessage());
*/
public static File getSiftsFile(String pdbId) throws SiftsException
{
- File siftsFile = new File(SiftsSettings.getSiftDownloadDirectory()
- + pdbId.toLowerCase() + ".xml.gz");
+ String siftsFileName = SiftsSettings.getSiftDownloadDirectory()
+ + pdbId.toLowerCase() + ".xml.gz";
+ File siftsFile = new File(siftsFileName);
if (siftsFile.exists())
{
// The line below is required for unit testing... don't comment it out!!!
if (isFileOlderThanThreshold(siftsFile,
SiftsSettings.getCacheThresholdInDays()))
{
- // System.out.println("Downloaded file is out of date, hence re-downloading...");
- siftsFile = downloadSiftsFile(pdbId.toLowerCase());
+ 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);
+ }
}
- return siftsFile;
}
- siftsFile = downloadSiftsFile(pdbId.toLowerCase());
+ try
+ {
+ siftsFile = downloadSiftsFile(pdbId.toLowerCase());
+ } catch (IOException e)
+ {
+ throw new SiftsException(e.getMessage());
+ }
return siftsFile;
}
* @param pdbId
* @return downloaded SIFTs XML file
* @throws SiftsException
+ * @throws IOException
*/
- public static File downloadSiftsFile(String pdbId) throws SiftsException
+ public static File downloadSiftsFile(String pdbId) throws SiftsException,
+ IOException
{
if (pdbId.contains(".cif"))
{
{
siftsDownloadDir.mkdirs();
}
- try
- {
// System.out.println(">> Download ftp url : " + siftsFileFTPURL);
URL url = new URL(siftsFileFTPURL);
URLConnection conn = url.openConnection();
outputStream.close();
inputStream.close();
// System.out.println(">>> File downloaded : " + downloadedSiftsFile);
- } catch (IOException ex)
- {
- throw new SiftsException(ex.getMessage());
- }
return new File(downloadedSiftsFile);
}
DBRefEntry[] dbRefs = seq.getDBRefs();
if (dbRefs == null || dbRefs.length < 1)
{
- throw new SiftsException("Could not get source DB Ref");
+ throw new SiftsException(
+ "Source DBRef could not be determined. DBRefs might not have been retrieved.");
}
for (DBRefEntryI dbRef : dbRefs)
&& (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT) || dbRef
.getSource().equalsIgnoreCase(DBRefSource.PDB)))
{
+ seq.setSourceDBRef(dbRef);
return dbRef;
}
}
* - 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());
.getMapRegion();
for (MapRegion mapRegion : mapRegions)
{
- accessions.add(mapRegion.getDb().getDbAccessionId());
+ accessions
+ .add(mapRegion.getDb().getDbAccessionId().toLowerCase());
}
}
}
public HashMap<Integer, int[]> getGreedyMapping(String entityId,
SequenceI seq, java.io.PrintStream os) throws SiftsException
{
- ArrayList<Integer> omitNonObserved = new ArrayList<Integer>();
+ List<Integer> omitNonObserved = new ArrayList<Integer>();
int nonObservedShiftIndex = 0;
- System.out.println("Generating mappings for : " + entityId);
+ // System.out.println("Generating mappings for : " + entityId);
Entity entity = null;
entity = getEntityById(entityId);
String originalSeq = AlignSeq.extractGaps(
jalview.util.Comparison.GapChars, seq.getSequenceAsString());
HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>();
DBRefEntryI sourceDBRef = seq.getSourceDBRef();
- if (sourceDBRef == null)
- {
- sourceDBRef = getValidSourceDBRef(seq);
- // TODO ensure sequence start/end is in the same coordinate system and
- // consistent with the choosen 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))
List<Segment> segments = entity.getSegment();
for (Segment segment : segments)
{
- segStartEnd = segment.getStart() + " - " + segment.getEnd();
- System.out.println("Mappging segments : " + segment.getSegId() + "\\"
- + segStartEnd);
+ // segStartEnd = segment.getStart() + " - " + segment.getEnd();
+ // System.out.println("Mapping segments : " + segment.getSegId() + "\\"
+ // + segStartEnd);
List<Residue> residues = segment.getListResidue().getResidue();
