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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/omssamerge_8cpp_source.html below:

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

96

argDesc->AddDefaultKey(

"i"

"infiles"

97 "file containing list of input files on separate lines"

101

argDesc->AddFlag(

"sw"

"output search results without spectra"

);

103

argDesc->AddFlag(

"it"

"input as text asn.1 formatted search results"

);

104

argDesc->AddFlag(

"ib"

"input as binary asn.1 formatted search results"

);

105

argDesc->AddFlag(

"ix"

"input as xml formatted search results"

);

106

argDesc->AddFlag(

"ibz2"

"input as xml formatted search results compressed by bzip2"

);

111

argDesc->AddFlag(

"ot"

"output as text asn.1 formatted search results"

);

112

argDesc->AddFlag(

"ob"

"output as binary asn.1 formatted search results"

);

113

argDesc->AddFlag(

"ox"

"output as xml formatted search results"

);

114

argDesc->AddFlag(

"obz2"

"output as xml formatted search results compressed by bzip2"

);

125 int main

(

int

argc,

const char

* argv[])

152 else if

(args[

"obz2"

]) {

161 else if

(args[

"ibz2"

]) {

169 if

( args[

"i"

].AsString() !=

""

) {

170

ifstream is(args[

"i"

].AsString().c_str());

173 ERR_POST

(

Fatal

"unable to open input file list "

<< args[

"i"

].AsString());

177 if

(iFileName ==

""

|| is.eof())

continue

;

184

MySearch->CopyCMSSearch(InSearch);

188

MySearch->AppendSearch(InSearch);

198 for

(

size_t

extra = 1; extra <= args.

GetNExtra

(); extra++) {

205

MySearch->CopyCMSSearch(InSearch);

209

MySearch->AppendSearch(InSearch);

221

unique_ptr <CNcbiOfstream> raw_out;

222

unique_ptr <CCompressionOStream> compress_out;

223

unique_ptr <CObjectOStream> txt_out;

226

raw_out.reset(

new CNcbiOfstream

(args[

"o"

].AsString().c_str()));

243

txt_out->Write(

ObjectInfo

(*(*MySearch->SetResponse().begin())));

253

}

catch

(NCBI_NS_STD::exception& e) {

254 ERR_POST

(

Fatal

"Exception in COMSSAMerge::Run: "

<< e.what());

CBZip2StreamCompressor â bzip2 based compression stream processor.

virtual int Run()

Run the application.

virtual void Init()

Initialize the application.

static int ReadCompleteSearch(const string &Filename, const ESerialDataFormat DataFormat, bool bz2, CMSSearch &MySearch)

Read in a complete search (typically for an iterative search)

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.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

void SetVersion(const CVersionInfo &version)

Set the version number for the program.

size_t GetNExtra(void) const

Get the number of unnamed positional (a.k.a. extra) args.

@ eString

An arbitrary string.

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_Info

Informational message.

void Fatal(CExceptionArgs_Base &args)

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

ESerialDataFormat

Data file format.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

CBeginInfo Begin(C &obj)

Get starting point of object hierarchy.

pair< TObjectPtr, TTypeInfo > ObjectInfo(C &obj)

static CObjectOStream * Open(ESerialDataFormat format, CNcbiOstream &outStream, bool deleteOutStream)

Create serial object writer and attach it to an output stream.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

CNcbiIstream & NcbiGetline(CNcbiIstream &is, string &str, char delim, string::size_type *count=NULL)

Read from "is" to "str" up to the delimiter symbol "delim" (or EOF)

CObjectOStream * SetUpOutputFile(CObjectOStream *os, ESerialDataFormat DataFormat)

sets up output file based on DataFormat in particular, initializes xml stream appropriately

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,...

The NCBI C++/STL use hints.

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

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

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