missed a zero for xcorr rounding in standard (non FI) Comet in prevou…

…s commit; other useless cleanup that do nothing

CometSearch/CometFragmentIndex.cpp

@@ -229,7 +229,7 @@ void CometFragmentIndex::GenerateFragmentIndex(ThreadPool *tp)
 
    // sort list of peptides at each fragment bin by peptide mass
    for (int iWhichThread = 0; iWhichThread < iNumIndexingThreads; ++iWhichThread)
-      pFragmentIndexPool->doJob(std::bind(SortFragmentThreadProc, iWhichThread, iNumIndexingThreads, pFragmentIndexPool));
+      pFragmentIndexPool->doJob(std::bind(SortFragmentThreadProc, iWhichThread, pFragmentIndexPool));
 
    pFragmentIndexPool->wait_on_threads();
 
@@ -372,7 +372,6 @@ void CometFragmentIndex::AddFragmentsThreadProc(int iWhichThread,
 
 
 void CometFragmentIndex::SortFragmentThreadProc(int iWhichThread,
-                                                int iNumIndexingThreads,
                                                 ThreadPool *tp)
 {
    for (int iPrecursorBin = 0; iPrecursorBin < FRAGINDEX_PRECURSORBINS; ++iPrecursorBin)
@@ -1019,26 +1018,26 @@ bool CometFragmentIndex::ReadPlainPeptideIndex(void)
    comet_fileoffset_t clPermutationsFilePos;  // file position of permutations variables
 
    comet_fseek(fp, -clSizeCometFileOffset*3, SEEK_END);
-   fread(&clPeptidesFilePos, clSizeCometFileOffset, 1, fp);
-   fread(&clProteinsFilePos, clSizeCometFileOffset, 1, fp);
-   fread(&clPermutationsFilePos, clSizeCometFileOffset, 1, fp);
+   tTmp = fread(&clPeptidesFilePos, clSizeCometFileOffset, 1, fp);
+   tTmp = fread(&clProteinsFilePos, clSizeCometFileOffset, 1, fp);
+   tTmp = fread(&clPermutationsFilePos, clSizeCometFileOffset, 1, fp);
 
    comet_fseek(fp, clPeptidesFilePos, SEEK_SET);
 
    size_t tNumPeptides;
-   fread(&tNumPeptides, sizeof(size_t), 1, fp);  // read # of peptides
+   tTmp = fread(&tNumPeptides, sizeof(size_t), 1, fp);  // read # of peptides
 
    struct PlainPeptideIndex sTmp;
    int iLen;
    char szPeptide[MAX_PEPTIDE_LEN];
    for (size_t it = 0; it < tNumPeptides; ++it)
    {
-      fread(&iLen, sizeof(int), 1, fp);
-      fread(szPeptide, sizeof(char), iLen, fp);
+      tTmp = fread(&iLen, sizeof(int), 1, fp);
+      tTmp = fread(szPeptide, sizeof(char), iLen, fp);
       szPeptide[iLen] = '\0';
       sTmp.sPeptide = szPeptide;
-      fread(&(sTmp.dPepMass), sizeof(double), 1, fp);
-      fread(&(sTmp.lIndexProteinFilePosition), clSizeCometFileOffset, 1, fp);
+      tTmp = fread(&(sTmp.dPepMass), sizeof(double), 1, fp);
+      tTmp = fread(&(sTmp.lIndexProteinFilePosition), clSizeCometFileOffset, 1, fp);
 
       g_vRawPeptides.push_back(sTmp);
    }
@@ -1047,20 +1046,21 @@ bool CometFragmentIndex::ReadPlainPeptideIndex(void)
 
