PRD_SequenceIterator.cxx

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#include "PRD_SequenceIterator.hxx"
#include <cstdio>

using namespace std;

const int SequenceIterator::FORWARD;
const int SequenceIterator::BACKWARD;

//
// Constructor
//
SequenceIterator::SequenceIterator (const char *sequence_, PRD_Sequence_Pos start_pos_, PRD_Sequence_Pos stop_pos_, int max_length_, int direction_) {
    sequence      = sequence_;
    max_length    = max_length_;
    stop_position = stop_pos_;
    direction     = (direction_ < 0) ? BACKWARD : FORWARD;
    pos           = start_pos_ - direction; // -direction because nextBase() starts with pos+direction
    delivered     = 0;
}

SequenceIterator::SequenceIterator (const char *sequence_) {
    sequence      = sequence_;
    max_length    = IGNORE;
    stop_position = IGNORE;
    direction     = FORWARD;
    pos           = 0;
    delivered     = 0;
}


//
// restart at new position
//
void SequenceIterator::restart (PRD_Sequence_Pos start_pos_, PRD_Sequence_Pos stop_pos_, int max_length_, int direction_) {
    max_length    = max_length_;
    stop_position = stop_pos_;
    direction     = (direction_ < 0) ? BACKWARD : FORWARD;
    pos           = start_pos_ - direction; // -direction because nextBase() starts with pos+direction
    delivered     = 0;
}


//
// get next base if not at the end of sequence or already delivered max_length bases
//
unsigned char SequenceIterator::nextBase () {
    if (((max_length != IGNORE) && (delivered >= max_length)) ||
        ((stop_position != IGNORE) && (pos == stop_position))) return EOS;

    char cur_char;

    pos += direction;                                                 // <=> pos++ if direction=FORWARD else pos--
    if (pos < 0) return EOS;                                          // reached front end ?
    cur_char = sequence[pos];
    if (cur_char > 'Z') cur_char = cur_char - ('a' - 'A');            // convert to upper case

    while ((cur_char != 'A') &&
           (cur_char != 'T') &&
           (cur_char != 'U') &&
           (cur_char != 'C') &&
           (cur_char != 'G') &&
           (cur_char != 'N') &&
           (cur_char != 'R') &&
           (cur_char != 'Y') &&
           (cur_char != 'M') &&
           (cur_char != 'K') &&
           (cur_char != 'W') &&
           (cur_char != 'S') &&
           (cur_char != 'B') &&
           (cur_char != 'D') &&
           (cur_char != 'H') &&
           (cur_char != 'V') &&
           (cur_char != EOS))
    {
        pos += direction;                                               // <=> pos++ if direction=FORWARD else pos--
        if (pos < 0) return EOS;                                        // reached front end ?
        cur_char = sequence[pos];
        if (cur_char > 'Z') cur_char = cur_char - ('a' - 'A');          // convert to upper case
    };

    if (cur_char != EOS) delivered++;

    return cur_char;
}