coor.hpp

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/*
 * Copyright 2008,2009,2010,2011,2012 Stephan Ossowski, Korbinian Schneeberger,
 * Felix Ott, Joerg Hagmann, Alf Scotland, Sebastian Bender
 * 
 * This file is part of SHORE.
 * 
 * SHORE is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 * 
 * SHORE is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with SHORE.  If not, see <http://www.gnu.org/licenses/>.
 */


#ifndef SHORE_GENOME_COOR_HPP__
#define SHORE_GENOME_COOR_HPP__

#include <string>
#include <utility>

namespace shore {

struct refseq_coor
{
        typedef int chr_t;
        typedef long pos_t;
        typedef long diff_t;

        chr_t chromosome;
        pos_t position;

        refseq_coor();
        refseq_coor(chr_t c,pos_t p);

        static refseq_coor max();
        static refseq_coor min();

        refseq_coor &operator++();
        refseq_coor &operator--();
        refseq_coor operator++(int);
        refseq_coor operator--(int);
        refseq_coor &operator+=(const diff_t d);
        refseq_coor &operator-=(const diff_t d);
};

refseq_coor operator+(const refseq_coor& c0,const refseq_coor::diff_t d);
refseq_coor operator-(const refseq_coor& c0,const refseq_coor::diff_t d);
refseq_coor::diff_t operator-(const refseq_coor& c0,const refseq_coor& c1);

bool operator<(const refseq_coor& gc1,const refseq_coor& gc2);
bool operator>(const refseq_coor& gc1,const refseq_coor& gc2);
bool operator<=(const refseq_coor& gc1,const refseq_coor& gc2);
bool operator>=(const refseq_coor& gc1,const refseq_coor& gc2);

bool operator==(const refseq_coor& gc1,const refseq_coor& gc2);
bool operator!=(const refseq_coor& gc1,const refseq_coor& gc2);

std::ostream &operator<<(std::ostream &os,const refseq_coor &gc);
std::istream &operator>>(std::istream &is,refseq_coor &gc);

struct refseq_region
{
        refseq_coor coor;
        size_t size;

        refseq_region();
        refseq_region(const refseq_coor &c,const size_t s);

        refseq_region &operator=(const refseq_coor &c);
};

bool operator==(const refseq_region& gc1,const refseq_region& gc2);
bool operator!=(const refseq_region& gc1,const refseq_region& gc2);

struct refseq_range
{
        refseq_coor start;
        refseq_coor end;

        refseq_range();
        refseq_range(const refseq_coor &s,const refseq_coor &e);
        refseq_range(const refseq_region &region);

        refseq_range &operator=(const refseq_coor &c);
        refseq_range &operator=(const refseq_region &region);
};

bool operator==(const refseq_range& gc1,const refseq_range& gc2);
bool operator!=(const refseq_range& gc1,const refseq_range& gc2);

std::ostream &operator<<(std::ostream &os,const refseq_range &gr);
std::istream &operator>>(std::istream &is,refseq_range &gr);

struct genomic_coor
{
        std::string sequence;
        long position;
    

        genomic_coor();
        genomic_coor(const std::string &seq,const long pos);
};

struct genomic_region
{
        genomic_coor coor;
        size_t size;


        genomic_region();
};

struct genomic_range
{
    genomic_coor start;
    genomic_coor end;

    genomic_range();
    genomic_range(
      const std::string& startseq,const long startpos,
      const std::string& endseq,const long endpos);
    genomic_range(
      const std::string& startseq,const long startpos,const long endpos);

    static std::string esc(const std::string& seqstr);
};

enum Strand
{
    STR_FWD=1,STR_REV=2
};

std::istream& operator>>(std::istream& in,Strand& s);
std::ostream& operator<<(std::ostream& out,const Strand& s);
Strand other_strand(const Strand strand);

enum OptionalStrand
{
    STR_NA_OPT=0,STR_FWD_OPT=STR_FWD,STR_REV_OPT=STR_REV
};

std::istream& operator>>(std::istream& in,OptionalStrand& s);
std::ostream& operator<<(std::ostream& out,const OptionalStrand& s);
OptionalStrand other_strand(const OptionalStrand strand);

enum ExtendedStrand
{
    STR_NA_EXT=STR_NA_OPT,STR_FWD_EXT=STR_FWD,STR_REV_EXT=STR_REV,STR_UNKNOWN_EXT=3
};

std::istream& operator>>(std::istream& in,ExtendedStrand& s);
std::ostream& operator<<(std::ostream& out,const ExtendedStrand& s);
ExtendedStrand other_strand(const ExtendedStrand strand);

std::istream& operator>>(std::istream& is,genomic_range& gr);

std::ostream& operator<<(std::ostream& os,const genomic_range& gr);

} // namespace

#endif // SHORE_GENOME_COOR_HPP__