footprintHelper.h File Reference

#include <mysql++.h>
#include <iostream>
#include "Match.h"
#include <fstream>
#include "FPGModel.h"

Go to the source code of this file.

Functions
bool	createFootprintKeyTable (Connection &conn, const string &tabname)
int	storeInFootprintKeyTable (vector< FPGModel * > &rm, Connection &conn, const string tabname)
void	newFootprintByDelete (Connection &conn, const string &intab, const string &deltab, const string &outtab)
void	newFootprintByPick (Connection &conn, const string &intab, const string &picktab, const string &outtab)
bool	remove_nrjunk (Connection &conn, const string &fptab)
void	create_footprint_exon (Connection &conn, const string &fptab, const string &fpdutab, const string &exontab)
void	filterFootprint (Connection &conn, const string &fptab)

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Function Documentation

void create_footprint_exon	(	Connection &	conn,
		const string &	fptab,
		const string &	fpdutab,
		const string &	exontab
	)

create footprintDetail type of table, from a know footprintDetail table, selecting a subset of detail according to fptab input: fptab, fpdutab output: exontab, is a subset of fpdutab according to fptab This is done after buildNewFootprintTable

Referenced by discardLowerFootprint(), and main().

bool createFootprintKeyTable	(	Connection &	conn,
		const string &	tabname
	)

create a table (tabname) with the primary key of footprint type of tables qid,tid,fpnum

Referenced by discardLowerFootprint().

void filterFootprint	(	Connection &	conn,
		const string &	fptab
	)

set the quality column to some negative numbers based on coverage, and identity, or very long models with low scores

Do some bassic filtering before the preparation step. Will add a quality column to the table No delete, just quality marking

Referenced by discardLowerFootprint().

void newFootprintByDelete	(	Connection &	conn,
		const string &	intab,
		const string &	deltab,
		const string &	outtab
	)

create a new footprint table outtab by removing entries in intab according the primary key stored in deltab input: intab, deltab output: outtab

void newFootprintByPick	(	Connection &	conn,
		const string &	intab,
		const string &	picktab,
		const string &	outtab
	)

Referenced by discardLowerFootprint().

bool remove_nrjunk	(	Connection &	conn,
		const string &	fptab
	)

procedures to do some clean up Remove models that are made from know junk protein from nr. This procesure should not be mingled here. In the futrue, this needs to be moved outside of this program.

int storeInFootprintKeyTable	(	vector< FPGModel * > &	rm,
		Connection &	conn,
		const string	tabname
	)

input: rm, this is a set<Blmodel*>. tabname, name of the tmpDelTable This function will write all the primary key(qid,tid,fpnum) into tabname. return the number of rows inserted.

References fpkey::fpnum, fpkey::qid, and fpkey::tid.

Referenced by discardLowerFootprint().