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Comet.cpp
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// Copyright 2023 Jimmy Eng
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
#include "Common.h"
#include "CometData.h"
#include "CometDataInternal.h"
#include "CometInterfaces.h"
#include <algorithm>
using namespace CometInterfaces;
void Usage(char *pszCmd);
void ProcessCmdLine(int argc,
char *argv[],
char *szParamsFile,
vector<InputFileInfo*> &pvInputFiles,
ICometSearchManager *pSearchMgr);
void SetOptions(char *arg,
char *szParamsFile,
int *iPrintParams,
ICometSearchManager *pSearchMgr);
void LoadParameters(char *pszParamsFile,
ICometSearchManager *pSearchMgr);
void PrintParams(int iPrintParams);
bool ValidateInputFile(char *pszInputFileName);
int main(int argc, char *argv[])
{
// add git hash to version string if present
if (strlen(GITHUBSHA) > 0)
{
string sTmp = std::string(GITHUBSHA);
if (sTmp.size() > 7)
sTmp.resize(7);
g_sCometVersion = std::string(comet_version) + " (" + sTmp + ")";
}
else
g_sCometVersion = std::string(comet_version);
if (argc < 2)
Usage(argv[0]);
vector<InputFileInfo*> pvInputFiles;
ICometSearchManager* pCometSearchMgr = GetCometSearchManager();
char szParamsFile[SIZE_FILE];
ProcessCmdLine(argc, argv, szParamsFile, pvInputFiles, pCometSearchMgr);
pCometSearchMgr->AddInputFiles(pvInputFiles);
bool bSearchSucceeded;
bSearchSucceeded = pCometSearchMgr->DoSearch();
CometInterfaces::ReleaseCometSearchManager();
if (!bSearchSucceeded)
{
// We already log errors when search fails, so no need to log the
// error message again via g_cometStatus
exit(1);
}
return (0);
} // main
void Usage(char *pszCmd)
{
char szTmp[1024];
logout("\n");
sprintf(szTmp, " Comet version \"%s\"\n %s\n", g_sCometVersion.c_str(), copyright);
logout(szTmp);
logout("\n");
sprintf(szTmp, " Comet usage: %s [options] <input_files>\n", pszCmd);
logout(szTmp);
logout("\n");
logout(" Supported input formats include mzXML, mzML, Thermo raw, mgf, and ms2 variants (cms2, bms2, ms2)\n");
logout("\n");
logout(" options: -p to print out a comet.params.new file\n");
logout(" -q to print out a comet.params.new file with more parameter entries\n");
logout(" -P<params> to specify an alternate parameters file (default comet.params)\n");
logout(" -N<name> to specify an alternate output base name; valid only with one input file\n");
logout(" -D<dbase> to specify a sequence database, overriding entry in parameters file\n");
logout(" -F<num> to specify the first/start scan to search, overriding entry in parameters file\n");
logout(" -L<num> to specify the last/end scan to search, overriding entry in parameters file\n");
logout(" (-L option is required if -F option is used)\n");
logout(" -i create .idx file for fragment ion indexing\n");
logout(" -j create .idx file for peptide indexing\n");
logout("\n");
sprintf(szTmp, " example: %s file1.mzXML file2.mzXML\n", pszCmd);
logout(szTmp);
sprintf(szTmp, " or %s -F1000 -L1500 file1.mzXML <- to search scans 1000 through 1500\n", pszCmd);
logout(szTmp);
sprintf(szTmp, " or %s -PParams.txt *.mzXML <- use parameters in the file 'Params.txt'\n", pszCmd);
logout(szTmp);
logout("\n");
exit(1);
}
void SetOptions(char *arg,
char *szParamsFile,
int *iPrintParams,
ICometSearchManager *pSearchMgr)
{
char szTmp[512];
char szParamStringVal[512];
switch (arg[1])
{
case 'D': // Alternate sequence database.
