Commits

radhesh  committed b42de00

fixed segfault occurring due to infinite recursion , gops_cluster. Added some pointer checks to avoid segfaults.

  • Participants
  • Parent commits 2792576

Comments (0)

Files changed (10)

File lib/bx/_seqmapping.c

-/* Generated by Pyrex 0.9.5.1a on Sat Mar 24 20:22:52 2007 */
+/* Generated by Pyrex 0.9.3.1 on Wed Oct 17 17:03:15 2007 */
 
 #include "Python.h"
 #include "structmember.h"
 #ifndef PY_LONG_LONG
   #define PY_LONG_LONG LONG_LONG
 #endif
-#ifdef __cplusplus
-#define __PYX_EXTERN_C extern "C"
-#else
-#define __PYX_EXTERN_C extern
-#endif
-__PYX_EXTERN_C double pow(double, double);
 #include "stdlib.h"
 
 
 typedef struct {PyObject **p; char *s;} __Pyx_InternTabEntry; /*proto*/
 typedef struct {PyObject **p; char *s; long n;} __Pyx_StringTabEntry; /*proto*/
+static PyObject *__Pyx_UnpackItem(PyObject *, int); /*proto*/
+static int __Pyx_EndUnpack(PyObject *, int); /*proto*/
+static int __Pyx_PrintItem(PyObject *); /*proto*/
+static int __Pyx_PrintNewline(void); /*proto*/
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+static void __Pyx_ReRaise(void); /*proto*/
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list); /*proto*/
+static PyObject *__Pyx_GetExcValue(void); /*proto*/
+static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, char *name); /*proto*/
+static int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); /*proto*/
+static int __Pyx_GetStarArgs(PyObject **args, PyObject **kwds, char *kwd_list[], int nargs, PyObject **args2, PyObject **kwds2); /*proto*/
+static void __Pyx_WriteUnraisable(char *name); /*proto*/
+static void __Pyx_AddTraceback(char *funcname); /*proto*/
+static PyTypeObject *__Pyx_ImportType(char *module_name, char *class_name, long size);  /*proto*/
+static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
+static int __Pyx_GetVtable(PyObject *dict, void *vtabptr); /*proto*/
+static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name, char *modname); /*proto*/
+static int __Pyx_InternStrings(__Pyx_InternTabEntry *t); /*proto*/
+static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
+static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
 
 static PyObject *__pyx_m;
 static PyObject *__pyx_b;
 static int __pyx_lineno;
 static char *__pyx_filename;
-static char **__pyx_f;
+staticforward char **__pyx_f;
 
 static char __pyx_mdoc[] = "\nPyrex extension classes used by `seqmapping.py`.\n";
 
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list); /*proto*/
-
-static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
-
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
-
-static int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); /*proto*/
-
-static int __Pyx_InternStrings(__Pyx_InternTabEntry *t); /*proto*/
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
-
-static void __Pyx_AddTraceback(char *funcname); /*proto*/
-
 /* Declarations from _seqmapping */
 
+staticforward PyTypeObject __pyx_type_11_seqmapping_CharToIntArrayMapping;
 
 struct __pyx_obj_11_seqmapping_CharToIntArrayMapping {
   PyObject_HEAD
   PyObject *reverse_table;
 };
 
+staticforward PyTypeObject __pyx_type_11_seqmapping_IntToIntMapping;
 
 struct __pyx_obj_11_seqmapping_IntToIntMapping {
   PyObject_HEAD
 static PyTypeObject *__pyx_ptype_11_seqmapping_CharToIntArrayMapping = 0;
 static PyTypeObject *__pyx_ptype_11_seqmapping_IntToIntMapping = 0;
 
-
 /* Implementation of _seqmapping */
 
 
   if (!PyArg_ParseTupleAndKeywords(__pyx_args, __pyx_kwds, "", __pyx_argnames)) return -1;
   Py_INCREF(__pyx_v_self);
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":29 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":29 */
   for (__pyx_v_i = 0; __pyx_v_i < 256; ++__pyx_v_i) {
     (((struct __pyx_obj_11_seqmapping_CharToIntArrayMapping *)__pyx_v_self)->table[__pyx_v_i]) = (-1);
+    __pyx_L2:;
   }
+  __pyx_L3:;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":30 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":30 */
   ((struct __pyx_obj_11_seqmapping_CharToIntArrayMapping *)__pyx_v_self)->out_size = 0;
 
   __pyx_r = 0;
+  goto __pyx_L0;
+  __pyx_L1:;
+  __Pyx_AddTraceback("_seqmapping.CharToIntArrayMapping.__new__");
+  __pyx_r = -1;
+  __pyx_L0:;
   Py_DECREF(__pyx_v_self);
   return __pyx_r;
 }
   int __pyx_r;
   PyObject *__pyx_1 = 0;
   PyObject *__pyx_2 = 0;
+  PyObject *__pyx_3 = 0;
   static char *__pyx_argnames[] = {0};
   if (!PyArg_ParseTupleAndKeywords(__pyx_args, __pyx_kwds, "", __pyx_argnames)) return -1;
   Py_INCREF(__pyx_v_self);
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":33 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":33 */
   __pyx_1 = __Pyx_GetName(__pyx_b, __pyx_n_dict); if (!__pyx_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; goto __pyx_L1;}
-  __pyx_2 = PyObject_CallObject(__pyx_1, 0); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; goto __pyx_L1;}
+  __pyx_2 = PyTuple_New(0); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; goto __pyx_L1;}
+  __pyx_3 = PyObject_CallObject(__pyx_1, __pyx_2); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; goto __pyx_L1;}
   Py_DECREF(__pyx_1); __pyx_1 = 0;
+  Py_DECREF(__pyx_2); __pyx_2 = 0;
   Py_DECREF(((struct __pyx_obj_11_seqmapping_CharToIntArrayMapping *)__pyx_v_self)->reverse_table);
-  ((struct __pyx_obj_11_seqmapping_CharToIntArrayMapping *)__pyx_v_self)->reverse_table = __pyx_2;
-  __pyx_2 = 0;
+  ((struct __pyx_obj_11_seqmapping_CharToIntArrayMapping *)__pyx_v_self)->reverse_table = __pyx_3;
+  __pyx_3 = 0;
 
   __pyx_r = 0;
   goto __pyx_L0;
   __pyx_L1:;
   Py_XDECREF(__pyx_1);
   Py_XDECREF(__pyx_2);
+  Py_XDECREF(__pyx_3);
   __Pyx_AddTraceback("_seqmapping.CharToIntArrayMapping.__init__");
   __pyx_r = -1;
   __pyx_L0:;
   if (!PyArg_ParseTupleAndKeywords(__pyx_args, __pyx_kwds, "ci", __pyx_argnames, &__pyx_v_char, &__pyx_v_symbol)) return 0;
   Py_INCREF(__pyx_v_self);
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":37 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":37 */
   (((struct __pyx_obj_11_seqmapping_CharToIntArrayMapping *)__pyx_v_self)->table[__pyx_v_char]) = __pyx_v_symbol;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":38 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":38 */
   __pyx_1 = (((struct __pyx_obj_11_seqmapping_CharToIntArrayMapping *)__pyx_v_self)->out_size <= __pyx_v_symbol);
   if (__pyx_1) {
 
