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NCBI C++ ToolKit: src/algo/ms/omssa/omssaapp.cpp Source File

79

cout <<

" # : Name"

<< endl;

81

cout << setw(3) << iModMap->second <<

": "

<< iModMap->first << endl;

114

argDesc->PrintUsageIfNoArgs();

116

argDesc->AddDefaultKey(

"pm"

"param"

117 "search parameter input in xml format (overrides command line)"

120

argDesc->AddDefaultKey(

"d"

"blastdb"

"Blast sequence library to search. Do not include .p* filename suffixes."

122

argDesc->AddFlag(

"umm"

"use memory mapped sequence libraries"

);

123

argDesc->AddDefaultKey(

"f"

"infile"

"single dta file to search"

125

argDesc->AddDefaultKey(

"fx"

"xmlinfile"

"multiple xml-encapsulated dta files to search"

127

argDesc->AddDefaultKey(

"fb"

"dtainfile"

"multiple dta files separated by blank lines to search"

129

argDesc->AddDefaultKey(

"fp"

"pklinfile"

"pkl formatted file"

131

argDesc->AddDefaultKey(

"fm"

"pklinfile"

"mgf formatted file"

133

argDesc->AddDefaultKey(

"foms"

"omsinfile"

"omssa oms file"

135

argDesc->AddDefaultKey(

"fomx"

"omxinfile"

"omssa omx file"

137

argDesc->AddDefaultKey(

"fbz2"

"bz2infile"

"omssa omx file compressed by bzip2"

139

argDesc->AddDefaultKey(

"fxml"

"omxinfile"

"omssa xml search request file"

141

argDesc->AddDefaultKey(

"o"

"textasnoutfile"

"filename for text asn.1 formatted search results"

143

argDesc->AddDefaultKey(

"ob"

"binaryasnoutfile"

"filename for binary asn.1 formatted search results"

145

argDesc->AddDefaultKey(

"ox"

"xmloutfile"

"filename for xml formatted search results"

147

argDesc->AddDefaultKey(

"obz2"

"bz2outfile"

"filename for bzip2 compressed xml formatted search results"

149

argDesc->AddDefaultKey(

"op"

"pepxmloutfile"

"filename for pepXML formatted search results"

151

argDesc->AddDefaultKey(

"oc"

"csvfile"

"filename for csv formatted search summary"

153

argDesc->AddFlag(

"w"

"include spectra and search params in search results"

);

154

argDesc->AddDefaultKey(

"to"

"pretol"

"product ion m/z tolerance in Da"

156

argDesc->AddDefaultKey(

"te"

"protol"

"precursor ion m/z tolerance in Da (or ppm if -teppm flag set)"

158

argDesc->AddDefaultKey(

"tom"

"promass"

"product ion search type (0 = mono, 1 = avg, 2 = N15, 3 = exact)"

160

argDesc->AddDefaultKey(

"tem"

"premass"

"precursor ion search type (0 = mono, 1 = avg, 2 = N15, 3 = exact, 4 = multiisotope)"

162

argDesc->AddDefaultKey(

"tez"

"prozdep"

"charge dependency of precursor mass tolerance (0 = none, 1 = linear)"

164

argDesc->AddDefaultKey(

"ti"

"isotopes"

"when doing multiisotope search, number of isotopic peaks to search. 0 = monoisotopic peak only"

166

argDesc->AddFlag(

"teppm"

"search precursor masses in units of ppm"

);

167

argDesc->AddDefaultKey(

"ta"

"autotol"

168 "automatic mass tolerance adjustment fraction"

171

argDesc->AddDefaultKey(

"tex"

"exact"

172 "threshold in Da above which the mass of neutron should be added in exact mass search"

175

argDesc->AddDefaultKey(

"i"

"ions"

176 "id numbers of ions to search (comma delimited, no spaces)"

179

argDesc->AddDefaultKey(

"cl"

"cutlo"

"low intensity cutoff as a fraction of max peak"

181

argDesc->AddDefaultKey(

"ch"

"cuthi"

"high intensity cutoff as a fraction of max peak"

183

argDesc->AddDefaultKey(

"ci"

