diff --git a/ChargeDetermination/AutoCorrelationChargeDetermination.cpp b/ChargeDetermination/AutoCorrelationChargeDetermination.cpp index de55d70..d744d6c 100644 --- a/ChargeDetermination/AutoCorrelationChargeDetermination.cpp +++ b/ChargeDetermination/AutoCorrelationChargeDetermination.cpp @@ -35,26 +35,27 @@ namespace Engine void AutoCorrelationChargeDetermine::ACss(std::vector &Iv, std::vector &Ov) { - int i,j; - float sum,ave; + int i,j,topIndex; + double sum,ave; int IvN = (int)Iv.size() ; ave=0.0; for(j=0;j 0) { // too much weight given to high charges this way. DJ Jan 07 2007 - Ov.push_back(sum/IvN) ; + Ov.push_back((float)(sum/IvN)) ; //Ov.push_back(sum/j) ; } else @@ -64,7 +65,8 @@ namespace Engine short AutoCorrelationChargeDetermine::GetChargeState(PeakProcessing::Peak &pk, PeakProcessing::PeakData &peak_data, bool debug) { - clock_t auto_start_t = clock() ; + // Disable timing (MEM 2013) + // clock_t auto_start_t = clock() ; debug = false ; double minMZ, maxMZ ; @@ -102,7 +104,8 @@ namespace Engine mvect_Y.push_back(intensity) ; } - clock_t start_t = clock() ; + // Disable timing (MEM 2013) + // clock_t start_t = clock() ; mobj_interpolation.Spline(mvect_X, mvect_Y, 0, 0) ; minMZ = mvect_X[0]; @@ -118,8 +121,9 @@ namespace Engine fVal = mobj_interpolation.Splint(mvect_X, mvect_Y, xVal); mvect_Iv.push_back(fVal) ; } - clock_t stop_t = clock() ; - mint_spline_time += (stop_t - start_t) ; + // Disable timing (MEM 2013) + // clock_t stop_t = clock() ; + // mint_spline_time += (stop_t - start_t) ; if (debug) { @@ -132,7 +136,9 @@ namespace Engine } } - start_t = clock() ; + // Disable timing (MEM 2013) + // start_t = clock() ; + ACss(mvect_Iv, mvect_autocorrelation_scores); if (debug) { @@ -145,8 +151,9 @@ namespace Engine } } - stop_t = clock() ; - mint_autocorrelation_time += (stop_t - start_t) ; + // Disable timing (MEM 2013) + // stop_t = clock() ; + // mint_autocorrelation_time += (stop_t - start_t) ; int j=0; int minN ; @@ -209,7 +216,8 @@ namespace Engine found = peak_data.GetPeakFromAllOriginalIntensity(peakA - FWHM, peakA + FWHM, iso_peak) ; if (found) { - mint_total_cs_time += (clock() - auto_start_t) ; + // Disable timing (MEM 2013) + // mint_total_cs_time += (clock() - auto_start_t) ; return tmp ; } } @@ -219,14 +227,16 @@ namespace Engine found = peak_data.GetPeakFromAllOriginalIntensity(peakA - FWHM, peakA + FWHM, iso_peak) ; if (found && iso_peak.mdbl_mz * tmp < 3000) { - mint_total_cs_time += (clock() - auto_start_t) ; + // Disable timing (MEM 2013) + // mint_total_cs_time += (clock() - auto_start_t) ; return tmp ; } } } } - mint_total_cs_time += (clock() - auto_start_t) ; + // Disable timing (MEM 2013) + // mint_total_cs_time += (clock() - auto_start_t) ; return returnCSVal; } diff --git a/DeconEngine.sdf.REMOVED.git-id b/DeconEngine.sdf.REMOVED.git-id index 5f89a07..5afa581 100644 --- a/DeconEngine.sdf.REMOVED.git-id +++ b/DeconEngine.sdf.REMOVED.git-id @@ -1 +1 @@ -1cbead774513b91da7785109ff6d94f1a7c1bd3a \ No newline at end of file +c4ea9077030eabdeb273d15369f98081f813e204 \ No newline at end of file diff --git a/DeconEngine.sln b/DeconEngine.sln index 279f9c6..9ac6590 100644 --- a/DeconEngine.sln +++ b/DeconEngine.sln @@ -5,8 +5,6 @@ Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "DeconEngineV2", "DeconEngin EndProject Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "UnitTests", "UnitTests\UnitTests\UnitTests.csproj", "{0B6C729C-17D9-4960-BDC4-2BEB56FED18E}" EndProject -Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "ConsoleBasedTesting", "..