-    /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":39 */
+    /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":39 */
     ((struct __pyx_obj_11_seqmapping_CharToIntArrayMapping *)__pyx_v_self)->out_size = (__pyx_v_symbol + 1);
     goto __pyx_L2;
   }
   __pyx_L2:;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":40 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":40 */
   __pyx_2 = __Pyx_GetName(__pyx_b, __pyx_n_chr); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 40; goto __pyx_L1;}
   __pyx_3 = PyInt_FromLong(__pyx_v_char); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 40; goto __pyx_L1;}
   __pyx_4 = PyTuple_New(1); if (!__pyx_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 40; goto __pyx_L1;}
   Py_DECREF(__pyx_2); __pyx_2 = 0;
   Py_DECREF(__pyx_3); __pyx_3 = 0;
 
-  __pyx_r = Py_None; Py_INCREF(Py_None);
+  __pyx_r = Py_None; Py_INCREF(__pyx_r);
   goto __pyx_L0;
   __pyx_L1:;
   Py_XDECREF(__pyx_2);
   if (!PyArg_ParseTupleAndKeywords(__pyx_args, __pyx_kwds, "O", __pyx_argnames, &__pyx_v_string)) return 0;
   Py_INCREF(__pyx_v_self);
   Py_INCREF(__pyx_v_string);
-  __pyx_v_rval = Py_None; Py_INCREF(Py_None);
-  __pyx_v_i = Py_None; Py_INCREF(Py_None);
+  __pyx_v_rval = Py_None; Py_INCREF(__pyx_v_rval);
+  __pyx_v_i = Py_None; Py_INCREF(__pyx_v_i);
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":48 */
-  __pyx_1 = PyString_AsStringAndSize(__pyx_v_string,((char (*(*)))(&__pyx_v_s_buf)),(&__pyx_v_s_len)); if (__pyx_1 == (-1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; goto __pyx_L1;}
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":48 */
+  __pyx_1 = PyString_AsStringAndSize(__pyx_v_string,((char (*(*)))(&__pyx_v_s_buf)),(&__pyx_v_s_len)); if (__pyx_1 == -1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; goto __pyx_L1;}
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":50 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":50 */
   __pyx_2 = __Pyx_GetName(__pyx_m, __pyx_n_zeros); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; goto __pyx_L1;}
   __pyx_3 = PyInt_FromLong(__pyx_v_s_len); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; goto __pyx_L1;}
   __pyx_4 = PyTuple_New(2); if (!__pyx_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; goto __pyx_L1;}
   __pyx_v_rval = __pyx_3;
   __pyx_3 = 0;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":51 */
-  __pyx_1 = PyObject_AsWriteBuffer(__pyx_v_rval,((void (*(*)))(&__pyx_v_t_buf)),(&__pyx_v_t_len)); if (__pyx_1 == (-1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 51; goto __pyx_L1;}
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":51 */
+  __pyx_1 = PyObject_AsWriteBuffer(__pyx_v_rval,((void (*(*)))(&__pyx_v_t_buf)),(&__pyx_v_t_len)); if (__pyx_1 == -1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 51; goto __pyx_L1;}
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":53 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":53 */
   for (__pyx_5 = 0; __pyx_5 < __pyx_v_s_len; ++__pyx_5) {
     __pyx_2 = PyInt_FromLong(__pyx_5); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; goto __pyx_L1;}
     Py_DECREF(__pyx_v_i);
     __pyx_v_i = __pyx_2;
     __pyx_2 = 0;
 
-    /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":54 */
+    /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":54 */
     __pyx_1 = PyInt_AsLong(__pyx_v_i); if (PyErr_Occurred()) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; goto __pyx_L1;}
     __pyx_6 = PyInt_AsLong(__pyx_v_i); if (PyErr_Occurred()) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; goto __pyx_L1;}
     (__pyx_v_t_buf[__pyx_6]) = (((struct __pyx_obj_11_seqmapping_CharToIntArrayMapping *)__pyx_v_self)->table[(__pyx_v_s_buf[__pyx_1])]);
+    __pyx_L2:;
   }
+  __pyx_L3:;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":56 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":56 */
   Py_INCREF(__pyx_v_rval);
   __pyx_r = __pyx_v_rval;
   goto __pyx_L0;
 
-  __pyx_r = Py_None; Py_INCREF(Py_None);
+  __pyx_r = Py_None; Py_INCREF(__pyx_r);
   goto __pyx_L0;
   __pyx_L1:;
   Py_XDECREF(__pyx_2);
   if (!PyArg_ParseTupleAndKeywords(__pyx_args, __pyx_kwds, "O", __pyx_argnames, &__pyx_v_strings)) return 0;
   Py_INCREF(__pyx_v_self);
   Py_INCREF(__pyx_v_strings);
-  __pyx_v_rval = Py_None; Py_INCREF(Py_None);
-  __pyx_v_string = Py_None; Py_INCREF(Py_None);
+  __pyx_v_rval = Py_None; Py_INCREF(__pyx_v_rval);
+  __pyx_v_string = Py_None; Py_INCREF(__pyx_v_string);
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":66 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":66 */
   __pyx_1 = __Pyx_GetName(__pyx_b, __pyx_n_len); if (!__pyx_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; goto __pyx_L1;}
   __pyx_2 = PyTuple_New(1); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; goto __pyx_L1;}
   Py_INCREF(__pyx_v_strings);
   }
   __pyx_L2:;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":69 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":69 */
   __pyx_2 = __Pyx_GetName(__pyx_b, __pyx_n_len); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; goto __pyx_L1;}
   __pyx_3 = PyInt_FromLong(0); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; goto __pyx_L1;}
   __pyx_1 = PyObject_GetItem(__pyx_v_strings, __pyx_3); if (!__pyx_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; goto __pyx_L1;}
   Py_DECREF(__pyx_1); __pyx_1 = 0;
   __pyx_v_text_len = __pyx_4;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":72 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":72 */
   __pyx_2 = __Pyx_GetName(__pyx_m, __pyx_n_zeros); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; goto __pyx_L1;}
   __pyx_3 = PyInt_FromLong(__pyx_v_text_len); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; goto __pyx_L1;}
   __pyx_1 = PyTuple_New(2); if (!__pyx_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; goto __pyx_L1;}
   __pyx_v_rval = __pyx_3;
   __pyx_3 = 0;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":73 */
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+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":73 */
+  __pyx_4 = PyObject_AsWriteBuffer(__pyx_v_rval,((void (*(*)))(&__pyx_v_t_buf)),(&__pyx_v_t_len)); if (__pyx_4 == -1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 73; goto __pyx_L1;}
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":76 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":76 */
   __pyx_v_factor = 1;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":77 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":77 */
   __pyx_2 = PyObject_GetIter(__pyx_v_strings); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; goto __pyx_L1;}
   for (;;) {
+    __pyx_L3:;
     __pyx_1 = PyIter_Next(__pyx_2);
     if (!__pyx_1) {
       if (PyErr_Occurred()) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; goto __pyx_L1;}
     __pyx_v_string = __pyx_1;
     __pyx_1 = 0;
 
-    /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":78 */
-    __pyx_4 = PyString_AsStringAndSize(__pyx_v_string,((char (*(*)))(&__pyx_v_s_buf)),(&__pyx_v_s_len)); if (__pyx_4 == (-1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; goto __pyx_L1;}
+    /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":78 */
+    __pyx_4 = PyString_AsStringAndSize(__pyx_v_string,((char (*(*)))(&__pyx_v_s_buf)),(&__pyx_v_s_len)); if (__pyx_4 == -1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; goto __pyx_L1;}
 
-    /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":79 */
+    /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":79 */
     for (__pyx_v_i = 0; __pyx_v_i < __pyx_v_text_len; ++__pyx_v_i) {
 
