void DataSetUpdaterTest::CreateReferenceFile()
{
// Create the data object.
GenericData data;
data.Header().SetFilename(TEST_FILE);
DataGroupHeader dgHdr(L"data");
DataSetHeader dsHdr;
dsHdr.SetName(L"test");
dsHdr.AddAsciiColumn(L"string8", 64);
dsHdr.AddUnicodeColumn(L"string16", 64);
dsHdr.AddByteColumn(L"int8");
dsHdr.AddShortColumn(L"int16");
dsHdr.AddIntColumn(L"int32");
dsHdr.AddUByteColumn(L"uint8");
dsHdr.AddUShortColumn(L"uint16");
dsHdr.AddUIntColumn(L"uint32");
dsHdr.AddFloatColumn(L"float");
dsHdr.SetRowCnt(3);
dgHdr.AddDataSetHdr(dsHdr);
data.Header().AddDataGroupHdr(dgHdr);
data.Header().GetGenericDataHdr()->SetFileTypeId("affymetrix.test.data");
// Write the data object to the file
GenericFileWriter writer(&data.Header());
writer.WriteHeader();
DataGroupWriter &dataGroupWriter = writer.GetDataGroupWriter(0);
dataGroupWriter.WriteHeader();
//int iSet=0;
DataSetWriterIt beginSet;
DataSetWriterIt endSet;
dataGroupWriter.GetDataSetWriters(beginSet, endSet);
beginSet->WriteHeader();
int32_t dataSetSz = beginSet->GetDataSetSize();
int32_t offset = writer.GetFilePos();
writer.SeekFromCurrentPos(dataSetSz + 1);
beginSet->UpdateNextDataSetOffset();
dataGroupWriter.UpdateNextDataGroupPos();
writer.SeekFromBeginPos(offset);
// Write the data.
beginSet->Write("first_row", 64);
beginSet->Write(L"first_row", 64);
beginSet->Write((int8_t) 1);
beginSet->Write((int16_t) 1);
beginSet->Write((int32_t) 1);
beginSet->Write((u_int8_t) 1);
beginSet->Write((u_int16_t) 1);
beginSet->Write((u_int32_t) 1);
beginSet->Write(1.0f);
beginSet->Write("second_row", 64);
beginSet->Write(L"second_row", 64);
beginSet->Write((int8_t) 2);
beginSet->Write((int16_t) 2);
beginSet->Write((int32_t) 2);
beginSet->Write((u_int8_t) 2);
beginSet->Write((u_int16_t) 2);
beginSet->Write((u_int32_t) 2);
beginSet->Write(2.0f);
beginSet->Write("third_row", 64);
beginSet->Write(L"third_row", 64);
beginSet->Write((int8_t) 3);
beginSet->Write((int16_t) 3);
beginSet->Write((int32_t) 3);
beginSet->Write((u_int8_t) 3);
beginSet->Write((u_int16_t) 3);
beginSet->Write((u_int32_t) 3);
beginSet->Write(3.0f);
}
/*
* 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();
}
/*
* Create a results file with the CEL file header and other parameters.
*/
void CopyNumberResultWriter::CreateResultFile(affymetrix_fusion_io::FusionCELData& cel, const std::string& fileName)
{
try
{
// Create the results file with the header.
CHPMultiDataData *data = new CHPMultiDataData(fileName);
data->SetEntryCount(CopyNumberMultiDataType, numberProbeSets, maxProbeSetNameLength[CopyNumberMultiDataType], columns);
if (numberCytoRegions > 0)
data->SetEntryCount(CytoMultiDataType, numberCytoRegions, maxProbeSetNameLength[CytoMultiDataType],cytoRegionColumns);
if (numberGenotypeProbeSets > 0)
data->SetEntryCount(GenotypeMultiDataType, numberGenotypeProbeSets, maxProbeSetNameLength[GenotypeMultiDataType], genotypeColumns);
data->SetAlgName(StringUtils::ConvertMBSToWCS(algName));
data->SetAlgVersion(StringUtils::ConvertMBSToWCS(algVersion));
data->SetArrayType(cel.GetChipType());
GenericDataHeader *gdh = data->GetFileHeader()->GetGenericDataHdr();
ParameterNameValueType param;
param.SetName(PROGRAM_NAME);
param.SetValueText(StringUtils::ConvertMBSToWCS(programName));
gdh->AddNameValParam(param);
param.SetName(L"program-version");
param.SetValueText(StringUtils::ConvertMBSToWCS(programVersion));
gdh->AddNameValParam(param);
param.SetName(PROGRAM_COMPANY);
param.SetValueText(StringUtils::ConvertMBSToWCS(programCompany));
gdh->AddNameValParam(param);
ParameterNameValueTypeList params = algParams;
param.SetName(L"ArraySet");
param.SetValueText(cel.GetChipType());
params.push_back(param);
data->AddAlgParams(params);
data->AddSummaryParams(summaryParams);
DataSetHeader *dsh = data->GetDataSetHeader(CopyNumberMultiDataType);
for (ParameterNameValueTypeList::iterator it=chrStartStop.begin(); it!=chrStartStop.end(); it++)
dsh->AddNameValParam(*it);
GenericData *gdata = cel.GetGenericData();
if (gdata != NULL)
gdh->AddParent(*gdata->Header().GetGenericDataHdr());
CHPMultiDataFileWriter *writer = new CHPMultiDataFileWriter(*data);
delete writer;
delete data;
// Create a buffer writer object
outputFiles.clear();
outputFiles.push_back(fileName);
vector<MultiDataType> dataTypes;
dataTypes.push_back(CopyNumberMultiDataType);
if (numberCytoRegions > 0)
dataTypes.push_back(CytoMultiDataType);
if (numberGenotypeProbeSets > 0)
dataTypes.push_back(GenotypeMultiDataType);
bufferWriter = new CHPMultiDataFileBufferWriter();
bufferWriter->Initialize(&outputFiles, dataTypes, maxProbeSetNameLength);
}
catch (CalvinException &ex)
{
string err = "Error creating the output file: " + fileName;
wstring msg = ex.ToString();
if (msg.empty() == false)
err += " " + StringUtils::ConvertWCSToMBS(msg);
throw err;
}
catch (...)
{
string err = "Error creating the output file: " + fileName;
throw err;
}
}
