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 GenericDataTest_MinDPH::setUp()
{
// Create generic data header
data = new GenericData;
GenericFileReader reader;
std::string name = TEST_DATA_DAT_FILE;
reader.SetFilename(name);
reader.ReadHeader(*data, GenericFileReader::ReadMinDataGroupHeader);
}
void CHPTilingFileReader::Read(CHPTilingData& data)
{
data.Clear();
GenericFileReader reader;
if (fileName.empty())
{
fileName = data.GetFilename();
}
reader.SetFilename(fileName);
reader.ReadHeader(data.GetGenericData());
}
void CHPQuantificationDetectionFileReader::Read(CHPQuantificationDetectionData& data)
{
data.Clear();
GenericFileReader reader;
if (fileName.empty())
{
fileName = data.GetFilename();
}
reader.SetFilename(fileName);
reader.ReadHeader(data.GetGenericData());
}
/*
* Determines if a CDF file is of the Calvin format.
*/
bool FusionCDFData::IsCalvinCompatibleFile(const char *fileName)
{
GenericData data;
GenericFileReader reader;
reader.SetFilename(fileName);
try
{
reader.ReadHeader(data, GenericFileReader::ReadNoDataGroupHeader);
return true;
}
catch (affymetrix_calvin_exceptions::CalvinException)
{
}
return false;
}
void DataSetTest_DATGridSet::setUp()
{
data = new GenericData;
GenericFileReader reader;
std::string name = TEST_DATA_DAT_FILE_WITH_GRIDS;
reader.SetFilename(name);
reader.ReadHeader(*data);
try
{
dataPlane = data->DataSet(0,1); // grids is the second DataSet of the first DataGroup.
}
catch(affymetrix_calvin_exceptions::CalvinException&)
{
dataPlane = 0;
}
}
void DataSetTest_GenericData::ColsFromDataSetWithZeroRows()
{
GenericData gd;
GenericFileReader reader;
reader.SetFilename("../data/small_cel_file_with_dataset_of_zero_rows");
reader.ReadHeader(gd);
// Open a DataSet that has 0 rows.
DataSet* ds = gd.DataSet(0,3);
CPPUNIT_ASSERT(ds);
CPPUNIT_ASSERT(ds->Cols() == 2);
CPPUNIT_ASSERT(ds->Rows() == 0);
ds->Delete();
// Open another DataSet that has 0 rows.
ds = gd.DataSet(0,4);
CPPUNIT_ASSERT(ds);
CPPUNIT_ASSERT(ds->Cols() == 2);
CPPUNIT_ASSERT(ds->Rows() == 0);
ds->Delete();
}
/**
* No more probesets will be processed, this is a chance to finish outputting
* results and clean up.
* @param qMethod - Quantification method that was used.
* @return true if success, false otherwise.
*/
bool QuantMethodExprCCCHPReport::finish(QuantMethod &qMethod)
{
// Sanity to check we saw all the probe sets we were expecting.
if (m_CurrentProbeSetCount != m_Info.m_NumProbeSets) {
Err::errAbort("QuantMethodExprCCCHPReport::finish() - Expecting: " + ToStr(m_Info.m_NumProbeSets) +
" but got: " + ToStr(m_CurrentProbeSetCount) + ". Command Console CHP file will be corrupt.");
}
// Flush remaining signal entries in the buffer.