-      /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":80 */
+      /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":80 */
       __pyx_4 = ((__pyx_v_t_buf[__pyx_v_i]) >= 0);
       if (__pyx_4) {
 
-        /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":81 */
+        /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":81 */
         __pyx_4 = ((((struct __pyx_obj_11_seqmapping_CharToIntArrayMapping *)__pyx_v_self)->table[(__pyx_v_s_buf[__pyx_v_i])]) == (-1));
         if (__pyx_4) {
 
-          /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":82 */
+          /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":82 */
           (__pyx_v_t_buf[__pyx_v_i]) = (-1);
           goto __pyx_L8;
         }
         /*else*/ {
 
-          /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":84 */
+          /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":84 */
           (__pyx_v_t_buf[__pyx_v_i]) = ((__pyx_v_t_buf[__pyx_v_i]) + ((((struct __pyx_obj_11_seqmapping_CharToIntArrayMapping *)__pyx_v_self)->table[(__pyx_v_s_buf[__pyx_v_i])]) * __pyx_v_factor));
         }
         __pyx_L8:;
         goto __pyx_L7;
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       __pyx_L7:;
+      __pyx_L5:;
     }
+    __pyx_L6:;
 
-    /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":85 */
+    /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":85 */
     __pyx_v_factor = (__pyx_v_factor * ((struct __pyx_obj_11_seqmapping_CharToIntArrayMapping *)__pyx_v_self)->out_size);
   }
+  __pyx_L4:;
   Py_DECREF(__pyx_2); __pyx_2 = 0;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":86 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":86 */
   Py_INCREF(__pyx_v_rval);
   __pyx_r = __pyx_v_rval;
   goto __pyx_L0;
 
-  __pyx_r = Py_None; Py_INCREF(Py_None);
+  __pyx_r = Py_None; Py_INCREF(__pyx_r);
   goto __pyx_L0;
   __pyx_L1:;
   Py_XDECREF(__pyx_1);
   PyObject *__pyx_5 = 0;
   PyObject *__pyx_6 = 0;
   static char *__pyx_argnames[] = {"val","nseqs",0};
+  extern double pow(double, double);
   if (!PyArg_ParseTupleAndKeywords(__pyx_args, __pyx_kwds, "OO", __pyx_argnames, &__pyx_v_val, &__pyx_v_nseqs)) return 0;
   Py_INCREF(__pyx_v_self);
   Py_INCREF(__pyx_v_val);
   Py_INCREF(__pyx_v_nseqs);
-  __pyx_v_factor = Py_None; Py_INCREF(Py_None);
-  __pyx_v_rval = Py_None; Py_INCREF(Py_None);
+  __pyx_v_factor = Py_None; Py_INCREF(__pyx_v_factor);
+  __pyx_v_rval = Py_None; Py_INCREF(__pyx_v_rval);
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":89 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":89 */
   __pyx_1 = PyInt_FromLong(((struct __pyx_obj_11_seqmapping_CharToIntArrayMapping *)__pyx_v_self)->out_size); if (!__pyx_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; goto __pyx_L1;}
   __pyx_2 = PyInt_FromLong(1); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; goto __pyx_L1;}
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   __pyx_v_factor = __pyx_2;
   __pyx_2 = 0;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":90 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":90 */
   __pyx_1 = PyList_New(0); if (!__pyx_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 90; goto __pyx_L1;}
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   __pyx_v_rval = __pyx_1;
   __pyx_1 = 0;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":91 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":91 */
   while (1) {
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     __pyx_3 = PyInt_FromLong(0); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 91; goto __pyx_L1;}
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     if (!__pyx_4) break;
 
-    /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":92 */
+    /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":92 */
     __pyx_2 = PyObject_GetAttr(__pyx_v_rval, __pyx_n_append); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 92; goto __pyx_L1;}
     __pyx_1 = __Pyx_GetName(__pyx_b, __pyx_n_int); if (!__pyx_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 92; goto __pyx_L1;}
     __pyx_3 = __Pyx_GetName(__pyx_m, __pyx_n_floor); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 92; goto __pyx_L1;}
     Py_DECREF(__pyx_1); __pyx_1 = 0;
     Py_DECREF(__pyx_3); __pyx_3 = 0;
 
-    /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":93 */
+    /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":93 */
     __pyx_6 = __Pyx_GetName(__pyx_m, __pyx_n_floor); if (!__pyx_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 93; goto __pyx_L1;}
     __pyx_5 = PyNumber_Divide(__pyx_v_val, __pyx_v_factor); if (!__pyx_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 93; goto __pyx_L1;}
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     __pyx_v_val = __pyx_5;
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-    /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":94 */
+    /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":94 */
     __pyx_6 = __Pyx_GetName(__pyx_m, __pyx_n_floor); if (!__pyx_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; goto __pyx_L1;}
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     __pyx_v_factor = __pyx_5;
     __pyx_5 = 0;
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-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":95 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":95 */
   __pyx_2 = PyObject_GetAttr(__pyx_v_rval, __pyx_n_reverse); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; goto __pyx_L1;}
-  __pyx_1 = PyObject_CallObject(__pyx_2, 0); if (!__pyx_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; goto __pyx_L1;}
+  __pyx_1 = PyTuple_New(0); if (!__pyx_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; goto __pyx_L1;}
+  __pyx_6 = PyObject_CallObject(__pyx_2, __pyx_1); if (!__pyx_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; goto __pyx_L1;}
   Py_DECREF(__pyx_2); __pyx_2 = 0;
   Py_DECREF(__pyx_1); __pyx_1 = 0;
+  Py_DECREF(__pyx_6); __pyx_6 = 0;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":96 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":96 */
   Py_INCREF(__pyx_v_rval);
   __pyx_r = __pyx_v_rval;
   goto __pyx_L0;
 
-  __pyx_r = Py_None; Py_INCREF(Py_None);
+  __pyx_r = Py_None; Py_INCREF(__pyx_r);
   goto __pyx_L0;
   __pyx_L1:;
   Py_XDECREF(__pyx_1);
   if (!PyArg_ParseTupleAndKeywords(__pyx_args, __pyx_kwds, "", __pyx_argnames)) return 0;
   Py_INCREF(__pyx_v_self);
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":99 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":99 */
   __pyx_1 = PyInt_FromLong(((struct __pyx_obj_11_seqmapping_CharToIntArrayMapping *)__pyx_v_self)->out_size); if (!__pyx_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 99; goto __pyx_L1;}
   __pyx_r = __pyx_1;
   __pyx_1 = 0;
   goto __pyx_L0;
 
-  __pyx_r = Py_None; Py_INCREF(Py_None);
+  __pyx_r = Py_None; Py_INCREF(__pyx_r);
   goto __pyx_L0;
   __pyx_L1:;
   Py_XDECREF(__pyx_1);
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 }
 
+static PyObject *__pyx_n_stderr;
+static PyObject *__pyx_n_write;
+static PyObject *__pyx_n_flush;
+
 static PyObject *__pyx_k9p;
+static PyObject *__pyx_k10p;
 
