boost::shared_ptr<IsobaricQuantitationMethod> IBSpectraFile::guessExperimentType_(const ConsensusMap& cm)
{
if (cm.getExperimentType() != "labeled_MS2" && cm.getExperimentType() != "itraq")
{
throw Exception::InvalidParameter(__FILE__,
__LINE__,
__PRETTY_FUNCTION__,
"Given ConsensusMap does not hold any isobaric quantification data.");
}
// we take the mapcount as approximation
if (cm.getFileDescriptions().size() == 4)
{
return boost::shared_ptr<IsobaricQuantitationMethod>(new ItraqFourPlexQuantitationMethod);
}
else if (cm.getFileDescriptions().size() == 6)
{
return boost::shared_ptr<IsobaricQuantitationMethod>(new TMTSixPlexQuantitationMethod);
}
else if (cm.getFileDescriptions().size() == 8)
{
return boost::shared_ptr<IsobaricQuantitationMethod>(new ItraqEightPlexQuantitationMethod);
}
else
{
throw Exception::InvalidParameter(__FILE__,
__LINE__,
__PRETTY_FUNCTION__,
"Could not guess isobaric quantification data from ConsensusMap due to non-matching number of input maps.");
}
}
file.getOptions().addMSLevel(1);
TEST_EQUAL(file.getOptions().hasMSLevels(), true);
END_SECTION
START_SECTION((void load(const String &filename, ConsensusMap & map)))
ConsensusMap map;
ConsensusXMLFile file;
file.load(OPENMS_GET_TEST_DATA_PATH("ConsensusXMLFile_1.consensusXML"), map);
//test DocumentIdentifier addition
TEST_STRING_EQUAL(map.getLoadedFilePath(), OPENMS_GET_TEST_DATA_PATH("ConsensusXMLFile_1.consensusXML"));
TEST_STRING_EQUAL(FileTypes::typeToName(map.getLoadedFileType()), "consensusXML");
//meta data
TEST_EQUAL(map.getIdentifier(), "lsid")
TEST_EQUAL(map.getExperimentType() == "label-free", true)
TEST_EQUAL(map.getMetaValue("name1") == DataValue("value1"), true)
TEST_EQUAL(map.getMetaValue("name2") == DataValue(2), true)
//file descriptions
TEST_EQUAL(map.getFileDescriptions()[0].filename == "data/MapAlignmentFeatureMap1.xml", true)
TEST_EQUAL(map.getFileDescriptions()[0].label, "label")
TEST_EQUAL(map.getFileDescriptions()[0].size, 144)
TEST_EQUAL(map.getFileDescriptions()[0].getMetaValue("name3") == DataValue("value3"), true)
TEST_EQUAL(map.getFileDescriptions()[0].getMetaValue("name4") == DataValue(4), true)
TEST_STRING_EQUAL(map.getFileDescriptions()[1].filename, "data/MapAlignmentFeatureMap2.xml")
TEST_EQUAL(map.getFileDescriptions()[1].label, "")
TEST_EQUAL(map.getFileDescriptions()[1].size, 0)
TEST_EQUAL(map.getFileDescriptions()[1].getMetaValue("name5") == DataValue("value5"), true)
TEST_EQUAL(map.getFileDescriptions()[1].getMetaValue("name6") == DataValue(6.0), true)
//data processing
TEST_EQUAL(map.getDataProcessing().size(), 2)