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 CHPQuantificationDataTest::test_AlgParams() { ParameterNameValueTypeList params; ParameterNameValueType param; CHPQuantificationData data; param.SetName(L"n1"); param.SetValueText(L"v1"); params.push_back(param); param.SetName(L"n2"); param.SetValueText(L"v2"); params.push_back(param); data.AddAlgParams(params); ParameterNameValueTypeList params_out = data.GetAlgParams(); CPPUNIT_ASSERT(params_out.size() == 2); ParameterNameValueTypeList::iterator it = params_out.begin(); param = *it; CPPUNIT_ASSERT(param.GetName() == L"n1"); CPPUNIT_ASSERT(param.GetValueText() == L"v1"); ++it; param = *it; CPPUNIT_ASSERT(param.GetName() == L"n2"); CPPUNIT_ASSERT(param.GetValueText() == L"v2"); }
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 CHPMultiDataDataTest::test_SumParams() { ParameterNameValueTypeList params; ParameterNameValueType param; CHPMultiDataData data; param.SetName(L"n1"); param.SetValueText(L"v1"); params.push_back(param); param.SetName(L"n2"); param.SetValueText(L"v2"); params.push_back(param); data.AddSummaryParams(params); ParameterNameValueTypeList params_out = data.GetSummaryParams(); CPPUNIT_ASSERT(params_out.size() == 2); ParameterNameValueTypeList::iterator it = params_out.begin(); param = *it; CPPUNIT_ASSERT(param.GetName() == L"n1"); CPPUNIT_ASSERT(param.GetValueText() == L"v1"); ++it; param = *it; CPPUNIT_ASSERT(param.GetName() == L"n2"); CPPUNIT_ASSERT(param.GetValueText() == L"v2"); }
void TestFileGenerator::WriteSmallCelFileNoStdev() { CelFileData data("small_cel_file_no_stdev"); data.SetIntensityCount(25); data.SetStdDevCount(0); data.SetPixelCount(25); data.SetOutlierCount(2); data.SetMaskCount(3); data.SetRows(5); data.SetCols(5); data.SetArrayType(L"Hg-small"); data.SetAlgorithmName(L"Feature Extraction"); ParameterNameValueType nvt; nvt.SetName(L"percentile"); nvt.SetValueFloat(0.75f); data.AddAlgorithmParameter(nvt); nvt.SetName(L"outlierlow"); nvt.SetValueFloat(1.004f); data.AddAlgorithmParameter(nvt); CelFileWriter* writer = new CelFileWriter(data); FloatVector vInten; Int16Vector vPixels; for (int i=0; i<25; ++i) { vInten.push_back(100.0f*i); vPixels.push_back(25); } // Do some writing writer->WriteIntensities(vInten); writer->WritePixels(vPixels); // XYCoordVector XYCoordVector outlier; XYCoord xy(0,0); outlier.push_back(xy); xy.xCoord = 1; xy.yCoord = 2; outlier.push_back(xy); writer->WriteOutlierCoords(outlier); XYCoordVector masked; xy.xCoord = 1; xy.yCoord = 0; masked.push_back(xy); xy.xCoord = 2; xy.yCoord = 1; masked.push_back(xy); xy.xCoord = 3; xy.yCoord = 2; masked.push_back(xy); writer->WriteMaskCoords(masked); delete writer; }
void TestFileGenerator::WriteOutGenericDATDataFileNoGrid() { GenericDataHeader gdh; AddStandardGenericDataHeader(gdh); // Fill the DataGroupHeader DataGroupHeader dch; dch.SetName(L"First Data Cube"); // Fill the DataSetHeader DataSetHeader dph; dph.SetName(L"acquired data"); ParameterNameValueType nvt; nvt.SetName(L"Scanner"); nvt.SetValueText(L"M10"); dph.AddNameValParam(nvt); nvt.SetName(L"Pixel Size"); nvt.SetValueFloat(0.051f); dph.AddNameValParam(nvt); dph.AddColumn(UShortColumn(L"Pixel")); int32_t rows = 100; dph.SetRowCnt(rows); dch.AddDataSetHdr(dph); // Set the FileHeader FileHeader fh; fh.SetFilename("test.file.data_dat"); fh.SetGenericDataHdr(gdh); fh.AddDataGroupHdr(dch); // Create the generic file writer GenericFileWriter gfWriter(&fh); gfWriter.WriteHeader(); DataGroupWriterIt dcwBegin, dcwEnd; gfWriter.GetDataGroupWriters(dcwBegin, dcwEnd); DataGroupWriter d = *dcwBegin; dcwBegin->WriteHeader(); DataSetWriterIt dpwBegin, dpwEnd; dcwBegin->GetDataSetWriters(dpwBegin, dpwEnd); dpwBegin->WriteHeader(); // Write out the data for( int32_t i=0; i < rows; ++i ) { u_int16_t value = (u_int16_t)(i*10+i); dpwBegin->Write(value); } dpwBegin->UpdateNextDataSetOffset(); dcwBegin->Close(); }