-static char (__pyx_k9[]) = "Malloc Failed";
+static char (__pyx_k9[]) = "From IntToIntMapping, _seqmapping.pyx, malloc failed\n";
+static char (__pyx_k10[]) = "Malloc Failed in IntToIntMapping, _seqmapping.pyx";
 
 static int __pyx_f_11_seqmapping_15IntToIntMapping___new__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
 static int __pyx_f_11_seqmapping_15IntToIntMapping___new__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_i;
   int __pyx_r;
   int __pyx_1;
-  long __pyx_2;
+  PyObject *__pyx_2 = 0;
   PyObject *__pyx_3 = 0;
+  PyObject *__pyx_4 = 0;
+  long __pyx_5;
   static char *__pyx_argnames[] = {"in_size",0};
   if (!PyArg_ParseTupleAndKeywords(__pyx_args, __pyx_kwds, "i", __pyx_argnames, &__pyx_v_in_size)) return -1;
   Py_INCREF(__pyx_v_self);
-  __pyx_v_i = Py_None; Py_INCREF(Py_None);
+  __pyx_v_i = Py_None; Py_INCREF(__pyx_v_i);
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":108 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":108 */
   ((struct __pyx_obj_11_seqmapping_IntToIntMapping *)__pyx_v_self)->in_size = __pyx_v_in_size;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":109 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":109 */
   ((struct __pyx_obj_11_seqmapping_IntToIntMapping *)__pyx_v_self)->table = ((int (*))malloc((__pyx_v_in_size * (sizeof(int )))));
 
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-  __pyx_1 = (((struct __pyx_obj_11_seqmapping_IntToIntMapping *)__pyx_v_self)->table == NULL);
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":110 */
+  __pyx_1 = (((struct __pyx_obj_11_seqmapping_IntToIntMapping *)__pyx_v_self)->table == 0);
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-    __Pyx_Raise(__pyx_k9p, 0, 0);
-    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; goto __pyx_L1;}
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+    /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":111 */
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+    __pyx_3 = PyObject_GetAttr(__pyx_2, __pyx_n_stderr); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 111; goto __pyx_L1;}
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+    Py_DECREF(__pyx_3); __pyx_3 = 0;
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+    /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":111 */
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+    __pyx_3 = PyObject_GetAttr(__pyx_2, __pyx_n_stderr); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 111; goto __pyx_L1;}
+    Py_DECREF(__pyx_2); __pyx_2 = 0;
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+    Py_DECREF(__pyx_4); __pyx_4 = 0;
+    Py_DECREF(__pyx_2); __pyx_2 = 0;
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+    /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":112 */
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     goto __pyx_L2;
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   __pyx_L2:;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":111 */
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-    __pyx_3 = PyInt_FromLong(__pyx_2); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 111; goto __pyx_L1;}
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":113 */
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     Py_DECREF(__pyx_v_i);
-    __pyx_v_i = __pyx_3;
-    __pyx_3 = 0;
-    __pyx_1 = PyInt_AsLong(__pyx_v_i); if (PyErr_Occurred()) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 111; goto __pyx_L1;}
+    __pyx_v_i = __pyx_4;
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     (((struct __pyx_obj_11_seqmapping_IntToIntMapping *)__pyx_v_self)->table[__pyx_1]) = (-1);
+    __pyx_L3:;
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+  __pyx_L4:;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":112 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":114 */
   ((struct __pyx_obj_11_seqmapping_IntToIntMapping *)__pyx_v_self)->out_size = 0;
 
   __pyx_r = 0;
   goto __pyx_L0;
   __pyx_L1:;
+  Py_XDECREF(__pyx_2);
   Py_XDECREF(__pyx_3);
+  Py_XDECREF(__pyx_4);
   __Pyx_AddTraceback("_seqmapping.IntToIntMapping.__new__");
   __pyx_r = -1;
   __pyx_L0:;
   return __pyx_r;
 }
 
+static PyObject *__pyx_k11p;
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+static char (__pyx_k11[]) = "Free Failed in IntToIntMapping, _seqmapping.pyx";
+
 static void __pyx_f_11_seqmapping_15IntToIntMapping___dealloc__(PyObject *__pyx_v_self); /*proto*/
 static void __pyx_f_11_seqmapping_15IntToIntMapping___dealloc__(PyObject *__pyx_v_self) {
+  int __pyx_1;
   Py_INCREF(__pyx_v_self);
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":116 */
-  free(((struct __pyx_obj_11_seqmapping_IntToIntMapping *)__pyx_v_self)->table);
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":118 */
+  __pyx_1 = (((struct __pyx_obj_11_seqmapping_IntToIntMapping *)__pyx_v_self)->table == 0);
+  if (__pyx_1) {
 
+    /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":119 */
+    __Pyx_Raise(__pyx_k11p, 0, 0);
+    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 119; goto __pyx_L1;}
+    goto __pyx_L2;
+  }
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+    /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":121 */
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+  goto __pyx_L0;
+  __pyx_L1:;
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   Py_DECREF(__pyx_v_self);
 }
 
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 static PyObject *__pyx_f_11_seqmapping_15IntToIntMapping_set_mapping(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
 static PyObject *__pyx_f_11_seqmapping_15IntToIntMapping_set_mapping(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   if (!PyArg_ParseTupleAndKeywords(__pyx_args, __pyx_kwds, "ii", __pyx_argnames, &__pyx_v_index, &__pyx_v_symbol)) return 0;
   Py_INCREF(__pyx_v_self);
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":119 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":124 */
   __pyx_1 = (-1) <= __pyx_v_index;
   if (__pyx_1) {
     __pyx_1 = __pyx_v_index < ((struct __pyx_obj_11_seqmapping_IntToIntMapping *)__pyx_v_self)->in_size;
   }
-  __pyx_2 = PyInt_FromLong(__pyx_v_index); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 119; goto __pyx_L1;}
-  __pyx_3 = PyInt_FromLong(((struct __pyx_obj_11_seqmapping_IntToIntMapping *)__pyx_v_self)->in_size); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 119; goto __pyx_L1;}
-  __pyx_4 = PyTuple_New(2); if (!__pyx_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 119; goto __pyx_L1;}
+  __pyx_2 = PyInt_FromLong(__pyx_v_index); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 124; goto __pyx_L1;}
+  __pyx_3 = PyInt_FromLong(((struct __pyx_obj_11_seqmapping_IntToIntMapping *)__pyx_v_self)->in_size); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 124; goto __pyx_L1;}
+  __pyx_4 = PyTuple_New(2); if (!__pyx_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 124; goto __pyx_L1;}
   PyTuple_SET_ITEM(__pyx_4, 0, __pyx_2);
   PyTuple_SET_ITEM(__pyx_4, 1, __pyx_3);
   __pyx_2 = 0;
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-  __pyx_2 = PyNumber_Remainder(__pyx_k10p, __pyx_4); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 119; goto __pyx_L1;}
+  __pyx_2 = PyNumber_Remainder(__pyx_k12p, __pyx_4); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 124; goto __pyx_L1;}
   Py_DECREF(__pyx_4); __pyx_4 = 0;
   if (!__pyx_1) {
     PyErr_SetObject(PyExc_AssertionError, __pyx_2);
-    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 119; goto __pyx_L1;}
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   }
   Py_DECREF(__pyx_2); __pyx_2 = 0;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":120 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":125 */
   (((struct __pyx_obj_11_seqmapping_IntToIntMapping *)__pyx_v_self)->table[__pyx_v_index]) = __pyx_v_symbol;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":121 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":126 */
   __pyx_1 = (((struct __pyx_obj_11_seqmapping_IntToIntMapping *)__pyx_v_self)->out_size <= __pyx_v_symbol);
   if (__pyx_1) {
 
-    /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":122 */
+    /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":127 */
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-  __pyx_r = Py_None; Py_INCREF(Py_None);
+  __pyx_r = Py_None; Py_INCREF(__pyx_r);
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 }
 
