CompressedString.h

/**
 * @file    CompressedString.h
 * @author  MohammadJavad Rezaei Seraji <mjrezaei (at) ce (.) sharif (.) edu>
 *
 * @section LICENCE
 *
 * Copyright (C) 2017-2020
 *   MohammadJavad Rezaei Seraji <mjrezaei (at) ce.sharif.edu>
 *	 Seyed Abolfazl Motahari <motahari (at) sharif.edu
 *
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
 * files (the "Software"), to deal in the Software without
 * restriction, including without limitation the rights to use,
 * copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the
 * Software is furnished to do so, subject to the following
 * conditions:
 *
 * The above copyright notice and this permission notice shall be
 * included in all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
 * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
 * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
 * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
 * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
 * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
 * OTHER DEALINGS IN THE SOFTWARE.
 **/
#include <string>
#include <cstdlib>
#include <cstdio>
#include "BitArray.h"

using namespace std;

struct CompressedString{
    char dna[4];
    BitArray invalidPos;
    uint32_t sz;
    uint8_t* encodedStr;
    uint32_t zeroPos;

    CompressedString(){
        sz = 0;
        dna[0] = 'a', dna[1] = 'c', dna[2] = 'g', dna[3] = 't';
        encodedStr = NULL;
    }

    void save( FILE* fout ){
        fwrite((const void*)& sz,sizeof(uint32_t),1,fout);
        if( sz > 0 ){
            invalidPos.save( fout );
            for( uint32_t i = 0; i < ( sz + 3 ) / 4; i++ )
                fwrite((const void*)& encodedStr[i],sizeof(uint8_t),1,fout);
            fwrite((const void*)& zeroPos,sizeof(uint32_t),1,fout);
        }
    }

    void load( FILE* fin ){
        fread( &sz, sizeof( uint32_t ), 1, fin );
        if( sz > 0 ){
            invalidPos.load( fin );
            encodedStr = new uint8_t[( sz + 3 ) / 4];
            fread( encodedStr, sizeof( uint8_t ), ( sz + 3 ) / 4, fin );
            fread( &zeroPos, sizeof( uint32_t ), 1, fin );
        }
    }

    void set( const uint8_t* T, uint32_t n ){
        sz = n;
        invalidPos.reset( n );
        encodedStr = new uint8_t[( n + 3 ) / 4];
        for( uint32_t i = 0; i < ( n + 3 ) / 4; i++ )
            encodedStr[i] = 0;
        for( unsigned int i = 0; i < n; i++ )
            if( T[i] == 'n' )
                invalidPos.setBit( i );
            else if( T[i] == 0 )
                zeroPos = i;
            else{
                int idx = 0;
                while( dna[idx] != T[i] )
                    idx++;
                encodedStr[i >> 2] |= ( idx << ( ( i & 3 ) << 1 ) );
            }
    }

    uint8_t charAt( uint32_t pos ){
        if( pos == zeroPos )
            return 0;
        if( invalidPos.getPos( pos ) )
            return 'n';
        return dna[( encodedStr[pos>>2] >> ( ( pos & 3 ) << 1 ) ) & 3];
    }

    uint32_t getBytes(){
        long long ret = 0;
        ret += sz / 4;
        ret += invalidPos.getBytes();
        return ret;
    }
};