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#ifndef SEQ_H
#define SEQ_H
#ifndef FUN_H
#include "fun.h"
#endif
#ifndef GLOBAL_H
#include "global.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(strdup(id_)),
len(len_),
max(len+1),
seq((char*)malloc(max))
{
memcpy(seq, seq_, len);
check_valid(seq, len);
}
Seq() {
id = NULL;
len = 0;
max = INITSEQ;
seq = (char *)calloc(1, (unsigned)(sizeof(char) * INITSEQ + 1));
}
~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;
seq = (char*)Reallocspace(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
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