void DATFileUpdaterTest::AddParameters(DATData& data) { ParameterNameValueType nvt; nvt.SetName(L"Santa Clara"); nvt.SetValueUInt8(56); data.AddGridAlignmentAlgorithmParameter(nvt); nvt.SetName(L"San Mateo"); nvt.SetValueFloat(4.56f); data.AddGridAlignmentAlgorithmParameter(nvt); }
/* * Save the program information to the AGCC file. */ void MAS5CHPUtils::StoreProgramInfo() { ParameterNameValueType p; p.SetName(PROGRAM_NAME); p.SetValueText(programName); cc_data->GetGenericData().Header().GetGenericDataHdr()->AddNameValParam(p); p.SetName(PROGRAM_ID); p.SetValueText(programId); cc_data->GetGenericData().Header().GetGenericDataHdr()->AddNameValParam(p); p.SetName(PROGRAM_COMPANY); p.SetValueText(programCompany); cc_data->GetGenericData().Header().GetGenericDataHdr()->AddNameValParam(p); }
void DataGroupHeaderTest::FindDataSetHeaderTest() { // Create DataSetHeaders DataSetHeader dph1; dph1.SetName(L"pixel intensity"); ParameterNameValueType param; param.SetName(L"Scanner"); param.SetValueText(L"M10"); dph1.AddNameValParam(param); dph1.AddUShortColumn(L""); dph1.SetRowCnt(1); DataSetHeader dph2; dph2.SetName(L"grid coordinates"); param.SetName(L"Corner Pattern"); param.SetValueText(L"Checkerboard"); dph2.AddNameValParam(param); dph2.AddUShortColumn(L""); dph2.AddUShortColumn(L""); dph2.AddUShortColumn(L""); dph2.AddUShortColumn(L""); dph2.AddUShortColumn(L""); dph2.AddUShortColumn(L""); dph2.AddUShortColumn(L""); dph2.AddUShortColumn(L""); dph2.AddUShortColumn(L""); dph2.AddUShortColumn(L""); dph2.AddUShortColumn(L""); dph2.AddUShortColumn(L""); dph2.AddUShortColumn(L""); dph2.AddUShortColumn(L""); dph2.AddUShortColumn(L""); dph2.AddUShortColumn(L""); dph2.SetRowCnt(1); header->AddDataSetHdr(dph1); header->AddDataSetHdr(dph2); const DataSetHeader* dph = header->FindDataSetHeader(L"none"); CPPUNIT_ASSERT(0 == dph); dph = header->FindDataSetHeader(dph1.GetName()); CPPUNIT_ASSERT(0 != dph); CPPUNIT_ASSERT(dph->GetName() == dph1.GetName()); dph = header->FindDataSetHeader(dph2.GetName()); CPPUNIT_ASSERT(0 != dph); CPPUNIT_ASSERT(dph->GetName() == dph2.GetName()); }
/* * Store the start index and count of probe sets for the given chromosome. */ void CopyNumberResultWriter::SetChromosomeProbeSetIndexInformation(u_int8_t chr, int startIndex, int count) { ostringstream str; str << (int) chr; wstring schr = StringUtils::ConvertMBSToWCS(str.str()); ParameterNameValueType param; param.SetName(schr + L":start"); param.SetValueInt32(startIndex); chrStartStop.push_back(param); param.SetName(schr + L":count"); param.SetValueInt32(count); chrStartStop.push_back(param); param.SetName(schr + L":display"); param.SetValueAscii(ChromosomeToString(chr)); chrStartStop.push_back(param); }
