wolm.cpp File Reference

#include <mysql++.h>
#include <iostream>
#include <map>
#include <fstream>
#include "Range.h"
#include <functional>

Classes
class	Rangewid
Functions
void	getLongIntrons (Connection &conn, const string &intab, map< string, vector< Rangewid > * > &ins, const string &cdstab, int minintron)
void	storeCDS (Connection &conn, const string &cdstab, map< string, vector< Range > * > &cdsm)
int	countIncludedRange (const Rangewid &rwi, const vector< Range > *vr)
bool	gtint (const Range &r, const int i)
void	cleanup (map< string, vector< Rangewid > * > &in, map< string, vector< Range > * > &cd)
void	updateCDS (Connection &conn, const string &cdstab, const map< string, int > &lc, const int literSizeCut)
int	main (int argc, char *argv[])
bool	sortop (const Range &r, const int i)

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Function Documentation

void cleanup	(	map< string, vector< Rangewid > * > &	in,
		map< string, vector< Range > * > &	cd
	)

Referenced by main().

int countIncludedRange	(	const Rangewid &	rwi,
		const vector< Range > *	vr
	)

rwi is the intron Range, vr is the CDS Range vector of pointers rwi is one intron vr is a pointer to the vector of CDS_ranges return: The number of CDS included inside this intron.

References Range::begin(), Range::end(), and sortop().

Referenced by main().

void getLongIntrons	(	Connection &	conn,
		const string &	intab,
		map< string, vector< Rangewid > * > &	ins,
		const string &	cdstab,
		int	minintron
	)

genes with introns longer than minintron will be stored in ins which is index by tid -> vector<Rangewid>. the vector is [subseqid, exon_min, exon_max] Input: intab (intron table with absolute coordinates) cdstab (cds table)

References string().

Referenced by main().

bool gtint	(	const Range &	r,
		const int	i
	)

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

References cleanup(), countIncludedRange(), Rangewid::getId(), getLongIntrons(), Range::length(), storeCDS(), updateCDS(), and user.

bool sortop	(	const Range &	r,
		const int	i
	)

References Range::begin().

Referenced by countIncludedRange().

void storeCDS	(	Connection &	conn,
		const string &	cdstab,
		map< string, vector< Range > * > &	cdsm
	)

indexed by chromosome We only use CDS whose quality is better than 0 or pep longer than 300 this can eliminate some false CDS the result is stored in cdsm which is tid => vector<Range> The vector contain [min_end, max_end] of each CDS

References string().

Referenced by main().

void updateCDS	(	Connection &	conn,
		const string &	cdstab,
		const map< string, int > &	lc,
		const int	literSizeCut
	)

Referenced by main().