private String structId;
- // private String segStartEnd;
-
private CoordinateSys seqCoordSys = CoordinateSys.UNIPROT;
private static final int BUFFER_SIZE = 4096;
private HashSet<String> curDBRefAccessionIdsString;
- public enum CoordinateSys
+ private enum CoordinateSys
{
UNIPROT("UniProt"), PDB("PDBresnum"), PDBe("PDBe");
private String name;
}
};
- public enum ResidueDetailType
+ private enum ResidueDetailType
{
NAME_SEC_STRUCTURE("nameSecondaryStructure"), CODE_SEC_STRUCTURE(
"codeSecondaryStructure"), ANNOTATION("Annotation");
TreeMap<Integer, String> resNumMap = new TreeMap<Integer, String>();
List<Segment> segments = entity.getSegment();
+ SegmentHelperPojo shp = new SegmentHelperPojo(seq, mapping, resNumMap,
+ omitNonObserved, nonObservedShiftIndex);
+ processSegments(segments, shp);
+ try
+ {
+ populateAtomPositions(entityId, mapping);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ if (seqCoordSys == CoordinateSys.UNIPROT)
+ {
+ padWithGaps(resNumMap, omitNonObserved);
+ }
+ int seqStart = UNASSIGNED;
+ int seqEnd = UNASSIGNED;
+ int pdbStart = UNASSIGNED;
+ int pdbEnd = UNASSIGNED;
+
+ 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];
+
+ String matchedSeq = originalSeq;
+ if (seqStart != UNASSIGNED)
+ {
+ 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) ? 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();
+ for (String res : resNumMap.values())
+ {
+ targetStrucSeqs.append(res);
+ }
+
+ if (os != null)
+ {
+ MappingOutputPojo mop = new MappingOutputPojo();
+ mop.setSeqStart(pdbStart);
+ mop.setSeqEnd(pdbEnd);
+ mop.setSeqName(seq.getName());
+ mop.setSeqResidue(matchedSeq);
+
+ mop.setStrStart(seqStart);
+ mop.setStrEnd(seqEnd);
+ mop.setStrName(structId);
+ mop.setStrResidue(targetStrucSeqs.toString());
+
+ mop.setType("pep");
+ os.print(getMappingOutput(mop).toString());
+ os.println();
+ }
+ return mapping;
+ }
+
+ void processSegments(List<Segment> segments, SegmentHelperPojo shp)
+ {
+ SequenceI seq = shp.getSeq();
+ HashMap<Integer, int[]> mapping = shp.getMapping();
+ TreeMap<Integer, String> resNumMap = shp.getResNumMap();
+ List<Integer> omitNonObserved = shp.getOmitNonObserved();
+ int nonObservedShiftIndex = shp.getNonObservedShiftIndex();
for (Segment segment : segments)
{
- // segStartEnd = segment.getStart() + " - " + segment.getEnd();
- // System.out.println("Mapping segments : " + segment.getSegId() + "\\"
+ // System.out.println("Mapping segments : " + segment.getSegId() + "\\"s
// + segStartEnd);
List<Residue> residues = segment.getListResidue().getResidue();
for (Residue residue : residues)
}
}
}
- try
- {
- populateAtomPositions(entityId, mapping);
- } catch (Exception e)
- {
- e.printStackTrace();
- }
- if (seqCoordSys == CoordinateSys.UNIPROT)
- {
- padWithGaps(resNumMap, omitNonObserved);
- }
- int seqStart = UNASSIGNED;
- int seqEnd = UNASSIGNED;
- int pdbStart = UNASSIGNED;
- int pdbEnd = UNASSIGNED;
-
- 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];
-
- String matchedSeq = originalSeq;
- if (seqStart != UNASSIGNED)
- {
- 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) ? 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();
- for (String res : resNumMap.values())
- {
- targetStrucSeqs.append(res);
- }
-
- if (os != null)
- {
- MappingOutputPojo mop = new MappingOutputPojo();
- mop.setSeqStart(pdbStart);
- mop.setSeqEnd(pdbEnd);
- mop.setSeqName(seq.getName());
- mop.setSeqResidue(matchedSeq);
-
- mop.setStrStart(seqStart);
- mop.setStrEnd(seqEnd);
- mop.setStrName(structId);
- mop.setStrResidue(targetStrucSeqs.toString());
-
- mop.setType("pep");
- os.print(getMappingOutput(mop).toString());
- os.println();
- }
- return mapping;
}
-
/**
*
* @param chainId
return;
}
Integer[] keys = resNumMap.keySet().toArray(new Integer[0]);
- Arrays.sort(keys);
+ // Arrays.sort(keys);
int firstIndex = keys[0];
int lastIndex = keys[keys.length - 1];
// System.out.println("Min value " + firstIndex);
@Override
public Entity getEntityById(String id) throws SiftsException
{
- // 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)
- // {
- // List<Entity> entities = siftsEntry.getEntity();
- // for (Entity entity : entities)
- // {
- // if (!entity.getEntityId().equalsIgnoreCase(id))
- // {
- // continue;
- // }
- // return entity;
- // }
- // }
+ // Determines an entity to process by performing a heuristic matching of all
+ // Entities with the given chainId and choosing the best matching Entity
Entity entity = getEntityByMostOptimalMatchedId(id);
if (entity != null)
{
return null;
}
- public class SiftsEntitySortPojo implements
+ private class SiftsEntitySortPojo implements
Comparable<SiftsEntitySortPojo>
{
public String entityId;
}
}
+ private class SegmentHelperPojo
+ {
+ private SequenceI seq;
+
+ private HashMap<Integer, int[]> mapping;
+
+ private TreeMap<Integer, String> resNumMap;
+
+ private List<Integer> omitNonObserved;
+
+ private int nonObservedShiftIndex;
+
+ public SegmentHelperPojo(SequenceI seq,
+ HashMap<Integer, int[]> mapping,
+ TreeMap<Integer, String> resNumMap,
+ List<Integer> omitNonObserved, int nonObservedShiftIndex)
+ {
+ setSeq(seq);
+ setMapping(mapping);
+ setResNumMap(resNumMap);
+ setOmitNonObserved(omitNonObserved);
+ setNonObservedShiftIndex(nonObservedShiftIndex);
+ }
+
+ public SequenceI getSeq()
+ {
+ return seq;
+ }
+
+ public void setSeq(SequenceI seq)
+ {
+ this.seq = seq;
+ }
+
+ public HashMap<Integer, int[]> getMapping()
+ {
+ return mapping;
+ }
+
+ public void setMapping(HashMap<Integer, int[]> mapping)
+ {
+ this.mapping = mapping;
+ }
+
+ public TreeMap<Integer, String> getResNumMap()
+ {
+ return resNumMap;
+ }
+
+ public void setResNumMap(TreeMap<Integer, String> resNumMap)
+ {
+ this.resNumMap = resNumMap;
+ }
+
+ public List<Integer> getOmitNonObserved()
+ {
+ return omitNonObserved;
+ }
+
+ public void setOmitNonObserved(List<Integer> omitNonObserved)
+ {
+ this.omitNonObserved = omitNonObserved;
+ }
+
+ public int getNonObservedShiftIndex()
+ {
+ return nonObservedShiftIndex;
+ }
+
+ public void setNonObservedShiftIndex(int nonObservedShiftIndex)
+ {
+ this.nonObservedShiftIndex = nonObservedShiftIndex;
+ }
+ }
@Override
public StringBuffer getMappingOutput(MappingOutputPojo mp)