\ConsoleBasedTesting\ConsoleBasedTesting.csproj", "{9E48169B-1AE5-442F-AC76-F0B543906886}" -EndProject Global GlobalSection(SolutionConfigurationPlatforms) = preSolution Debug|Any CPU = Debug|Any CPU @@ -35,29 +33,15 @@ Global {0B6C729C-17D9-4960-BDC4-2BEB56FED18E}.Debug|Any CPU.ActiveCfg = Debug|x86 {0B6C729C-17D9-4960-BDC4-2BEB56FED18E}.Debug|Any CPU.Build.0 = Debug|x86 {0B6C729C-17D9-4960-BDC4-2BEB56FED18E}.Debug|Mixed Platforms.ActiveCfg = Debug|x86 - {0B6C729C-17D9-4960-BDC4-2BEB56FED18E}.Debug|Mixed Platforms.Build.0 = Debug|x86 {0B6C729C-17D9-4960-BDC4-2BEB56FED18E}.Debug|Win32.ActiveCfg = Debug|Any CPU {0B6C729C-17D9-4960-BDC4-2BEB56FED18E}.Debug|x86.ActiveCfg = Debug|x86 {0B6C729C-17D9-4960-BDC4-2BEB56FED18E}.Debug|x86.Build.0 = Debug|x86 {0B6C729C-17D9-4960-BDC4-2BEB56FED18E}.Release|Any CPU.ActiveCfg = Release|Any CPU {0B6C729C-17D9-4960-BDC4-2BEB56FED18E}.Release|Any CPU.Build.0 = Release|Any CPU {0B6C729C-17D9-4960-BDC4-2BEB56FED18E}.Release|Mixed Platforms.ActiveCfg = Release|Any CPU - {0B6C729C-17D9-4960-BDC4-2BEB56FED18E}.Release|Mixed Platforms.Build.0 = Release|Any CPU {0B6C729C-17D9-4960-BDC4-2BEB56FED18E}.Release|Win32.ActiveCfg = Release|Any CPU {0B6C729C-17D9-4960-BDC4-2BEB56FED18E}.Release|x86.ActiveCfg = Release|x86 {0B6C729C-17D9-4960-BDC4-2BEB56FED18E}.Release|x86.Build.0 = Release|x86 - {9E48169B-1AE5-442F-AC76-F0B543906886}.Debug|Any CPU.ActiveCfg = Debug|x86 - {9E48169B-1AE5-442F-AC76-F0B543906886}.Debug|Mixed Platforms.ActiveCfg = Debug|x86 - {9E48169B-1AE5-442F-AC76-F0B543906886}.Debug|Mixed Platforms.Build.0 = Debug|x86 - {9E48169B-1AE5-442F-AC76-F0B543906886}.Debug|Win32.ActiveCfg = Debug|x86 - {9E48169B-1AE5-442F-AC76-F0B543906886}.Debug|x86.ActiveCfg = Debug|x86 - {9E48169B-1AE5-442F-AC76-F0B543906886}.Debug|x86.Build.0 = Debug|x86 - {9E48169B-1AE5-442F-AC76-F0B543906886}.Release|Any CPU.ActiveCfg = Release|x86 - {9E48169B-1AE5-442F-AC76-F0B543906886}.Release|Mixed Platforms.ActiveCfg = Release|x86 - {9E48169B-1AE5-442F-AC76-F0B543906886}.Release|Mixed Platforms.Build.0 = Release|x86 - {9E48169B-1AE5-442F-AC76-F0B543906886}.Release|Win32.ActiveCfg = Release|x86 - {9E48169B-1AE5-442F-AC76-F0B543906886}.Release|x86.ActiveCfg = Release|x86 - {9E48169B-1AE5-442F-AC76-F0B543906886}.Release|x86.Build.0 = Release|x86 EndGlobalSection GlobalSection(SolutionProperties) = preSolution HideSolutionNode = FALSE diff --git a/DeconEngine.vcxproj b/DeconEngine.vcxproj index c815577..d8fc2eb 100644 --- a/DeconEngine.vcxproj +++ b/DeconEngine.vcxproj @@ -68,7 +68,7 @@ mscoree.lib;msvcrtd.lib;Ws2_32.lib;xerces-c_2.lib;msvcrt.lib;xerces-c_2D.lib;%(AdditionalDependencies) $(OutDir)$(ProjectName).dll - C:\xerces\xerces-c-windows_2000-msvc_60\lib;C:\xerces\xerces-c_2_8_0-x86-windows-vc_7_1\lib;%(AdditionalLibraryDirectories) + C:\xerces\xerces-c_2_8_0-x86-windows-vc_7_1\lib;C:\xerces\xerces-c-windows_2000-msvc_60\lib;%(AdditionalLibraryDirectories) __DllMainCRTStartup%4012;%(ForceSymbolReferences) true true @@ -79,7 +79,7 @@ - C:\xerces\xerces-c-windows_2000-msvc_60\include\;C:\PNL\LTE\Proteomics\xerces-c-windows_2000-msvc_60\include;%(AdditionalIncludeDirectories) + C:\xerces\xerces-c_2_8_0-x86-windows-vc_7_1\include\;C:\xerces\xerces-c-windows_2000-msvc_60\include\;%(AdditionalIncludeDirectories) WIN32;NDEBUG;MASSLYNX_4_INSTALLED;ANALYST_INSTALLED;XCALIBUR_INSTALLED;%(PreprocessorDefinitions) false