strncpy(szTmp, arg+2, 511);
szTmp[511]='\0';
if (strlen(szTmp) == 0 )
logerr("Missing text for parameter option -D<database>. Ignored.\n");
else
pSearchMgr->SetParam("database_name", szTmp, szTmp);
break;
case 'P': // Alternate parameters file.
strncpy(szTmp, arg+2, 511);
szTmp[511]='\0';
if (strlen(szTmp) == 0 )
logerr("Missing text for parameter option -P<params>. Ignored.\n");
else
strcpy(szParamsFile, szTmp);
break;
case 'N': // Set basename of output file (for .out, SQT, and pepXML)
strncpy(szTmp, arg+2, 511);
szTmp[511]='\0';
if (strlen(szTmp) == 0 )
logerr("Missing text for parameter option -N<basename>. Ignored.\n");
else
pSearchMgr->SetOutputFileBaseName(szTmp);
break;
case 'F': // first scan
if (sscanf(arg+2, "%511s", szTmp) == 0 )
logerr("Missing text for parameter option -F<num>. Ignored.\n");
else
{
IntRange iScanRange;
pSearchMgr->GetParamValue("scan_range", iScanRange);
iScanRange.iStart = atoi(szTmp);
szParamStringVal[0] = '\0';
sprintf(szParamStringVal, "%d %d", iScanRange.iStart, iScanRange.iEnd);
pSearchMgr->SetParam("scan_range", szParamStringVal, iScanRange);
}
break;
case 'L': // last scan
if (sscanf(arg+2, "%511s", szTmp) == 0 )
logerr("Missing text for parameter option -L<num>. Ignored.\n");
else
{
IntRange iScanRange;
pSearchMgr->GetParamValue("scan_range", iScanRange);
iScanRange.iEnd = atoi(szTmp);
szParamStringVal[0] = '\0';
sprintf(szParamStringVal, "%d %d", iScanRange.iStart, iScanRange.iEnd);
pSearchMgr->SetParam("scan_range", szParamStringVal, iScanRange);
}
break;
case 'B': // batch size
if (sscanf(arg+2, "%511s", szTmp) == 0 )
logerr("Missing text for parameter option -B<num>. Ignored.\n");
else
{
int iSpectrumBatchSize = atoi(szTmp);
szParamStringVal[0] = '\0';
sprintf(szParamStringVal, "%d", iSpectrumBatchSize);
pSearchMgr->SetParam("spectrum_batch_size", szParamStringVal, iSpectrumBatchSize);
}
break;
case 'p':
*iPrintParams = 1; // default set of parameters
break;
case 'q':
*iPrintParams = 2; // include additional parameters such as PEFF, fragment ion index
break;
case 'i':
sprintf(szParamStringVal, "1");
pSearchMgr->SetParam("create_fragment_index", szParamStringVal, 1);
sprintf(szParamStringVal, "0");
pSearchMgr->SetParam("create_peptide_index", szParamStringVal, 0);
break;
case 'j':
sprintf(szParamStringVal, "0");
pSearchMgr->SetParam("create_fragment_index", szParamStringVal, 0);
sprintf(szParamStringVal, "1");
pSearchMgr->SetParam("create_peptide_index", szParamStringVal, 1);
break;
default:
break;
}
}
// Reads comet.params parameter file.
void LoadParameters(char *pszParamsFile,
ICometSearchManager *pSearchMgr)
{
double dTempMass,
dDoubleParam;
int iSearchEnzymeNumber = 1,
iSearchEnzyme2Number = 0,
iSampleEnzymeNumber = 1,
iIntParam,
iAllowedMissedCleavages = 2;
long lLongParam;
char szParamBuf[SIZE_BUF],
szParamName[128],
szParamVal[512],
szParamStringVal[512],
szVersion[128],
szErrorMsg[512];
FILE *fp;
bool bCurrentParamsFile = 0, // Track a parameter to make sure present.
