fix backwards support of retired parameter 'peptide_mass_tolerance' i…

…n issue 60
UWPR · Jul 2, 2024 · 23a3901 · 23a3901
1 parent d7882a2
commit 23a3901
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Showing 2 changed files with 5 additions and 6 deletions.
diff --git a/CometSearch/CometFragmentIndex.cpp b/CometSearch/CometFragmentIndex.cpp
@@ -284,7 +284,7 @@ void CometFragmentIndex::AddFragmentsThreadProc(int iWhichThread,
    // each thread will loop through a subset of the g_vRawPeptides
    for (size_t iWhichPeptide = iWhichThread; iWhichPeptide < g_vRawPeptides.size(); iWhichPeptide += iNumIndexingThreads)
    {
-      // AddFragments(iWhichPeptide, modNumIdx) for unmodified peptide
+      // AddFragments for unmodified peptide
       // FIX: if require variable mod is set, this would not be called here
       AddFragments(g_vRawPeptides, iWhichThread, iWhichPeptide, -1, -1, -1, bCountOnly);
 

diff --git a/CometSearch/CometSearchManager.cpp b/CometSearch/CometSearchManager.cpp
@@ -736,12 +736,11 @@ bool CometSearchManager::InitializeStaticParams()
    GetParamValue("peptide_mass_tolerance", g_staticParams.tolerances.dInputTolerancePlus);
    g_staticParams.tolerances.dInputToleranceMinus = -1.0 * g_staticParams.tolerances.dInputTolerancePlus;
 
-   GetParamValue("peptide_mass_tolerance_upper", g_staticParams.tolerances.dInputToleranceMinus);
+   if (GetParamValue("peptide_mass_tolerance_upper", g_staticParams.tolerances.dInputToleranceMinus))
+      g_staticParams.tolerances.dInputToleranceMinus *= -1.0;
 
-   GetParamValue("peptide_mass_tolerance_lower", g_staticParams.tolerances.dInputTolerancePlus);
-
-   g_staticParams.tolerances.dInputToleranceMinus *= -1.0;  // hack to address reversing logic in how these were applieed
-   g_staticParams.tolerances.dInputTolerancePlus *= -1.0;
+   if (GetParamValue("peptide_mass_tolerance_lower", g_staticParams.tolerances.dInputTolerancePlus))
+      g_staticParams.tolerances.dInputTolerancePlus *= -1.0;
 
    GetParamValue("precursor_tolerance_type", g_staticParams.tolerances.iMassToleranceType);
    if ((g_staticParams.tolerances.iMassToleranceType < 0) || (g_staticParams.tolerances.iMassToleranceType > 1))