MultiThreadedDLL @@ -93,7 +93,7 @@ mscoree.lib;msvcrt.lib;Ws2_32.lib;xerces-c_2.lib;%(AdditionalDependencies) $(OutDir)$(ProjectName).dll - C:\xerces\xerces-c-windows_2000-msvc_60\lib;C:\PNL\LTE\Proteomics\xerces-c-windows_2000-msvc_60\lib;C:\Projects\Decon2LS\DeconEngine\bin;%(AdditionalLibraryDirectories) + C:\xerces\xerces-c_2_8_0-x86-windows-vc_7_1\lib;C:\xerces\xerces-c-windows_2000-msvc_60\lib;%(AdditionalLibraryDirectories) __DllMainCRTStartup%4012;%(ForceSymbolReferences) true false diff --git a/HornTransform/AreaFit.cpp b/HornTransform/AreaFit.cpp index 4e069fc..7a712ea 100644 --- a/HornTransform/AreaFit.cpp +++ b/HornTransform/AreaFit.cpp @@ -30,7 +30,8 @@ namespace Engine bool debug) { - clock_t start_t = clock() ; + // Disable timing (MEM 2013) + // clock_t start_t = clock() ; int num_points = (int)mvect_distribution_mzs.size() ; if (num_points < 3) return 1 ; @@ -63,8 +64,9 @@ namespace Engine } } - clock_t stop_t = clock() ; - mint_fit_processing_time += (stop_t - start_t) ; + // Disable timing (MEM 2013) + // clock_t stop_t = clock() ; + // mint_fit_processing_time += (stop_t - start_t) ; return fit/(sum + 0.001) ; } @@ -73,7 +75,8 @@ namespace Engine double intensity_normalizer, double mz_delta, double min_intensity_for_score, bool debug ) { - clock_t start_t = clock() ; + // Disable timing (MEM 2013) + // clock_t start_t = clock() ; int num_points = (int)mvect_distribution_mzs.size() ; if (num_points < 3) return 1 ; @@ -95,8 +98,10 @@ namespace Engine sum += theoretical_intensity * theoretical_intensity ; } } - clock_t stop_t = clock() ; - mint_fit_processing_time += (stop_t - start_t) ; + + // Disable timing (MEM 2013) + // clock_t stop_t = clock() ; + // mint_fit_processing_time += (stop_t - start_t) ; return fit/(sum + 0.001) ; } diff --git a/HornTransform/ChiSqFit.cpp b/HornTransform/ChiSqFit.cpp index 7a1dc42..38cd2e7 100644 --- a/HornTransform/ChiSqFit.cpp +++ b/HornTransform/ChiSqFit.cpp @@ -26,7 +26,8 @@ namespace Engine double ChiSqFit::FitScore(PeakProcessing::PeakData &pk_data, short cs, PeakProcessing::Peak &pk, double mz_delta, double min_intensity_for_score, bool debug) { - clock_t start_t = clock() ; + // Disable timing (MEM 2013) + // clock_t start_t = clock() ; int num_points = (int)mvect_distribution_mzs.size() ; if (num_points < 3) return 1 ; @@ -50,15 +51,17 @@ namespace Engine } } - clock_t stop_t = clock() ; - mint_fit_processing_time += (stop_t - start_t) ; + // Disable timing (MEM 2013) + // clock_t stop_t = clock() ; + // mint_fit_processing_time += (stop_t - start_t) ; return fit/(sum + 0.001) ; } double ChiSqFit::FitScore(PeakProcessing::PeakData &pk_data, short cs, double intensity_normalizer, double mz_delta, double min_intensity_for_score, bool debug) { - clock_t start_t = clock() ; + // Disable timing (MEM 2013) + // clock_t start_t = clock() ; int num_points = (int)mvect_distribution_mzs.size() ; if (num_points < 3) @@ -82,8 +85,9 @@ namespace Engine sum += theoretical_intensity * observed_intensity ; } } - clock_t stop_t = clock() ; - mint_fit_processing_time += (stop_t - start_t) ; + // Disable timing (MEM 2013) + // clock_t stop_t = clock() ; + // mint_fit_processing_time += (stop_t - start_t) ; return fit/(sum + 0.001) ; } diff --git a/HornTransform/IsotopeFit.cpp b/HornTransform/IsotopeFit.cpp index 9cfca0d..b93f38f 100644 --- a/HornTransform/IsotopeFit.cpp +++ b/HornTransform/IsotopeFit.cpp @@ -54,11 +54,13 @@ namespace Engine bool IsotopeFit::FindPeak(double min_mz, double max_mz, double &mz_value, double &intensity, bool debug) { - clock_t start_t = clock() ; + // Disable timing (MEM 2013) + // clock_t start_t = clock() ; if (!mbln_last_value_was_cached) { bool found = mobj_isotope_dist.FindPeak(min_mz, max_mz, mz_value, intensity) ; - mint_find_peak_calc += (clock() - start_t) ; + // Disable timing (MEM 2013) + // mint_find_peak_calc += (clock() - start_t) ; return found ; } @@ -106,7 +108,8 @@ namespace Engine } if (max_index == -1) { - mint_find_peak_cached += (clock() - start_t) ; + // Disable timing (MEM 2013) + // mint_find_peak_cached += (clock() - start_t) ; return false ; } @@ -141,13 +144,16 @@ namespace Engine mz_value = X2 ; intensity = mvect_distribution_intensities[max_index] ; } - mint_find_peak_cached += (clock() - start_t) ; + // Disable timing (MEM 2013) + // mint_find_peak_cached += (clock() - start_t) ; return true ; } mz_value = X2 ; intensity = mvect_distribution_intensities[max_index] ; - mint_find_peak_cached += (clock() - start_t) ; + + // Disable timing (MEM 2013) + // mint_find_peak_cached += (clock() - start_t) ; return true ; } @@ -687,9 +693,9 @@ namespace Engine { double current_mz = most_abundant_mass/charge + mdbl_cc_mass ; double FWHM = current_mz / resolution ; - clock_t start_t = clock() ; - - + + // Disable timing (MEM 2013) + // clock_t start_t = clock() ; //first check the UseCaching option; then check if it is in the cache or not. //if it is in the cache, the data is retrieved and the method returns true @@ -733,8 +739,10 @@ namespace Engine mobj_isotope_dist.mdbl_most_intense_mw = mobj_mercury_cache.mdbl_most_intense_mw ; mobj_isotope_dist.mdbl_max_peak_mz = mobj_mercury_cache.mdbl_most_intense_mw/charge + mdbl_cc_mass - ELECTRON_MASS ; } - clock_t stop_t = clock() ; - mint_distribution_processing_time += (stop_t - start_t) ; + + // Disable timing (MEM 2013) + // clock_t stop_t = clock() ; + // mint_distribution_processing_time += (stop_t - start_t) ; return ; } diff --git a/HornTransform/MassTransform.cpp b/HornTransform/MassTransform.cpp index d80f40d..7108dcc 100644 --- a/HornTransform/MassTransform.cpp +++ b/HornTransform/MassTransform.cpp @@ -214,8 +214,9 @@ namespace Engine } } double best_fit = 0 ; - clock_t start_t = clock() ; - + + // Disable timing (MEM 2013) + // clock_t start_t = clock() ; PeakProcessing::Peak pkCharge1 = pk ; @@ -255,7 +256,8 @@ namespace Engine } } - mint_get_fit_score_time += (clock() - start_t) ; + // Disable timing (MEM 2013) + // mint_get_fit_score_time += (clock() - start_t) ; if (best_fit > mdbl_max_fit) // check if fit is good enough return false ; @@ -273,11 +275,14 @@ namespace Engine PeakProcessing::Peak m3_peak ; double mono_pls_two_mz = record.mdbl_mono_mw / record.mshort_cs + 2.0/record.mshort_cs + mdbl_cc_mass ; - start_t = clock() ; + // Disable timing (MEM 2013) + // start_t = clock() ; pk_data.FindPeak(mono_mz - pk.mdbl_FWHM, mono_mz + pk.mdbl_FWHM, mono_peak) ; pk_data.FindPeak(mono_pls_two_mz - pk.mdbl_FWHM, mono_pls_two_mz + pk.mdbl_FWHM, m3_peak) ; - mint_remaining_time += (clock() - start_t) ; + + // Disable timing (MEM 2013) + // mint_remaining_time += (clock() - start_t) ; record.mint_mono_intensity = (int) mono_peak.mdbl_intensity ; record.mint_iplus2_intensity = (int) m3_peak.mdbl_intensity ; diff --git a/HornTransform/PeakFit.cpp