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#include "utils/alignment_pharaoh.h"
#include <set>
using namespace std;
static bool is_digit(char x) { return x >= '0' && x <= '9'; }
boost::shared_ptr<Array2D<bool> > AlignmentPharaoh::ReadPharaohAlignmentGrid(const string& al) {
int max_x = 0;
int max_y = 0;
int i = 0;
size_t pos = al.rfind(" ||| ");
if (pos != string::npos) { i = pos + 5; }
while (i < al.size()) {
if (al[i] == '\n' || al[i] == '\r') break;
int x = 0;
while(i < al.size() && is_digit(al[i])) {
x *= 10;
x += al[i] - '0';
++i;
}
if (x > max_x) max_x = x;
assert(i < al.size());
if(al[i] != '-') {
cerr << "BAD ALIGNMENT: " << al << endl;
abort();
}
++i;
int y = 0;
while(i < al.size() && is_digit(al[i])) {
y *= 10;
y += al[i] - '0';
++i;
}
if (y > max_y) max_y = y;
while(i < al.size() && al[i] == ' ') { ++i; }
}
boost::shared_ptr<Array2D<bool> > grid(new Array2D<bool>(max_x + 1, max_y + 1));
i = 0;
if (pos != string::npos) { i = pos + 5; }
while (i < al.size()) {
if (al[i] == '\n' || al[i] == '\r') break;
int x = 0;
while(i < al.size() && is_digit(al[i])) {
x *= 10;
x += al[i] - '0';
++i;
}
assert(i < al.size());
assert(al[i] == '-');
++i;
int y = 0;
while(i < al.size() && is_digit(al[i])) {
y *= 10;
y += al[i] - '0';
++i;
}
(*grid)(x, y) = true;
while(i < al.size() && al[i] == ' ') { ++i; }
}
// cerr << *grid << endl;
return grid;
}
void AlignmentPharaoh::SerializePharaohFormat(const Array2D<bool>& alignment, ostream* out) {
bool need_space = false;
for (int i = 0; i < alignment.width(); ++i)
for (int j = 0; j < alignment.height(); ++j)
if (alignment(i,j)) {
if (need_space) (*out) << ' '; else need_space = true;
(*out) << i << '-' << j;
}
(*out) << endl;
}
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