Esempi in C++ (Cpp) per ConsensusFeature::getMZ

Esempio n. 1

File: EDTAFile.cpp Progetto: BioinformaticsArchive/OpenMS

  void EDTAFile::store(const String& filename, const ConsensusMap& map) const
  {
    TextFile tf;

    // search for maximum number of sub-features (since this determines the number of columns)
    Size max_sub(0);
    for (Size i = 0; i < map.size(); ++i)
    {
      max_sub = std::max(max_sub, map[i].getFeatures().size());
    }

    // write header
    String header("RT\tm/z\tintensity\tcharge");
    for (Size i = 1; i <= max_sub; ++i)
    {
      header += "\tRT" + String(i) + "\tm/z" + String(i) + "\tintensity" + String(i) + "\tcharge" + String(i);
    }
    tf.addLine(header);

    for (Size i = 0; i < map.size(); ++i)
    {
      ConsensusFeature f = map[i];
      // consensus
      String entry = String(f.getRT()) + "\t" + f.getMZ() + "\t" + f.getIntensity() + "\t" + f.getCharge();
      // sub-features
      ConsensusFeature::HandleSetType handle = f.getFeatures();
      for (ConsensusFeature::HandleSetType::const_iterator it = handle.begin(); it != handle.end(); ++it)
      {
        entry += String("\t") + it->getRT() + "\t" + it->getMZ() + "\t" + it->getIntensity() + "\t" + it->getCharge();
      }
      // missing sub-features
      for (Size j = handle.size(); j < max_sub; ++j)
      {
        entry += "\tNA\tNA\tNA\tNA";
      }
      tf.addLine(entry);
    }


    tf.store(filename);
  }

Esempio n. 2

File: ConsensusFeature_test.C Progetto: BioITer/OpenMS

	
	TEST_EQUAL(ml(c1,c1), 0);
	TEST_EQUAL(ml(c1,c2), 1);
	TEST_EQUAL(ml(c2,c1), 0);
	TEST_EQUAL(ml(c2,c2), 0);
END_SECTION

START_SECTION((ConsensusFeature& operator=(const ConsensusFeature &rhs)))
  ConsensusFeature cons(tmp_feature);
  cons.insert(1,tmp_feature);

  ConsensusFeature cons_copy;
  cons_copy = cons;

  TEST_REAL_SIMILAR(cons_copy.getRT(),1.0)
  TEST_REAL_SIMILAR(cons_copy.getMZ(),2.0)
  TEST_REAL_SIMILAR(cons_copy.getIntensity(),200.0)
  TEST_EQUAL((cons_copy.begin())->getMapIndex(),1)
  TEST_EQUAL((cons_copy.begin())->getUniqueId(),3)
  TEST_EQUAL((cons_copy.begin())->getIntensity(),200)
END_SECTION

START_SECTION((ConsensusFeature(const ConsensusFeature &rhs)))

  ConsensusFeature cons(tmp_feature);
  cons.insert(1,tmp_feature);
  ConsensusFeature cons_copy(cons);

  TEST_REAL_SIMILAR(cons_copy.getRT(),1.0)
  TEST_REAL_SIMILAR(cons_copy.getMZ(),2.0)
  TEST_REAL_SIMILAR(cons_copy.getIntensity(),200.0)

Esempio n. 3

File: ConsensusXMLFile_test.C Progetto: aiche/open-ms-mirror

TEST_EQUAL(map[1].getPeptideIdentifications().size(), 1)
TEST_EQUAL(map[1].getPeptideIdentifications()[0].getHits().size(), 1)
TEST_EQUAL(map[1].getPeptideIdentifications()[0].getHits()[0].getSequence(), "E")
//unassigned peptide identifications
TEST_EQUAL(map.getUnassignedPeptideIdentifications().size(), 2)
TEST_EQUAL(map.getUnassignedPeptideIdentifications()[0].getHits().size(), 1)
TEST_EQUAL(map.getUnassignedPeptideIdentifications()[0].getHits()[0].getSequence(), "F")
TEST_EQUAL(map.getUnassignedPeptideIdentifications()[1].getHits().size(), 2)
TEST_EQUAL(map.getUnassignedPeptideIdentifications()[1].getHits()[0].getSequence(), "G")
TEST_EQUAL(map.getUnassignedPeptideIdentifications()[1].getHits()[1].getSequence(), "H")

//features
TEST_EQUAL(map.size(), 6)
ConsensusFeature cons_feature = map[0];
TEST_REAL_SIMILAR(cons_feature.getRT(), 1273.27)
TEST_REAL_SIMILAR(cons_feature.getMZ(), 904.47)
TEST_REAL_SIMILAR(cons_feature.getIntensity(), 3.12539e+07)
TEST_REAL_SIMILAR(cons_feature.getPositionRange().minPosition()[0], 1273.27)
TEST_REAL_SIMILAR(cons_feature.getPositionRange().maxPosition()[0], 1273.27)
TEST_REAL_SIMILAR(cons_feature.getPositionRange().minPosition()[1], 904.47)
TEST_REAL_SIMILAR(cons_feature.getPositionRange().maxPosition()[1], 904.47)
TEST_REAL_SIMILAR(cons_feature.getIntensityRange().minPosition()[0], 3.12539e+07)
TEST_REAL_SIMILAR(cons_feature.getIntensityRange().maxPosition()[0], 3.12539e+07)
TEST_REAL_SIMILAR(cons_feature.getQuality(), 1.1)
TEST_EQUAL(cons_feature.getMetaValue("peptide_id") == DataValue("RefSeq:NC_1234"), true)
ConsensusFeature::HandleSetType::const_iterator it = cons_feature.begin();
TEST_REAL_SIMILAR(it->getIntensity(), 3.12539e+07)

cons_feature = map[5];
TEST_REAL_SIMILAR(cons_feature.getRT(), 1194.82)
TEST_REAL_SIMILAR(cons_feature.getMZ(), 777.101)