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;
{
private Entry siftsEntry;
- private PDBfile pdb;
+ private StructureFile pdb;
private String pdbId;
private final static String NEWLINE = System.lineSeparator();
- // private final static int CACHE_THRESHOLD_IN_DAYS = 2;
- //
- // private final static int FAIL_SAFE_PID_THRESHOLD = 30;
-
private String curSourceDBRef;
private HashSet<String> curDBRefAccessionIdsString;
* @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);
}
public SiftsClient(PDBfile pdb, File siftsFile) throws SiftsException
{
this.pdb = pdb;
- this.pdbId = pdb.id;
+ this.pdbId = pdb.getId();
siftsEntry = parseSIFTs(siftsFile);
}
{
ArrayList<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(
for (Segment segment : segments)
{
segStartEnd = segment.getStart() + " - " + segment.getEnd();
- System.out.println("Mappging segments : " + segment.getSegId() + "\\"
- + segStartEnd);
+ // 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)
{
{
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)
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());
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())
+ 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 (Exception e)
+ {
+ e.printStackTrace();
}
}
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))
@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;
++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)
{
// output mappings
StringBuffer output = new StringBuffer();
output.append(NEWLINE);
- output.append("Sequence ⟷ Structure mapping details").append(NEWLINE);
+ output.append("Sequence \u27f7 Structure mapping details").append(
+ NEWLINE);
output.append("Method: SIFTS");
output.append(NEWLINE).append(NEWLINE);
float pid = (float) matchedSeqCount / seqRes.length() * 100;
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);