"cutinc"

"intensity cutoff increment as a fraction of max peak"

185

argDesc->AddDefaultKey(

"cp"

"precursorcull"

186 "eliminate charge reduced precursors in spectra (0=no, 1=yes)"

188

argDesc->AddDefaultKey(

"v"

"cleave"

189 "number of missed cleavages allowed"

191

argDesc->AddDefaultKey(

"x"

"taxid"

192 "comma delimited list of taxids to search (0 = all)"

194

argDesc->AddDefaultKey(

"w1"

"window1"

195 "single charge window in Da"

197

argDesc->AddDefaultKey(

"w2"

"window2"

198 "double charge window in Da"

200

argDesc->AddDefaultKey(

"h1"

"hit1"

201 "number of peaks allowed in single charge window (0 = number of ion species)"

203

argDesc->AddDefaultKey(

"h2"

"hit2"

204 "number of peaks allowed in double charge window (0 = number of ion species)"

206

argDesc->AddDefaultKey(

"hl"

"hitlist"

207 "maximum number of hits retained per precursor charge state per spectrum during the search"

209

argDesc->AddDefaultKey(

"hc"

"hitcount"

210 "maximum number of hits reported per spectrum (0 = all)"

212

argDesc->AddDefaultKey(

"ht"

"tophitnum"

213 "number of m/z values corresponding to the most intense peaks that must include one match to the theoretical peptide"

215

argDesc->AddDefaultKey(

"hm"

"minhit"

216 "the minimum number of m/z matches a sequence library peptide must have for the hit to the peptide to be recorded"

218

argDesc->AddDefaultKey(

"hs"

"minspectra"

219 "the minimum number of m/z values a spectrum must have to be searched"

221

argDesc->AddDefaultKey(

"he"

"evalcut"

222 "the maximum evalue allowed in the hit list"

224

argDesc->AddDefaultKey(

"mf"

"fixedmod"

225 "comma delimited (no spaces) list of id numbers for fixed modifications"

228

argDesc->AddDefaultKey(

"mv"

"variablemod"

229 "comma delimited (no spaces) list of id numbers for variable modifications"

232

argDesc->AddFlag(

"mnm"

"n-term methionine should not be cleaved"

);

233

argDesc->AddDefaultKey(

"mm"

"maxmod"

234 "the maximum number of mass ladders to generate per database peptide"

236

argDesc->AddDefaultKey(

"e"

"enzyme"

237 "id number of enzyme to use"

240

argDesc->AddDefaultKey(

"zh"

"maxcharge"

241 "maximum precursor charge to search when not 1+"

244

argDesc->AddDefaultKey(

"zl"

"mincharge"

245 "minimum precursor charge to search when not 1+"

248

argDesc->AddDefaultKey(

"zoh"

"maxprodcharge"

249 "maximum product charge to search"

252

argDesc->AddDefaultKey(

"zt"

"chargethresh"

253 "minimum precursor charge to start considering multiply charged products"

256

argDesc->AddDefaultKey(

"z1"

"plusone"

257 "fraction of peaks below precursor used to determine if spectrum is charge 1"

260

argDesc->AddDefaultKey(

"zc"

"calcplusone"

261 "should charge plus one be determined algorithmically? (1=yes)"

264

argDesc->AddDefaultKey(

"zcc"

"calccharge"

265 "how should precursor charges be determined? (1=believe the input file, 2=use a range)"

268

argDesc->AddDefaultKey(

"zn"

"negions"

269 "search using negative or positive ions (1=positive, -1=negative)"

272

argDesc->AddDefaultKey(

"pc"

"pseudocount"

273 "minimum number of precursors that match a spectrum"

276

argDesc->AddDefaultKey(

"sb1"

"searchb1"

277 "should first forward (b1) product ions be in search (1=no)"

280

argDesc->AddDefaultKey(

"sct"

"searchcterm"

281 "should c terminus ions be searched (1=no)"

284

argDesc->AddDefaultKey(

"sp"

"productnum"

285 "max number of ions in each series being searched (0=all)"

288

argDesc->AddDefaultKey(

"scorr"

