C++ (Cpp) CDFData Examples

Example #1

void CDFFileReaderTest::BadFilenameTest()
{
	CDFData data;
	CDFFileReader reader;
	data.SetFilename("CDFMetaDataBad");
	CPPUNIT_ASSERT_THROW(reader.Read(data, CDFFileReader::ReadSequential), affymetrix_calvin_exceptions::FileNotFoundException);
}

Example #2

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);
}

Example #3

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);
}

Example #4

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);
}

Example #5

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);
}

Example #6

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);
}

Example #7

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);
	}
}

Example #8

File: CDFCntrlFileWriter.cpp Project: HenrikBengtsson/affxparser

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();
}

Example #9

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;
	}
}

Example #10

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);
}

Example #11

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);
}

Example #12

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);
}

Example #13

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);
}