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 static PyObject *__pyx_f_11_seqmapping_15IntToIntMapping_translate(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
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-  __pyx_v_i = Py_None; Py_INCREF(Py_None);
+  __pyx_v_rval = Py_None; Py_INCREF(__pyx_v_rval);
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-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":130 */
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-  __pyx_4 = PyTuple_New(1); if (!__pyx_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; goto __pyx_L1;}
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+  __pyx_3 = __Pyx_GetName(__pyx_b, __pyx_n_len); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; goto __pyx_L1;}
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+  __pyx_5 = PyObject_CallObject(__pyx_3, __pyx_4); if (!__pyx_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; goto __pyx_L1;}
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+  __pyx_5 = PyObject_CallObject(__pyx_3, __pyx_2); if (!__pyx_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 138; goto __pyx_L1;}
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+    __pyx_4 = PyInt_FromLong(__pyx_6); if (!__pyx_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; goto __pyx_L1;}
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+    /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":142 */
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     __pyx_7 = ((__pyx_v_s_buf[__pyx_1]) == (-1));
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-      /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":138 */
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+      /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":143 */
+      __pyx_1 = PyInt_AsLong(__pyx_v_i); if (PyErr_Occurred()) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 143; goto __pyx_L1;}
       (__pyx_v_t_buf[__pyx_1]) = (-1);
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-      /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":140 */
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-      __pyx_1 = PyInt_AsLong(__pyx_v_i); if (PyErr_Occurred()) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; goto __pyx_L1;}
+      /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":145 */
+      __pyx_7 = PyInt_AsLong(__pyx_v_i); if (PyErr_Occurred()) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; goto __pyx_L1;}
+      __pyx_1 = PyInt_AsLong(__pyx_v_i); if (PyErr_Occurred()) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; goto __pyx_L1;}
       (__pyx_v_t_buf[__pyx_1]) = (((struct __pyx_obj_11_seqmapping_IntToIntMapping *)__pyx_v_self)->table[(__pyx_v_s_buf[__pyx_7])]);
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+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":147 */
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-  __pyx_r = Py_None; Py_INCREF(Py_None);
+  __pyx_r = Py_None; Py_INCREF(__pyx_r);
   goto __pyx_L0;
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-  __pyx_v_x = PyInt_AsLong(__pyx_arg_x); if (PyErr_Occurred()) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 144; goto __pyx_L1;}
+  __pyx_v_x = PyInt_AsLong(__pyx_arg_x); if (PyErr_Occurred()) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 149; goto __pyx_L1;}
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":145 */
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-    __pyx_2 = PyInt_FromLong((-1)); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; goto __pyx_L1;}
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     goto __pyx_L0;
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-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":146 */
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   if (!__pyx_1) {
     PyErr_SetNone(PyExc_AssertionError);
-    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 146; goto __pyx_L1;}
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-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":147 */
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+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":152 */
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   __pyx_r = __pyx_2;
   __pyx_2 = 0;
   goto __pyx_L0;
 
-  __pyx_r = Py_None; Py_INCREF(Py_None);
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   goto __pyx_L0;
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   Py_XDECREF(__pyx_2);
   static char *__pyx_argnames[] = {"a","b",0};
   if (!PyArg_ParseTupleAndKeywords(__pyx_args, __pyx_kwds, "ii", __pyx_argnames, &__pyx_v_a, &__pyx_v_b)) return 0;
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-  __pyx_v_copy = ((struct __pyx_obj_11_seqmapping_IntToIntMapping *)Py_None); Py_INCREF(Py_None);
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-  __pyx_2 = PyTuple_New(1); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 152; goto __pyx_L1;}
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":157 */
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   PyTuple_SET_ITEM(__pyx_2, 0, __pyx_1);
   __pyx_1 = 0;
-  __pyx_1 = PyObject_CallObject(((PyObject*)__pyx_ptype_11_seqmapping_IntToIntMapping), __pyx_2); if (!__pyx_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 152; goto __pyx_L1;}
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   Py_DECREF(((PyObject *)__pyx_v_copy));
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-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":153 */
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-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":154 */
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   __pyx_L2:;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":155 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":160 */
   __pyx_3 = ((struct __pyx_obj_11_seqmapping_IntToIntMapping *)__pyx_v_self)->in_size;
   for (__pyx_v_i = 0; __pyx_v_i < __pyx_3; ++__pyx_v_i) {
 
-    /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":156 */
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     __pyx_L5:;
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-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":159 */
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-  __pyx_r = Py_None; Py_INCREF(Py_None);
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   __pyx_L1:;
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   int __pyx_v_i;
   int __pyx_v_count;
   int __pyx_v_a;
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   struct __pyx_obj_11_seqmapping_IntToIntMapping *__pyx_v_copy;
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   int __pyx_1;
   static char *__pyx_argnames[] = {"x",0};
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-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":166 */
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   __pyx_L2:;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":170 */
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-    /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":172 */
+    /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":177 */
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       __pyx_v_count = (__pyx_v_count + 1);
       goto __pyx_L5;
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     __pyx_L5:;
+    __pyx_L3:;
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+  __pyx_L4:;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":174 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":179 */
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-  __pyx_4 = PyTuple_New(1); if (!__pyx_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 176; goto __pyx_L1;}
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":181 */
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-  __pyx_3 = PyObject_CallObject(((PyObject*)__pyx_ptype_11_seqmapping_IntToIntMapping), __pyx_4); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 176; goto __pyx_L1;}
+  __pyx_3 = PyObject_CallObject(((PyObject*)__pyx_ptype_11_seqmapping_IntToIntMapping), __pyx_4); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; goto __pyx_L1;}
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-  if (!__Pyx_TypeTest(__pyx_3, __pyx_ptype_11_seqmapping_IntToIntMapping)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 176; goto __pyx_L1;}
+  if (!__Pyx_TypeTest(__pyx_3, __pyx_ptype_11_seqmapping_IntToIntMapping)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; goto __pyx_L1;}
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-  __pyx_v_copy = ((struct __pyx_obj_11_seqmapping_IntToIntMapping *)__pyx_3);
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-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":177 */
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-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":178 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":183 */
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-    /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":179 */
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     (__pyx_v_copy->table[__pyx_v_i]) = (((struct __pyx_obj_11_seqmapping_IntToIntMapping *)__pyx_v_self)->table[__pyx_v_i]);
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-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":180 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":185 */
   (__pyx_v_copy->table[__pyx_v_x]) = ((struct __pyx_obj_11_seqmapping_IntToIntMapping *)__pyx_v_self)->out_size;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":181 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":186 */
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   __pyx_r = ((PyObject *)__pyx_v_copy);
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-  __pyx_r = Py_None; Py_INCREF(Py_None);
+  __pyx_r = Py_None; Py_INCREF(__pyx_r);
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   Py_INCREF(__pyx_v_self);
-  __pyx_v_copy = ((struct __pyx_obj_11_seqmapping_IntToIntMapping *)Py_None); Py_INCREF(Py_None);
+  __pyx_v_copy = Py_None; Py_INCREF((PyObject *) __pyx_v_copy);
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":187 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":192 */
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-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":188 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":193 */
   __pyx_1 = ((struct __pyx_obj_11_seqmapping_IntToIntMapping *)__pyx_v_self)->in_size;
   for (__pyx_v_i = 0; __pyx_v_i < __pyx_1; ++__pyx_v_i) {
 
