void CDFFileReaderTest::BadFilenameTest() { CDFData data; CDFFileReader reader; data.SetFilename("CDFMetaDataBad"); CPPUNIT_ASSERT_THROW(reader.Read(data, CDFFileReader::ReadSequential), affymetrix_calvin_exceptions::FileNotFoundException); }
void CDFFileReaderTest::UnknownQCProbeSetNameTest() { CDFData data; CDFFileReader reader; reader.SetFilename(SMALL_QCCDF_FILE); reader.Read(data, CDFFileReader::ReadByProbeSetName); CDFQCProbeSetInformation info; CPPUNIT_ASSERT_THROW(data.GetQCProbeSetInformation(L"hello", info), ProbeSetNotFoundException); }
void CDFFileReaderTest::GetQCProbeSetInformationWithProbeSetNumberOutOfBoundsTest() { CDFData data; CDFFileReader reader; reader.SetFilename(SMALL_QCCDF_FILE); reader.Read(data, CDFFileReader::ReadByProbeSetNumber); CDFQCProbeSetInformation info; CPPUNIT_ASSERT_THROW(data.GetQCProbeSetInformation(11, info), ProbeSetNotFoundException); }
void CDFFileReaderTest::ReadQCCDFProbeSetInformationOpenProbeNameModeInWrongMode() { CDFData data; CDFFileReader reader; reader.SetFilename(SMALL_QCCDF_FILE); reader.Read(data, CDFFileReader::ReadByProbeSetName); CDFQCProbeSetInformation info; CPPUNIT_ASSERT_THROW(data.GetQCProbeSetInformation(3, info), CDFAccessNotSupportedByModeException); }
void CDFFileReaderTest::ReadCDFProbeSetInformationOpenProbeIndexModeInWrongMode() { CDFData data; CDFFileReader reader; reader.SetFilename(SMALL_CDF_FILE); reader.Read(data, CDFFileReader::ReadByProbeSetNumber); CDFProbeSetInformation info; CPPUNIT_ASSERT_THROW(data.GetProbeSetInformation(L"hello", info), CDFAccessNotSupportedByModeException); }
void CDFFileReaderTest::UseGetProbeSEtInformationTOReadQCCDFFileTest() { CDFData data; CDFFileReader reader; reader.SetFilename(SMALL_QCCDF_FILE); reader.Read(data, CDFFileReader::ReadByProbeSetNumber); CDFProbeSetInformation info; CPPUNIT_ASSERT_THROW(data.GetProbeSetInformation(0, info), ProbeSetNotFoundException); CPPUNIT_ASSERT_THROW(data.GetProbeSetInformation(L"hello", info), ProbeSetNotFoundException); }
void CDFFileReaderTest::CheckQCGetProbeSetName(CDFData& data) { int32_t probeSetCnt = data.GetProbeSetCnt(); wchar_t name[100]; for (int32_t i = 0; i < probeSetCnt; ++i) { FormatString1(name, 100, L"control_%d", i); CPPUNIT_ASSERT(data.GetProbeSetName(i) == name); } }
CDFCntrlFileWriter::CDFCntrlFileWriter(CDFData &p) { writer = new GenericFileWriter(p.GetFileHeader()); contentsPos = 0; WriteHeaders(); dataGroupWriter = 0; //skip ahead to the position of the first probe set dataSet int32_t probes = p.GetProbeSetCnt(); int32_t size = probes * ((MAX_CDF_PROBE_SET_NAME_LENGTH * 2) + 8); writer->SeekFromCurrentPos(size); // Set the file position of the next DataGroup writer->GetDataGroupWriter(0).UpdateNextDataGroupPos(); }
void CDFFileReader::Read(CDFData& data, ReadMode mode) { data.Clear(); //data.GetGenericData().UseMemoryMapping(false); GenericFileReader reader; if (fileName.empty()) fileName = data.GetFilename(); reader.SetFilename(fileName); reader.ReadHeader(data.GetGenericData(), GenericFileReader::ReadNoDataGroupHeader); switch(mode) { case ReadSequential: data.PrepareForSequentialAccess(); break; case ReadByProbeSetNumber: data.PrepareForAccessByProbeSetIndex(); break; case ReadByProbeSetName: data.PrepareForAccessByProbeSetName(); break; default: data.PrepareForSequentialAccess(); break; } }
void CDFFileReaderTest::ReadSmallCDFFileSeqModeTest() { CDFData data; CDFFileReader reader; CPPUNIT_ASSERT_NO_THROW(reader.SetFilename(SMALL_CDF_FILE)); CPPUNIT_ASSERT_NO_THROW(reader.Read(data, CDFFileReader::ReadSequential)); int32_t probeSetCnt = data.GetProbeSetCnt(); for (int32_t i = 0; i < probeSetCnt; ++i) { CDFProbeSetInformation info; data.GetProbeSetInformation(i, info); CheckSmallCDFProbeSetInformation(i, info); } CheckGetProbeSetName(data); }
void CDFFileReaderTest::ReadSmallCDFFileProbeSetNumberModeTest() { CDFData data; CDFFileReader reader; CPPUNIT_ASSERT_NO_THROW(reader.SetFilename(SMALL_CDF_FILE)); CPPUNIT_ASSERT_NO_THROW(reader.Read(data, CDFFileReader::ReadByProbeSetNumber)); int32_t probeSetCnt = data.GetProbeSetCnt(); // go backwards for (int32_t i = probeSetCnt-1; i >= 0; --i) { CDFProbeSetInformation info; data.GetProbeSetInformation(i, info); CheckSmallCDFProbeSetInformation(i, info); } CheckGetProbeSetName(data); }
void CDFFileReaderTest::ReadSmallQCCDFFileProbeSetNameModeTest() { CDFData data; CDFFileReader reader; CPPUNIT_ASSERT_NO_THROW(reader.SetFilename(SMALL_QCCDF_FILE)); CPPUNIT_ASSERT_NO_THROW(reader.Read(data, CDFFileReader::ReadByProbeSetName)); int32_t probeSetCnt = data.GetProbeSetCnt(); // go backwards for (int32_t i = probeSetCnt-1; i >= 0; --i) { wchar_t name[100]; FormatString1(name, 100, L"control_%d", i); CDFQCProbeSetInformation info; data.GetQCProbeSetInformation(name, info); CheckSmallQCCDFProbeSetInformation(i, info); } CheckQCGetProbeSetName(data); }
void CDFFileReaderTest::ReadSmallCDFFileBasicTest() { CDFData data; CDFFileReader reader; CPPUNIT_ASSERT_NO_THROW(reader.SetFilename(SMALL_CDF_FILE)); CPPUNIT_ASSERT_NO_THROW(reader.Read(data)); CPPUNIT_ASSERT(data.GetFilename() == SMALL_CDF_FILE); FileHeader* fh = data.GetFileHeader(); u_int32_t pos = fh->GetFirstDataGroupFilePos(); CPPUNIT_ASSERT(pos == 0x1BD); CPPUNIT_ASSERT(data.GetProbeSetCnt() == 10); CPPUNIT_ASSERT(data.GetArrayRows() == 10*2); CPPUNIT_ASSERT(data.GetArrayCols() == 11); }