dbaln_chimerathread.cpp File Reference

#include "mysql++.h"
#include <string>
#include "bioseq.h"
#include "dynaln.h"
#include <math.h>
#include <fstream>
#include "dbinfo.h"
#include <map>
#include "strformat.h"
#include "dbalnhelper.h"
#include <boost/thread/thread.hpp>
#include <boost/thread/condition.hpp>

Classes
class	loadprt
class	loadpair
class	alignmentRunner
Defines
#define	MYSQLPLUS2
Functions
void	alignProtein (const string &pairtab)
void	usage ()
int	main (int argc, char *argv[])
Variables
boost::mutex	io_mutex
string	user
string	passwd

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Define Documentation

#define MYSQLPLUS2

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Function Documentation

void alignProtein

(

const string &

pairtab

)

for loading input to instruct the alignment pairtab columns must be: (db1pid int, db2pid int) query protein: chimera_query_protein (id,seq) target protein: chimera_target_protein (id,seq)

These will be variables in future version of the function.

References MysqlDBInfo::getAuthenInfo(), MysqlDBInfo::getPassword(), MysqlDBInfo::getUser(), passwd, and user.

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

References alignProtein().

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

boost::mutex io_mutex

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.

format I am adding a format for bootstrap where a vector of 0,1,2 are output that stands for mismatch, similar, and match respectively.

string passwd

string user