    // now read in: vector<vector<comet_fileoffset_t>> g_pvProteinsList
    size_t tSize;
-   fread(&tSize, clSizeCometFileOffset, 1, fp);
+   tTmp = fread(&tSize, clSizeCometFileOffset, 1, fp);
    vector<comet_fileoffset_t> vTmp;
 
    g_pvProteinsList.clear();
    g_pvProteinsList.reserve(tSize);
 
    for (size_t it = 0; it < tSize; ++it)
    {
-      fread(&tTmp, clSizeCometFileOffset, 1, fp);
+      size_t tNumProteinOffsets;
+      tTmp = fread(&tNumProteinOffsets, clSizeCometFileOffset, 1, fp);
 
       vTmp.clear();
-      for (size_t it2 = 0; it2 < tTmp; ++it2)
+      for (size_t it2 = 0; it2 < tNumProteinOffsets; ++it2)
       {
-         fread(&clTmp, clSizeCometFileOffset, 1, fp);
+         tTmp = fread(&clTmp, clSizeCometFileOffset, 1, fp);
          vTmp.push_back(clTmp);
       }
       g_pvProteinsList.push_back(vTmp);
@@ -1072,31 +1072,32 @@ bool CometFragmentIndex::ReadPlainPeptideIndex(void)
    unsigned long ulSizevRawPeptides;   // size of g_vRawPeptides
    unsigned long ulModNumSize;         // size of MOD_NUMBERS
 
-   fread(&ulSizeModSeqs, sizeof(unsigned long), 1, fp);
-   fread(&ulSizevRawPeptides, sizeof(unsigned long), 1, fp);
-   fread(&ulModNumSize, sizeof(unsigned long), 1, fp);
+   tTmp = fread(&ulSizeModSeqs, sizeof(unsigned long), 1, fp);
+   tTmp = fread(&ulSizevRawPeptides, sizeof(unsigned long), 1, fp);
+   tTmp = fread(&ulModNumSize, sizeof(unsigned long), 1, fp);
 
    MOD_SEQ_MOD_NUM_START = new int[ulSizeModSeqs];
    MOD_SEQ_MOD_NUM_CNT = new int[ulSizeModSeqs];
    PEPTIDE_MOD_SEQ_IDXS = new int[ulSizevRawPeptides];
 
-   fread(MOD_SEQ_MOD_NUM_START, sizeof(int), ulSizeModSeqs, fp);
-   fread(MOD_SEQ_MOD_NUM_CNT, sizeof(int), ulSizeModSeqs, fp);
-   fread(PEPTIDE_MOD_SEQ_IDXS, sizeof(int), ulSizevRawPeptides, fp);  //FIX
+   tTmp = fread(MOD_SEQ_MOD_NUM_START, sizeof(int), ulSizeModSeqs, fp);
+   tTmp = fread(MOD_SEQ_MOD_NUM_CNT, sizeof(int), ulSizeModSeqs, fp);
+   tTmp = fread(PEPTIDE_MOD_SEQ_IDXS, sizeof(int), ulSizevRawPeptides, fp);  //FIX
+
    int iTmp;
    char szTmp[MAX_PEPTIDE_LEN];
    for (unsigned long i = 0; i < ulSizeModSeqs; ++i)
    {
-      fread(&iTmp, sizeof(int), 1, fp); // read length
-      fread(szTmp, 1, iTmp, fp);
+      tTmp = fread(&iTmp, sizeof(int), 1, fp); // read length
+      tTmp = fread(szTmp, 1, iTmp, fp);
       szTmp[iTmp]='\0';
       MOD_SEQS.push_back(szTmp);
    }
    for (unsigned long i = 0; i < ulModNumSize; ++i)
    {
       ModificationNumber sTmp;
-      fread(&iTmp, sizeof(int), 1, fp); // read length
-      fread(szTmp, 1, iTmp, fp);
+      tTmp = fread(&iTmp, sizeof(int), 1, fp); // read length
+      tTmp = fread(szTmp, 1, iTmp, fp);
       szTmp[iTmp]='\0';
       sTmp.modStringLen = iTmp;
       sTmp.modifications = new char[iTmp];

CometSearch/CometFragmentIndex.h

@@ -51,7 +51,6 @@ class CometFragmentIndex
    static bool SortFragmentsByPepMass(unsigned int x,
                                       unsigned int y);
    static void SortFragmentThreadProc(int iWhichThread,
-                                      int iNumIndexingThreads,
                                       ThreadPool* tp);
    static bool CompareByPeptide(const DBIndex &lhs,
                                 const DBIndex &rhs);

