Add a new field that tracks the abundance of a peak as a double

When converting the intensity of a peak to a 32-bit integer, now preventing 32-bit overflow errors by reporting 2147483648 instead
PNNL-Comp-Mass-Spec · Jul 14, 2015 · fa5c4a1 · fa5c4a1
1 parent b2df3a2
commit fa5c4a1
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Showing 15 changed files with 27 additions and 12 deletions.
diff --git a/HornTransform/IsotopeFitRecord.cpp b/HornTransform/IsotopeFitRecord.cpp
@@ -8,6 +8,7 @@ namespace Engine
 		IsotopeFitRecord::IsotopeFitRecord()
 		{
 			mint_abundance = 0 ;
+			mdbl_abundance = 0;
 			mshort_cs = -1 ;
 			mdbl_mz = 0 ;
 			mdbl_fit = 1 ;

diff --git a/HornTransform/IsotopeFitRecord.h b/HornTransform/IsotopeFitRecord.h
@@ -17,8 +17,10 @@ namespace Engine
 			int mint_scan_num ; 
 			//! charge state 
 			short mshort_cs ;
-			//! intensity of feature.
+			//! intensity of feature; maximum value that can be represented is 2147483648
 			int mint_abundance ;
+			//! intensity of feature (as a double)
+			double mdbl_abundance;
 			//! m/z value of most abundant peak in the feature.
 			double mdbl_mz ;
 			//! fit value .

diff --git a/HornTransform/MassTransform.cpp b/HornTransform/MassTransform.cpp
@@ -271,7 +271,18 @@ namespace Engine
 			if (mbln_debug)
 				std::cerr<<"\tBack with fit = "<<record.mdbl_fit<<std::endl ; 
 
-			record.mint_abundance = (int) pk.mdbl_intensity ; 
+			// Abundance has always been reported as a 32-bit integer
+			// Added field mdbl_abundance in 2015 to allow tracking it as a double
+			// For backwards compatibility, if the peak intensity is too large for a 32-bit integer, mint_abundance will be 2147483648
+
+			if (pk.mdbl_intensity < 2147483648)
+				record.mint_abundance = (int)pk.mdbl_intensity; 
+			else
+				record.mint_abundance = 2147483648;
+
+			// Applications using this DLL should use mdbl_abundance instead of mint_abundance
+			record.mdbl_abundance = pk.mdbl_intensity;
+
 			record.mshort_cs = chargeState ; 
 
 			PeakProcessing::Peak mono_peak ; 

diff --git a/Library/xerces-c_2_7.dll b/Library/xerces-c_2_7.dll
diff --git a/Library/xerces-c_2_7D.dll b/Library/xerces-c_2_7D.dll
diff --git a/Library/xerces-c_2_8.dll b/Library/xerces-c_2_8.dll
diff --git a/Library/xerces-c_2_8D.dll b/Library/xerces-c_2_8D.dll
diff --git a/Readme_DeconTools_and_DeconEngine_Versions.txt b/Readme_DeconTools_and_DeconEngine_Versions.txt
@@ -13,5 +13,5 @@ C# DeconTools (with ThrashV2)
 	Port of DeconEngine to C#
 	See file DeconTools.Backend\ProcessingTasks\Deconvoluters\HornDeconvolutor\ThrashDeconvolutorV2.cs
 	Used by DeconConsole if parameter file has:
-		<UseThrashV1>true</UseThrashV1>
+		<DeconvolutionType>ThrashV2</DeconvolutionType>
 
diff --git a/UnitTests/UnitTests/UnitTests.csproj b/UnitTests/UnitTests/UnitTests.csproj
@@ -71,12 +71,8 @@
     <Compile Include="Reader_Tests\MZXMLReaderTests.cs" />
   </ItemGroup>
   <ItemGroup>
-    <Content Include="xerces-c_2_7.dll">
-      <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
-    </Content>
-    <Content Include="xerces-c_2_7D.dll">
-      <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
-    </Content>
+    <Content Include="xerces-c_2_8.dll" />
+    <Content Include="xerces-c_2_8D.dll" />
   </ItemGroup>
   <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
   <!-- To modify your build process, add your task inside one of the targets below and uncomment it. 

diff --git a/UnitTests/UnitTests/xerces-c_2_7.dll b/UnitTests/UnitTests/xerces-c_2_7.dll
diff --git a/UnitTests/UnitTests/xerces-c_2_7D.dll b/UnitTests/UnitTests/xerces-c_2_7D.dll
diff --git a/UnitTests/UnitTests/xerces-c_2_8.dll b/UnitTests/UnitTests/xerces-c_2_8.dll
diff --git a/UnitTests/UnitTests/xerces-c_2_8D.dll b/UnitTests/UnitTests/xerces-c_2_8D.dll
diff --git a/clsHornTransformResults.h b/clsHornTransformResults.h
@@ -23,8 +23,10 @@ namespace DeconToolsV2
 			int mint_scan_num ; 
 			//! charge state 
 			short mshort_cs ;
-			//! intensity of feature.
-			int mint_abundance ;
+			//! intensity of feature; maximum value that can be represented is 2147483648
+			int mint_abundance;
+			//! intensity of feature (as a double)
+			double mdbl_abundance;
 			//! m/z value of most abundant peak in the feature.
 			double mdbl_mz ;
 			//! fit value .
@@ -64,6 +66,7 @@ namespace DeconToolsV2
 				result->mint_scan_num = this->mint_scan_num ; 
 				result->mshort_cs = this->mshort_cs ;
 				result->mint_abundance = this->mint_abundance ;
+				result->mdbl_abundance = this->mdbl_abundance;
 				result->mdbl_mz = this->mdbl_mz ;
 				result->mdbl_fit = this->mdbl_fit ;
 				result->mint_fit_count_basis = this->mint_fit_count_basis ;
@@ -90,6 +93,7 @@ namespace DeconToolsV2
 				mint_scan_num = fitRecord.mint_scan_num ; 
 				mshort_cs = fitRecord.mshort_cs ;
 				mint_abundance = fitRecord.mint_abundance ;
+				mdbl_abundance = fitRecord.mdbl_abundance;
 				mdbl_mz = fitRecord.mdbl_mz ;
 				mdbl_fit = fitRecord.mdbl_fit ;
 				mint_fit_count_basis = fitRecord.mint_fit_count_basis ;

diff --git a/clsProcRunner.cpp b/clsProcRunner.cpp
@@ -482,7 +482,7 @@ namespace DeconToolsV2
 							// Disable timing (MEM 2013)
 							// transform_time += (clock() - current_time) ; 
 
-							// AM: if summing over a window, reinsert the original intensity     // [gord]  why?
+							// AM (anoop?): if summing over a window, reinsert the original intensity     // [gord]  why?
 							if(found_transform && transformRecord.mshort_cs <= transform_parameters->get_MaxCharge()
 								 && transform_parameters->get_SumSpectraAcrossScanRange())
 							{
@@ -493,6 +493,7 @@ namespace DeconToolsV2
  								if (originalPeak.mdbl_intensity > 0) 
 								{	
 									transformRecord.mint_abundance =  (int)originalPeak.mdbl_intensity ; 
+									transformRecord.mdbl_abundance = originalPeak.mdbl_intensity;
 									transformRecord.mdbl_fwhm = originalPeak.mdbl_FWHM   ;       // [gord] this might be the source of why FWHM is sometimes 0
 								}
 								else