add hidden parameter 'pinfile_protein_delimiter' to change default protein tab delimiter; remove undocumented 'pin_mod_proteindelim' parameter that set this same delmiter to a comma

Author: jke000

Comet.cpp

@@ -351,7 +351,6 @@ void LoadParameters(char *pszParamsFile,
                szDecoyPrefix[0] = '\0';
                sscanf(szParamVal, "%255s", szDecoyPrefix);
                pSearchMgr->SetParam("decoy_prefix", szDecoyPrefix, szDecoyPrefix);
-
             }
             else if (!strcmp(szParamName, "output_suffix"))
             {
@@ -500,12 +499,6 @@ void LoadParameters(char *pszParamsFile,
                sprintf(szParamStringVal, "%d", iIntParam);
                pSearchMgr->SetParam("clip_nterm_aa", szParamStringVal, iIntParam);
             }
-            else if (!strcmp(szParamName, "pin_mod_proteindelim"))
-            {
-               sscanf(szParamVal, "%d", &iIntParam);
-               sprintf(szParamStringVal, "%d", iIntParam);
-               pSearchMgr->SetParam("pin_proteindelim_comma", szParamStringVal, iIntParam);
-            }
             else if (!strcmp(szParamName, "minimum_xcorr"))
             {
                sscanf(szParamVal, "%lf", &dDoubleParam);
@@ -1335,6 +1328,13 @@ void LoadParameters(char *pszParamsFile,
                   sprintf(szParamStringVal, "%d", iIntParam);
                   pSearchMgr->SetParam("scale_fragmentNL", szParamStringVal, iIntParam);
                }
+               else if (!strcmp(szParamName, "pinfile_protein_delimiter"))
+               {
+                  char szDelimiter[256];
+                  szDelimiter[0] = '\0';
+                  sscanf(szParamVal, "%255s", szDelimiter);
+                  pSearchMgr->SetParam("pinfile_protein_delimiter", szDelimiter, szDelimiter);
+               }
                else if (!strcmp(szParamName, "max_iterations"))
                {
                   sscanf(szParamVal, "%ld", &lLongParam);
@@ -1815,6 +1815,8 @@ peptide_length_range = 5 50            # minimum and maximum peptide length to a
    if (iPrintParams == 2)
    {
       fprintf(fp,
+"pinfile_protein_delimiter =            # blank = default 'tab' delimiter between proteins; enter a char/string to use in place of the tab; Percolator pin output only\n");
+      fprintf(fp,
 "num_results = 100                      # number of results to store internally for Sp rank only; if Sp rank is not used, set this to num_output_lines\n");
    }
 

CometSearch/CometDataInternal.h

@@ -101,7 +101,7 @@ struct msdata                    // used in the preprocessing
    double dIntensity;
 };
 
-struct Options             // output parameters
+struct Options
 {
    int iNumPeptideOutputLines;
    int iWhichReadingFrame;
@@ -129,7 +129,6 @@ struct Options             // output parameters
    int bOutputOutFiles;
    int bClipNtermMet;            // 0=leave protein sequences alone; 1=also consider w/o N-term methionine
    int bClipNtermAA;             // 0=leave peptide sequences as-is; 1=clip N-term amino acid from every peptide
-   int bPinModProteinDelim;      // 0=default pin output format; 1=change protein delimiter to comma
    int bSkipAlreadyDone;         // 0=search everything; 1=don't re-search if .out exists
 // int bSkipUpdateCheck;         // 0=do not check for updates; 1=check for updates
    int bMango;                   // 0=normal; 1=Mango x-link ms2 input
@@ -162,6 +161,7 @@ struct Options             // output parameters
    IntRange peptideLengthRange;
    DoubleRange clearMzRange;
    char szActivationMethod[24];  // mzXML only
+   string sPinProteinDelimiter;  // PIN file protein delimiter; default tab
 
