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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/omssa2pepXML_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/ms/omssa/omssa2pepXML.cpp Source File

75 virtual void Init

(

void

);

76 virtual int Run

(

void

);

77 virtual void Exit

(

void

);

91

arg_desc->PrintUsageIfNoArgs();

94

arg_desc->SetUsageContext(

GetArguments

().GetProgramBasename(),

95 "Convert OMSSA ASN.1 and XML output files to PepXML"

);

98

arg_desc->AddFlag(

"xml"

"Input file is XML"

);

99

arg_desc->AddFlag(

"bz2"

"Input file is bzipped XML"

);

100

arg_desc->AddFlag(

"asn"

"Input file is ASN.1"

);

101

arg_desc->AddFlag(

"asntext"

"Input file is ASN.1 text"

);

103

arg_desc->AddOptionalKey(

"o"

"outfile"

104 "filename for pepXML formatted search results"

107

arg_desc->AddPositional

109 "The name of the XML file to load"

129 string

filename = args[

"filename"

].AsString();

132 string

fullpath, path, base, ext;

134

fullpath =

file

.GetPath();

142

newname = args[

"o"

].AsString();

149 if

(args[

"xml"

] || args[

"bz2"

]) {

152

}

else if

(args[

"asn"

]) {

155

}

else if

(args[

"asntext"

]) {

161 if

(ext ==

".oms"

) {

163

}

else if

(ext ==

".omx"

) {

165

}

else if

(ext ==

".omt"

) {

169

cout <<

"Reading "

<< filename <<

" as "

;

172

cout <<

"ASN"

<< endl;

break

;

174

cout <<

"XML"

<< endl;

break

;

176

cout <<

"ASN text"

<< endl;

break

;

178

cout <<

"Unable to determine type of file"

<< endl;

185

cout <<

"Sorry, this file cannot be converted."

<< endl;

186

cout <<

"The original search needs to have been executed with the '-w' flag set."

<< endl;

187

cout <<

"The search settings are not availiable in this file. Aborting"

<< endl;

205

*xml_out << outPepXML;

225 int main

(

int

argc,

const char

* argv[] )

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

void CreateArrays(void)

creates arrays for the existing set

virtual void Init(void)

Initialize the application.

COmssa2pepxmlApplication()

virtual int Run(void)

Run the application.

virtual void Exit(void)

Cleanup on application exit.

void ConvertFromOMSSA(CMSSearch &inOMSSA, CRef< CMSModSpecSet > Modset, string basename, string newname)

convert OMSSA to PepXML

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

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

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

read in modification files.

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.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

const CNcbiArguments & GetArguments(void) const

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

void SetVersion(const CVersionInfo &version)

Set the version number for the program.

@ eString

An arbitrary string.

void SetDiagStream(CNcbiOstream *os, bool quick_flush=true, FDiagCleanup cleanup=0, void *cleanup_data=0, const string &stream_name="")

Set diagnostic stream.

@ eDS_Default

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

static string CreateAbsolutePath(const string &path, ERelativeToWhat rtw=eRelativeToCwd)

Get an absolute path from some, possibly relative, path.

static bool IsAbsolutePath(const string &path)

Check if a "path" is absolute for the current OS.

static void SplitPath(const string &path, string *dir=0, string *base=0, string *ext=0)

Split a path string into its basic components.

ESerialDataFormat

Data file format.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

void SetReferenceSchema(bool use_schema=true)

Make generated XML document reference XML schema.

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

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

void SetDefaultSchemaNamespace(const string &schema_ns)

Set default value of namespace name of generated DTD documents.

bool CanGetRequest(void) const

Check if it is safe to call GetRequest method.

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

Magic spell ;-) needed for some weird compilers... very empiric.

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,...

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

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