private final static String NEWLINE = System.lineSeparator();
- private final static int THRESHOLD_IN_DAYS = 2;
-
private String curSourceDBRef;
private HashSet<String> curDBRefAccessionIdsString;
// 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))
+ if (isFileOlderThanThreshold(siftsFile,
+ SiftsSettings.getCacheThresholdInDays()))
{
// System.out.println("Downloaded file is out of date, hence re-downloading...");
siftsFile = downloadSiftsFile(pdbId.toLowerCase());
*/
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 = SiftsSettings.getSiftDownloadDirectory()
{
continue;
}
- if (currSeqIndex > seq.getStart() && currSeqIndex <= seq.getEnd())
+ if (currSeqIndex >= seq.getStart() && currSeqIndex <= seq.getEnd())
{
int resNum;
try
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(residue.getDbResName());
+ .getSingleCharacterCode(ResidueProperties
+ .getCanonicalAminoAcid(residue.getDbResName()));
resNumMap.put(currSeqIndex, String.valueOf(resCharCode));
}
else
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];
int orignalSeqStart = seq.getStart();
if (orignalSeqStart >= 1)
{
- int subSeqStart = seqStart - orignalSeqStart;
+ 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
+ {
+ matchedSeq = originalSeq.substring(1, originalSeq.length());
+ }
}
StringBuilder targetStrucSeqs = new StringBuilder();
if (os != null)
{
MappingOutputPojo mop = new MappingOutputPojo();
- mop.setSeqStart(seqStart);
- mop.setSeqEnd(seqEnd);
+ mop.setSeqStart(pdbStart);
+ mop.setSeqEnd(pdbEnd);
mop.setSeqName(seq.getName());
mop.setSeqResidue(matchedSeq);
- mop.setStrStart(pdbStart);
- mop.setStrEnd(pdbEnd);
+ mop.setStrStart(seqStart);
+ mop.setStrEnd(seqEnd);
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
+ */
+ void populateAtomPositions(String chainId,
+ HashMap<Integer, 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.values())
+ {
+ 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;
+ }
+
+ /**
* Checks if the residue instance is marked 'Not_observed' or not
*
* @param residue
*/
private boolean isResidueObserved(Residue residue)
{
- String annotation = getResidueAnnotaiton(residue,
+ HashSet<String> annotations = getResidueAnnotaitons(residue,
ResidueDetailType.ANNOTATION);
- if (annotation == null)
+ if (annotations == null || annotations.isEmpty())
{
return true;
}
- if (!annotation.equalsIgnoreCase(NOT_FOUND)
- && annotation.equalsIgnoreCase(NOT_OBSERVED))
+ for (String annotation : annotations)
{
- return false;
+ if (annotation.equalsIgnoreCase(NOT_OBSERVED))
+ {
+ return false;
+ }
}
return true;
}
* @param type
* @return
*/
- private String getResidueAnnotaiton(Residue residue,
+ private HashSet<String> getResidueAnnotaitons(Residue residue,
ResidueDetailType type)
{
+ HashSet<String> foundAnnotations = new HashSet<String>();
List<ResidueDetail> resDetails = residue.getResidueDetail();
for (ResidueDetail resDetail : resDetails)
{
if (resDetail.getProperty().equalsIgnoreCase(type.getCode()))
{
- return resDetail.getContent();
+ foundAnnotations.add(resDetail.getContent());
}
}
- return NOT_FOUND;
+ return foundAnnotations;
}
@Override
}
}
- /**
- *
- * @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<Integer, 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.values())
- {
- 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
{
- List<Entity> entities = siftsEntry.getEntity();
- for (Entity entity : entities)
+ // 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)
{
- if (!entity.getEntityId().equalsIgnoreCase(id))
+ List<Entity> entities = siftsEntry.getEntity();
+ for (Entity entity : entities)
{
- continue;
+ if (!entity.getEntityId().equalsIgnoreCase(id))
+ {
+ continue;
+ }
+ return entity;
}
- return entity;
}
Entity entity = getEntityByMostOptimalMatchedId(id);
if (entity != null)
*/
public Entity getEntityByMostOptimalMatchedId(String chainId)
{
- System.out
- .println("--------------> advanced greedy entityId matching block entered..");
+ // System.out.println("---> advanced greedy entityId matching block entered..");
List<Entity> entities = siftsEntry.getEntity();
SiftsEntitySortPojo[] sPojo = new SiftsEntitySortPojo[entities.size()];
int count = 0;
output.append(NEWLINE).append(NEWLINE);
}
float pid = (float) matchedSeqCount / seqRes.length() * 100;
- if (pid < 2)
+ if (pid < SiftsSettings.getFailSafePIDThreshold())
{
- throw new SiftsException("Low PID detected for SIFTs mapping...");
+ throw new SiftsException(">>> Low PID detected for SIFTs mapping...");
}
output.append("Length of alignment = " + seqRes.length()).append(
NEWLINE);
git://source.jalview.org / jalview.git / blobdiff