void TestFileGenerator::WriteCelFileWithADataSetWithZeroRows() { CelFileData data("small_cel_file_with_dataset_of_zero_rows"); data.SetIntensityCount(25); data.SetStdDevCount(25); data.SetPixelCount(25); data.SetOutlierCount(0); data.SetMaskCount(0); data.SetRows(5); data.SetCols(5); data.SetArrayType(L"Hg-small"); data.SetAlgorithmName(L"Feature Extraction"); ParameterNameValueType nvt; nvt.SetName(L"percentile"); nvt.SetValueFloat(0.75f); data.AddAlgorithmParameter(nvt); nvt.SetName(L"outlierlow"); nvt.SetValueFloat(1.004f); data.AddAlgorithmParameter(nvt); CelFileWriter* writer = new CelFileWriter(data); FloatVector vInten; FloatVector vStdev; Int16Vector vPixels; for (int i=0; i<25; ++i) { vInten.push_back(100.0f*i); vStdev.push_back(.123f); vPixels.push_back(25); } // Do some writing writer->WriteIntensities(vInten); writer->WriteStdDevs(vStdev); writer->WritePixels(vPixels); XYCoordVector outlier; writer->WriteOutlierCoords(outlier); XYCoordVector masked; writer->WriteMaskCoords(masked); delete writer; }
void CHPQuantificationData::SetWStringToGenericHdr(const std::wstring& name, const std::wstring value, int32_t reserve) { ParameterNameValueType paramType; paramType.SetName(name); paramType.SetValueText(value, reserve); GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr(); hdr->AddNameValParam(paramType); }
void CHPData::SetFloatToGenericHdr(const std::wstring& name, float value) { ParameterNameValueType paramType; paramType.SetName(name); paramType.SetValueFloat(value); GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr(); hdr->AddNameValParam(paramType); }
void CDFData::SetUInt32ToGenericHdr(const std::wstring& name, u_int32_t value) { ParameterNameValueType paramType; paramType.SetName(name); paramType.SetValueUInt32(value); GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr(); hdr->AddNameValParam(paramType); }
void CDFData::SetRefSequence(const std::string &seq) { GenericDataHeader* gPtr = genericData.Header().GetGenericDataHdr(); ParameterNameValueType paramType; paramType.SetName(CDF_REFSEQ_PARAM); paramType.SetValueAscii(seq); gPtr->AddNameValParam(paramType); }
ParameterNameValueType CHPData::GetChipSum(const std::wstring& tag) { std::wstring name = CHIP_SUMMARY_PARAMETER_NAME_PREFIX_S + tag; ParameterNameValueType paramType; GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr(); hdr->FindNameValParam(name, paramType); ParameterNameValueType type = paramType; type.SetName(tag); return type; }
void TestFileGenerator::WriteSmallDatFileWithGridAndSubgridsAndParameters() { std::string filename = "small_DAT_file_with_subgrids_and_parameters"; WriteDatFile(filename, L"Hg-small", 4, 5, true); DATData data(filename); AddGridAndSubgrids(data, 2.5, 10); ParameterNameValueType nvt; nvt.SetName(L"Zip Code"); nvt.SetValueInt32(95051); data.AddGridAlignmentAlgorithmParameter(nvt); nvt.SetName(L"County"); nvt.SetValueText(L"Santa Clara"); data.AddGridAlignmentAlgorithmParameter(nvt); DATFileUpdater update(data); update.Update(); }
ParameterNameValueType CHPData::GetAlgParam(const std::wstring& tag) { std::wstring name = ALGORITHM_PARAM_NAME_PREFIX_S + tag; ParameterNameValueType paramType; GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr(); hdr->FindNameValParam(name, paramType); ParameterNameValueType type = paramType; type.SetName(tag); return type; }
void CHPMultiDataData::AddAppMetaInfo(const ParameterNameValueTypeList& params) { ParameterNameValueType param; GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr(); for (ParameterNameValueTypeList::const_iterator it=params.begin(); it != params.end(); ++it) { param = *it; param.SetName(APPLICATION_META_INFO_PREFIX_S + param.GetName()); hdr->AddNameValParam(param); } }
