pfogfile.cpp File Reference

#include "Range.h"
#include "Match.h"
#include <iostream>
#include <map>
#include <fstream>
#include "bioseq.h"
#include "dbinfo.h"

Classes
struct	ProgParameters
Functions
void	bufferProteinsFromFile (const string &infile, map< string, Protein > &store)
void	bufferGenomicFromFile (const string &file, map< string, DNA > &store)
void	storeBestModels (Tblastn &tbn, ostream &SUM, ostream &DET, const ProgParameters &par)
void	usage (const ProgParameters &param)
bool	processAll (const map< string, Protein > &pepstore, const map< string, DNA > &genomicstore, const ProgParameters &par)
int	main (int argc, char *argv[])

---

Function Documentation

void bufferGenomicFromFile	(	const string &	file,
		map< string, DNA > &	store
	)

Store all genomic from one genome int a map

References bioseq::empty(), bioseq::getName(), ifstream(), and bioseq::read().

Referenced by main().

void bufferProteinsFromFile	(	const string &	infile,
		map< string, Protein > &	store
	)

store protein into a map<string,string> so the program can randomly access the sequence by the proteinid

References bioseq::empty(), bioseq::getName(), ifstream(), and bioseq::read().

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

References bufferGenomicFromFile(), bufferProteinsFromFile(), ProgParameters::detailfile, ProgParameters::enough(), ProgParameters::genomicfile, ProgParameters::identitycut, processAll(), ProgParameters::prtinfile, ProgParameters::qcovcut, Tblastn::readConfig(), ProgParameters::scorecut, ProgParameters::summaryfile, ProgParameters::tbnfile, and usage.

bool processAll	(	const map< string, Protein > &	pepstore,
		const map< string, DNA > &	genomicstore,
		const ProgParameters &	par
	)

process a subset from the whole table. In this particular case, I am picking a Reverse transcriptase scanning against different databases. I used RT from SwissProt and searched against a dozen fungal gnomic databases using tblastn. Because this program only deals with the whole table. I have the choice to write a wrapper to use a dozen tables or use a sql to select a portion of the tables.

map of pid => protein sequence map of gid => genomic DNA sequence

parameters for this program

Returns:

true if success, false if fail.

References ProgParameters::detailfile, E, gap(), ifstream(), ProgParameters::showevery, storeBestModels(), ProgParameters::summaryfile, and ProgParameters::tbnfile.

Referenced by main().

void storeBestModels	(	Tblastn &	tbn,
		ostream &	SUM,
		ostream &	DET,
		const ProgParameters &	par
	)

helper function used by processOneBatch and Main

make it work into different streams

The par mainly provide the cutoff information.

Only best chains with maxScore() > par.scorecut will be outputed.

Store information into output streams SUM and DET

make it work into different streams

The par mainly provide the cutoff information. Store information into output streams SUM and DET

References Linkmatch::bestModel(), ProgParameters::identitycut, Tblastn::numMatches(), Tblastn::outputModel(), ProgParameters::qcovcut, ProgParameters::qcovlencut, Tblastn::queryLength(), and ProgParameters::scorecut.

void usage

(

const ProgParameters &

param

)

this describe how to use this program After calling this function the program will terminate.