Use NUM_ION_SERIES in place of MAX_FRAGMENT_IONS_TYPE. Discovered tha…

…t the latter was set too large causing segfaults in Windows searches.
UWPR · May 31, 2024 · f00df0c · f00df0c
1 parent e658123
commit f00df0c
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Showing 4 changed files with 8 additions and 9 deletions.
diff --git a/CometSearch/CometDataInternal.h b/CometSearch/CometDataInternal.h
@@ -30,7 +30,6 @@ class CometSearchManager;
 #define MIN_PEPTIDE_LEN             1        // min # of AA for a petpide
 #define MAX_PEPTIDE_LEN             51       // max # of AA for a peptide; one more than actual # to account for terminating char
 #define MAX_PEPTIDE_LEN_P2          53       // max # of AA for a peptide plus 2 for N/C-term
-#define MAX_FRAGMENT_IONS_TYPE      9        // allowed fragment ions (aka a/b/c/x/y/z) ; check why this is 9!
 
 #define FRAGINDEX_MIN_IONS_SCORE    3        // min # of matched ions for peptide to register for E-value xcorr histogram
 #define FRAGINDEX_MIN_IONS_REPORT   3        // min # of matched ions for peptide to be reported

diff --git a/CometSearch/CometFragmentIndex.h b/CometSearch/CometFragmentIndex.h
@@ -58,8 +58,8 @@ class CometFragmentIndex
    static bool CompareByMass(const DBIndex &lhs,
                              const DBIndex &rhs);
 
-   unsigned int       _uiBinnedIonMasses[MAX_FRAGMENT_CHARGE+1][MAX_FRAGMENT_IONS_TYPE][MAX_PEPTIDE_LEN][BIN_MOD_COUNT];
-   unsigned int       _uiBinnedIonMassesDecoy[MAX_FRAGMENT_CHARGE+1][MAX_FRAGMENT_IONS_TYPE][MAX_PEPTIDE_LEN][BIN_MOD_COUNT];
+   unsigned int       _uiBinnedIonMasses[MAX_FRAGMENT_CHARGE+1][NUM_ION_SERIES][MAX_PEPTIDE_LEN][BIN_MOD_COUNT];
+   unsigned int       _uiBinnedIonMassesDecoy[MAX_FRAGMENT_CHARGE+1][NUM_ION_SERIES][MAX_PEPTIDE_LEN][BIN_MOD_COUNT];
    unsigned int       _uiBinnedPrecursorNL[MAX_PRECURSOR_NL_SIZE][MAX_PRECURSOR_CHARGE];
    unsigned int       _uiBinnedPrecursorNLDecoy[MAX_PRECURSOR_NL_SIZE][MAX_PRECURSOR_CHARGE];
 

diff --git a/CometSearch/CometSearch.cpp b/CometSearch/CometSearch.cpp
@@ -1200,7 +1200,7 @@ void CometSearch::SearchFragmentIndex(size_t iWhichQuery,
    unsigned int uiFragmentMass;
    int iArraySize = (int)((g_staticParams.options.dPeptideMassHigh + 100.0) * g_staticParams.dInverseBinWidth);
 
-   unsigned int uiBinnedIonMasses[MAX_FRAGMENT_CHARGE + 1][MAX_FRAGMENT_IONS_TYPE][MAX_PEPTIDE_LEN][BIN_MOD_COUNT];
+   unsigned int uiBinnedIonMasses[MAX_FRAGMENT_CHARGE + 1][NUM_ION_SERIES][MAX_PEPTIDE_LEN][BIN_MOD_COUNT];
    unsigned int uiBinnedPrecursorNL[MAX_PRECURSOR_NL_SIZE][MAX_PRECURSOR_CHARGE];
 
    bool* pbDuplFragment = new bool[iArraySize];
@@ -3622,7 +3622,7 @@ void CometSearch::XcorrScore(char *szProteinSeq,
    int iLenPeptideMinus1 = iLenPeptide - 1;
 