bValidParamsFile;
char *pStr;
VarMods varModsParam;
IntRange intRangeParam;
DoubleRange doubleRangeParam;
if ((fp=fopen(pszParamsFile, "r")) == NULL)
{
sprintf(szErrorMsg, "\n Comet version %s\n\n", g_sCometVersion.c_str());
sprintf(szErrorMsg+strlen(szErrorMsg), " Error - cannot open parameter file \"%s\".\n", pszParamsFile);
logerr(szErrorMsg);
exit(1);
}
// validate not using incompatible params file by checking "# comet_version" in first line of file
strcpy(szVersion, "unknown");
bValidParamsFile = false;
while (!feof(fp))
{
if (fgets(szParamBuf, SIZE_BUF, fp) != NULL)
{
if (!strncmp(szParamBuf, "# comet_version ", 16))
{
char szRev1[12],
szRev2[12];
sscanf(szParamBuf, "%*s %*s %127s %11s %11s", szVersion, szRev1, szRev2);
if (pSearchMgr->IsValidCometVersion(string(szVersion)))
{
bValidParamsFile = true;
char szVersion2[128];
sprintf(szVersion2, "%.100s %.11s %.11s", szVersion, szRev1, szRev2);
strcpy(szVersion, szVersion2);
pSearchMgr->SetParam("# comet_version", szVersion, szVersion);
break;
}
}
}
}
if (!bValidParamsFile)
{
sprintf(szErrorMsg, "\n Comet version %s\n\n", g_sCometVersion.c_str());
sprintf(szErrorMsg+strlen(szErrorMsg), " The comet.params file is from version %s\n", szVersion);
sprintf(szErrorMsg+strlen(szErrorMsg), " Please update your comet.params file. You can generate\n");
sprintf(szErrorMsg+strlen(szErrorMsg), " a new parameters file using \"comet -p\"\n\n");
logerr(szErrorMsg);
exit(1);
}
rewind(fp);
// now parse the parameter entries
while (!feof(fp))
{
if (fgets(szParamBuf, SIZE_BUF, fp) != NULL)
{
if (!strncmp(szParamBuf, "[COMET_ENZYME_INFO]", 19))
break;
if ( (pStr = strchr(szParamBuf, '#')) != NULL) // take care of comments
*pStr = 0;
if ( (pStr = strchr(szParamBuf, '=')) != NULL)
{
strcpy(szParamVal, pStr + 1); // Copy over value.
*pStr = 0; // Null rest of szParamName at equal char.
sscanf(szParamBuf, "%127s", szParamName);
bool bParameterEntryNotFoundYet = false;
if (!strcmp(szParamName, "database_name"))
{
char szFile[SIZE_FILE];
// Support parsing a database string from params file that
// includes spaces in the path.
// Remove white spaces at beginning/end of szParamVal
int iLen = (int)strlen(szParamVal);
char *szTrimmed = szParamVal;
while (iLen > 0 && isspace(szTrimmed[iLen -1])) // trim end
szTrimmed[--iLen] = 0;
while (*szTrimmed && isspace(*szTrimmed)) // trim beginning
{
++szTrimmed;
--iLen;
}
memmove(szParamVal, szTrimmed, iLen+1);
strcpy(szFile, szParamVal);
pSearchMgr->SetParam("database_name", szFile, szFile);
}
else if (!strcmp(szParamName, "peff_obo"))
{
char szFile[SIZE_FILE];
// Remove white spaces at beginning/end of szParamVal
int iLen = (int)strlen(szParamVal);
char *szTrimmed = szParamVal;
while (iLen > 0 && isspace(szTrimmed[iLen -1])) // trim end
szTrimmed[--iLen] = 0;
while (*szTrimmed && isspace(*szTrimmed)) // trim beginning
{
++szTrimmed;
--iLen;
}
memmove(szParamVal, szTrimmed, iLen+1);
strcpy(szFile, szParamVal);
pSearchMgr->SetParam("peff_obo", szFile, szFile);
}
else if (!strcmp(szParamName, "decoy_prefix"))
{
char szDecoyPrefix[256];
szDecoyPrefix[0] = '\0';
sscanf(szParamVal, "%255s", szDecoyPrefix);
pSearchMgr->SetParam("decoy_prefix", szDecoyPrefix, szDecoyPrefix);
}
else if (!strcmp(szParamName, "output_suffix"))
{
char szOutputSuffix[256];
szOutputSuffix[0] = '\0';
sscanf(szParamVal, "%255s", szOutputSuffix);
pSearchMgr->SetParam("output_suffix", szOutputSuffix, szOutputSuffix);
}
else if (!strcmp(szParamName, "text_file_extension"))
{
char szTxtFileExt[256];
szTxtFileExt[0] = '\0';
sscanf(szParamVal, "%255s", szTxtFileExt);
pSearchMgr->SetParam("text_file_extension", szTxtFileExt, szTxtFileExt);
}
else if (!strcmp(szParamName, "protein_modslist_file"))
{
char szTmp[256];
szTmp[0] = '\0';
sscanf(szParamVal, "%255s", szTmp);
pSearchMgr->SetParam("protein_modslist_file", szTmp, szTmp);
}
else if (!strcmp(szParamName, "explicit_deltacn"))
{
sscanf(szParamVal, "%d", &iIntParam);
szParamStringVal[0] = '\0';
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("explicit_deltacn", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "mass_offsets"))
{
// Remove white spaces at beginning/end of szParamVal
int iLen = (int)strlen(szParamVal);
char *szTrimmed = szParamVal;
while (iLen > 0 && isspace(szTrimmed[iLen -1])) // trim end
szTrimmed[--iLen] = 0;
while (*szTrimmed && isspace(*szTrimmed)) // trim beginning
{
++szTrimmed;
--iLen;
}
memmove(szParamVal, szTrimmed, iLen+1);
char szMassOffsets[512];
vector<double> vectorSetMassOffsets;
char *tok;
char delims[] = " \t"; // tokenize by space and tab
double dMass;
strcpy(szMassOffsets, szParamVal); // need to copy as strtok below destroys szParamVal
tok = strtok(szParamVal, delims);
while (tok != NULL)
{
if (sscanf(tok, "%lf", &dMass) == 1)
{
if (dMass >= 0.0)
vectorSetMassOffsets.push_back(dMass);
tok = strtok(NULL, delims);
}
}
sort(vectorSetMassOffsets.begin(), vectorSetMassOffsets.end());
