mergefootprint.cpp File Reference

#include <mysql++.h>
#include <iostream>
#include <fstream>
#include <list>
#include "Range.h"
#include <string>
#include "strformat.h"

Classes
struct	ProgParam
Functions
bool	createSummaryTable (Connection &dbh, const string &tab)
void	topfp (Connection &conn, Connection &conn2, const ProgParam &par)
void	usage ()
void	mergeNeighbor (Connection &conn, Connection &conn2, const ProgParam &par)
int	main (int argc, char *argv[])
ostream &	operator<< (ostream &ous, const ProgParam &par)

---

Function Documentation

bool createSummaryTable	(	Connection &	dbh,
		const string &	tab
	)

always drop existing table create a summary table Here the exon is the merged homology part, not strictly.

Referenced by mergeNeighbor().

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

References ProgParam::fpdetailtab, ProgParam::fptoptab, mergeNeighbor(), ProgParam::oufile, ProgParam::outab, and user.

void mergeNeighbor	(	Connection &	conn,
		Connection &	conn2,
		const ProgParam &	par
	)

this version deals with multiple target databases Normally you don't do this. It is one search db. I am using this test case to develope this application

References ProgParam::avgidencut, RangeChain::begin(), createSummaryTable(), RangeChain::end(), ProgParam::exolpcut, ProgParam::exolpfrcut, RangeChain::exonMerge(), RangeChain::exonOverlap(), ProgParam::fpdetailtab, ProgParam::fptoptab, itos(), RangeChain::numberOfRanges(), ProgParam::oufile, ProgParam::outab, string(), RangeChain::sumLength(), and RangeChain::tableRows().

Referenced by main().

ostream& operator<<	(	ostream &	ous,
		const ProgParam &	par
	)

only check intab and outab for not emptyness

References ProgParam::avgidencut, ProgParam::exolpcut, ProgParam::exolpfrcut, ProgParam::fpdetailtab, ProgParam::fptoptab, ProgParam::oufile, and ProgParam::outab.

void topfp	(	Connection &	conn,
		Connection &	conn2,
		const ProgParam &	par
	)

this version deals with multiple target databases Normally you don't do this. It is one search db. I am using this test case to develope this application

Make sure the quality of the table has been set to non-null. This program will only pick quality >= 0.

References Range::begin(), createUniqueTable(), del(), Range::end(), ProgParam::fpmaxlen, ProgParam::intab, Range::merge(), ProgParam::oufile, ProgParam::outab, Range::output(), Range::overlap(), and string().

Referenced by main().

void usage

(

)

Input file: ngiden.tab format +----------+----------+------------+ | db1 | db2 | avgngiden | +----------+----------+------------+ | Aspni1 | Aspni1 | 0.42651027 | | Aspni1 | Batde5 | 0.37095312 | | Aspni1 | Lacbi1 | 0.38920021 | ...

I will generate file format suitable for bionj

The input file must have header.

The input could be a full matrix or one half of (triangle) if the matrix is symmetric.