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) ))
<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" >