    // Pointer to either regular or decoy uiBinnedIonMasses[][][][][].
-   unsigned int (*p_uiBinnedIonMasses)[MAX_FRAGMENT_CHARGE+1][MAX_FRAGMENT_IONS_TYPE][MAX_PEPTIDE_LEN][BIN_MOD_COUNT];
+   unsigned int (*p_uiBinnedIonMasses)[MAX_FRAGMENT_CHARGE+1][NUM_ION_SERIES][MAX_PEPTIDE_LEN][BIN_MOD_COUNT];
    unsigned int (*p_uiBinnedPrecursorNL)[MAX_PRECURSOR_NL_SIZE][MAX_PRECURSOR_CHARGE];
 
    // Point to right set of arrays depending on target or decoy search.
@@ -3804,7 +3804,7 @@ void CometSearch::XcorrScoreI(char *szProteinSeq,
                              int iLenPeptide,
                              int *piVarModSites,
                              struct sDBEntry *dbe,
-                             unsigned int uiBinnedIonMasses[MAX_FRAGMENT_CHARGE+1][MAX_FRAGMENT_IONS_TYPE][MAX_PEPTIDE_LEN][BIN_MOD_COUNT],
+                             unsigned int uiBinnedIonMasses[MAX_FRAGMENT_CHARGE+1][NUM_ION_SERIES][MAX_PEPTIDE_LEN][BIN_MOD_COUNT],
                              unsigned int uiBinnedPrecursorNL[MAX_PRECURSOR_NL_SIZE][MAX_PRECURSOR_CHARGE],
                              int iNumMatchedFragmentIons)
 {

diff --git a/CometSearch/CometSearch.h b/CometSearch/CometSearch.h
@@ -138,7 +138,7 @@ class CometSearch
                    int iLenPeptide,
                    int *piVarModSites,
                    struct sDBEntry *dbe,
-                   unsigned int uiBinnedIonMasses[MAX_FRAGMENT_CHARGE+1][MAX_FRAGMENT_IONS_TYPE][MAX_PEPTIDE_LEN][BIN_MOD_COUNT],
+                   unsigned int uiBinnedIonMasses[MAX_FRAGMENT_CHARGE+1][NUM_ION_SERIES][MAX_PEPTIDE_LEN][BIN_MOD_COUNT],
                    unsigned int uiBinnedPrecursorNL[MAX_PRECURSOR_NL_SIZE][MAX_PRECURSOR_CHARGE],
                    int iNumMatchedFragmentIons);
 
@@ -305,8 +305,8 @@ class CometSearch
    VarModInfo         _varModInfo;
    ProteinInfo        _proteinInfo;
 
-   unsigned int       _uiBinnedIonMasses[MAX_FRAGMENT_CHARGE+1][MAX_FRAGMENT_IONS_TYPE][MAX_PEPTIDE_LEN][BIN_MOD_COUNT];
-   unsigned int       _uiBinnedIonMassesDecoy[MAX_FRAGMENT_CHARGE+1][MAX_FRAGMENT_IONS_TYPE][MAX_PEPTIDE_LEN][BIN_MOD_COUNT];
+   unsigned int       _uiBinnedIonMasses[MAX_FRAGMENT_CHARGE+1][NUM_ION_SERIES][MAX_PEPTIDE_LEN][BIN_MOD_COUNT];
+   unsigned int       _uiBinnedIonMassesDecoy[MAX_FRAGMENT_CHARGE+1][NUM_ION_SERIES][MAX_PEPTIDE_LEN][BIN_MOD_COUNT];
    unsigned int       _uiBinnedPrecursorNL[MAX_PRECURSOR_NL_SIZE][MAX_PRECURSOR_CHARGE];
    unsigned int       _uiBinnedPrecursorNLDecoy[MAX_PRECURSOR_NL_SIZE][MAX_PRECURSOR_CHARGE];