void CHPMultiDataData::AddAlgParams(const ParameterNameValueTypeList& params) { ParameterNameValueType param; GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr(); for (ParameterNameValueTypeList::const_iterator it=params.begin(); it != params.end(); it++) { param = *it; param.SetName(ALGORITHM_PARAM_NAME_PREFIX_S + param.GetName()); hdr->AddNameValParam(param); } }
void CHPQuantificationData::AddSummaryParams(const ParameterNameValueTypeList& params) { ParameterNameValueType param; GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr(); for (ParameterNameValueTypeList::const_iterator it=params.begin(); it != params.end(); it++) { param = *it; param.SetName(CHIP_SUMMARY_PARAMETER_NAME_PREFIX_S + param.GetName()); hdr->AddNameValParam(param); } }
void TestFileGenerator::WriteSmallCelFileNoOutlierNoMask() { CelFileData data("small_cel_file_no_outlier_no_mask"); data.SetIntensityCount(10); data.SetStdDevCount(10); data.SetPixelCount(10); data.SetOutlierCount(0); data.SetMaskCount(0); data.SetRows(2); data.SetCols(5); data.SetArrayType(L"Hg-small"); data.SetAlgorithmName(L"Feature Extraction"); ParameterNameValueType nvt; nvt.SetName(L"percentile"); nvt.SetValueFloat(0.75f); data.AddAlgorithmParameter(nvt); nvt.SetName(L"outlierlow"); nvt.SetValueFloat(1.004f); data.AddAlgorithmParameter(nvt); CelFileWriter* writer = new CelFileWriter(data); FloatVector vInten; FloatVector vStdev; Int16Vector vPixels; for (int i=0; i<10; ++i) { vInten.push_back(100.0f*i); vStdev.push_back(.5*i); vPixels.push_back(25); } // Do some writing writer->WriteIntensities(vInten); writer->WriteStdDevs(vStdev); writer->WritePixels(vPixels); delete writer; }
bool DataSetHeader::FindNameValParam(const std::wstring& name, ParameterNameValueType& result) const { ParameterNameValueType t; t.SetName(name); t.SetValueText(L""); ParameterNameValueTypeConstIt found = FindNameValParam(t); if (found != nameValParams.end()) { result = *found; return true; } return false; }
void TestFileGenerator::WriteSmallDatFileWithReservedStringParameters() { int32_t rows = 4; int32_t cols = 5; int32_t pixelCount = rows*cols; DATData data("small_dat_file_with_reserved_string_parameters"); data.SetPixelCount(pixelCount); data.SetStatsCount(1); data.SetArrayType(L"Hg_small"); data.SetPixelSize(0.71f); data.SetScannerType(L"M10"); data.SetScannerID(L"main"); DateTime dt = DateTime::Parse(L"2005-12-25T11:12:13Z"); data.SetScanDate(dt); data.SetRows(rows); data.SetCols(cols); std::string arrayId = "smellsliketeenspirit"; data.SetArrayId(arrayId); ParameterNameValueType nvt; nvt.SetName(L"fixedlen"); nvt.SetValueText(L"twenty-five", 25); data.GetFileHeader()->GetGenericDataHdr()->AddNameValParam(nvt); DATFileWriter writer(data); Uint16Vector pixels; pixels.reserve(pixelCount); u_int16_t inten = 10; for (int32_t i=0; i<pixelCount; ++i, ++inten) { if (inten > 46000) { inten = 0; } pixels.push_back(inten); } Uint16Vector stats; stats.push_back(pixels[0]); // min stats.push_back(pixels[19]); // max writer.WriteStats(stats); writer.WritePixels(pixels); }
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); }
ParameterNameValueTypeList CHPQuantificationData::GetSummaryParams() { ParameterNameValueTypeList nvt; ParameterNameValueTypeIt begin, end; ParameterNameValueType param; genericData.Header().GetGenericDataHdr()->GetNameValIterators(begin, end); while(begin != end) { std::wstring key = begin->GetName(); if(key.compare(0, CHIP_SUMMARY_PARAMETER_NAME_PREFIX_S.size(),CHIP_SUMMARY_PARAMETER_NAME_PREFIX_S) == 0) { param = *begin; key.erase(0, CHIP_SUMMARY_PARAMETER_NAME_PREFIX_S.size()); param.SetName(key); nvt.push_back(param); } begin++; } return nvt; }