"corrscore"

289 "turn off correlation correction to score (1=off, 0=use correlation)"

292

argDesc->AddDefaultKey(

"scorp"

"corrprob"

293 "probability of consecutive ion (used in correlation correction)"

296

argDesc->AddDefaultKey(

"no"

"minno"

297 "minimum size of peptides for no-enzyme and semi-tryptic searches"

300

argDesc->AddDefaultKey(

"nox"

"maxno"

301 "maximum size of peptides for no-enzyme and semi-tryptic searches (0=none)"

304

argDesc->AddDefaultKey(

"is"

"subsetthresh"

305 "evalue threshold to include a sequence in the iterative search, 0 = all"

308

argDesc->AddDefaultKey(

"ir"

"replacethresh"

309 "evalue threshold to replace a hit, 0 = only if better"

312

argDesc->AddDefaultKey(

"ii"

"iterativethresh"

313 "evalue threshold to iteratively search a spectrum again, 0 = always"

316

argDesc->AddDefaultKey(

"p"

"prolineruleions"

317 "id numbers of ion series to apply no product ions at proline rule at (comma delimited, no spaces)"

321

argDesc->AddFlag(

"il"

"print a list of ions and their corresponding id number"

);

322

argDesc->AddFlag(

"el"

"print a list of enzymes and their corresponding id number"

);

323

argDesc->AddFlag(

"ml"

"print a list of modifications and their corresponding id number"

);

325

argDesc->AddDefaultKey(

"mx"

"modinputfile"

326 "file containing modification data"

329

argDesc->AddDefaultKey(

"mux"

"usermodinputfile"

330 "file containing user modification data"

333

argDesc->AddDefaultKey(

"nt"

"numthreads"

334 "number of search threads to use, 0=autodetect"

337

argDesc->AddFlag(

"ni"

"don't print informational messages"

);

361

Outfile->SetOutfile(FileName);

362

Outfile->SetOutfiletype(FileFormat);

364 if

(IncludeSpectra) {

365

Outfile->SetIncluderequest(

true

);

368

Outfile->SetIncluderequest(

false

);

381 if

(args[

"fx"

].AsString().

size

() != 0) {

382

Infile->SetInfile(args[

"fx"

].AsString());

385 else if

(args[

"f"

].AsString().

size

() != 0) {

386

Infile->SetInfile(args[

"f"

].AsString());

389 else if

(args[

"fb"

].AsString().

size

() != 0) {

390

Infile->SetInfile(args[

"fb"

].AsString());

393 else if

(args[

"fp"

].AsString().

size

() != 0) {

394

Infile->SetInfile(args[

"fp"

].AsString());

397 else if

(args[

"fm"

].AsString().

size

() != 0) {

398

Infile->SetInfile(args[

"fm"

].AsString());

401 else if

(args[

"fomx"

].AsString().

size

() != 0) {

402

Infile->SetInfile(args[

"fomx"

].AsString());

405 else if

(args[

"fbz2"

].AsString().

size

() != 0) {

406

Infile->SetInfile(args[

"fbz2"

].AsString());

409 else if

(args[

"foms"

].AsString().

size

() != 0) {

410

Infile->SetInfile(args[

"foms"

].AsString());

413 else if

(args[

"fxml"

].AsString().

size

() != 0) {

414

Infile->SetInfile(args[

"fxml"

].AsString());

422 bool

IncludeSpectra = args[

"w"

];

425 if

(args[

"o"

].AsString() !=

""

) {

428 if

(args[

"ob"

].AsString() !=

""

) {

431 if

(args[

"ox"

].AsString() !=

""

) {

434 if

(args[

"obz2"

].AsString() !=

""

) {

437 if

(args[

"op"

].AsString() !=

""

) {

440 if

(args[

"oc"

].AsString() !=

""

) {

448

Settings->

SetPeptol

(args[

"te"

].AsDouble());

449

Settings->

SetMsmstol

(args[

"to"

].AsDouble());

450

Settings->

SetZdep

(args[

"tez"

].AsInteger());

454 if

(args[

"ti"

].AsInteger() != 0)

460

Settings->

SetCutlo

(args[

"cl"

].AsDouble());

461

Settings->

SetCuthi

(args[

"ch"

].AsDouble());

462

Settings->

SetCutinc

(args[

"ci"

].AsDouble());

468

Settings->

SetEnzyme

(args[

"e"

].AsInteger());

473

Settings->

SetDb

(args[

"d"

].AsString());

476

Settings->

SetMinhit

(args[

"hm"

].AsInteger());

479

Settings->

SetCutoff

(args[

"he"

].AsDouble());

480 if

(args[

"hc"

].AsInteger() != 0)

482

Settings->

SetMaxmods

(args[

"mm"

].AsInteger());

484

Settings->

SetSearchb1

(args[

"sb1"

].AsInteger());

492 if

(args[

"x"

].AsString() !=

"0"

) {

536 _TRACE

(

"omssa: search begin"

);

char const *const kEnzymeNames[eMSEnzymes_max]

@MSEnzymes.hpp User-defined methods of the data storage class.

map< TModPair, bool > TModMap

const char * GetModName(int Mod) const

get modification friendly name

int GetModMass(int Mod) const

get modification mass

virtual void AppInit(CArgDescriptions *argDesc)

application specific initialization

void SetThreadCount(int NumThreads)

set up number of threads

void RunSearch(CRef< CSearch > SearchEngine)

run multithreaded search

void PrintEnzymes(void)

print out a list of enzymes that can be used in OMSSA

void PrintMods(CRef< CMSModSpecSet > Modset)

print out a list of modification that can be used in OMSSA

void SetOutFile(bool IncludeSpectra, EMSSerialDataFormat FileFormat, std::string FileName, CRef< CMSSearchSettings > &Settings)

Set the out files.

void PrintIons(void)

print out a list of ions that can be used in OMSSA

TSearchThreads & SetsearchThreads(void)

return a settable list of search engine threads

virtual void Init()

Initialize the application.

const int GetnThreads(void) const

return number of threads

int & SetnThreads(void)

return settable number of threads

void SetSearchSettings(const CArgs &args, CRef< CMSSearchSettings > Settings)

Set search settings given args.

void CopySettings(CRef< CSearch > fromObj)

iterator_bool insert(const value_type &val)

container_type::value_type value_type

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

void SetVersion(const CVersionInfo &version)

Set the version number for the program.

@ eDouble

Convertible into a floating point number (double)

@ eString

An arbitrary string.

@ eInteger

Convertible into an integer number (int or Int8)

EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)

Set the threshold severity for posting the messages.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

@ eDiag_Info

Informational message.

void Fatal(CExceptionArgs_Base &args)

void Info(CExceptionArgs_Base &args)

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

@ fRunAllowST

Allow threads to run in single thread builds.

void SetMaxmods(TMaxmods value)

Assign a value to Maxmods data member.

TFixed & SetFixed(void)

Assign a value to Fixed data member.

void SetMaxproductions(TMaxproductions value)

Assign a value to Maxproductions data member.

void SetIterativesettings(TIterativesettings &value)

Assign a value to Iterativesettings data member.

TVariable & SetVariable(void)

Assign a value to Variable data member.

void SetSinglenum(TSinglenum value)

Assign a value to Singlenum data member.

void SetPrecursorsearchtype(TPrecursorsearchtype value)

Assign a value to Precursorsearchtype data member.

TInfiles & SetInfiles(void)

Assign a value to Infiles data member.

void SetSearchctermproduct(TSearchctermproduct value)

Assign a value to Searchctermproduct data member.

void SetReportedhitcount(TReportedhitcount value)

Assign a value to Reportedhitcount data member.

void SetPrecursorcull(TPrecursorcull value)

Assign a value to Precursorcull data member.

TNoprolineions & SetNoprolineions(void)

Assign a value to Noprolineions data member.

void SetMinspectra(TMinspectra value)

Assign a value to Minspectra data member.

TOutfiles & SetOutfiles(void)

Assign a value to Outfiles data member.

TIonstosearch & SetIonstosearch(void)

Assign a value to Ionstosearch data member.

EMSSerialDataFormat

Access to EMSSerialDataFormat's attributes (values, names) as defined in spec.

void SetMinnoenzyme(TMinnoenzyme value)

Assign a value to Minnoenzyme data member.

void SetPseudocount(TPseudocount value)

Assign a value to Pseudocount data member.

void SetExactmass(TExactmass value)

Assign a value to Exactmass data member.

void SetDb(const TDb &value)

Assign a value to Db data member.

void SetMissedcleave(TMissedcleave value)

Assign a value to Missedcleave data member.

void SetCutinc(TCutinc value)

Assign a value to Cutinc data member.

void SetZdep(TZdep value)

Assign a value to Zdep data member.

void SetProductsearchtype(TProductsearchtype value)

Assign a value to Productsearchtype data member.

void SetProbfollowingion(TProbfollowingion value)

Assign a value to Probfollowingion data member.

void SetDoublewin(TDoublewin value)

Assign a value to Doublewin data member.

void SetCutlo(TCutlo value)

Assign a value to Cutlo data member.

void SetTophitnum(TTophitnum value)

Assign a value to Tophitnum data member.

void SetSinglewin(TSinglewin value)

Assign a value to Singlewin data member.

void SetDoublenum(TDoublenum value)

Assign a value to Doublenum data member.

void SetNocorrelationscore(TNocorrelationscore value)

Assign a value to Nocorrelationscore data member.

void SetMsmstol(TMsmstol value)

Assign a value to Msmstol data member.

void SetNmethionine(TNmethionine value)

Assign a value to Nmethionine data member.

TTaxids & SetTaxids(void)

Assign a value to Taxids data member.

void SetPepppm(TPepppm value)

Assign a value to Pepppm data member.

void SetCuthi(TCuthi value)

Assign a value to Cuthi data member.

void SetMaxnoenzyme(TMaxnoenzyme value)

Assign a value to Maxnoenzyme data member.

void SetSearchb1(TSearchb1 value)

Assign a value to Searchb1 data member.

void SetMinhit(TMinhit value)

Assign a value to Minhit data member.

void SetCutoff(TCutoff value)

Assign a value to Cutoff data member.

void SetAutomassadjust(TAutomassadjust value)

Assign a value to Automassadjust data member.

void SetEnzyme(TEnzyme value)

Assign a value to Enzyme data member.

void SetHitlistlen(THitlistlen value)

Assign a value to Hitlistlen data member.

void SetNumisotopes(TNumisotopes value)

Assign a value to Numisotopes data member.

void SetChargehandling(TChargehandling &value)

Assign a value to Chargehandling data member.

void SetPeptol(TPeptol value)

Assign a value to Peptol data member.

void SetScale(TScale value)

Assign a value to Scale data member.

@ eMSSerialDataFormat_csv

csv (excel)

@ eMSSerialDataFormat_xml

open XML format

@ eMSSerialDataFormat_asnbinary

open ASN.1 binary format

@ eMSSerialDataFormat_pepxml

pepXML format

@ eMSSerialDataFormat_asntext

open ASN.1 text format

@ eMSSerialDataFormat_xmlbz2

bzip2 XML format

@ eMSCalcPlusOne_calc

guess charge one

@ eMSSpectrumFileType_mgf

@ eMSSpectrumFileType_omxbz2

bzip2 omx file

@ eMSSpectrumFileType_dtablank

@ eMSSpectrumFileType_pkl

@ eMSSpectrumFileType_omx

xml for iterative search

@ eMSSpectrumFileType_dtaxml

@ eMSSpectrumFileType_dta

@ eMSSpectrumFileType_xml

xml MSRequest

@ eMSSpectrumFileType_oms

asn.1 binary for iterative search

@ eMSMod_max

maximum number of mods

const struct ncbi::grid::netcache::search::fields::SIZE size

unsigned int GetCpuCount(void)

Return number of active CPUs (never less than 1).

void InsertList(const string &Input, T &ToInsert, string error)

template for inserting elements of comma delimited string of ints into a list

char const *const kIonLabels[eMSIonType_max]

some friendly names for ion series

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