b/HornTransform/PeakFit.cpp index 4aab0c1..b9e2096 100644 --- a/HornTransform/PeakFit.cpp +++ b/HornTransform/PeakFit.cpp @@ -27,7 +27,8 @@ namespace Engine double PeakFit::FitScore(PeakProcessing::PeakData &pk_data, short cs, PeakProcessing::Peak &pk, double mz_delta, double min_intensity_for_score, bool debug) { - clock_t start_t = clock() ; + // Disable timing (MEM 2013) + // clock_t start_t = clock() ; int num_points = (int)mvect_distribution_mzs.size() ; if (num_points < 3) return 1 ; @@ -79,8 +80,10 @@ namespace Engine diff = theoretical_intensity - last_yval ; last_yval = theoretical_intensity ; } - clock_t stop_t = clock() ; - mint_fit_processing_time += (stop_t - start_t) ; + + // Disable timing (MEM 2013) + // clock_t stop_t = clock() ; + // mint_fit_processing_time += (stop_t - start_t) ; return fit/(sum + 0.001) ; } @@ -90,7 +93,9 @@ namespace Engine { throw "Don't Ever come into this FitScore overload in PeakFit" ; - clock_t start_t = clock() ; + + // Disable timing (MEM 2013) + // clock_t start_t = clock() ; int num_points = (int)mvect_distribution_mzs.size() ; if (num_points < 3) return 1 ; @@ -129,8 +134,9 @@ namespace Engine last_yval = theoretical_intensity ; } - clock_t stop_t = clock() ; - mint_fit_processing_time += (stop_t - start_t) ; + // Disable timing (MEM 2013) + // clock_t stop_t = clock() ; + // mint_fit_processing_time += (stop_t - start_t) ; return fit/(sum + 0.001) ; } diff --git a/clsProcRunner.cpp b/clsProcRunner.cpp index 672c6c5..59f33c0 100644 --- a/clsProcRunner.cpp +++ b/clsProcRunner.cpp @@ -218,7 +218,8 @@ namespace DeconToolsV2 for(int scan_num = min_scan ; scan_num <= max_scan && scan_num != -1 ; scan_num = raw_data->GetNextScanNum(scan_num)) { - clock_t start_time = clock() ; + // Disable timing (MEM 2013) + // clock_t start_time = clock() ; peak_processor->Clear() ; original_peak_processor->Clear() ; mint_current_scan = scan_num ; @@ -229,7 +230,8 @@ namespace DeconToolsV2 temp_vect_mzs.clear() ; temp_vect_intensities.clear() ; - clock_t current_time = clock() ; + // Disable timing (MEM 2013) + // clock_t current_time = clock() ; //Check if it needs to be processed if (raw_data->IsMSScan(scan_num)) @@ -312,7 +314,8 @@ namespace DeconToolsV2 raw_data->GetSummedSpectra(&vect_mzs, &vect_intensities, scan_num, scan_range) ; } - raw_data_read_time += (clock() - current_time) ; + // Disable timing (MEM 2013) + // raw_data_read_time += (clock() - current_time) ; scan_time = raw_data->GetScanTime(scan_num) ; //if (file_type == DeconToolsV2::Readers::PNNL_UIMF) @@ -353,12 +356,19 @@ namespace DeconToolsV2 double minMZ = vect_mzs[0] ; double maxMZ = vect_mzs[(int)vect_mzs.size()-1] ; - current_time = clock() ; + // Disable timing (MEM 2013) + // current_time = clock() ; double thres = DeconEngine::Utils::GetAverage(vect_intensities, FLT_MAX) ; double background_intensity = DeconEngine::Utils::GetAverage(vect_intensities, (float)(5*thres)) ; - average_time += clock() - current_time ; + + // Disable timing (MEM 2013) + // average_time += clock() - current_time ; + double bpi = 0, bp_mz = 0 ; - current_time = clock() ; + + // Disable timing (MEM 2013) + // current_time = clock() ; + double tic_intensity = 0 ; if (mobj_transform_parameters->get_UseMZRange()) { @@ -372,38 +382,55 @@ namespace DeconToolsV2 tic_intensity = DeconEngine::Utils::GetTIC(400.0, 2000.0, vect_mzs, vect_intensities, (float)(background_intensity * peak_parameters->get_PeakBackgroundRatio()), bpi, bp_mz) ; } - tic_time += clock() - current_time ; + + // Disable timing (MEM 2013) + // tic_time += clock() - current_time ; peak_processor->SetPeakIntensityThreshold(background_intensity * peak_parameters->get_PeakBackgroundRatio()) ; int numPeaks = 0 ; if (mobj_transform_parameters->get_UseMZRange()) { - current_time = clock() ; + // Disable timing (MEM 2013) + // current_time = clock() ; numPeaks = peak_processor->DiscoverPeaks(&vect_mzs, &vect_intensities, mobj_transform_parameters->get_MinMZ(), mobj_transform_parameters->get_MaxMZ()) ; - peak_discover_time += clock() - current_time ; + + // Disable timing (MEM 2013) + // peak_discover_time += clock() - current_time ; } else { - current_time = clock() ; + // Disable timing (MEM 2013) + // current_time = clock() ; + numPeaks = peak_processor->DiscoverPeaks(&vect_mzs, &vect_intensities) ; - peak_discover_time += clock() - current_time ; + + // Disable timing (MEM 2013) + // peak_discover_time += clock() - current_time ; } if (save_peaks) { - current_time = clock() ; + // Disable timing (MEM 2013) + // current_time = clock() ; lcms_results->AddPeaksForScan(scan_num, peak_processor->mobj_peak_data->mvect_peak_tops) ; - peak_save_time += clock() - current_time ; + // Disable timing (MEM 2013) + // peak_save_time += clock() - current_time ; } - preprocessing_time += (clock() - current_time) ; + // Disable timing (MEM 2013) + // preprocessing_time += (clock() - current_time) ; int numDeisotoped = 0 ; - preprocessing_time += clock() - start_time ; + + // Disable timing (MEM 2013) + // preprocessing_time += clock() - start_time ; if (file_type != DeconToolsV2::Readers::PNNL_UIMF && scan_num % 20 == 0) { - clock_t current_t = clock() ; - int all = current_t - start_t ; + // Disable timing (MEM 2013) + // clock_t current_t = clock() ; + // int all = current_t - start_t ; + + /* Console::WriteLine(System::String::Concat( S" Raw Reading Time = ", Convert::ToString(raw_data_read_time), S" Average Time = ", Convert::ToString(average_time), @@ -413,6 +440,7 @@ namespace DeconToolsV2 S" PreProcessing Time = ", Convert::ToString(preprocessing_time), S" preprocess-read= ", Convert::ToString(preprocessing_time-raw_data_read_time) )) ; + */ } @@ -443,12 +471,16 @@ namespace DeconToolsV2 break ; bool found_transform = false ; - current_time = clock() ; + + // Disable timing (MEM 2013) + // current_time = clock() ; try { found_transform = mass_transform->FindTransform(*peak_processor->mobj_peak_data, currentPeak, transformRecord, background_intensity) ; - transform_time += (clock() - current_time) ; + + // Disable timing (MEM 2013) + // transform_time += (clock() - current_time) ; // AM: if summing over a window, reinsert the original intensity // [gord] why? if(found_transform && transformRecord.mshort_cs <= transform_parameters->get_MaxCharge() @@ -523,10 +555,13 @@ namespace DeconToolsV2 { int iso_time=0, spline_time=0, ac_time=0, fit_time = 0, cs_time =0, get_fit_score_time = 0, remainder_time = 0, find_peak_calc = 0, find_peak_cached = 0 ; + clock_t current_t = clock() ; int all = current_t - start_t ; + mass_transform->GetProcessingTimes(cs_time, ac_time, spline_time, iso_time, fit_time, remainder_time, get_fit_score_time, find_peak_calc, find_peak_cached) ; + Console::WriteLine(System::String::Concat(S"Scan # =", Convert::ToString(scan_num), S" CS= ", Convert::ToString(cs_time), S" Isotope= ", Convert::ToString(iso_time),