testGModel.cpp File Reference

#include "GenModel.h"
#include "RNAModel.h"
#include <mysql++.h>
#include <dbinfo.h>
#include "bioseq.h"
#include <set>
#include <list>

Functions
string *	getGenomicSeq (Query &gquery, const string &gname)
void	bestORF (Query &gquery)
void	testBreakup (Query &gquery)
int	main (int argc, char *argv[])

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Function Documentation

void bestORF

(

Query &

gquery

)

References mRNAModel::FivePrimeUTR(), getGenomicSeq(), mRNAModel::getProtein(), Noschain::numberOfRanges(), and mRNAModel::ThreePrimeUTRLength().

string * getGenomicSeq	(	Query &	gquery,
		const string &	gname
	)

References string().

Referenced by bestORF(), main(), and testBreakup().

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

References GenModel::CDSSeq(), Noschain::compareChainAndFix(), MysqlDBInfo::getAuthenInfo(), getGenomicSeq(), MysqlDBInfo::getPassword(), MysqlDBInfo::getUser(), GenModel::makeProtein(), Range::overlay(), GenModel::pepstr(), Noschain::show(), testBreakup(), and GenModel::valid().

void testBreakup

(

Query &

gquery

)

References ESTAssemblyid::breakup(), getGenomicSeq(), ESTAssembly::isChimera(), and mRNAModel::ThreePrimeUTRLength().

Referenced by main().