C++ (Cpp) SpectrumPtr::getMZArray Examples

Example #1

File: IndexedMzMLFile_test.cpp Project: chahuistle/OpenMS

  IndexedMzMLFile file(OPENMS_GET_TEST_DATA_PATH("IndexedmzMLFile_1.mzML"));
  TEST_EQUAL(file.getNrChromatograms(), 1)
}
END_SECTION

START_SECTION(( OpenMS::Interfaces::SpectrumPtr getSpectrumById(int id)  ))
{
  IndexedMzMLFile file(OPENMS_GET_TEST_DATA_PATH("IndexedmzMLFile_1.mzML"));

	MSExperiment<> exp;
	MzMLFile().load(OPENMS_GET_TEST_DATA_PATH("IndexedmzMLFile_1.mzML"),exp);

  TEST_EQUAL(file.getNrSpectra(), exp.getSpectra().size())

  OpenMS::Interfaces::SpectrumPtr spec = file.getSpectrumById(0);
  TEST_EQUAL(spec->getMZArray()->data.size(), exp.getSpectra()[0].size() )
  TEST_EQUAL(spec->getIntensityArray()->data.size(), exp.getSpectra()[0].size() )

  // Test Exceptions
  TEST_EXCEPTION(Exception::IllegalArgument,file.getSpectrumById(-1));
  TEST_EXCEPTION(Exception::IllegalArgument,file.getSpectrumById( file.getNrSpectra()+1));

  {
    IndexedMzMLFile file(OPENMS_GET_TEST_DATA_PATH("fileDoesNotExist"));
    TEST_EQUAL(file.getParsingSuccess(), false)
    TEST_EXCEPTION(Exception::ParseError,file.getSpectrumById( 0 ));
  }
}
END_SECTION

START_SECTION(( OpenMS::Interfaces::ChromatogramPtr getChromatogramById(int id) ))

Example #2

File: MzMLSpectrumDecoder_test.C Project: BioITer/OpenMS

            <binary>AAAAAAAAAAAAAAAAAADwPwAAAAAAAABAAAAAAAAACEAAAAAAAAAQQAAAAAAAABRAAAAAAAAAGEAAAAAAAAAcQAAAAAAAACBAAAAAAAAAIkAAAAAAAAAkQAAAAAAAACZAAAAAAAAAKEAAAAAAAAAqQAAAAAAAACxA</binary>
          </binaryDataArray>
          <binaryDataArray encodedLength="160" >
            <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
            <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
            <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitAccession="MS:1000131" unitName="number of counts" unitCvRef="MS"/>
            <binary>AAAAAAAALkAAAAAAAAAsQAAAAAAAACpAAAAAAAAAKEAAAAAAAAAmQAAAAAAAACRAAAAAAAAAIkAAAAAAAAAgQAAAAAAAABxAAAAAAAAAGEAAAAAAAAAUQAAAAAAAABBAAAAAAAAACEAAAAAAAAAAQAAAAAAAAPA/</binary>
          </binaryDataArray>
        </binaryDataArrayList>
      </spectrum>
  );

  OpenMS::Interfaces::SpectrumPtr cptr(new OpenMS::Interfaces::Spectrum);
  ptr->domParseSpectrum(testString, cptr);

  TEST_EQUAL(cptr->getMZArray()->data.size(), 15)
  TEST_EQUAL(cptr->getIntensityArray()->data.size(), 15)

  TEST_REAL_SIMILAR(cptr->getMZArray()->data[7], 7)
  TEST_REAL_SIMILAR(cptr->getIntensityArray()->data[7], 8)
}
END_SECTION

START_SECTION(([EXTRA] void domParseSpectrum(std::string& in, OpenMS::Interfaces::SpectrumPtr & sptr) ))
{
  // missing defaultArrayLength -> should give an exception of ParseError
  ptr = new MzMLSpectrumDecoder();
  std::string testString = MULTI_LINE_STRING(
      <spectrum index="2" id="index=2">
        <binaryDataArrayList count="2">
          <binaryDataArray encodedLength="160" >