Cassiopee.h

#include <iostream>
#include <fstream>
#include <list>

#include "tree/tree.hh"

#include "CassiopeeConfig.h"

#include <boost/archive/text_oarchive.hpp>
#include <boost/archive/text_iarchive.hpp>
#include <boost/archive/binary_oarchive.hpp>
#include <boost/archive/binary_iarchive.hpp>
// Provide an implementation of serialize for std::list
#include <boost/serialization/list.hpp>

using namespace std;




class Match {
public:

        bool operator==(const Match& p) const {
                return pos == p.pos && in+del == p.in + p.del;
        }

        int in;
        int del;
        int subst;


        long pos;

        Match();


};

class TreeNode {
public:
        char c;


        list<long> positions;

        long next_pos;

        long next_length;


        TreeNode(char nc);

        TreeNode(char nc, long pos);
        TreeNode();


private:
          friend class boost::serialization::access;
          template<class Archive>
          void serialize(Archive & ar, const unsigned int /*version*/)
          {
            ar & c;
            ar & next_pos;
            ar & next_length;
            ar & positions;
          }

};



#ifndef __CASSIOPEE_H_
#define __CASSIOPEE_H_
//inline std::ostream& operator<<(std::ostream &strm, const TreeNode &a) {
//  return strm << "TreeNode(" << a.c << ")";
//}
#endif


class CassieIndexer {
public:


        CassieIndexer(const char* path);

        ~CassieIndexer();

        void save();

        void load();


        void graph();

        void graph(int depth);

        string getSuffix(long pos);

        void index();

        tree<TreeNode>* getTree();

        list<Match> matches;

        bool do_reduction;

        char getCharAtSuffix(long pos);

        void filltree(long pos);

        long max_depth;

    long max_index_depth;

        long seq_length;

        bool index_loaded_from_file();

private:
        list<TreeNode> serialized_nodes;

        bool loaded_from_file;

        const char* filename;
        ifstream seqstream;
        tree<TreeNode> tr;

        const long MAX_SUFFIX;
        long suffix_position;
        char* suffix;

        long graphNode(tree<TreeNode>::iterator node, long counter, ofstream& myfile, int maxdepth);

        char* loadSuffix(long pos);


        void reset_suffix();



        void fillTreeWithSuffix(tree<TreeNode>::iterator sib, long suffix_pos, long pos);
        void fillTreeWithSuffix(long suffix_pos, long pos);



};


class CassiopeeUtils {
public:
        static void transform_fasta(const string in, const string out);
};

class Ambiguous {
public:
        static bool isequal(char a, char b);
private:
        static bool ismatchequal(char a, const char b[], int len);
        static const char K_MATCH[];
        static const char M_MATCH[];
        static const char R_MATCH[];
        static const char Y_MATCH[];
        static const char S_MATCH[];
        static const char W_MATCH[];
        static const char B_MATCH[];
        static const char V_MATCH[];
        static const char H_MATCH[];
        static const char D_MATCH[];
        static const char N_MATCH[];
};


struct per_position
{
    inline bool operator() (const Match* struct1, const Match* struct2)
    {
        return (struct1->pos < struct2->pos);
    }
};

class CassieSearch {

public:
        CassieSearch(CassieIndexer* index_ref);

        ~CassieSearch();

        void removeDuplicates();

        Match* match_limits;

        list<Match*> matches;

        bool ambiguity;

        int nmax;

        int mode;

        void search(string suffix, bool clear);


        void search(string suffix);

        void search(string suffixes[]);

        bool isequal(char a,char b);


        int max_indel;
        int max_subst;

    long pattern_length;

        void sort();

private:

        static bool same_match (Match* first, Match* second)
        { return ( *first == *second ); }

        CassieIndexer* indexer;

        void getMatchesFromNode(tree<TreeNode>::iterator sib, const int nbSubst, const int nbIn, const int nbDel);



        void searchAtNode(string suffix, const long suffix_pos, const tree<TreeNode>::iterator root, int nbSubst, int nbIn, int nbDel, int nbN);

        void searchAtNode(string suffix, const long suffix_pos, const tree<TreeNode>::iterator root, const tree<TreeNode>::iterator start_node, int nbSubst, int nbIn, int nbDel, int nbN);

        bool searchAtreduction(const string suffix, const tree<TreeNode>::iterator sib, long counter, long tree_reducted_pos, int nbSubst, int nbIn, int nbDel, int nbN);


};