pSearchMgr->SetParam("mass_offsets", szMassOffsets, vectorSetMassOffsets);
}
else if (!strcmp(szParamName, "precursor_NL_ions"))
{
// Remove white spaces at beginning/end of szParamVal
int iLen = (int)strlen(szParamVal);
char *szTrimmed = szParamVal;
while (iLen > 0 && isspace(szTrimmed[iLen -1])) // trim end
szTrimmed[--iLen] = 0;
while (*szTrimmed && isspace(*szTrimmed)) // trim beginning
{
++szTrimmed;
--iLen;
}
memmove(szParamVal, szTrimmed, iLen+1);
char szMassOffsets[512];
vector<double> vectorPrecursorNLIons;
char *tok;
char delims[] = " \t"; // tokenize by space and tab
double dMass;
strcpy(szMassOffsets, szParamVal); // need to copy as strtok below destroys szParamVal
tok = strtok(szParamVal, delims);
while (tok != NULL)
{
sscanf(tok, "%lf", &dMass);
if (dMass >= 0.0)
vectorPrecursorNLIons.push_back(dMass);
tok = strtok(NULL, delims);
}
sort(vectorPrecursorNLIons.begin(), vectorPrecursorNLIons.end());
pSearchMgr->SetParam("precursor_NL_ions", szMassOffsets, vectorPrecursorNLIons);
}
else if (!strcmp(szParamName, "old_mods_encoding"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("old_mods_encoding", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "nucleotide_reading_frame"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("nucleotide_reading_frame", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "mass_type_parent"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("mass_type_parent", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "mass_type_fragment"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("mass_type_fragment", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "show_fragment_ions"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("show_fragment_ions", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "num_threads"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("num_threads", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "clip_nterm_methionine"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("clip_nterm_methionine", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "clip_nterm_aa"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("clip_nterm_aa", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "minimum_xcorr"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("minimum_xcorr", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "theoretical_fragment_ions"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("theoretical_fragment_ions", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "use_A_ions"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("use_A_ions", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "use_B_ions"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("use_B_ions", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "use_C_ions"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("use_C_ions", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "use_X_ions"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("use_X_ions", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "use_Y_ions"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("use_Y_ions", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "use_Z_ions"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("use_Z_ions", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "use_Z1_ions"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("use_Z1_ions", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "use_NL_ions"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("use_NL_ions", szParamStringVal, iIntParam);
}
else if (!strncmp(szParamName, "variable_mod", 12) && strlen(szParamName)==14)
{
char szTmp[512];
char szTmp1[512];
varModsParam.szVarModChar[0] = '\0';
sscanf(szParamVal, "%lf %31s %d %511s %d %d %d %s",
&varModsParam.dVarModMass,
varModsParam.szVarModChar,
&varModsParam.iBinaryMod,
szTmp,
&varModsParam.iVarModTermDistance,
&varModsParam.iWhichTerm,
&varModsParam.iRequireThisMod,
szTmp1);
char *pStr;
// the 8th entry can have to fragment NL values, comma separated
if ( (pStr = strchr(szTmp1, ',')) )
sscanf(szTmp1, "%lf,%lf", &varModsParam.dNeutralLoss, &varModsParam.dNeutralLoss2);
else
sscanf(szTmp1, "%lf", &varModsParam.dNeutralLoss);
// the 4th entry can either be just the max_num_var_mod or a comma separated
// value composed of min_num,max_num
if ( (pStr=strchr(szTmp, ',')) == NULL)
{
sscanf(szTmp, "%d", &varModsParam.iMaxNumVarModAAPerMod);
}
else
{
*pStr = ' ';
sscanf(szTmp, "%d %d", &varModsParam.iMinNumVarModAAPerMod, &varModsParam.iMaxNumVarModAAPerMod);
}
#ifdef _WIN32
szParamVal[strlen(szParamVal)-2] = '\0'; // remove CR/LF
#else
szParamVal[strlen(szParamVal)-1] = '\0'; // remove LF
#endif
sprintf(szParamStringVal, "%s", szParamVal); // FIX: confirm that this is OK
pSearchMgr->SetParam(szParamName, szParamStringVal, varModsParam);
}
else if (!strcmp(szParamName, "max_variable_mods_in_peptide"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("max_variable_mods_in_peptide", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "require_variable_mod"))
{
char szRequireVariableMod[256];
szRequireVariableMod[0] = '\0';
sscanf(szParamVal, "%255s", szRequireVariableMod);
pSearchMgr->SetParam("require_variable_mod", szRequireVariableMod, szRequireVariableMod);
}
else if (!strcmp(szParamName, "fragment_bin_tol"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("fragment_bin_tol", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "fragment_bin_offset"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("fragment_bin_offset", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "peptide_mass_tolerance"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("peptide_mass_tolerance", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "peptide_mass_tolerance_upper"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("peptide_mass_tolerance_upper", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "peptide_mass_tolerance_lower"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("peptide_mass_tolerance_lower", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "precursor_tolerance_type"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("precursor_tolerance_type", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "peptide_mass_units"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("peptide_mass_units", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "isotope_error"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("isotope_error", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "num_output_lines"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("num_output_lines", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "num_results"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("num_results", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "max_duplicate_proteins"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("max_duplicate_proteins", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "remove_precursor_peak"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("remove_precursor_peak", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "remove_precursor_tolerance"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("remove_precursor_tolerance", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "clear_mz_range"))
{
doubleRangeParam.dStart = 0.0;
doubleRangeParam.dEnd = 0.0;
sscanf(szParamVal, "%lf %lf", &doubleRangeParam.dStart, &doubleRangeParam.dEnd);
sprintf(szParamStringVal, "%lf %lf", doubleRangeParam.dStart, doubleRangeParam.dEnd);
pSearchMgr->SetParam("clear_mz_range", szParamStringVal, doubleRangeParam);
}
else if (!strcmp(szParamName, "percentage_base_peak"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("percentage_base_peak", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "export_additional_pepxml_scores"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("export_additional_pepxml_scores", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "print_expect_score"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("print_expect_score", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "resolve_fullpaths"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("resolve_fullpaths", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "output_sqtstream"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("output_sqtstream", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "output_sqtfile"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("output_sqtfile", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "output_txtfile"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("output_txtfile", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "output_pepxmlfile"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("output_pepxmlfile", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "output_mzidentmlfile"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("output_mzidentmlfile", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "output_percolatorfile"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("output_percolatorfile", szParamStringVal, iIntParam);
bCurrentParamsFile = 1; // this is the new parameter; if this is missing then complain & exit
}
else if (!strcmp(szParamName, "output_outfiles"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("output_outfiles", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "skip_researching"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("skip_researching", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "skip_updatecheck"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("skip_updatecheck", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "peff_verbose_output"))
{
sscanf(szParamVal, "%d", &iIntParam);
