dbaln_fungalrmsimp.cpp File Reference

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

Classes
struct	ProgParam
Functions
pair< double, double >	computeZvalue (Protein &p1, Protein &p2, int n)
double	computeIdentityZValue (Protein &p1, Protein &p2, const int n, double *v)
pair< double, double >	avgstd (vector< double > nums)
void	createTmpTable (const string &tab, mysqlpp::Connection &conn)
void	bufferProtein (map< int, string > &store, Connection &conn, const string &idcol)
void	bufferAllProteins (const ProgParam &par, Connection &conn, map< int, string > &qstore, map< int, string > &tstore)
bool	addEntropyColumn (Connection &conn, const string &tab)
int	main (int argc, char *argv[])

---

Function Documentation

bool addEntropyColumn	(	Connection &	conn,
		const string &	tab
	)

Referenced by main().

pair< double, double > avgstd

(

vector< double >

nums

)

Referenced by breakonecl().

void bufferAllProteins	(	const ProgParam &	par,
		Connection &	conn,
		map< int, string > &	qstore,
		map< int, string > &	tstore
	)

connects to two protein databases to cache all proteins from the query database and the target database.

Parameters:

conn

is a mysql connection to the main database containing the alignment table.

References ProgParam::alntab, bufferProtein(), ProgParam::db1, ProgParam::db2, ProgParam::entropycut, MysqlDBInfo::getAuthenInfo(), MysqlDBInfo::getPassword(), MysqlDBInfo::getUser(), ProgParam::host1, ProgParam::host2, ProgParam::id1, and ProgParam::id2.

Referenced by main().

void bufferProtein	(	map< int, string > &	store,
		Connection &	conn,
		const string &	idcol
	)

store serve both as the input and output The input is the id list, the output fills in the sequence

Fetch 100 proteins at a time.

References string().

double computeIdentityZValue	(	Protein &	p1,
		Protein &	p2,
		const int	n,
		double *	v
	)

References Dynaln::getIdentity(), bioseq::randomize(), Dynaln::runglobal(), and Dynaln::setSeq().

Referenced by main().

pair<double,double> computeZvalue	(	Protein &	p1,
		Protein &	p2,
		int	n
	)

return a pair of z-score for (score,identity)

void createTmpTable	(	const string &	tab,
		mysqlpp::Connection &	conn
	)

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

References ProgParam::alntab, bufferAllProteins(), computeIdentityZValue(), ProgParam::db, ProgParam::db1, ProgParam::db2, ProgParam::entropycut, MysqlDBInfo::getAuthenInfo(), MysqlDBInfo::getPassword(), MysqlDBInfo::getUser(), ProgParam::host, ProgParam::host1, ProgParam::host2, ProgParam::id1, ProgParam::id2, bioseq::substr(), and ProgParam::valid().