dbalnhelper.h File Reference

#include <mysql++.h>
#include <string>

Go to the source code of this file.

Classes
struct	Alnrange
Functions
int	table2map (map< int, string > &store, mysqlpp::Connection &conn, const string &tab, string idcol="id", string seqcol="seq")
int	tableFillMap (map< int, string > &store, mysqlpp::Connection &conn, const string &tab, string idcol="id", string seqcol="seq")
int	tableFillMapFirst (map< int, string > &store, const vector< pair< int, int > > &guide, mysqlpp::Connection &conn, const string &tab, string idcol="proteinId", string seqcol="seq")
int	table2pair (vector< pair< int, int > > &pairs, mysqlpp::Connection &conn, const string &tab, string id1col="seq1id", string id2col="seq2id")
int	table2vector (vector< Alnrange > &store, mysqlpp::Connection &conn, const string &tab, string id1col="seq1id", string id2col="seq2id")
bool	tableExists (mysqlpp::Connection &conn, const string &tab)

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Function Documentation

int table2map	(	map< int, string > &	store,
		mysqlpp::Connection &	conn,
		const string &	tab,
		string	idcol = "id",
		string	seqcol = "seq"
	)

store all id => seq from tab in the database connection conn into buff.

Parameters:

	conn	Mysql database connection
	buff	result to store the id=>seq map
	tab	table name
	idcol	name of the idcolumn, default id
	seqcol	name of the sequence column default seq

Returns:

the number of proteins stored.

Referenced by alignProtein(), and loadprt::operator()().

int table2pair	(	vector< pair< int, int > > &	pairs,
		mysqlpp::Connection &	conn,
		const string &	tab,
		string	id1col = "seq1id",
		string	id2col = "seq2id"
	)

Store a cross of two ids into a vector of pair of integers for future usage.

Parameters:

pairs

is an empty vector to be filled.

Returns:

the number of distinct pairs.

Note we are only using int,int type. Future extention could convert this to a template function.

Referenced by alignProtein(), and loadpair::operator()().

int table2vector	(	vector< Alnrange > &	store,
		mysqlpp::Connection &	conn,
		const string &	tab,
		string	id1col = "seq1id",
		string	id2col = "seq2id"
	)

Referenced by loadpair::operator()().

bool tableExists	(	mysqlpp::Connection &	conn,
		const string &	tab
	)

int tableFillMap	(	map< int, string > &	store,
		mysqlpp::Connection &	conn,
		const string &	tab,
		string	idcol = "id",
		string	seqcol = "seq"
	)

Store proteinsequence into a map structure

Parameters:

store

serve both as the input and output, this program fills the value part. The key part of the map serves as input. mysql Connection object table name

Fetch 100 proteins at a time from the table.

References string().

Referenced by tableFillMapFirst().

int tableFillMapFirst	(	map< int, string > &	store,
		const vector< pair< int, int > > &	guide,
		mysqlpp::Connection &	conn,
		const string &	tab,
		string	idcol = "proteinId",
		string	seqcol = "seq"
	)

overloaded version that uses a vector pair as input

References tableFillMap().

Referenced by alignProtein().