preparegw.cpp File Reference

#include <mysql++.h>
#include <cmath>
#include <iostream>
#include "Match.h"
#include <fstream>
#include "bioseq.h"
#include "strformat.h"
#include <list>
#include "Blmodel.h"
#include <iomanip>
#include "FPGModel.h"
#include "footprintHelper.h"
#include <iterator>

Classes
struct	pregcut
class	Progparam
Functions
void	loadProtein (Query &query, map< string, string > &prt, Connection &nrdb)
void	writeJobToFile (list< string > &jobs, const string &dirname)
void	loadProtein (Connection &cn, map< string, string > &prt, Connection &nrdb, const string &intab, const Progparam &par)
void	discardLowerFootprint (Connection &conn, Progparam &par, Connection &conn2)
void	longPregnant (const vector< FPGModel * > &models, const Progparam &par, map< fpkey, int > &lap, vector< FPGModel * > &nonpregnant, vector< FPGModel * > &pregnant, vector< FPGModel * > &pregnantandlong)
void	deallocateMem (vector< FPGModel * > &m)
int	pickTop (vector< FPGModel * > &model, vector< FPGModel * > &bad, float fr)
void	writeLongPregToFile (const map< fpkey, int > &longNpregnant, ostream &ous)
void	writeJobInstruction (Connection &conn, Connection &conn2, Connection &nrdb, Progparam &params, const int jobsperdir)
int	main (int argc, char *argv[])

---

Function Documentation

void deallocateMem

(

vector< FPGModel * > &

m

)

Referenced by discardLowerFootprint().

void discardLowerFootprint	(	Connection &	conn,
		Progparam &	par,
		Connection &	conn2
	)

References GModel< T >::addExon(), create_footprint_exon(), createFootprintKeyTable(), deallocateMem(), filterFootprint(), Progparam::identityCut, Progparam::inputfootprint_exon_tab, Progparam::inputfootprint_tab, longPregnant(), newFootprintByPick(), Progparam::outputfootprint_exon_tab, Progparam::outputfootprint_tab, pickTop(), Progparam::qcovCut, remove_nrjunk(), storeInFootprintKeyTable(), string(), Progparam::topmodel_fraction, and writeLongPregToFile().

Referenced by main().

void loadProtein	(	Connection &	cn,
		map< string, string > &	prt,
		Connection &	nrdb,
		const string &	intab,
		const Progparam &	par
	)

References Progparam::identityCut, Progparam::qcovCut, and string().

void loadProtein	(	Query &	query,
		map< string, string > &	prt,
		Connection &	nrdb
	)

void longPregnant	(	const vector< FPGModel * > &	models,
		const Progparam &	par,
		map< fpkey, int > &	lap,
		vector< FPGModel * > &	nonpregnant,
		vector< FPGModel * > &	pregnant,
		vector< FPGModel * > &	pregnantandlong
	)

lap contains the long and pregant models selected based on the elipses selection method based on parameter pregcut pc. The non pregnant models will be stored in nonpregnant vector This one can be used to do filtering.

References pregcut::a, pregcut::b, pregcut::c, pregcut::d, Progparam::intronsizeCut, max, min, and Progparam::pc.

Referenced by discardLowerFootprint().

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

References Progparam::bufferZone, discardLowerFootprint(), Progparam::identityCut, Progparam::inputfootprint_exon_tab, Progparam::inputfootprint_tab, Progparam::intronsizeCut, Progparam::nuc2pepratio, Progparam::outputfootprint_exon_tab, Progparam::outputfootprint_tab, Progparam::qcovCut, user, and writeJobInstruction().

int pickTop	(	vector< FPGModel * > &	model,
		vector< FPGModel * > &	bad,
		float	fr
	)

return the number of good entries those elements that are not marked as zero.

References Range::merge(), and Range::overlap().

Referenced by discardLowerFootprint().

void writeJobInstruction	(	Connection &	conn,
		Connection &	conn2,
		Connection &	nrdb,
		Progparam &	params,
		const int	jobsperdir
	)

References Progparam::bufferZone, bioseq::computeEntropy(), Progparam::genomicTable, Blmodel::getExpectedTargetRange(), Blmodel::getFpnum(), Progparam::identityCut, itos(), bioseq::length(), loadProtein(), Progparam::nuc2pepratio, Progparam::outputfootprint_tab, bioseq::printFastaWithHeader(), Progparam::qcovCut, string(), bioseq::subseq(), and writeJobToFile().

Referenced by main().

void writeJobToFile	(	list< string > &	jobs,
		const string &	dirname
	)

Referenced by writeJobInstruction().

void writeLongPregToFile	(	const map< fpkey, int > &	longNpregnant,
		ostream &	ous
	)

Referenced by discardLowerFootprint().