void CHPMultiDataDataTest::test_SumParams() { ParameterNameValueTypeList params; ParameterNameValueType param; CHPMultiDataData data; param.SetName(L"n1"); param.SetValueText(L"v1"); params.push_back(param); param.SetName(L"n2"); param.SetValueText(L"v2"); params.push_back(param); data.AddSummaryParams(params); ParameterNameValueTypeList params_out = data.GetSummaryParams(); CPPUNIT_ASSERT(params_out.size() == 2); ParameterNameValueTypeList::iterator it = params_out.begin(); param = *it; CPPUNIT_ASSERT(param.GetName() == L"n1"); CPPUNIT_ASSERT(param.GetValueText() == L"v1"); ++it; param = *it; CPPUNIT_ASSERT(param.GetName() == L"n2"); CPPUNIT_ASSERT(param.GetValueText() == L"v2"); }
void CHPQuantificationDataTest::test_AlgParams() { ParameterNameValueTypeList params; ParameterNameValueType param; CHPQuantificationData data; param.SetName(L"n1"); param.SetValueText(L"v1"); params.push_back(param); param.SetName(L"n2"); param.SetValueText(L"v2"); params.push_back(param); data.AddAlgParams(params); ParameterNameValueTypeList params_out = data.GetAlgParams(); CPPUNIT_ASSERT(params_out.size() == 2); ParameterNameValueTypeList::iterator it = params_out.begin(); param = *it; CPPUNIT_ASSERT(param.GetName() == L"n1"); CPPUNIT_ASSERT(param.GetValueText() == L"v1"); ++it; param = *it; CPPUNIT_ASSERT(param.GetName() == L"n2"); CPPUNIT_ASSERT(param.GetValueText() == L"v2"); }
void CHPQuantificationData::AddSummaryParams(const ParameterNameValueTypeList& params) { ParameterNameValueType param; GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr(); for (ParameterNameValueTypeList::const_iterator it=params.begin(); it != params.end(); it++) { param = *it; param.SetName(CHIP_SUMMARY_PARAMETER_NAME_PREFIX_S + param.GetName()); hdr->AddNameValParam(param); } }
void CHPMultiDataData::AddAppMetaInfo(const ParameterNameValueTypeList& params) { ParameterNameValueType param; GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr(); for (ParameterNameValueTypeList::const_iterator it=params.begin(); it != params.end(); ++it) { param = *it; param.SetName(APPLICATION_META_INFO_PREFIX_S + param.GetName()); hdr->AddNameValParam(param); } }
void CHPMultiDataData::AddAlgParams(const ParameterNameValueTypeList& params) { ParameterNameValueType param; GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr(); for (ParameterNameValueTypeList::const_iterator it=params.begin(); it != params.end(); it++) { param = *it; param.SetName(ALGORITHM_PARAM_NAME_PREFIX_S + param.GetName()); hdr->AddNameValParam(param); } }
void CHPMultiDataFileReaderTest::testReadCNV() { affymetrix_calvin_data::ProbeSetMultiDataCopyNumberVariationRegionData e; ParameterNameValueType param; CHPMultiDataData data2; CHPMultiDataFileReader reader; reader.SetFilename("../data/CHP_MultiData_file_cnv"); reader.Read(data2); CPPUNIT_ASSERT(data2.GetAlgName() == L"canary"); CPPUNIT_ASSERT(data2.GetAlgVersion() == L"1.0"); CPPUNIT_ASSERT(data2.GetArrayType() == L"test3"); CPPUNIT_ASSERT(data2.GetEntryCount(CopyNumberVariationMultiDataType) == 2); CPPUNIT_ASSERT(data2.GetEntryCount(CopyNumberMultiDataType) == 0); CPPUNIT_ASSERT(data2.GetEntryCount(GenotypeMultiDataType) == 0); CPPUNIT_ASSERT(data2.GetEntryCount(ExpressionMultiDataType) == 0); ParameterNameValueTypeList p = data2.GetAlgParams(); ParameterNameValueTypeList::iterator it = p.begin(); param = *it; CPPUNIT_ASSERT(param.GetName() == L"an1"); CPPUNIT_ASSERT(param.GetValueText() == L"av1"); p = data2.GetSummaryParams(); it = p.begin(); param = *it; CPPUNIT_ASSERT(param.GetName() == L"sn1"); CPPUNIT_ASSERT(param.GetValueText() == L"sv1"); data2.GetCopyNumberVariationEntry(CopyNumberVariationMultiDataType, 0, e); CPPUNIT_ASSERT(e.call == 1); CPPUNIT_ASSERT(e.name == "abc"); CPPUNIT_ASSERT_DOUBLES_EQUAL(e.confidenceScore, 1.1f, 0.0001f); CPPUNIT_ASSERT(e.signal == 100); data2.GetCopyNumberVariationEntry(CopyNumberVariationMultiDataType, 1, e); CPPUNIT_ASSERT(e.call == 2); CPPUNIT_ASSERT(e.name == "xyz"); CPPUNIT_ASSERT_DOUBLES_EQUAL(e.confidenceScore, 2.2, 0.0001f); CPPUNIT_ASSERT(e.signal == 200); }
