gwseedaln.cpp File Reference

#include "mysql++.h"
#include <string>
#include "bioseq.h"
#include "dynaln.h"
#include <math.h>
#include <fstream>
#include "dbalnhelper.h"

Defines
#define	MYSQLPLUS2
Functions
void	getPrt (Query &q, const string &id, string &prt)
string	getModelprt (Query &q, const string &id, string &prt)
string	getPrtByModelId (Query &q, const string &id, string &prt, string &prtid)
void	getnrPrt (Query &q, const string &id, string &prt, const string &nrtab)
void	alignProtein (ostream &ous, const string &id, Connection &conn, Connection &nrconn, const string &nrtab, const char idtype)
void	usage ()
int	main (int argc, char *argv[])
Variables
string	user = "kzhou"
string	passwd = "Hotcreek2800"

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Define Documentation

#define MYSQLPLUS2

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Function Documentation

void alignProtein	(	ostream &	ous,
		const string &	id,
		Connection &	conn,
		Connection &	nrconn,
		const string &	nrtab,
		const char	idtype
	)

References getModelprt(), getnrPrt(), getPrtByModelId(), Dynaln::printAlign(), prtid, and Dynaln::runlocal().

string getModelprt	(	Query &	q,
		const string &	id,
		string &	prt
	)

References string().

Referenced by alignProtein().

void getnrPrt	(	Query &	q,
		const string &	id,
		string &	prt,
		const string &	nrtab
	)

References string().

Referenced by alignProtein().

void getPrt	(	Query &	q,
		const string &	id,
		string &	prt
	)

the tab must have id and seq column

References string().

string getPrtByModelId	(	Query &	q,
		const string &	id,
		string &	prt,
		string &	prtid
	)

References string().

Referenced by alignProtein().

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

References alignProtein(), passwd, usage, and user.

void usage

(

)

given gmap summary format, this program converts it into combest archive format (*.car)

It can be used a pipe, or given specific file names.

this is a helper program to count distinct estids in the ESTId column of the combest result. So it is the actual number of ESTs mapped. This could be lower for deeply covered genome because of the coverage depth-dependent filtering.

given gmap summary format, this program converts it into combest archive format (*.car)

It can be used a pipe, or given specific file names.

this is a helper program to count distinct estids in the ESTId column of the combest result. So it is the actual number of ESTs mapped. This could be lower for deeply covered genome because of the coverage depth-dependent filtering.

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Variable Documentation

string passwd = "Hotcreek2800"

string user = "kzhou"

DESCRIPTION For looking at Genewise seed alignment.

use three connections, the first connection provide the alignment pairs. the second and the third provided the raw sequences All three connections can be the same. each connection provide a table.