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NCBI C++ ToolKit: src/app/formatguess/formatguess.cpp Source File

std::map<ncbi::CFormatGuess::EFormat, std::string>

;

(

);

(

);

(

);

arg_desc->SetUsageContext

);

arg_desc->AddDefaultKey

(

,

,

,

);

arg_desc->AddDefaultKey(

,

,

,

( args[

] ) {

;

;

it = FormatStrings.find( uFormat );

( it == FormatStrings.end() ) {

format_name = it->second;

object_type_to_show(

);

( args[

] ) {

output_format = args[

].AsString();

name_of_input_stream = args[

].AsString();

( name_of_input_stream.empty() || name_of_input_stream ==

) {

name_of_input_stream =

;

( output_format ==

) {

cout << name_of_input_stream <<

;

( ! format_name.empty() );

( ! object_type_to_show.empty() ) {

cout <<

<< object_type_to_show;

}

( output_format ==

) {

input_stream_node(

);

stream_attribs.

(

, name_of_input_stream.c_str());

stream_attribs.

(

, format_name.c_str());

( ! object_type_to_show.empty() ) {

stream_attribs.

(

, object_type_to_show.c_str());

output_node.

(input_stream_node);

(

argc,

* argv[])

User-defined methods of the data storage class.

This file contains the definition of the xml::attributes class.

static string guess_object_type(CObjectIStream &obj_istrm)

virtual int Run(void)

Run the application.

virtual void Init(void)

Initialize the application.

virtual void Exit(void)

Cleanup on application exit.

Wraps CFormatGuess, and if CFormatGuess's result is Unknown, it tries every file reader until one wor...

CFormatGuess::EFormat GuessFormatAndContent(CFileContentInfo &contentInfo)

void SetRecognizedGenbankTypes(const set< TTypeInfo > &recognizedGenbankTypes)

EFormat

The formats are checked in the same order as declared here.

@ eFiveColFeatureTable

Five-column feature table.

@ eBinaryASN

Binary ASN.1.

@ eGff2

GFF2, CGff2Reader, any GFF-like that doesn't fit the others.

@ eBed

UCSC BED file format, CBedReader.

@ eGtf

New GTF, CGtfReader.

@ eSnpMarkers

SNP Marker flat file.

@ eHgvs

HGVS, CHgvsParser.

@ eAgp

AGP format assembly, AgpRead.

@ eDistanceMatrix

Distance matrix file.

@ ePhrapAce

Phrap ACE assembly file.

@ eFlatFileSequence

GenBank/GenPept/DDBJ/EMBL flat-file sequence portion.

@ eGff3

GFF3, CGff3Reader.

@ eGlimmer3

Glimmer3 predictions.

@ eFasta

FASTA format sequence record, CFastaReader.

@ eUnknown

unknown format

@ eRmo

RepeatMasker Output.

@ eAlignment

Text alignment.

@ eBed15

UCSC BED15 or microarray format.

@ eWiggle

UCSC WIGGLE file format.

static const char * GetFormatName(EFormat format)

The xml::attributes class is used to access all the attributes of one xml::node.

void insert(const char *name, const char *value, const ns *nspace=NULL)

Add an attribute to the attributes list.

The xml::document class is used to hold the XML tree and various bits of information about it.

void save_to_stream(std::ostream &stream, save_option_flags flags=save_op_default) const

Convert the XML document tree into XML text data and then insert it into the given stream.

The xml::node class is used to hold information about one XML node.

void push_back(const node &child)

Add a child xml::node to this node.

xml::attributes & get_attributes(void)

Get the list of attributes.

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

FormatMap::iterator FormatIter

std::map< ncbi::CFormatGuess::EFormat, std::string > FormatMap

set< TTypeInfo > sDefaultRecognizedGenbankObjectTypes

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.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ fBinary

Open file in binary mode.

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 TTypeInfo GetTypeInfo(void)

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

This file contains the definition of the xml::document class.

This file contains the definition of the xml::node class.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

CFileContentInfoGenbank mInfoGenbank

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