ParameterNameValueTypeVector CHPData::GetAlgParams() { ParameterNameValueTypeVector nvt; ParameterNameValueTypeIt begin, end; ParameterNameValueType param; genericData.Header().GetGenericDataHdr()->GetNameValIterators(begin, end); while(begin != end) { std::wstring key = begin->GetName(); if(key.compare(0, ALGORITHM_PARAM_NAME_PREFIX_S.size(),ALGORITHM_PARAM_NAME_PREFIX_S) == 0) { param = *begin; key.erase(0, ALGORITHM_PARAM_NAME_PREFIX_S.size()); param.SetName(key); nvt.push_back(param); } begin++; } return nvt; }
void CalvinCHPMultiDataFileUpdaterTest::CreateReferenceFile2() { CHPMultiDataData data(TEST2_FILE); vector<ColumnInfo> cols; ParameterNameValueType nv; ByteColumn bcol(L"byte"); cols.push_back(bcol); UByteColumn ubcol(L"ubyte"); cols.push_back(ubcol); ShortColumn scol(L"short"); cols.push_back(scol); UShortColumn uscol(L"ushort"); cols.push_back(uscol); IntColumn icol(L"int"); cols.push_back(icol); UIntColumn uicol(L"uint"); cols.push_back(uicol); FloatColumn fcol(L"float"); cols.push_back(fcol); ASCIIColumn acol(L"ascii", 7); cols.push_back(acol); UnicodeColumn tcol(L"text", 10); cols.push_back(tcol); ProbeSetMultiDataGenotypeData e; data.SetEntryCount(GenotypeMultiDataType, 4, 10, cols); CHPMultiDataFileWriter *writer = new CHPMultiDataFileWriter(data); nv.SetName(L"byte"); nv.SetValueInt8(8); e.metrics.push_back(nv); nv.SetName(L"ubyte"); nv.SetValueUInt8(8); e.metrics.push_back(nv); nv.SetName(L"short"); nv.SetValueInt16(16); e.metrics.push_back(nv); nv.SetName(L"ushort"); nv.SetValueUInt16(16); e.metrics.push_back(nv); nv.SetName(L"int"); nv.SetValueInt32(32); e.metrics.push_back(nv); nv.SetName(L"uint"); nv.SetValueUInt32(32); e.metrics.push_back(nv); nv.SetName(L"float"); nv.SetValueFloat(44.0f); e.metrics.push_back(nv); nv.SetName(L"ascii"); nv.SetValueAscii("ascii"); e.metrics.push_back(nv); nv.SetName(L"text"); nv.SetValueText(L"text"); e.metrics.push_back(nv); writer->SeekToDataSet(GenotypeMultiDataType); e.name = "1"; e.call = 1; e.confidence = 10.0f; writer->WriteEntry(e); e.name = "2"; e.call = 2; e.confidence = 20.0f; writer->WriteEntry(e); e.name = "3"; e.call = 3; e.confidence = 30.0f; writer->WriteEntry(e); e.name = "4"; e.call = 4; e.confidence = 40.0f; writer->WriteEntry(e); delete writer; }
/** * Get set up for a run of reporting probesets. Often used to open file * streams and print headers to files etc. * * @param qMethod - Quantification method to be used. * @param layout - Where the probesets, probes, etc are on the chip. * * @return true if success, false otherwise. */ bool QuantMethodExprCCCHPReport::prepare(QuantMethod &qMethod, const IntensityMart &iMart) { QuantExprMethod *eMethod = dynamic_cast<QuantExprMethod *>(&qMethod); if (eMethod == NULL) { Err::errAbort("Can only use a QuantMethodExprReport with a QuantExprMethod."); } setupFileNames(iMart); int nfiles = m_CHPFileNames.size(); // Make sure our output directory exists. if (!Fs::isWriteableDir(m_Prefix.c_str()) && (Fs::mkdirPath(m_Prefix, false) != APT_OK)) { APT_ERR_ABORT("Can't make or write to directory: " + m_Prefix); } removeAllChps(); // Get CEL file GUIDs ///@todo This be computed by the engine and passed in via AnalysisInfo m_celGuids.resize(nfiles); std::string tmp_unc_name; for (int chip=0; chip<nfiles; chip++) { FusionCELData cel; try { tmp_unc_name=Fs::convertToUncPath(m_CELFileNames[chip]); cel.SetFileName(tmp_unc_name.c_str()); if (!cel.ReadHeader()) { Err::errAbort("Unable to read CEL file: "+FS_QUOTE_PATH(tmp_unc_name)); } GenericData *gdata = cel.GetGenericData(); if (gdata != NULL) { m_celGuids[chip] = gdata->Header().GetGenericDataHdr()->GetFileId(); } cel.Close(); } catch (...) { Err::errAbort("Unable to read CEL file " + tmp_unc_name); } } int maxProbeSetNameLength = 0; for (int i=0; i<m_Info.m_ProbesetNames.size(); i++) { int len = (int)strlen(m_Info.m_ProbesetNames.at(i)); if (m_Info.m_ProbesetDisplayNames.size() > 0 && m_Info.m_ProbesetDisplayNames.at(i) != NULL) len = (int)strlen(m_Info.m_ProbesetDisplayNames.at(i)); maxProbeSetNameLength = Max(maxProbeSetNameLength, len); } // Prepare headers for all CHP files. wstring algName = StringUtils::ConvertMBSToWCS(m_Info.m_AlgName); wstring algVersion = StringUtils::ConvertMBSToWCS(m_Info.m_AlgVersion); wstring chipType = StringUtils::ConvertMBSToWCS(m_Info.m_ChipType); // For each chip, precreate all probeset signal entries (default to 0.0). Verbose::out(1,"QuantMethodExprCCCHPReport: Creating temporary files for CHP output"); for (int chip=0; chip<nfiles; chip++) { try { ParameterNameValueType param; // Create tmp chp file std::string tmp_chp_name=m_CHPFileNames[chip] + ".tmp"; CHPQuantificationData *data = new CHPQuantificationData(tmp_chp_name); m_TmpChpFiles.push_back(tmp_chp_name); // set parent header FusionCELData cel; try { tmp_unc_name=Fs::convertToUncPath(m_CELFileNames[chip]); cel.SetFileName(tmp_unc_name.c_str()); if (!cel.ReadHeader()) { Err::errAbort("Unable to read CEL file: "+FS_QUOTE_PATH(tmp_unc_name)); } GenericData *gdata = cel.GetGenericData(); if (gdata != NULL) { data->GetFileHeader()->GetGenericDataHdr()->AddParent(*gdata->Header().GetGenericDataHdr()); } cel.Close(); } catch (...) { Err::errAbort("Unable to read CEL file: "+FS_QUOTE_PATH(tmp_unc_name)); } data->SetEntryCount(m_Info.m_NumProbeSets, maxProbeSetNameLength); data->SetAlgName(algName); data->SetAlgVersion(algVersion); data->SetArrayType(chipType); param.SetName(L"program-name"); param.SetValueText(StringUtils::ConvertMBSToWCS(m_Info.m_ProgramName)); data->GetGenericData().Header().GetGenericDataHdr()->AddNameValParam(param); param.SetName(L"program-version"); param.SetValueText(StringUtils::ConvertMBSToWCS(m_Info.m_ProgramVersion)); data->GetGenericData().Header().GetGenericDataHdr()->AddNameValParam(param); param.SetName(L"program-company"); param.SetValueText(StringUtils::ConvertMBSToWCS(m_Info.m_ProgramCompany)); data->GetGenericData().Header().GetGenericDataHdr()->AddNameValParam(param); // Add algorithm parameters to list. ParameterNameValueTypeList paramList; assert(m_Info.m_ParamNames.size() == m_Info.m_ParamValues.size()); for (int i=0; i<m_Info.m_ParamNames.size(); i++) { if (m_Info.m_ParamValues[i].length() > 0) { param.SetName(StringUtils::ConvertMBSToWCS(m_Info.m_ParamNames[i])); param.SetValueText(StringUtils::ConvertMBSToWCS(m_Info.m_ParamValues[i])); paramList.push_back(param); } } // Add list of all CEL GUIDs in batch ///@todo should this be computed by the engine and passed in via AnalysisInfo? string prefix = "apt-opt-"; for (int chip=0; chip<m_CHPFileNames.size(); chip++) { if (m_celGuids[chip].empty() == false) { string paramName = prefix + "cel-guid-" + ToStr(chip+1); param.SetName(StringUtils::ConvertMBSToWCS(paramName)); param.SetValueText(StringUtils::ConvertMBSToWCS(m_celGuids[chip])); paramList.push_back(param); } } data->AddAlgParams(paramList); // Add the run report parameters to the list ParameterNameValueTypeList summaryParamList; std::string