void TestFileGenerator::AddStandardGenericDataHeader(GenericDataHeader& gdh)
{
// Fill the GenericDataHeader.
gdh.SetFileTypeId(SCAN_ACQUISITION_DATA_TYPE);
gdh.SetFileId("test-dat-guid");
gdh.SetFileCreationTime(L"2004-07-04T11:12:13Z");
gdh.SetLocale(L"en-US");
ParameterNameValueType nvt;
nvt.SetName(ARRAY_TYPE_PARAM_NAME);
nvt.SetValueText(L"Hg-U133A");
gdh.AddNameValParam(nvt);
nvt.SetName(ARRAY_BARCODE_PARAM_NAME);
nvt.SetValueText(L"Barcode");
gdh.AddNameValParam(nvt);
nvt.SetName(L"Parameter1");
nvt.SetValueText(L"Value1");
gdh.AddNameValParam(nvt);
GenericDataHeader gdhParent;
gdhParent.SetFileTypeId(ARRAY_TYPE_IDENTIFIER);
gdhParent.SetFileId("test-array-guid");
gdhParent.SetFileCreationTime(L"2004-07-01T13:14:15Z");
gdhParent.SetLocale(L"en-US");
nvt.SetName(ARRAY_TYPE_PARAM_NAME);
nvt.SetValueText(L"Hg-U133A");
gdhParent.AddNameValParam(nvt);
nvt.SetName(ARRAY_LOT_PARAM_NAME);
nvt.SetValueText(L"Thanks alot");
gdhParent.AddNameValParam(nvt);
gdh.AddParent(gdhParent);
}
void CDFData::SetDataTypeId(CDFDataTypeIds p, int32_t probesetCnt)
{
GenericDataHeader* gPtr = genericData.Header().GetGenericDataHdr();
std::string typeId;
std::wstring groupName;
if(p == Expression)
{
typeId = AFFY_EXPR_PS;
groupName = CDF_PS_GROUP_LBL;
}
else if(p == Genotyping)
{
typeId = AFFY_GENO_PS;
groupName = CDF_PS_GROUP_LBL;
}
else if(p == Tag)
{
typeId = AFFY_TAG_PS;
groupName = CDF_PS_GROUP_LBL;
}
else if(p == Resequencing)
{
typeId = AFFY_RESEQ_PS;
groupName = CDF_PS_GROUP_LBL;
}
else
{
typeId = AFFY_CNTRL_PS;
groupName = CDF_QC_GROUP_LBL;
}
gPtr->SetFileTypeId(typeId);
CreateDataGroups(groupName, probesetCnt);
}
void TestFileGenerator::WriteSmallCelFileWithAPartialDatHeaderTest()
{
CelFileData data("small_cel_file_partial_datheader");
// Write
ParameterNameValueType nvt;
GenericDataHeader datHdr;
datHdr.SetFileId(AffymetrixGuid::GenerateNewGuid());
datHdr.SetFileTypeId("affymetrix-calvin-scan-acquisition");
datHdr.SetFileCreationTime(L"2004-07-01T13:14:15Z");
nvt.SetName(L"affymetrix-partial-dat-header");
std::wstring datHeaderString = L" small_cel_file_partial_datheader:CLS=25 RWS=25 XIN=1 YIN=1 VE=0 0 05/19/05 02:45:59 ScannerID: ScannerTyp \x14 \x14 Hg-Small.1sq \x14 \x14 \x14 \x14 \x14 570 \x14 45.200001 \x14 0.340000 \x14 1.0900 \x14 3";
nvt.SetValueText(datHeaderString);
datHdr.AddNameValParam(nvt);
nvt.SetName(L"affymetrix-max-pixel-intensity");
nvt.SetValueUInt16(46001);
datHdr.AddNameValParam(nvt);
nvt.SetName(L"affymetrix-min-pixel-intensity");
nvt.SetValueUInt16(1);
datHdr.AddNameValParam(nvt);
// Add DAT GenericDataHeader as parent.
data.GetFileHeader()->GetGenericDataHdr()->AddParent(datHdr);
WriteRemaingSmallCelFileWithGridParameters(data);
}
void TestFileGenerator::WriteSmallCelFileWithAFullDatHeaderTest() // Files converted from GCOS will have a full DatHeader
{
CelFileData data("small_cel_file_full_datheader");
// Write
ParameterNameValueType nvt;
GenericDataHeader datHdr;
datHdr.SetFileId(AffymetrixGuid::GenerateNewGuid());
datHdr.SetFileTypeId("affymetrix-calvin-scan-acquisition");
datHdr.SetFileCreationTime(L"2004-07-01T13:14:15Z");
nvt.SetName(L"affymetrix-dat-header");
std::wstring datHeaderString = L"[45..56789] small_cel_file_full_datheader:CLS=25 RWS=25 XIN=1 YIN=1 VE=0 0 05/19/05 02:45:59 ScannerID: ScannerTyp \x14 \x14 Hg-Small.1sq \x14 \x14 \x14 \x14 \x14 570 \x14 45.200001 \x14 0.340000 \x14 1.0900 \x14 3";
nvt.SetValueText(datHeaderString);
datHdr.AddNameValParam(nvt);
// Add DAT GenericDataHeader as parent.
data.GetFileHeader()->GetGenericDataHdr()->AddParent(datHdr);
WriteRemaingSmallCelFileWithGridParameters(data);
}
