Changeset 78

Timestamp:

11/28/06 00:42:17 (2 years ago)

Author:

t

Message:

Python interface to the N-way comparison stuff.

Files:

• trunk/paircomp/lib/NwayComparison.cc (modified) (1 diff)
• trunk/paircomp/lib/paircomp.hh (modified) (1 diff)
• trunk/paircomp/python/c++-ext/_paircomp_parser.cc (modified) (2 diffs)
• trunk/paircomp/tests/nway.py (modified) (1 diff)

trunk/paircomp/lib/NwayComparison.cc

@@ -97 +97 @@
-std::vector<NwayPath> NwayComparison::filter()
-{
+  do_comparisons();
+
-  std::string seq0 = _sequences[0];
-  std::vector<NwayPath> ret_paths;

trunk/paircomp/lib/paircomp.hh

@@ -11 +11 @@
-#include "MutableComparison.hh"
-#include "ImmutableComparison.hh"
+#include "NwayComparison.hh"
-
-#include "algorithms.hh"

trunk/paircomp/python/c++-ext/_paircomp_parser.cc

@@ -550 +550 @@
-
-  return ret;
+}
+
+static PyObject * create_nway(PyObject * self, PyObject * args)
+{
+  unsigned int windowsize;
+  float threshold;
+
+  if (!PyArg_ParseTuple(args, "If", &windowsize, &threshold)) {
+    return NULL;
+  }
+
+  NwayComparison * nway = new NwayComparison(windowsize, threshold);
+
+  return PyCObject_FromVoidPtr(nway, NULL); // @CTB
+}
+
+static PyObject * add_sequence_to_nway(PyObject * self, PyObject * args)
+{
+  char * seq;
+  PyObject * p;
+
+  if (!PyArg_ParseTuple(args, "Os", &p, &seq)) {
+    return NULL;
+  }
+
+  NwayComparison * nway = (NwayComparison *) PyCObject_AsVoidPtr(p);
+  nway->add_sequence(seq);
+
+  Py_INCREF(Py_None);
+  return Py_None;
+}
+
+std::string print_poso_v(NwayPath v)
+{
+  char buf[50];
+  std::string ret;
+  for (unsigned int i = 0; i < v.size(); i++) {
+    PosAndO p = v[i];
+    sprintf(buf, "%d(%c) ", p.pos, p.orient > 0 ? '+' : '-');
+    ret += buf;
+  }
+  ret += "\n";
+
+  return ret;
+}
+
+static PyObject * get_nway_filtered_paths(PyObject * self, PyObject * args)
+{
+  PyObject * p;
+
+  if (!PyArg_ParseTuple(args, "O", &p)) {
+    return NULL;
+  }
+
+  NwayComparison * nway = (NwayComparison *) PyCObject_AsVoidPtr(p);
+
+  std::string ret;
+  std::vector<NwayPath> paths = nway->filter();
+  for (unsigned int i = 0; i < paths.size(); i++) {
+    NwayPath path = paths[i];
+    ret += print_poso_v(path);
+  }
+  
+  return PyString_FromString(ret.c_str());
-}
-
@@ -577 +641 @@
-  { "is_empty", is_empty, METH_VARARGS },
-  { "subtract", subtract, METH_VARARGS },
+  { "create_nway", create_nway, METH_VARARGS },
+  { "add_sequence_to_nway", add_sequence_to_nway, METH_VARARGS },
+  { "get_nway_filtered_paths", get_nway_filtered_paths, METH_VARARGS },
-  { NULL, NULL }
-};

trunk/paircomp/tests/nway.py

@@ -322 +322 @@
-if __name__ == '__main__':
-    test()
+
+    from paircomp import _paircomp_parser
+    o = _paircomp_parser.create_nway(10, 0.7)
+    _paircomp_parser.add_sequence_to_nway(o, 'AAAAAAAAAA')
+    _paircomp_parser.add_sequence_to_nway(o, 'AAAAAAAAAA')
+    _paircomp_parser.add_sequence_to_nway(o, 'AAAAAAAAAA')
+    _paircomp_parser.add_sequence_to_nway(o, 'TTTTTTTTTT')
+    print _paircomp_parser.get_nway_filtered_paths(o)