    Options& operator=(Options& a)
    {
@@ -190,7 +190,6 @@ struct Options             // output parameters
       bOutputOutFiles = a.bOutputOutFiles;
       bClipNtermMet = a.bClipNtermMet;
       bClipNtermAA = a.bClipNtermAA;
-      bPinModProteinDelim = a.bPinModProteinDelim;
       bSkipAlreadyDone = a.bSkipAlreadyDone;
 //    bSkipUpdateCheck = a.bSkipUpdateCheck;
       bMango = a.bMango;
@@ -216,6 +215,7 @@ struct Options             // output parameters
       peptideLengthRange = a.peptideLengthRange;
       clearMzRange = a.clearMzRange;
       strcpy(szActivationMethod, a.szActivationMethod);
+      sPinProteinDelimiter = a.sPinProteinDelimiter;
 
       dFragIndexMinMass = a.dFragIndexMinMass;
       dFragIndexMaxMass = a.dFragIndexMaxMass;
@@ -874,7 +874,6 @@ struct StaticParams
       options.iNumFragmentThreads = 4;
       options.bClipNtermMet = 0;
       options.bClipNtermAA = 0;
-      options.bPinModProteinDelim = 0;
 
       options.lMaxIterations = 0;
 
@@ -898,6 +897,7 @@ struct StaticParams
       strcpy(options.szActivationMethod, "ALL");
       // End of mzXML specific parameters.
 
+      options.sPinProteinDelimiter = '\t';
 
       options.dFragIndexMinMass = FRAGINDEX_MIN_MASS;
       options.dFragIndexMaxMass = FRAGINDEX_MAX_MASS;

CometSearch/CometSearchManager.cpp

@@ -649,8 +649,6 @@ bool CometSearchManager::InitializeStaticParams()
 
    GetParamValue("clip_nterm_aa", g_staticParams.options.bClipNtermAA);
 
-   GetParamValue("pin_mod_proteindelim", g_staticParams.options.bPinModProteinDelim);
-
    GetParamValue("minimum_xcorr", g_staticParams.options.dMinimumXcorr);
 
    GetParamValue("theoretical_fragment_ions", g_staticParams.ionInformation.iTheoreticalFragmentIons);
@@ -1192,6 +1190,12 @@ bool CometSearchManager::InitializeStaticParams()
    if (GetParamValue("activation_method", strData))
       strcpy(g_staticParams.options.szActivationMethod, strData.c_str());
 
+   if (GetParamValue("pinfile_protein_delimiter", strData))
+   {
+      if (strData.length() > 0)
+         g_staticParams.options.sPinProteinDelimiter = strData;
+   }
+
    GetParamValue("minimum_intensity", g_staticParams.options.dMinIntensity);
    if (g_staticParams.options.dMinIntensity < 0.0)
       g_staticParams.options.dMinIntensity = 0.0;
@@ -1627,6 +1631,12 @@ bool CometSearchManager::InitializeStaticParams()
       }
    }
 
+   if (g_staticParams.tolerances.dInputToleranceMinus > g_staticParams.tolerances.dInputTolerancePlus)
+   {
+      printf("\n Error: mass_tolerance_lower is greater than mass_tolerance_upper so no peptides will be analyzed.\n");
+      return false;
+   }
+
    return true;
 }
 

CometSearch/CometWritePercolator.cpp

@@ -280,12 +280,7 @@ void CometWritePercolator::PrintPercolatorSearchHit(int iWhichQuery,
       for (it = vProteinTargets.begin(); it != vProteinTargets.end(); ++it)
       {
          if (bPrintTab)
-         {
-            if (g_staticParams.options.bPinModProteinDelim)
-               fprintf(fpout, ",");
-            else
-               fprintf(fpout, "\t");
-         }
+            fprintf(fpout, "%s", g_staticParams.options.sPinProteinDelimiter.c_str());
 
          fprintf(fpout, "%s", (*it).c_str());
          bPrintTab = true;
@@ -297,12 +292,7 @@ void CometWritePercolator::PrintPercolatorSearchHit(int iWhichQuery,
       for (it = vProteinDecoys.begin(); it != vProteinDecoys.end(); ++it)
       {
          if (bPrintTab)
-         {
-            if (g_staticParams.options.bPinModProteinDelim)
-               fprintf(fpout, ",");
-            else
-               fprintf(fpout, "\t");
-         }
+            fprintf(fpout, "%s", g_staticParams.options.sPinProteinDelimiter.c_str());
 
          fprintf(fpout, "%s", (*it).c_str());
          bPrintTab = true;