source: tags/ms_r16q3/CONVERTALN/seq.h

#ifndef SEQ_H
#define SEQ_H

#ifndef FUN_H
#include "fun.h"
#endif
#ifndef GLOBAL_H
#include "global.h"
#endif
#ifndef ARB_STRING_H
#include <arb_string.h>
#endif
#ifndef _GLIBCXX_CCTYPE
#include <cctype>
#endif


#define INITSEQ 6000

struct BaseCounts {
    int a;
    int c;
    int g;
    int t;
    int other;

    BaseCounts()
        : a(0), c(0), g(0), t(0), other(0)
    {}

    void add(char ch) {
        switch (tolower(ch)) {
            case 'a': a++; break;
            case 'c': c++; break;
            case 'g': g++; break;
            case 'u':
            case 't': t++; break;
            default: other++; break;
        }
    }
};

class Seq : virtual Noncopyable {
    // - holds sequence data

    char *id;
    int   len;     // sequence length
    int   max;     // space allocated for 'sequence'
    char *seq;     // sequence data

    void zeroTerminate() { add(0); len--; }

    static void check_valid(char ch) {
        if (isalpha(ch) || is_gapchar(ch)) return;
        throw_errorf(43, "Invalid character '%c' in sequence data", ch);
    }
    static void check_valid(const char *s, int len) {
        for (int i = 0; i<len; ++i) {
            check_valid(s[i]);
        }
    }

public:
    Seq(const char *id_, const char *seq_, int len_) :
        id(ARB_strdup(id_)),
        len(len_),
        max(len+1),
        seq(strndup(seq_, len))
    {
        check_valid(seq, len);
    }
    Seq() :
        id(NULL),
        len(0),
        max(INITSEQ),
        seq(ARB_alloc<char>(INITSEQ))
    {
    }
    ~Seq() {
        ca_assert(seq); // otherwise 'this' is useless!
        freenull(id);
        freenull(seq);
    }

    void set_id(const char *id_) {
        ca_assert(!id);
        ca_assert(id_);
        freedup(id, id_);
    }
    void replace_id(const char *id_) {
        freenull(id);
        set_id(id_);
    }
    const char *get_id() const {
        ca_assert(id);
        return id;
    }

    void add(char c) {
        if (c) check_valid(c);
        if (len >= max) {
            max = max*1.5+100;
            ARB_realloc(seq, max);
        }
        seq[len++] = c;
    }

    int get_len() const { return len; }
    bool is_empty() const { return len == 0; }

    const char *get_seq() const {
        const_cast<Seq*>(this)->zeroTerminate();
        return seq;
    }

    void count(BaseCounts& counter) const {
        for (int i = 0; i<len; ++i)
            counter.add(seq[i]);
    }

    int count_gaps() const {
        int gaps = 0;
        for (int i = 0; i<len; ++i) {
            gaps += is_gapchar(seq[i]);
        }
        return gaps;
    }

    void out(Writer& write, Format outType) const;
};
typedef SmartPtr<Seq> SeqPtr;

#else
#error seq.h included twice
#endif // SEQ_H