CometSearch/CometMassSpecUtils.cpp

@@ -133,25 +133,27 @@ void CometMassSpecUtils::GetProteinName(FILE *fpdb,
                                         comet_fileoffset_t lFilePosition,
                                         char *szProteinName)
 {
+   size_t tTmp;
+
    comet_fseek(fpdb, lFilePosition, SEEK_SET);
 
    if (g_staticParams.bIndexDb)  //index database
    {
       long lSize;
 
-      fread(&lSize, sizeof(long), 1, fpdb);
+      tTmp = fread(&lSize, sizeof(long), 1, fpdb);
       vector<comet_fileoffset_t> vOffsets;
       for (long x = 0; x < lSize; ++x) // read file offsets
       {
          comet_fileoffset_t tmpoffset;
-         fread(&tmpoffset, sizeof(comet_fileoffset_t), 1, fpdb);
+         tTmp = fread(&tmpoffset, sizeof(comet_fileoffset_t), 1, fpdb);
          vOffsets.push_back(tmpoffset);
       }
       for (long x = 0; x < lSize; ++x) // read name from fasta
       {
          char szTmp[WIDTH_REFERENCE];
          comet_fseek(fpdb, vOffsets.at(x), SEEK_SET);
-         fread(szTmp, sizeof(char)*WIDTH_REFERENCE, 1, fpdb);
+         tTmp = fread(szTmp, sizeof(char)*WIDTH_REFERENCE, 1, fpdb);
          sscanf(szTmp, "%511s", szProteinName);  // WIDTH_REFERENCE-1
          break;  //break here to only get first protein reference (out of lSize)
       }

CometSearch/CometPostAnalysis.cpp

@@ -328,7 +328,7 @@ void CometPostAnalysis::CalculateSP(Results *pOutput,
 
    int  _iSizepiVarModSites = sizeof(int)*MAX_PEPTIDE_LEN_P2;
 
-   for (i=0; i<iSize; ++i)
+   for (i = 0; i < iSize; ++i)
    {
       if (!g_staticParams.bIndexDb)
       {

CometSearch/CometSearch.cpp

@@ -3179,7 +3179,7 @@ void CometSearch::XcorrScore(char *szProteinSeq,
 
    dXcorr *= 0.005;  // Scale intensities to 50 and divide score by 1E4.
 
-   dXcorr= std::round(dXcorr* 10000.0) / 1000.0;  // round to 4 decimal points
+   dXcorr= std::round(dXcorr* 10000.0) / 10000.0;  // round to 4 decimal points
 
    Threading::LockMutex(pQuery->accessMutex);
 

CometSearch/CometSearchManager.cpp

@@ -3487,13 +3487,14 @@ bool CometSearchManager::DoSingleSpectrumSearchMultiResults(const int topN,
    if (!bSucceeded)
       goto cleanup_results;
 
-      g_massRange.dMinMass = g_pvQuery.at(0)->_pepMassInfo.dPeptideMassToleranceMinus;
+   g_massRange.dMinMass = g_pvQuery.at(0)->_pepMassInfo.dPeptideMassToleranceMinus;
    g_massRange.dMaxMass = g_pvQuery.at(g_pvQuery.size() - 1)->_pepMassInfo.dPeptideMassTolerancePlus;
 
    if (g_massRange.dMaxMass - g_massRange.dMinMass > g_massRange.dMinMass)
       g_massRange.bNarrowMassRange = true;  // unused in this context but setting here anyways
    else
       g_massRange.bNarrowMassRange = false;
+
    g_sCometVersion = comet_version;
 
    // Now that spectra are loaded to memory and sorted, do search.

CometSearch/CometWritePepXML.cpp

@@ -89,8 +89,7 @@ bool CometWritePepXML::WritePepXMLHeader(FILE *fpout,
       strcpy(szResolvedInputBaseName, g_staticParams.inputFile.szFileName);
 
    // now remove extension from szRunSummaryResolvedPath to leave just the base name
-   int  iLen = (int)strlen(szResolvedInputBaseName);
-   if ( (pStr = strrchr(szResolvedInputBaseName, '.')))
+   if ((pStr = strrchr(szResolvedInputBaseName, '.')))
       *pStr = '\0';
 
    if (g_staticParams.options.bResolveFullPaths)