m_ExpressionQuantificationBufferWriter.FlushBuffer();
// Rewrite CHP files to get chip summary entires
Verbose::out(1,"Creating final files for CHP output");
Verbose::progressBegin(1, ToStr("Finalizing Expression CHP Files"),
m_CHPFileNames.size(), 1, m_CHPFileNames.size());
try {
for (unsigned int chip = 0; chip < m_CHPFileNames.size(); chip++) {
// open up tmp chp file to pull results from
GenericData data;
GenericFileReader reader;
std::string filename = m_CHPFileNames[chip]+".tmp";
reader.SetFilename(filename);
reader.ReadHeader(data);
GenericDataHeader* hdr = data.Header().GetGenericDataHdr();
GenericDataHeader updateHdr;
for (int source = 0; source < m_ChipSummaries.size(); source++) {
ChipSummary::metricDefVec_t metricDefs = m_ChipSummaries[source]->getMetricDefs();
for (int i = 0; i < metricDefs.size(); i++) {
ChipSummary::Metric metric;
if (!m_ChipSummaries[source]->getMetric(chip, metricDefs[i].m_name, metric)) {
Err::errAbort("QuantMethodExprCCCHPReport: metric '" + metricDefs[i].m_name +
"' was not found");
}
std::wstring mName(CHIP_SUMMARY_PARAMETER_NAME_PREFIX);
mName += StringUtils::ConvertMBSToWCS(metric.m_Name);
ParameterNameValueType param;
if (hdr->FindNameValParam(mName, param) == false) {
Err::errAbort("QuantMethodExprCCCHPReport: metric name '" + StringUtils::ConvertWCSToMBS(mName) +
"' could not be found in the header of " + filename);
}
switch (param.GetParameterType()) {
case ParameterNameValueType::Int8Type:
param.SetValueInt8((int8_t)metric.m_Integer);
break;
case ParameterNameValueType::UInt8Type:
param.SetValueUInt8((u_int8_t)metric.m_Integer);
break;
case ParameterNameValueType::Int16Type:
param.SetValueInt16((int16_t)metric.m_Integer);
break;
case ParameterNameValueType::UInt16Type:
param.SetValueUInt16((u_int16_t)metric.m_Integer);
break;
case ParameterNameValueType::Int32Type:
param.SetValueInt32((int32_t)metric.m_Integer);
break;
case ParameterNameValueType::UInt32Type:
param.SetValueUInt32((u_int32_t)metric.m_Integer);
break;
case ParameterNameValueType::FloatType:
param.SetValueFloat((float)metric.m_Double);
break;
case ParameterNameValueType::TextType:
param.SetValueText(StringUtils::ConvertMBSToWCS(metric.m_String), (int) metric.m_String.length());
break;
case ParameterNameValueType::AsciiType:
if (metric.m_String.size() > 256) {
Err::errAbort("QuantMethodExprCCCHPReport: string header parameter too long, name = '" +
metric.m_Name + "', value = '" + metric.m_String + "'");
}
param.SetValueAscii(metric.m_String, (int) metric.m_String.length());
break;
default:
Err::errAbort("QuantMethodExprCCCHPReport: unknown header parameter type found in file " +
filename);
}
updateHdr.AddNameValParam(param);
}
}
std::ofstream os;
Fs::aptOpen(os, filename, std::ios::out|std::ios::binary|std::ios::in);
if (!os) {
Err::errAbort("QuantMethodExprCCCHPReport: file " + filename +
" could not be opened for writing");
}
GenericDataHeaderUpdater updater;
updater.Update(os, updateHdr, *hdr);
os.close();
Verbose::progressStep(1);
}
} catch (...) {
removeAllChps();
Err::errAbort("Error in creating final CHP output.");
}
Verbose::progressEnd(1, ToStr("Done."));
// Remove .tmp extension
for (unsigned int i = 0; i < m_CHPFileNames.size(); i++) {
std::string from = m_CHPFileNames[i] + ".tmp";
std::string to = m_CHPFileNames[i];
if (!Fs::fileRename(from.c_str(),to.c_str())) {
removeAllChps();
Err::errAbort("Unable to rename '" + from + "' to '" + to + "'");
}
}
removeTmpChps();
return true;
}
/*
* Read the file contents into the data object.
*/
void GridControlFileReader::Read(const std::string &fileName, GridControlData& data)
{
// Clear the old data and read the file.
data.Clear();
GenericFileReader reader;
GenericData gdata;
reader.SetFilename(fileName);
reader.ReadHeader(gdata);
// Check the file identifier
if (gdata.FileIdentifier() != GRD_FILE_TYPE_IDENTIFIER)
{
affymetrix_calvin_exceptions::InvalidFileTypeException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
throw e;
}
// Get the header parameters.
