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 FusionCHPQuantificationDataTest::testRead() { FusionCHPData *chp = FusionCHPDataReg::Read("../../parsers/data/CHP_quantification_file"); CPPUNIT_ASSERT(chp != NULL); FusionCHPQuantificationData *sigChp = FusionCHPQuantificationData::FromBase(chp); CPPUNIT_ASSERT(sigChp != NULL); CPPUNIT_ASSERT(sigChp->GetAlgName() == L"sig"); CPPUNIT_ASSERT(sigChp->GetAlgVersion() == L"1.0"); CPPUNIT_ASSERT(sigChp->GetArrayType() == L"test3"); CPPUNIT_ASSERT(sigChp->GetEntryCount() == 2); ParameterNameValueTypeList params = sigChp->GetAlgParams(); CPPUNIT_ASSERT(params.size() == 1); ParameterNameValueTypeList::iterator it=params.begin(); ParameterNameValueType ¶m = *it; CPPUNIT_ASSERT(param.GetName() == L"an1"); CPPUNIT_ASSERT(param.GetValueText() == L"av1"); params = sigChp->GetSummaryParams(); CPPUNIT_ASSERT(params.size() == 1); it=params.begin(); param = *it; CPPUNIT_ASSERT(param.GetName() == L"sn1"); CPPUNIT_ASSERT(param.GetValueText() == L"sv1"); affymetrix_calvin_data::ProbeSetQuantificationData e; sigChp->GetQuantificationEntry(0, e); CPPUNIT_ASSERT(e.name == "abc"); CPPUNIT_ASSERT(e.quantification == 10.0f); sigChp->GetQuantificationEntry(1, e); CPPUNIT_ASSERT(e.name == "xyz"); CPPUNIT_ASSERT(e.quantification == 20.0f); delete sigChp; }
void FusionCHPTilingDataTest::testRead() { FusionCHPData *chp = FusionCHPDataReg::Read("../../parsers/data/CHP_tiling_file"); CPPUNIT_ASSERT(chp != NULL); FusionCHPTilingData *tileChp = FusionCHPTilingData::FromBase(chp); CPPUNIT_ASSERT(tileChp != NULL); CPPUNIT_ASSERT(tileChp->GetNumberSequences() == 2); CPPUNIT_ASSERT(tileChp->GetAlgName() == L"tile"); CPPUNIT_ASSERT(tileChp->GetAlgVersion() == L"1.0"); ParameterNameValueTypeList params = tileChp->GetAlgParams(); CPPUNIT_ASSERT(params.size() == 1); ParameterNameValueTypeList::iterator it=params.begin(); ParameterNameValueType ¶m = *it; CPPUNIT_ASSERT(param.GetName() == L"p1"); CPPUNIT_ASSERT(param.GetValueText() == L"v1"); const double eps=0.00001; CHPTilingEntry e; TilingSequenceData seq; tileChp->OpenTilingSequenceDataSet(0); seq = tileChp->GetTilingSequenceData(); CPPUNIT_ASSERT(seq.name == L"n1"); CPPUNIT_ASSERT(seq.groupName == L"g1"); CPPUNIT_ASSERT(seq.version == L"v1"); CPPUNIT_ASSERT(seq.parameters.size() == 1); it = seq.parameters.begin(); param = *it; CPPUNIT_ASSERT(param.GetName() == L"seq1_p1"); CPPUNIT_ASSERT(param.GetValueText() == L"seq1_v1"); CPPUNIT_ASSERT(tileChp->GetTilingSequenceEntryCount(0) == 2); tileChp->GetTilingSequenceEntry(0, e); CPPUNIT_ASSERT(e.position == 10); CPPUNIT_ASSERT_DOUBLES_EQUAL(e.value, 10.0f, eps); tileChp->GetTilingSequenceEntry(1, e); CPPUNIT_ASSERT(e.position == 20); CPPUNIT_ASSERT_DOUBLES_EQUAL(e.value, 20.0f, eps); tileChp->OpenTilingSequenceDataSet(1); seq = tileChp->GetTilingSequenceData(); CPPUNIT_ASSERT(seq.name == L"n2"); CPPUNIT_ASSERT(seq.groupName == L"g2"); CPPUNIT_ASSERT(seq.version == L"v2"); CPPUNIT_ASSERT(seq.parameters.size() == 1); it = seq.parameters.begin(); param = *it; CPPUNIT_ASSERT(param.GetName() == L"seq2_p1"); CPPUNIT_ASSERT(param.GetValueText() == L"seq2_v1"); CPPUNIT_ASSERT(tileChp->GetTilingSequenceEntryCount(1) == 3); tileChp->GetTilingSequenceEntry(0, e); CPPUNIT_ASSERT(e.position == 11); CPPUNIT_ASSERT_DOUBLES_EQUAL(e.value, 11.0f, eps); tileChp->GetTilingSequenceEntry(1, e); CPPUNIT_ASSERT(e.position == 21); CPPUNIT_ASSERT_DOUBLES_EQUAL(e.value, 21.0f, eps); tileChp->GetTilingSequenceEntry(2, e); CPPUNIT_ASSERT(e.position == 31); CPPUNIT_ASSERT_DOUBLES_EQUAL(e.value, 31.0f, eps); delete tileChp; }