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/*
* compgenepred.hh
*
* License: Artistic License, see file LICENSE.TXT or
* https://opensource.org/licenses/artistic-license-1.0
*/
#ifndef _COMPGENEPRED_HH
#define _COMPGENEPRED_HH
// project includes
#include "extrinsicinfo.hh"
#include "randseqaccess.hh"
#include "phylotree.hh"
#include "geneMSA.hh"
#include "genomicMSA.hh"
#include "namgene.hh"
#include <stack>
// addeded for inetrval merging of generanges belonging to the same species
#ifdef TESTING
void mergeInterval(list<tuple<string,int,int> >& interval);
void mergeIntervals(vector<string>& speciesNames, vector<list<tuple<string,int,int> > >& intervals);
bool sortInterval(const tuple<string,int,int>& a, const tuple<string,int,int>& b);
void writeIntervals(string dirname, vector<string>& speciesNames, vector<list<tuple<string,int,int> > >& intervals);
bool shiftGFF(string filename);
#endif
/**
* @brief comparative gene prediction on multiple species
*
* @author Mario Stanke
* @author Alexander Gebauer
* @author Stefanie Koenig
*/
class CompGenePred {
public:
CompGenePred();
~CompGenePred() { delete rsa;}
void start();
void runPredictionOrTest();
#ifdef TESTING
// helpers for testing
void postprocTest();
bool readInterval(string filename, list<tuple<string,int,int> >& grlist);
#endif
RandSeqAccess *rsa;
PhyloTree tree;
};
#endif // _COMPGENEPRED_HH
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