ParameterNameValueType param;
gdata.Header().GetGenericDataHdr()->FindNameValParam(GRD_ROWS_PARAMETER_NAME, param);
data.SetRows(param.GetValueInt32());
gdata.Header().GetGenericDataHdr()->FindNameValParam(GRD_COLUMNS_PARAMETER_NAME, param);
data.SetColumns(param.GetValueInt32());
// Get the XY coordinates from the dataSets.
FeatureCoordinate coord;
u_int16_t x;
u_int16_t y;
int nRows;
DataSet *dataSet;
// First the B1 probes.
dataSet = gdata.DataSet(GRD_FILE_COORDINATE_GROUP_NAME, GRD_FILE_B1_SET_NAME);
if (dataSet->Open() == false)
{
affymetrix_calvin_exceptions::DataSetNotOpenException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
throw e;
}
nRows = dataSet->Rows();
data.ResizeB1(nRows);
for (int iRow=0; iRow<nRows; iRow++)
{
dataSet->GetData(iRow, 0, x);
dataSet->GetData(iRow, 1, y);
coord.x = x;
coord.y = y;
data.SetB1(iRow, coord);
}
dataSet->Close();
dataSet->Delete();
// Next the B2 probes.
dataSet = gdata.DataSet(GRD_FILE_COORDINATE_GROUP_NAME, GRD_FILE_B2_SET_NAME);
if (dataSet->Open() == false)
{
affymetrix_calvin_exceptions::DataSetNotOpenException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
throw e;
}
nRows = dataSet->Rows();
data.ResizeB2(nRows);
for (int iRow=0; iRow<nRows; iRow++)
{
dataSet->GetData(iRow, 0, x);
dataSet->GetData(iRow, 1, y);
coord.x = x;
coord.y = y;
data.SetB2(iRow, coord);
}
dataSet->Close();
dataSet->Delete();
// Last the NS probes.
dataSet = gdata.DataSet(GRD_FILE_COORDINATE_GROUP_NAME, GRD_FILE_NS_SET_NAME);
if (dataSet->Open() == false)
{
affymetrix_calvin_exceptions::DataSetNotOpenException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
throw e;
}
nRows = dataSet->Rows();
data.ResizeNS(nRows);
for (int iRow=0; iRow<nRows; iRow++)
{
dataSet->GetData(iRow, 0, x);
dataSet->GetData(iRow, 1, y);
coord.x = x;
coord.y = y;
data.SetNS(iRow, coord);
}
dataSet->Close();
dataSet->Delete();
}
static int Fusion_GetDataSetOffsetAndSize
(
const char *file_name,
const char *wavelength,
int &offset,
int &size,
char *err_msg,
int err_msg_alloc_sz
)
{
GenericFileReader reader;
string fname = file_name;
reader.SetFilename (fname);
GenericData hdr_data;
reader.ReadHeader (hdr_data);
GenericDataHeader *hdr = hdr_data.Header ().GetGenericDataHdr ();
ParameterNameValueType cel_cols,cel_rows;
if (hdr->FindNameValParam(L"affymetrix-cel-cols",cel_cols) == false ||
hdr->FindNameValParam(L"affymetrix-cel-cols",cel_rows) == false)
{
strncpy (err_msg,"Invalid cel file",sizeof(err_msg_alloc_sz)-1);
return FALSE;
}
string err_s;
while (1)
{
size_t len = strlen (wavelength)+1;
wchar_t *_wavelength = new wchar_t[len];
for (UINT i=0; i<len; i++)
{
_wavelength[i] = (WORD)wavelength[i];
}
wstring group_name = _wavelength;
delete [] _wavelength;
DataGroupHeader *data_group_header = hdr_data.Header ().FindDataGroupHeader (group_name);
if (data_group_header == 0)
{
err_s = "Missing data group ";
err_s += wavelength;
break;
}
DataSet *data_set = GetDataSet (L"Intensity", group_name, hdr_data);
if (data_set == 0)
{
err_s = "Missing data set \"Intensity\"";
break;
}
offset = data_set->Header ().GetDataStartFilePos ();
size = data_set->Header ().GetDataSize ();
break;
}
if (strlen (err_s.c_str ()))
{
strncpy (err_msg,err_s.c_str (),sizeof(err_msg_alloc_sz)-1);
return FALSE;
}
return TRUE;
}