for (Residue residue : residues)
{
{
currSeqIndex = Integer.valueOf(resNumIndexString
.split("[a-zA-Z]")[0]);
+ continue;
}
if (pdbRefDb != null)
{
mop.setType("pep");
os.print(getMappingOutput(mop).toString());
+ os.println();
}
return 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,
- HashMap<Integer, int[]> mapping) throws IllegalArgumentException
+ void populateAtomPositions(String chainId, Map<Integer, int[]> mapping)
+ throws IllegalArgumentException, SiftsException
{
- 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())
+ try
{
- if (map[PDB_RES_POS] != UNASSIGNED)
+ 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())
{
- map[PDB_ATOM_POS] = getAtomIndex(map[PDB_RES_POS], chain.atoms);
+ if (map[PDB_RES_POS] != UNASSIGNED)
+ {
+ map[PDB_ATOM_POS] = getAtomIndex(map[PDB_RES_POS], chain.atoms);
+ }
}
+ } catch (NullPointerException e)
+ {
+ throw new SiftsException(e.getMessage());
+ } catch (Exception e)
+ {
+ throw new SiftsException(e.getMessage());
}
}
*/
private boolean isResidueObserved(Residue residue)
{
- HashSet<String> annotations = getResidueAnnotaitons(residue,
+ Set<String> annotations = getResidueAnnotaitons(residue,
ResidueDetailType.ANNOTATION);
if (annotations == null || annotations.isEmpty())
{
* @param type
* @return
*/
- private HashSet<String> getResidueAnnotaitons(Residue residue,
+ private Set<String> getResidueAnnotaitons(Residue residue,
ResidueDetailType type)
{
HashSet<String> foundAnnotations = new HashSet<String>();
private boolean isFoundInSiftsEntry(String accessionId)
{
+ Set<String> siftsDBRefs = getAllMappingAccession();
return accessionId != null
- && getAllMappingAccession().contains(accessionId);
+ && siftsDBRefs.contains(accessionId.toLowerCase());
}
/**
*
* @param resNumMap
*/
- void padWithGaps(TreeMap<Integer, String> resNumMap,
- ArrayList<Integer> omitNonObserved)
+ void padWithGaps(Map<Integer, String> resNumMap,
+ List<Integer> omitNonObserved)
{
if (resNumMap == null || resNumMap.isEmpty())
{
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);
+ // 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))
// 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<Entity> entities = siftsEntry.getEntity();
- for (Entity entity : entities)
- {
- if (!entity.getEntityId().equalsIgnoreCase(id))
- {
- continue;
- }
- return entity;
- }
- }
+ // boolean isGetEntityIdDirectly = false;
+ // if (isGetEntityIdDirectly)
+ // {
+ // List<Entity> entities = siftsEntry.getEntity();
+ // for (Entity entity : entities)
+ // {
+ // if (!entity.getEntityId().equalsIgnoreCase(id))
+ // {
+ // continue;
+ // }
+ // return entity;
+ // }
+ // }
Entity entity = getEntityByMostOptimalMatchedId(id);
if (entity != null)
{
++count;
}
Arrays.sort(sPojo, Collections.reverseOrder());
- System.out.println("highest matched entity : " + sPojo[0].entityId);
- System.out.println("highest matched pid : " + sPojo[0].pid);
+ // System.out.println("highest matched entity : " + sPojo[0].entityId);
+ // System.out.println("highest matched pid : " + sPojo[0].pid);
if (sPojo[0].entityId != null)
{
}
}
- @Override
- public String[] getEntryDBs()
- {
- System.out.println("\nListing DB entries...");
- List<String> availDbs = new ArrayList<String>();
- List<Db> dbs = siftsEntry.getListDB().getDb();
- for (Db db : dbs)
- {
- availDbs.add(db.getDbSource());
- System.out.println(db.getDbSource() + " | " + db.getDbCoordSys());
- }
- return availDbs.toArray(new String[0]);
- }
@Override
public StringBuffer getMappingOutput(MappingOutputPojo mp)
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 String getDbEvidence()
- {
- return siftsEntry.getDbEvidence();
- }
-
- @Override
public String getDbSource()
{
return siftsEntry.getDbSource();
git://source.jalview.org / jalview.git / blobdiff