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"); }
/* * Get the DAT header from the DAT file header object. */ string CELConversionUtilities::GetDatHeader(CelFileData &inFile) { std::wstring datHeader; GenDataHdrVectorIt begin, end; inFile.GetFileHeader()->GetGenericDataHdr()->GetParentIterators(begin, end); // Find the DAT generic header for (GenDataHdrVectorIt ii = begin; ii != end; ++ii) { std::string s = ii->GetFileTypeId(); if (ii->GetFileTypeId() == SCAN_ACQUISITION_DATA_TYPE) { // found the right header, now look for the parameter ParameterNameValueType nvt; if (ii->FindNameValParam(DAT_HEADER_PARAM_NAME, nvt)) { if (nvt.GetParameterType() == ParameterNameValueType::TextType) datHeader = nvt.GetValueText(); } else if (ii->FindNameValParam(PARTIAL_DAT_HEADER_PARAM_NAME, nvt)) { if (nvt.GetParameterType() == ParameterNameValueType::TextType) { std::wstring partialDatHeader = nvt.GetValueText(); u_int16_t min = 0; u_int16_t max = 0; // Find the max and min parameters and append to the string. if (ii->FindNameValParam(MAX_PIXEL_INTENSITY_PARAM_NAME, nvt)) { if (nvt.GetParameterType() == ParameterNameValueType::UInt16Type) max = nvt.GetValueUInt16(); } if (ii->FindNameValParam(MIN_PIXEL_INTENSITY_PARAM_NAME, nvt)) { if (nvt.GetParameterType() == ParameterNameValueType::UInt16Type) min = nvt.GetValueUInt16(); } wchar_t buf[30]; FormatString2(buf, 30, L"[%d..%d]", min, max); datHeader = buf; datHeader += partialDatHeader; } } break; } } return StringUtils::ConvertWCSToMBS(datHeader); }
std::wstring CalvinCELDataAdapter::GetDatHeader() { std::wstring datHeader; //GenDataHdrVectorIt begin, end; GenericDataHeader* gdh = calvinCel.GetFileHeader()->GetGenericDataHdr()->FindParent(SCAN_ACQUISITION_DATA_TYPE); if (gdh) { // found the right header, now look for the parameter ParameterNameValueType nvt; if (gdh->FindNameValParam(DAT_HEADER_PARAM_NAME, nvt)) { if (nvt.GetParameterType() == ParameterNameValueType::TextType) datHeader = nvt.GetValueText(); } else if (gdh->FindNameValParam(PARTIAL_DAT_HEADER_PARAM_NAME, nvt)) { if (nvt.GetParameterType() == ParameterNameValueType::TextType) { std::wstring partialDatHeader = nvt.GetValueText(); u_int16_t min = 0; u_int16_t max = 0; // Find the max and min parameters and append to the string. if (gdh->FindNameValParam(MAX_PIXEL_INTENSITY_PARAM_NAME, nvt)) { if (nvt.GetParameterType() == ParameterNameValueType::UInt16Type) max = nvt.GetValueUInt16(); } if (gdh->FindNameValParam(MIN_PIXEL_INTENSITY_PARAM_NAME, nvt)) { if (nvt.GetParameterType() == ParameterNameValueType::UInt16Type) min = nvt.GetValueUInt16(); } wchar_t buf[30]=L""; FormatString2(buf, 30, L"[%d..%d]", min, max); datHeader = buf; datHeader += partialDatHeader; } } } return datHeader; }
std::wstring CHPQuantificationData::GetWStringFromGenericHdr(const std::wstring& name) { std::wstring result; ParameterNameValueType paramType; GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr(); if (hdr->FindNameValParam(name, paramType)) { result = paramType.GetValueText(); } return result; }
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"); }