-    /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":189 */
+    /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":194 */
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       goto __pyx_L4;
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     __pyx_L4:;
+    __pyx_L2:;
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-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":190 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":195 */
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-  __pyx_4 = PyTuple_New(1); if (!__pyx_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 191; goto __pyx_L1;}
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-  __pyx_3 = PyObject_CallObject(((PyObject*)__pyx_ptype_11_seqmapping_IntToIntMapping), __pyx_4); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 191; goto __pyx_L1;}
+  __pyx_3 = PyObject_CallObject(((PyObject*)__pyx_ptype_11_seqmapping_IntToIntMapping), __pyx_4); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; goto __pyx_L1;}
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-  if (!__Pyx_TypeTest(__pyx_3, __pyx_ptype_11_seqmapping_IntToIntMapping)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 191; goto __pyx_L1;}
+  if (!__Pyx_TypeTest(__pyx_3, __pyx_ptype_11_seqmapping_IntToIntMapping)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; goto __pyx_L1;}
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-  __pyx_v_copy = ((struct __pyx_obj_11_seqmapping_IntToIntMapping *)__pyx_3);
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-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":192 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":197 */
   __pyx_v_copy->out_size = (((struct __pyx_obj_11_seqmapping_IntToIntMapping *)__pyx_v_self)->out_size + 1);
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":193 */
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-  __pyx_4 = PyInt_FromLong(__pyx_v_count); if (!__pyx_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 194; goto __pyx_L1;}
-  __pyx_5 = PyTuple_New(1); if (!__pyx_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 194; goto __pyx_L1;}
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   __pyx_4 = 0;
-  __pyx_4 = PyObject_CallObject(__pyx_3, __pyx_5); if (!__pyx_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 194; goto __pyx_L1;}
+  __pyx_4 = PyObject_CallObject(__pyx_3, __pyx_5); if (!__pyx_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 199; goto __pyx_L1;}
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-  __pyx_1 = PyInt_AsLong(__pyx_4); if (PyErr_Occurred()) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 194; goto __pyx_L1;}
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-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":195 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":200 */
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-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":196 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":201 */
   __pyx_2 = ((struct __pyx_obj_11_seqmapping_IntToIntMapping *)__pyx_v_self)->in_size;
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-    /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":197 */
+    /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":202 */
     __pyx_1 = ((((struct __pyx_obj_11_seqmapping_IntToIntMapping *)__pyx_v_self)->table[__pyx_v_i]) == __pyx_v_a);
     if (__pyx_1) {
 
-      /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":198 */
+      /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":203 */
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       }
       __pyx_L9:;
 
-      /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":200 */
+      /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":205 */
       __pyx_v_count = (__pyx_v_count + 1);
       goto __pyx_L8;
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     /*else*/ {
 
-      /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":202 */
+      /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":207 */
       (__pyx_v_copy->table[__pyx_v_i]) = (((struct __pyx_obj_11_seqmapping_IntToIntMapping *)__pyx_v_self)->table[__pyx_v_i]);
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     __pyx_L8:;
+    __pyx_L6:;
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+  __pyx_L7:;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":203 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":208 */
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   goto __pyx_L0;
 
-  __pyx_r = Py_None; Py_INCREF(Py_None);
+  __pyx_r = Py_None; Py_INCREF(__pyx_r);
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   Py_XDECREF(__pyx_3);
   static char *__pyx_argnames[] = {"a",0};
   if (!PyArg_ParseTupleAndKeywords(__pyx_args, __pyx_kwds, "i", __pyx_argnames, &__pyx_v_a)) return 0;
   Py_INCREF(__pyx_v_self);
-  __pyx_v_copy = ((struct __pyx_obj_11_seqmapping_IntToIntMapping *)Py_None); Py_INCREF(Py_None);
-  __pyx_v_to_split = Py_None; Py_INCREF(Py_None);
+  __pyx_v_copy = Py_None; Py_INCREF((PyObject *) __pyx_v_copy);
+  __pyx_v_to_split = Py_None; Py_INCREF(__pyx_v_to_split);
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":209 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":214 */
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-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":210 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":215 */
   __pyx_1 = ((struct __pyx_obj_11_seqmapping_IntToIntMapping *)__pyx_v_self)->in_size;
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-    /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":211 */
+    /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":216 */
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     if (__pyx_2) {
       __pyx_v_count = (__pyx_v_count + 1);
       goto __pyx_L4;
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     __pyx_L4:;
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-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":212 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":217 */
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   __pyx_L5:;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":213 */
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-  __pyx_4 = PyTuple_New(1); if (!__pyx_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; goto __pyx_L1;}
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":218 */
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+  __pyx_4 = PyTuple_New(1); if (!__pyx_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; goto __pyx_L1;}
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   __pyx_3 = 0;
-  __pyx_3 = PyObject_CallObject(((PyObject*)__pyx_ptype_11_seqmapping_IntToIntMapping), __pyx_4); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; goto __pyx_L1;}
+  __pyx_3 = PyObject_CallObject(((PyObject*)__pyx_ptype_11_seqmapping_IntToIntMapping), __pyx_4); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; goto __pyx_L1;}
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-  if (!__Pyx_TypeTest(__pyx_3, __pyx_ptype_11_seqmapping_IntToIntMapping)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; goto __pyx_L1;}
+  if (!__Pyx_TypeTest(__pyx_3, __pyx_ptype_11_seqmapping_IntToIntMapping)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; goto __pyx_L1;}
   Py_DECREF(((PyObject *)__pyx_v_copy));
-  __pyx_v_copy = ((struct __pyx_obj_11_seqmapping_IntToIntMapping *)__pyx_3);
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   __pyx_3 = 0;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":214 */
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-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":215 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":220 */
   __pyx_v_b = ((struct __pyx_obj_11_seqmapping_IntToIntMapping *)__pyx_v_self)->out_size;
 
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-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":218 */
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-    /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":219 */
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-      /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":224 */
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-  __pyx_2 = PyTuple_New(1); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 235; goto __pyx_L1;}
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-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":237 */
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   Py_XDECREF(__pyx_1);
   {&__pyx_n_chr, "chr"},
   {&__pyx_n_dict, "dict"},
   {&__pyx_n_floor, "floor"},
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   {&__pyx_n_i, "i"},
   {&__pyx_n_int, "int"},
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   {&__pyx_n_range, "range"},
   {&__pyx_n_reverse, "reverse"},
   {&__pyx_n_sample, "sample"},
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 };
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 static PyObject *__pyx_tp_new_11_seqmapping_CharToIntArrayMapping(PyTypeObject *t, PyObject *a, PyObject *k) {
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   struct __pyx_obj_11_seqmapping_CharToIntArrayMapping *p = (struct __pyx_obj_11_seqmapping_CharToIntArrayMapping *)o;
-  p->reverse_table = Py_None; Py_INCREF(Py_None);
+  p->reverse_table = Py_None; Py_INCREF(p->reverse_table);
   if (__pyx_f_11_seqmapping_21CharToIntArrayMapping___new__(o, a, k) < 0) {
     Py_DECREF(o); o = 0;
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 static int __pyx_tp_clear_11_seqmapping_CharToIntArrayMapping(PyObject *o) {
   struct __pyx_obj_11_seqmapping_CharToIntArrayMapping *p = (struct __pyx_obj_11_seqmapping_CharToIntArrayMapping *)o;
   Py_XDECREF(p->reverse_table);
-  p->reverse_table = Py_None; Py_INCREF(Py_None);
+  p->reverse_table = Py_None; Py_INCREF(p->reverse_table);
   return 0;
 }
 
   0, /*bf_getcharbuffer*/
 };
 
