compgenepred.hh

/*
 * 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>
 
 
// added for interval merging of gene ranges 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
 
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;
    void test_2(double ctree_scaling_factor);
};
 
#endif  // _COMPGENEPRED_HH