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); }