blankStr(256, ' '); 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++) { param.SetName(StringUtils::ConvertMBSToWCS(metricDefs[i].m_name)); if (metricDefs[i].m_type == ChipSummary::Metric::Double) { param.SetValueFloat(-1.0); } else if (metricDefs[i].m_type == ChipSummary::Metric::Integer) { param.SetValueInt32(-1); } else if (metricDefs[i].m_type == ChipSummary::Metric::String) { param.SetValueAscii(blankStr); } else { Err::errAbort("QuantMethodExprCCCHPReport: Unable to handle unknown type: " + ToStr(metricDefs[i].m_type) ); } summaryParamList.push_back(param); } } data->AddSummaryParams(summaryParamList); ProbeSetQuantificationData entry; CHPQuantificationFileWriter writer(*data); writer.SeekToDataSet(); // seek to data table location for (int index=0; index<m_Info.m_ProbesetNames.size(); index++) { if (m_Info.m_ProbesetDisplayNames.size() > 0 && m_Info.m_ProbesetDisplayNames[index] != NULL) entry.name = m_Info.m_ProbesetDisplayNames[index]; else entry.name = m_Info.m_ProbesetNames[index]; entry.quantification = 0.0f; writer.WriteEntry(entry); } delete data; } catch (...) { Err::errAbort("QuantMethodExprCHPReport::prepare() - Unable to write header and/or precreate signal entries to file: " + m_CHPFileNames[chip] + ".tmp"); } } // initialize expression signal buffer writer m_ExpressionQuantificationBufferWriter.Initialize(&m_TmpChpFiles); return true; }
void CalvinCHPMultiDataFileUpdaterTest::CreateReferenceFile3() { CHPMultiDataData data(TEST3_FILE); vector<ColumnInfo> cols; ParameterNameValueType nv; ByteColumn bcol(L"byte"); cols.push_back(bcol); UByteColumn ubcol(L"ubyte"); cols.push_back(ubcol); ShortColumn scol(L"short"); cols.push_back(scol); UShortColumn uscol(L"ushort"); cols.push_back(uscol); IntColumn icol(L"int"); cols.push_back(icol); UIntColumn uicol(L"uint"); cols.push_back(uicol); FloatColumn fcol(L"float"); cols.push_back(fcol); ASCIIColumn acol(L"ascii", 7); cols.push_back(acol); UnicodeColumn tcol(L"text", 10); cols.push_back(tcol); ProbeSetMultiDataCopyNumberData e; ProbeSetMultiDataCytoRegionData c; data.SetEntryCount(CopyNumberMultiDataType, 4, 10, cols); data.SetEntryCount(CytoMultiDataType, 2, 10); CHPMultiDataFileWriter *writer = new CHPMultiDataFileWriter(data); nv.SetName(L"byte"); nv.SetValueInt8(8); e.metrics.push_back(nv); nv.SetName(L"ubyte"); nv.SetValueUInt8(8); e.metrics.push_back(nv); nv.SetName(L"short"); nv.SetValueInt16(16); e.metrics.push_back(nv); nv.SetName(L"ushort"); nv.SetValueUInt16(16); e.metrics.push_back(nv); nv.SetName(L"int"); nv.SetValueInt32(32); e.metrics.push_back(nv); nv.SetName(L"uint"); nv.SetValueUInt32(32); e.metrics.push_back(nv); nv.SetName(L"float"); nv.SetValueFloat(44.0f); e.metrics.push_back(nv); nv.SetName(L"ascii"); nv.SetValueAscii("ascii"); e.metrics.push_back(nv); nv.SetName(L"text"); nv.SetValueText(L"text"); e.metrics.push_back(nv); writer->SeekToDataSet(CopyNumberMultiDataType); e.name = "1"; e.chr = 1; e.position = 10; writer->WriteEntry(e); e.name = "2"; e.chr = 2; e.position = 20; writer->WriteEntry(e); e.name = "3"; e.chr = 3; e.position = 30; writer->WriteEntry(e); e.name = "4"; e.chr = 4; e.position = 40; writer->WriteEntry(e); writer->SeekToDataSet(CytoMultiDataType); c.name = "1"; c.chr= 1; c.startPosition = 1; c.stopPosition = 2; c.call = 1; c.confidenceScore = 10.0f; writer->WriteEntry(c); c.name = "2"; c.chr= 2; c.startPosition = 2; c.stopPosition = 3; c.call = 2; c.confidenceScore = 20.0f; writer->WriteEntry(c); delete writer; }