std::wstring CalvinCELDataAdapter::GetDatHeader() { std::wstring datHeader; //GenDataHdrVectorIt begin, end; GenericDataHeader* gdh = calvinCel.GetFileHeader()->GetGenericDataHdr()->FindParent(SCAN_ACQUISITION_DATA_TYPE); if (gdh) { // found the right header, now look for the parameter ParameterNameValueType nvt; if (gdh->FindNameValParam(DAT_HEADER_PARAM_NAME, nvt)) { if (nvt.GetParameterType() == ParameterNameValueType::TextType) datHeader = nvt.GetValueText(); } else if (gdh->FindNameValParam(PARTIAL_DAT_HEADER_PARAM_NAME, nvt)) { if (nvt.GetParameterType() == ParameterNameValueType::TextType) { std::wstring partialDatHeader = nvt.GetValueText(); u_int16_t min = 0; u_int16_t max = 0; // Find the max and min parameters and append to the string. if (gdh->FindNameValParam(MAX_PIXEL_INTENSITY_PARAM_NAME, nvt)) { if (nvt.GetParameterType() == ParameterNameValueType::UInt16Type) max = nvt.GetValueUInt16(); } if (gdh->FindNameValParam(MIN_PIXEL_INTENSITY_PARAM_NAME, nvt)) { if (nvt.GetParameterType() == ParameterNameValueType::UInt16Type) min = nvt.GetValueUInt16(); } wchar_t buf[30]=L""; FormatString2(buf, 30, L"[%d..%d]", min, max); datHeader = buf; datHeader += partialDatHeader; } } } return datHeader; }
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; }
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; }
std::wstring CHPQuantificationData::GetWStringFromGenericHdr(const std::wstring& name) { std::wstring result; ParameterNameValueType paramType; GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr(); if (hdr->FindNameValParam(name, paramType)) { result = paramType.GetValueText(); } return result; }
int32_t CHPData::GetInt32FromGenericHdr(const std::wstring& name) { int32_t result = 0; ParameterNameValueType paramType; GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr(); if (hdr->FindNameValParam(name, paramType)) { result = paramType.GetValueInt32(); } return result; }
std::string CDFData::GetRefSequence() { std::string result; ParameterNameValueType paramType; GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr(); if (hdr->FindNameValParam(CDF_REFSEQ_PARAM, paramType)) { result = paramType.GetValueAscii(); } return result; }
/** * 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; }
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; }