C++ (Cpp) CigarStrUtil_reverse Examples

Example #1

File: CigarStrUtilTest.c Project: Ensembl/ensc-core

int main(int argc, char *argv[]) {
  Vector *pieces;
  char *str;
  char *reverse;
  int testResult = 0;

  initEnsC(argc, argv);

  pieces = CigarStrUtil_getPieces(cigar1);

  testResult += ok(1, Vector_getNumElement(pieces) == 6);
  
  str = Vector_getElementAt(pieces,0);

  testResult += ok(2, !strcmp(str,"6M"));

  Vector_free(pieces);

  StrUtil_copyString(&str,cigar1,0);
  
  testResult += ok(3, !strcmp(str,cigar1));
  
  reverse = CigarStrUtil_reverse(str,strlen(str));
  free(str);

  pieces = CigarStrUtil_getPieces(reverse);

  testResult += ok(4, Vector_getNumElement(pieces) == 6);

  str = Vector_getElementAt(pieces,0);

  testResult += ok(5, !strcmp(str,"M"));

  return testResult;
}

Example #2

Vector *GenomicAlignAdaptor_objectsFromStatementHandle(GenomicAlignAdaptor *gaa, StatementHandle *sth,
                                                       int reverse) {
  Vector *results = Vector_new();
  ResultRow *row;
  DNAFragAdaptor *dfa;

  IDType consensusDNAFragId;
  IDType queryDNAFragId;
  int consensusStart;
  int consensusEnd;
  int queryStart;
  int queryEnd;
  int queryStrand;
  IDType methodLinkId;
  double score;
  double percId;
  char *cigarString;

  dfa = ComparaDBAdaptor_getDNAFragAdaptor(gaa->dba);

  while ((row = sth->fetchRow(sth))) {
    GenomicAlign *genomicAlign;
    char *alignmentType;
    
    if (reverse) {
      queryDNAFragId     = row->getLongLongAt(row,0);
      queryStart         = row->getIntAt(row,1);
      queryEnd           = row->getIntAt(row,2);
      consensusDNAFragId = row->getLongLongAt(row,3);
      consensusStart     = row->getIntAt(row,4);
      consensusEnd       = row->getIntAt(row,5);
    } else {
      consensusDNAFragId = row->getLongLongAt(row,0);
      consensusStart     = row->getIntAt(row,1);
      consensusEnd       = row->getIntAt(row,2);
      queryDNAFragId     = row->getLongLongAt(row,3);
      queryStart         = row->getIntAt(row,4);
      queryEnd           = row->getIntAt(row,5);
    }
    queryStrand  = row->getIntAt(row,6);
    methodLinkId = row->getLongLongAt(row,7);
    score        = row->getDoubleAt(row,8);
    percId       = row->getDoubleAt(row,9);
    cigarString  = row->getStringAt(row,10);

    alignmentType = GenomicAlignAdaptor_alignmentTypeByMethodLinkId(gaa, methodLinkId);

    if (reverse) {
      StrUtil_strReplChrs(cigarString,"DI","ID");

      // alignment of the opposite strand
      if (queryStrand == -1) {
        cigarString = CigarStrUtil_reverse(cigarString, strlen(cigarString));
      }
    }
    
    
    genomicAlign = GenomicAlign_new();
    GenomicAlign_setAdaptor(genomicAlign, (BaseAdaptor *)gaa);
    GenomicAlign_setConsensusDNAFrag(genomicAlign, DNAFragAdaptor_fetchByDbID(dfa,consensusDNAFragId));
    GenomicAlign_setConsensusStart(genomicAlign, consensusStart);
    GenomicAlign_setConsensusEnd(genomicAlign, consensusEnd);
    GenomicAlign_setQueryDNAFrag(genomicAlign, DNAFragAdaptor_fetchByDbID(dfa,queryDNAFragId));
    GenomicAlign_setQueryStart(genomicAlign, queryStart);
    GenomicAlign_setQueryEnd(genomicAlign, queryEnd);
    GenomicAlign_setQueryStrand(genomicAlign, queryStrand);
    GenomicAlign_setAlignmentType(genomicAlign, alignmentType);
    GenomicAlign_setScore(genomicAlign, score);
    GenomicAlign_setPercentId(genomicAlign, percId);
    GenomicAlign_setCigarString(genomicAlign, cigarString);

    Vector_addElement(results, genomicAlign);
  }

  return results;
}