import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureMapping;
+import jalview.structure.StructureMappingClient;
+import jalview.structures.models.MappingOutputModel;
+import jalview.util.Comparison;
+import jalview.util.DBRefUtils;
import jalview.util.Format;
import jalview.xml.binding.sifts.Entry;
import jalview.xml.binding.sifts.Entry.Entity;
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 javax.xml.stream.XMLInputFactory;
import javax.xml.stream.XMLStreamReader;
-import MCview.Atom;
-import MCview.PDBChain;
-
-public class SiftsClient implements SiftsClientI
+public class SiftsClient extends StructureMappingClient implements
+ SiftsClientI
{
- private Entry siftsEntry;
+ /*
+ * for use in mocking out file fetch for tests only
+ * - reset to null after testing!
+ */
+ private static File mockSiftsFile;
+
+ private static final int UNASSIGNED = StructureMapping.UNASSIGNED; // -1
+
+ private static final int PDB_RES_POS = StructureMapping.PDB_RES_NUM_INDEX; // 0
- private StructureFile pdb;
+ private Entry siftsEntry;
private String pdbId;
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 NOT_OBSERVED = "Not_Observed";
private static final String SIFTS_FTP_BASE_URL = "http://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
* @param pdbId
* @throws SiftsException
*/
- public SiftsClient(StructureFile pdb) throws SiftsException
+ public SiftsClient(StructureFile structureFile) throws SiftsException
{
- this.pdb = pdb;
- this.pdbId = pdb.getId();
+ this.structureFile = structureFile;
+ this.pdbId = structureFile.getId();
File siftsFile = getSiftsFile(pdbId);
siftsEntry = parseSIFTs(siftsFile);
}
-
/**
* Parse the given SIFTs File and return a JAXB POJO of parsed data
*
*/
public static File getSiftsFile(String pdbId) throws SiftsException
{
+ /*
+ * return mocked file if it has been set
+ */
+ if (mockSiftsFile != null)
+ {
+ return mockSiftsFile;
+ }
+
String siftsFileName = SiftsSettings.getSiftDownloadDirectory()
+ pdbId.toLowerCase() + ".xml.gz";
File siftsFile = new File(siftsFileName);
return new File(siftsFileName);
}
}
+ else
+ {
+ return siftsFile;
+ }
}
try
{
{
siftsDownloadDir.mkdirs();
}
- // System.out.println(">> Download ftp url : " + siftsFileFTPURL);
- URL url = new URL(siftsFileFTPURL);
- URLConnection conn = url.openConnection();
- InputStream inputStream = conn.getInputStream();
- FileOutputStream outputStream = new FileOutputStream(
- downloadedSiftsFile);
- byte[] buffer = new byte[BUFFER_SIZE];
- int bytesRead = -1;
- while ((bytesRead = inputStream.read(buffer)) != -1)
- {
- outputStream.write(buffer, 0, bytesRead);
- }
- outputStream.close();
- inputStream.close();
- // System.out.println(">>> File downloaded : " + downloadedSiftsFile);
+ // System.out.println(">> Download ftp url : " + siftsFileFTPURL);
+ // long now = System.currentTimeMillis();
+ URL url = new URL(siftsFileFTPURL);
+ URLConnection conn = url.openConnection();
+ InputStream inputStream = conn.getInputStream();
+ FileOutputStream outputStream = new FileOutputStream(
+ downloadedSiftsFile);
+ byte[] buffer = new byte[BUFFER_SIZE];
+ int bytesRead = -1;
+ while ((bytesRead = inputStream.read(buffer)) != -1)
+ {
+ outputStream.write(buffer, 0, bytesRead);
+ }
+ outputStream.close();
+ inputStream.close();
+// System.out.println(">>> File downloaded : " + downloadedSiftsFile
+// + " took " + (System.currentTimeMillis() - now) + "ms");
return new File(downloadedSiftsFile);
}
public DBRefEntryI getValidSourceDBRef(SequenceI seq)
throws SiftsException
{
- DBRefEntryI sourceDBRef = null;
- sourceDBRef = seq.getSourceDBRef();
- if (sourceDBRef != null && isValidDBRefEntry(sourceDBRef))
+ List<DBRefEntry> dbRefs = seq.getPrimaryDBRefs();
+ if (dbRefs == null || dbRefs.size() < 1)
{
- return sourceDBRef;
+ throw new SiftsException(
+ "Source DBRef could not be determined. DBRefs might not have been retrieved.");
}
- else
+
+ for (DBRefEntry dbRef : dbRefs)
{
- DBRefEntry[] dbRefs = seq.getDBRefs();
- if (dbRefs == null || dbRefs.length < 1)
+ if (dbRef == null || dbRef.getAccessionId() == null
+ || dbRef.getSource() == null)
{
- throw new SiftsException(
- "Source DBRef could not be determined. DBRefs might not have been retrieved.");
+ continue;
}
-
- for (DBRefEntryI dbRef : dbRefs)
+ String canonicalSource = DBRefUtils.getCanonicalName(dbRef
+ .getSource());
+ if (isValidDBRefEntry(dbRef)
+ && (canonicalSource.equalsIgnoreCase(DBRefSource.UNIPROT) || canonicalSource
+ .equalsIgnoreCase(DBRefSource.PDB)))
{
- if (dbRef == null || dbRef.getAccessionId() == null
- || dbRef.getSource() == null)
- {
- continue;
- }