-PyTypeObject __pyx_type_11_seqmapping_CharToIntArrayMapping = {
+statichere PyTypeObject __pyx_type_11_seqmapping_CharToIntArrayMapping = {
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   0, /*ob_size*/
   "_seqmapping.CharToIntArrayMapping", /*tp_name*/
 
 static PyObject *__pyx_tp_new_11_seqmapping_IntToIntMapping(PyTypeObject *t, PyObject *a, PyObject *k) {
   PyObject *o = (*t->tp_alloc)(t, 0);
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   if (__pyx_f_11_seqmapping_15IntToIntMapping___new__(o, a, k) < 0) {
     Py_DECREF(o); o = 0;
   }
 }
 
 static void __pyx_tp_dealloc_11_seqmapping_IntToIntMapping(PyObject *o) {
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   {
     PyObject *etype, *eval, *etb;
     PyErr_Fetch(&etype, &eval, &etb);
 }
 
 static int __pyx_tp_traverse_11_seqmapping_IntToIntMapping(PyObject *o, visitproc v, void *a) {
+  int e;
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   return 0;
 }
 
 static int __pyx_tp_clear_11_seqmapping_IntToIntMapping(PyObject *o) {
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   return 0;
 }
 static PyObject *__pyx_sq_item_11_seqmapping_IntToIntMapping(PyObject *o, int i) {
   0, /*bf_getcharbuffer*/
 };
 
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   0, /*ob_size*/
   "_seqmapping.IntToIntMapping", /*tp_name*/
   0, /*tp_getattro*/
   0, /*tp_setattro*/
   &__pyx_tp_as_buffer_IntToIntMapping, /*tp_as_buffer*/
-  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE, /*tp_flags*/
   0, /*tp_doc*/
   __pyx_tp_traverse_11_seqmapping_IntToIntMapping, /*tp_traverse*/
   __pyx_tp_clear_11_seqmapping_IntToIntMapping, /*tp_clear*/
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 };
 
-static void __pyx_init_filenames(void); /*proto*/
-
-PyMODINIT_FUNC init_seqmapping(void); /*proto*/
-PyMODINIT_FUNC init_seqmapping(void) {
+DL_EXPORT(void) init_seqmapping(void); /*proto*/
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   PyObject *__pyx_1 = 0;
   PyObject *__pyx_2 = 0;
-  __pyx_init_filenames();
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   __pyx_ptype_11_seqmapping_IntToIntMapping = &__pyx_type_11_seqmapping_IntToIntMapping;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":14 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":14 */
   __pyx_1 = PyList_New(1); if (!__pyx_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; goto __pyx_L1;}
   Py_INCREF(__pyx_n_zeros);
   PyList_SET_ITEM(__pyx_1, 0, __pyx_n_zeros);
   Py_DECREF(__pyx_1); __pyx_1 = 0;
   Py_DECREF(__pyx_2); __pyx_2 = 0;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":15 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":15 */
   __pyx_2 = PyList_New(1); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 15; goto __pyx_L1;}
   Py_INCREF(__pyx_n_floor);
   PyList_SET_ITEM(__pyx_2, 0, __pyx_n_floor);
   Py_DECREF(__pyx_2); __pyx_2 = 0;
   Py_DECREF(__pyx_1); __pyx_1 = 0;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":16 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":16 */
   __pyx_1 = __Pyx_Import(__pyx_n_random, 0); if (!__pyx_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 16; goto __pyx_L1;}
   if (PyObject_SetAttr(__pyx_m, __pyx_n_random, __pyx_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 16; goto __pyx_L1;}
   Py_DECREF(__pyx_1); __pyx_1 = 0;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":17 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":17 */
   __pyx_2 = __Pyx_Import(__pyx_n_sys, 0); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; goto __pyx_L1;}
   if (PyObject_SetAttr(__pyx_m, __pyx_n_sys, __pyx_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; goto __pyx_L1;}
   Py_DECREF(__pyx_2); __pyx_2 = 0;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/_seqmapping.pyx":233 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/_seqmapping.pyx":238 */
   return;
   __pyx_L1:;
   Py_XDECREF(__pyx_1);
 static char *__pyx_filenames[] = {
   "_seqmapping.pyx",
 };
+statichere char **__pyx_f = __pyx_filenames;
 
 /* Runtime support code */
 
-static void __pyx_init_filenames(void) {
-  __pyx_f = __pyx_filenames;
-}
-
 static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list) {
     PyObject *__import__ = 0;
     PyObject *empty_list = 0;
         Py_INCREF(type);
         Py_DECREF(tmp);
     }
-    if (PyString_Check(type)) {
-        if (PyErr_Warn(PyExc_DeprecationWarning,
-                "raising a string exception is deprecated"))
-            goto raise_error;
-    }
-    else if (PyType_Check(type) || PyClass_Check(type))
+    if (PyString_Check(type))
+        ;
+    else if (PyClass_Check(type))
         ; /*PyErr_NormalizeException(&type, &value, &tb);*/
-    else {
+    else if (PyInstance_Check(type)) {
         /* Raising an instance.  The value should be a dummy. */
         if (value != Py_None) {
             PyErr_SetString(PyExc_TypeError,
-                "instance exception may not have a separate value");
+              "instance exception may not have a separate value");
             goto raise_error;
         }
-        /* Normalize to raise <class>, <instance> */
-        Py_DECREF(value);
-        value = type;
-        if (PyInstance_Check(type))
+        else {
+            /* Normalize to raise <class>, <instance> */
+            Py_DECREF(value);
+            value = type;
             type = (PyObject*) ((PyInstanceObject*)type)->in_class;
-        else
-            type = (PyObject*) type->ob_type;
-        Py_INCREF(type);
+            Py_INCREF(type);
+        }
+    }
+    else {
+        /* Not something you can raise.  You get an exception
+           anyway, just not what you specified :-) */
+        PyErr_Format(PyExc_TypeError,
+                 "exceptions must be strings, classes, or "
+                 "instances, not %s", type->ob_type->tp_name);
+        goto raise_error;
     }
     PyErr_Restore(type, value, tb);
     return;

File lib/bx/_seqmapping.pyx

     def __new__( self, int in_size ):
         self.in_size = in_size
         self.table = <int *> malloc( in_size * sizeof( int ) )
-        if self.table == NULL: raise "Malloc Failed"
+        if self.table == NULL: 
+                sys.stderr.write("From IntToIntMapping, _seqmapping.pyx, malloc failed\n");sys.stderr.flush()
+                raise "Malloc Failed in IntToIntMapping, _seqmapping.pyx"
         for i from 0 <= i < in_size: self.table[i] = -1
         self.out_size = 0
         
     def __dealloc__( self ):
         # sys.stderr.write( "freeing mapping_helper.IntToIntMapping\n" ); sys.stderr.flush()
-        free( self.table )
+        if self.table == NULL:
+                raise "Free Failed in IntToIntMapping, _seqmapping.pyx"
+        else:
+                free( self.table )
 
     def set_mapping( self, int index, int symbol ):
         assert ( -1 <= index < self.in_size ), "%d not between 0 and %s" % ( index, self.in_size )

File lib/bx/bitset.c

-/* Generated by Pyrex 0.9.5.1a on Sat Mar 24 20:22:45 2007 */
+/* Generated by Pyrex 0.9.3.1 on Wed Oct 17 17:01:56 2007 */
 
