gbresub.cpp File Reference

#include "Gsubreader.h"
#include "gfeature.h"
#include <iostream>
#include <boost/filesystem.hpp>
#include "gsubarch.h"
#include <fstream>
#include <cstring>
#include "strformat.h"
#include <unistd.h>

Functions
bool	getTblFiles (vector< string > &tbl, const string &dirname)
bool	getGsubArchiveFiles (vector< string > &tbl, const string &dirname)
bool	getOldGsub (set< Gsubrecord > &oldsub, const vector< string > &files)
void	table2map (map< string, string > &lookup, const string &file)
void	prepareNewsubDir (string &dir, const string &prefix, const string &database, const string &gbsubmitopt)
int	main (int argc, char *argv[])

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Function Documentation

bool getGsubArchiveFiles	(	vector< string > &	tbl,
		const string &	dirname
	)

Referenced by main().

bool getOldGsub	(	set< Gsubrecord > &	oldsub,
		const vector< string > &	files
	)

References ifstream().

Referenced by main().

bool getTblFiles	(	vector< string > &	tbl,
		const string &	dirname
	)

Referenced by main().

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

References Gsubreader::clear(), deflineBetter(), Gsubreader::getGenes(), getGsubArchiveFiles(), getOldGsub(), getTblFiles(), Gsubreader::numberOfGenes(), prepareNewsubDir(), Gsubreader::read(), and table2map().

void prepareNewsubDir	(	string &	dir,
		const string &	prefix,
		const string &	database,
		const string &	gbsubmitopt
	)

Referenced by main().

void table2map	(	map< string, string > &	lookup,
		const string &	file
	)

generic function to suck file into map, only work on the first 2 columns. Can make column a parameter.

References ifstream(), and split().

Referenced by alignProtein(), main(), and loadprt::operator()().