1 files changed, 77 insertions, 0 deletions
diff --git a/utils/alignment_pharaoh.cc b/utils/alignment_pharaoh.cc
new file mode 100644
index 00000000..890ff565
--- /dev/null
+++ b/utils/alignment_pharaoh.cc
@@ -0,0 +1,77 @@
+#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;
+}
+