- if (isFoundInSiftsEntry(dbRef.getAccessionId())
- && (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT) || dbRef
- .getSource().equalsIgnoreCase(DBRefSource.PDB)))
- {
- seq.setSourceDBRef(dbRef);
- return dbRef;
- }
+ return dbRef;
}
}
- if (sourceDBRef != null && isValidDBRefEntry(sourceDBRef))
- {
- return sourceDBRef;
- }
throw new SiftsException("Could not get source DB Ref");
}
}
@Override
- public StructureMapping getSiftsStructureMapping(SequenceI seq,
- String pdbFile, String chain) throws SiftsException
+ public StructureMapping getStructureMapping(SequenceI seq,
+ String pdbFile, String chain) throws Exception,
+ StructureMappingException
{
structId = (chain == null) ? pdbId : pdbId + "|" + chain;
- System.out.println("Getting mapping for: " + pdbId + "|" + chain
- + " : seq- " + seq.getName());
+ System.out.println("Getting SIFTS mapping for " + structId + ": seq "
+ + seq.getName());
final StringBuilder mappingDetails = new StringBuilder(128);
PrintStream ps = new PrintStream(System.out)
@Override
public HashMap<Integer, int[]> getGreedyMapping(String entityId,
- SequenceI seq, java.io.PrintStream os) throws SiftsException
+ SequenceI seq, java.io.PrintStream os) throws SiftsException,
+ StructureMappingException
{
List<Integer> omitNonObserved = new ArrayList<Integer>();
int nonObservedShiftIndex = 0;
String originalSeq = AlignSeq.extractGaps(
jalview.util.Comparison.GapChars, seq.getSequenceAsString());
HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>();
- DBRefEntryI sourceDBRef = seq.getSourceDBRef();
+ DBRefEntryI sourceDBRef;
sourceDBRef = getValidSourceDBRef(seq);
// TODO ensure sequence start/end is in the same coordinate system and
// consistent with the choosen sourceDBRef
int pdbStart = UNASSIGNED;
int pdbEnd = UNASSIGNED;
- Integer[] keys = mapping.keySet().toArray(new Integer[0]);
- Arrays.sort(keys);
- if (keys.length < 1)
+ if (mapping.isEmpty())
{
- throw new SiftsException(">>> Empty SIFTS mapping generated!!");
+ throw new SiftsException("SIFTS mapping failed");
}
+
+ Integer[] keys = mapping.keySet().toArray(new Integer[0]);
+ Arrays.sort(keys);
seqStart = keys[0];
seqEnd = keys[keys.length - 1];
if (os != null)
{
- MappingOutputPojo mop = new MappingOutputPojo();
- mop.setSeqStart(pdbStart);
- mop.setSeqEnd(pdbEnd);
+ MappingOutputModel mop = new MappingOutputModel();
+ mop.setSeqStart(seqStart);
+ mop.setSeqEnd(seqEnd);
mop.setSeqName(seq.getName());
mop.setSeqResidue(matchedSeq);
- mop.setStrStart(seqStart);
- mop.setStrEnd(seqEnd);
+ mop.setStrStart(pdbStart);
+ mop.setStrEnd(pdbEnd);
mop.setStrName(structId);
mop.setStrResidue(targetStrucSeqs.toString());
}
}
}
- /**
- *
- * @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
- * @throws SiftsException
- */
- void populateAtomPositions(String chainId, Map<Integer, int[]> mapping)
- throws IllegalArgumentException, SiftsException
- {
- try
- {
- 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);
- }
- }
- } catch (NullPointerException e)
- {
- throw new SiftsException(e.getMessage());
- } catch (Exception e)
- {
- throw new SiftsException(e.getMessage());
- }
- }
-
- /**
- *
- * @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;
- }
/**
* Checks if the residue instance is marked 'Not_observed' or not
}
}
-
-
@Override
public Entity getEntityById(String id) throws SiftsException
{
if (sPojo[0].entityId != null)
{
+ if (sPojo[0].pid < 1)
+ {
+ return null;
+ }
for (Entity entity : entities)
{
if (!entity.getEntityId().equalsIgnoreCase(sPojo[0].entityId))
}
@Override
- public StringBuffer getMappingOutput(MappingOutputPojo mp)
- throws SiftsException
+ public StringBuffer getMappingOutput(MappingOutputModel mp)
+ throws StructureMappingException
{
String seqRes = mp.getSeqResidue();
String seqName = mp.getSeqName();
{
if ((i + (j * len)) < seqRes.length())
{
- if (seqRes.charAt(i + (j * len)) == strRes
- .charAt(i + (j * len))
+ boolean sameChar = Comparison.isSameResidue(
+ seqRes.charAt(i + (j * len)),
+ strRes.charAt(i + (j * len)), false);
+ if (sameChar
&& !jalview.util.Comparison.isGap(seqRes.charAt(i
+ (j * len))))
{
float pid = (float) matchedSeqCount / seqRes.length() * 100;
if (pid < SiftsSettings.getFailSafePIDThreshold())
{
- throw new SiftsException(">>> Low PID detected for SIFTs mapping...");
+ throw new StructureMappingException(
+ ">>> Low PID detected for SIFTs mapping...");
}
output.append("Length of alignment = " + seqRes.length()).append(
NEWLINE);
return siftsEntry.getDbVersion();
}
+ public static void setMockSiftsFile(File file)
+ {
+ mockSiftsFile = file;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff