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

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CMSHitSet::THits::const_iterator iHit;

CMSHits::TPephits::const_iterator iPephit;

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

void CreateArrays(void)

creates arrays for the existing set

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

int SetUpSearchSettings(CRef< CMSSearchSettings > &SearchSettings, bool IsIterative)

take a search settings object, give it an id, and put it in the right place

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 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

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

Set search settings given args.

virtual int Run()

Run the application.

virtual void AppInit(CArgDescriptions *argDesc)

application specific initialization

static int SaveAnyFile(CMSSearch &MySearch, CMSSearchSettings::TOutfiles OutFiles, CRef< CMSModSpecSet > Modset)

Write out a complete search.

static int ReadSearchRequest(const string &Filename, const ESerialDataFormat DataFormat, CMSSearch &MySearch)

Read in an MSRequest.

static void ValidateSearchSettings(CRef< CMSSearchSettings > &Settings)

Validates Search Settings.

static void CreateSearchSettings(string FileName, CRef< CMSSearchSettings > &Settings)

create search setting object from file or brand new

static int LoadAnyFile(CMSSearch &MySearch, CConstRef< CMSInFile > InFile, bool *SearchEngineIterative=0)

Read in any input file.

static int ReadModFiles(const string &ModFileName, const string &UserModFileName, const string &Path, CRef< CMSModSpecSet > Modset)

read in modification files.

bool & SetRankScore(void)

Sets the scoring to use rank statistics.

bool & SetIterative(void)

Sets iterate search.

const bool GetIterative(void) const

Gets iterate search.

int InitBlast(const char *blastdb, bool use_mmap=false)

init blast databases.

void SetupSearch(CRef< CMSRequest > MyRequestIn, CRef< CMSResponse > MyResponseIn, CRef< CMSModSpecSet > Modset, CRef< CMSSearchSettings > SettingsIn, TOMSSACallback Callback=0, void *CallbackData=0)

Setup the ms/ms search.

bool & SetPoissonOnly(void)

Sets the scoring to use rank statistics only with Poisson.

const string & GetProgramExecutablePath(EFollowLinks follow_links=eIgnoreLinks) const

Get the application's executable path.

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

int AppMain(int argc, const char *const *argv, const char *const *envp=0, EAppDiagStream diag=eDS_Default, const char *conf=NcbiEmptyCStr, const string &name=NcbiEmptyString)

Main function (entry point) for the NCBI application.

const CNcbiArguments & GetArguments(void) const

Get the application's cached unprocessed command-line arguments.

void AddFlag(const string &name, const string &comment, CBoolEnum< EFlagValue > set_value=eFlagHasValueIfSet, TFlags flags=0)

Add description for flag argument.

void SetUsageContext(const string &usage_name, const string &usage_description, bool usage_sort_args=false, SIZE_TYPE usage_width=78)

Set extra info to be used by PrintUsage().

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.

@ eDS_Default

Try standard log file (app.name + ".log") in /log/, use stderr on failure.

@ eDiag_Warning

Warning message.

void Fatal(CExceptionArgs_Base &args)

void Info(CExceptionArgs_Base &args)

void Reset(void)

Reset reference object.

const TDb & GetDb(void) const

Get the Db member data.

const TInfiles & GetInfiles(void) const

Get the Infiles member data.

TResponse & SetResponse(void)

Assign a value to Response data member.

TRequest & SetRequest(void)

Assign a value to Request data member.

const TOutfiles & GetOutfiles(void) const

Get the Outfiles member data.

@ eMSHitError_notenuffpeaks

not enough peaks to search

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

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

static void OMSSACallback(int TotalSeq, int Completed, void *Anything)

progress callback

int main(int argc, const char *argv[])

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