void CHPQuantificationDetectionFileReaderTest::testReadId() { CHPQuantificationDetectionData data; CHPQuantificationDetectionFileReader reader; CPPUNIT_ASSERT_NO_THROW(reader.SetFilename("../data/CHP_quantification_detection_file_id")); CPPUNIT_ASSERT_NO_THROW(reader.Read(data)); CPPUNIT_ASSERT(data.GetFilename() == "../data/CHP_quantification_detection_file_id"); CPPUNIT_ASSERT(data.GetAlgName() == L"sig"); CPPUNIT_ASSERT(data.GetAlgVersion() == L"1.0"); CPPUNIT_ASSERT(data.GetArrayType() == L"test3"); CPPUNIT_ASSERT(data.GetEntryCount() == 2); ParameterNameValueTypeList params = data.GetAlgParams(); CPPUNIT_ASSERT(params.size() == 1); ParameterNameValueTypeList::iterator it=params.begin(); ParameterNameValueType param = *it; CPPUNIT_ASSERT(param.GetName() == L"an1"); CPPUNIT_ASSERT(param.GetValueText() == L"av1"); params = data.GetSummaryParams(); CPPUNIT_ASSERT(params.size() == 1); it=params.begin(); param = *it; CPPUNIT_ASSERT(param.GetName() == L"sn1"); CPPUNIT_ASSERT(param.GetValueText() == L"sv1"); ProbeSetQuantificationDetectionData e; data.GetQuantificationDetectionEntry(0, e); CPPUNIT_ASSERT(e.id == 10); CPPUNIT_ASSERT(e.quantification == 10.0f); CPPUNIT_ASSERT(e.pvalue == 0.1f); CPPUNIT_ASSERT(e.name == ""); data.GetQuantificationDetectionEntry(1, e); CPPUNIT_ASSERT(e.id == 20); CPPUNIT_ASSERT(e.quantification == 20.0f); CPPUNIT_ASSERT(e.pvalue == 0.2f); CPPUNIT_ASSERT(e.name == ""); }
void CHPMultiDataFileReaderTest::testReadCN() { affymetrix_calvin_data::ProbeSetMultiDataCopyNumberData e; ParameterNameValueType param; CHPMultiDataData data2; CHPMultiDataFileReader reader; reader.SetFilename("../data/CHP_MultiData_file_cn"); reader.Read(data2); CPPUNIT_ASSERT(data2.GetAlgName() == L"sig"); CPPUNIT_ASSERT(data2.GetAlgVersion() == L"1.0"); CPPUNIT_ASSERT(data2.GetArrayType() == L"test3"); CPPUNIT_ASSERT(data2.GetEntryCount(CopyNumberMultiDataType) == 2); CPPUNIT_ASSERT(data2.GetEntryCount(GenotypeMultiDataType) == 0); CPPUNIT_ASSERT(data2.GetEntryCount(ExpressionMultiDataType) == 0); ParameterNameValueTypeList p = data2.GetAlgParams(); ParameterNameValueTypeList::iterator it = p.begin(); param = *it; CPPUNIT_ASSERT(param.GetName() == L"an1"); CPPUNIT_ASSERT(param.GetValueText() == L"av1"); p = data2.GetSummaryParams(); it = p.begin(); param = *it; CPPUNIT_ASSERT(param.GetName() == L"sn1"); CPPUNIT_ASSERT(param.GetValueText() == L"sv1"); data2.GetCopyNumberEntry(CopyNumberMultiDataType, 0, e); CPPUNIT_ASSERT(e.chr == 10); CPPUNIT_ASSERT(e.position == 11); CPPUNIT_ASSERT(e.name == "abc"); data2.GetCopyNumberEntry(CopyNumberMultiDataType, 1, e); CPPUNIT_ASSERT(e.chr == 20); CPPUNIT_ASSERT(e.position == 21); CPPUNIT_ASSERT(e.name == "xyz"); }
void CHPQuantificationFileWriterTest::WriteTest() { ParameterNameValueTypeList params; ParameterNameValueType param; CHPQuantificationData data("CHP_quantification_file"); data.SetAlgName(L"sig"); data.SetAlgVersion(L"1.0"); data.SetArrayType(L"test3"); data.SetEntryCount(2, 10); param.SetName(L"an1"); param.SetValueText(L"av1"); params.push_back(param); data.AddAlgParams(params); params.clear(); param.SetName(L"sn1"); param.SetValueText(L"sv1"); params.push_back(param); data.AddSummaryParams(params); CHPQuantificationFileWriter *writer = new CHPQuantificationFileWriter(data); affymetrix_calvin_data::ProbeSetQuantificationData e; writer->SeekToDataSet(); e.name = "abc"; e.quantification = 10.0f; writer->WriteEntry(e); e.name = "xyz"; e.quantification = 20.0f; writer->WriteEntry(e); delete writer; CPPUNIT_ASSERT(1); CHPQuantificationData data2; CHPQuantificationFileReader reader; reader.SetFilename("CHP_quantification_file"); reader.Read(data2); CPPUNIT_ASSERT(data2.GetAlgName() == L"sig"); CPPUNIT_ASSERT(data2.GetAlgVersion() == L"1.0"); CPPUNIT_ASSERT(data2.GetArrayType() == L"test3"); CPPUNIT_ASSERT(data2.GetEntryCount() == 2); ParameterNameValueTypeList p = data2.GetAlgParams(); ParameterNameValueTypeList::iterator it = p.begin(); param = *it; CPPUNIT_ASSERT(param.GetName() == L"an1"); CPPUNIT_ASSERT(param.GetValueText() == L"av1"); p = data2.GetSummaryParams(); it = p.begin(); param = *it; CPPUNIT_ASSERT(param.GetName() == L"sn1"); CPPUNIT_ASSERT(param.GetValueText() == L"sv1"); data2.GetQuantificationEntry(0, e); CPPUNIT_ASSERT_DOUBLES_EQUAL(e.quantification, 10.0f, 0.0001f); CPPUNIT_ASSERT(e.name == "abc"); data2.GetQuantificationEntry(1, e); CPPUNIT_ASSERT_DOUBLES_EQUAL(e.quantification, 20.0f, 0.0001f); CPPUNIT_ASSERT(e.name == "xyz"); }