sprintf(szParamStringVal, "%d", iIntParam);
pSearchMgr->SetParam("peff_verbose_output", szParamStringVal, iIntParam);
}
else if (!strcmp(szParamName, "add_Cterm_peptide"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("add_Cterm_peptide", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "add_Nterm_peptide"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("add_Nterm_peptide", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "add_Cterm_protein"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("add_Cterm_protein", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "add_Nterm_protein"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("add_Nterm_protein", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "set_G_glycine"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("set_G_glycine", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "set_A_alanine"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("set_A_alanine", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "set_S_serine"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("set_S_serine", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "set_P_proline"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("set_P_proline", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "set_V_valine"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("set_V_valine", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "set_T_threonine"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("set_T_threonine", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "set_C_cysteine"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("set_C_cysteine", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "set_U_selenocysteine"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("set_U_selenocysteine", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "set_L_leucine"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("set_L_leucine", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "set_I_isoleucine"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("set_I_isoleucine", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "set_N_asparagine"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("set_N_asparagine", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "set_O_pyrrolysine"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("set_O_pyrrolysine", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "set_D_aspartic_acid"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("set_D_aspartic_acid", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "set_Q_glutamine"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("set_Q_glutamine", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "set_K_lysine"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("set_K_lysine", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "set_E_glutamic_acid"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("set_E_glutamic_acid", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "set_M_methionine"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("set_M_methionine", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "set_H_histidine"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("set_H_histidine", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "set_F_phenylalanine"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("set_F_phenylalanine", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "set_R_arginine"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("set_R_arginine", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "set_Y_tyrosine"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("set_Y_tyrosine", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "set_W_tryptophan"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("set_W_tryptophan", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "set_B_user_amino_acid"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("set_B_user_amino_acid", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "set_J_user_amino_acid"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("set_J_user_amino_acid", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "set_X_user_amino_acid"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("set_X_user_amino_acid", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "set_Z_user_amino_acid"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("set_Z_user_amino_acid", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "add_G_glycine"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
szParamStringVal[0] = '\0';
sprintf(szParamStringVal, "%lf", dDoubleParam);
pSearchMgr->SetParam("add_G_glycine", szParamStringVal, dDoubleParam);
}
else if (!strcmp(szParamName, "add_A_alanine"))
{
sscanf(szParamVal, "%lf", &dDoubleParam);
szParamStringVal[0] = '\0';
sprintf(szParamStringVal, "%lf", dDoubleParam);