 #include "Python.h"
 #include "structmember.h"
 #ifndef PY_LONG_LONG
   #define PY_LONG_LONG LONG_LONG
 #endif
-#ifdef __cplusplus
-#define __PYX_EXTERN_C extern "C"
-#else
-#define __PYX_EXTERN_C extern
-#endif
-__PYX_EXTERN_C double pow(double, double);
 #include "common.h"
 #include "bits.h"
 #include "binBits.h"
 
 typedef struct {PyObject **p; char *s;} __Pyx_InternTabEntry; /*proto*/
 typedef struct {PyObject **p; char *s; long n;} __Pyx_StringTabEntry; /*proto*/
+static PyObject *__Pyx_UnpackItem(PyObject *, int); /*proto*/
+static int __Pyx_EndUnpack(PyObject *, int); /*proto*/
+static int __Pyx_PrintItem(PyObject *); /*proto*/
+static int __Pyx_PrintNewline(void); /*proto*/
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+static void __Pyx_ReRaise(void); /*proto*/
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list); /*proto*/
+static PyObject *__Pyx_GetExcValue(void); /*proto*/
+static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, char *name); /*proto*/
+static int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); /*proto*/
+static int __Pyx_GetStarArgs(PyObject **args, PyObject **kwds, char *kwd_list[], int nargs, PyObject **args2, PyObject **kwds2); /*proto*/
+static void __Pyx_WriteUnraisable(char *name); /*proto*/
+static void __Pyx_AddTraceback(char *funcname); /*proto*/
+static PyTypeObject *__Pyx_ImportType(char *module_name, char *class_name, long size);  /*proto*/
+static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
+static int __Pyx_GetVtable(PyObject *dict, void *vtabptr); /*proto*/
+static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name, char *modname); /*proto*/
+static int __Pyx_InternStrings(__Pyx_InternTabEntry *t); /*proto*/
+static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
+static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
 
 static PyObject *__pyx_m;
 static PyObject *__pyx_b;
 static int __pyx_lineno;
 static char *__pyx_filename;
-static char **__pyx_f;
+staticforward char **__pyx_f;
 
 static char __pyx_mdoc[] = "\nCompact mutable sequences of bits (vectors of 0s and 1s) supporting various\nboolean operations, and a \"binned\" variation which stores long runs of \nidentical bits compactly.\n\nBecause the binned implementation avoids a lot of memory allocation and access\nwhen working with either small subregions of the total interval or setting /\ntesting spans larger than the bin size, it an be much faster.\n";
 
-static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, char *name); /*proto*/
-
-static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
-
-static int __Pyx_InternStrings(__Pyx_InternTabEntry *t); /*proto*/
-
-static void __Pyx_AddTraceback(char *funcname); /*proto*/
-
 /* Declarations from bitset */
 
+staticforward PyTypeObject __pyx_type_6bitset_BitSet;
 
 struct __pyx_obj_6bitset_BitSet {
   PyObject_HEAD
   int bitCount;
 };
 
+staticforward PyTypeObject __pyx_type_6bitset_BinnedBitSet;
 
 struct __pyx_obj_6bitset_BinnedBitSet {
   PyObject_HEAD
 static int __pyx_k5;
 static int __pyx_k6;
 
-
 /* Implementation of bitset */
 
 static PyObject *__pyx_n_MAX;
 
+static PyObject *__pyx_n_sys;
+static PyObject *__pyx_n_stderr;
+static PyObject *__pyx_n_write;
+static PyObject *__pyx_n_flush;
+
+static PyObject *__pyx_k7p;
+static PyObject *__pyx_k8p;
+
+static char (__pyx_k7[]) = "From BitSet, bitset.pyx, bitAlloc failed\n";
+static char (__pyx_k8[]) = "Malloc Failed in BitSet, bitset.pyx";
+
 static int __pyx_f_6bitset_6BitSet___new__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
 static int __pyx_f_6bitset_6BitSet___new__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   int __pyx_v_bitCount;
   int __pyx_r;
+  int __pyx_1;
+  PyObject *__pyx_2 = 0;
+  PyObject *__pyx_3 = 0;
+  PyObject *__pyx_4 = 0;
   static char *__pyx_argnames[] = {"bitCount",0};
   if (!PyArg_ParseTupleAndKeywords(__pyx_args, __pyx_kwds, "i", __pyx_argnames, &__pyx_v_bitCount)) return -1;
   Py_INCREF(__pyx_v_self);
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/bitset.pyx":74 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/bitset.pyx":74 */
   ((struct __pyx_obj_6bitset_BitSet *)__pyx_v_self)->bitCount = __pyx_v_bitCount;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/bitset.pyx":75 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/bitset.pyx":75 */
   ((struct __pyx_obj_6bitset_BitSet *)__pyx_v_self)->bits = bitAlloc(__pyx_v_bitCount);
 
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/bitset.pyx":76 */
+  __pyx_1 = (((struct __pyx_obj_6bitset_BitSet *)__pyx_v_self)->bits == 0);
+  if (__pyx_1) {
+
+    /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/bitset.pyx":77 */
+    __pyx_2 = __Pyx_GetName(__pyx_b, __pyx_n_sys); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; goto __pyx_L1;}
+    __pyx_3 = PyObject_GetAttr(__pyx_2, __pyx_n_stderr); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; goto __pyx_L1;}
+    Py_DECREF(__pyx_2); __pyx_2 = 0;
+    __pyx_2 = PyObject_GetAttr(__pyx_3, __pyx_n_write); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; goto __pyx_L1;}
+    Py_DECREF(__pyx_3); __pyx_3 = 0;
+    __pyx_3 = PyTuple_New(1); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; goto __pyx_L1;}
+    Py_INCREF(__pyx_k7p);
+    PyTuple_SET_ITEM(__pyx_3, 0, __pyx_k7p);
+    __pyx_4 = PyObject_CallObject(__pyx_2, __pyx_3); if (!__pyx_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; goto __pyx_L1;}
+    Py_DECREF(__pyx_2); __pyx_2 = 0;
+    Py_DECREF(__pyx_3); __pyx_3 = 0;
+    Py_DECREF(__pyx_4); __pyx_4 = 0;
+
+    /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/bitset.pyx":77 */
+    __pyx_2 = __Pyx_GetName(__pyx_b, __pyx_n_sys); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; goto __pyx_L1;}
+    __pyx_3 = PyObject_GetAttr(__pyx_2, __pyx_n_stderr); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; goto __pyx_L1;}
+    Py_DECREF(__pyx_2); __pyx_2 = 0;
+    __pyx_4 = PyObject_GetAttr(__pyx_3, __pyx_n_flush); if (!__pyx_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; goto __pyx_L1;}
+    Py_DECREF(__pyx_3); __pyx_3 = 0;
+    __pyx_2 = PyTuple_New(0); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; goto __pyx_L1;}
+    __pyx_3 = PyObject_CallObject(__pyx_4, __pyx_2); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; goto __pyx_L1;}
+    Py_DECREF(__pyx_4); __pyx_4 = 0;
+    Py_DECREF(__pyx_2); __pyx_2 = 0;
+    Py_DECREF(__pyx_3); __pyx_3 = 0;
+
+    /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/bitset.pyx":78 */
+    __Pyx_Raise(__pyx_k8p, 0, 0);
+    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; goto __pyx_L1;}
+    goto __pyx_L2;
+  }
+  __pyx_L2:;
+
   __pyx_r = 0;
+  goto __pyx_L0;
+  __pyx_L1:;
+  Py_XDECREF(__pyx_2);
+  Py_XDECREF(__pyx_3);
+  Py_XDECREF(__pyx_4);
+  __Pyx_AddTraceback("bitset.BitSet.__new__");
+  __pyx_r = -1;
+  __pyx_L0:;
   Py_DECREF(__pyx_v_self);
   return __pyx_r;
 }
 
+static PyObject *__pyx_k9p;
+static PyObject *__pyx_k10p;
+
+static char (__pyx_k9[]) = "From BitSet, bitset.pyx, bitFree failed\n";
+static char (__pyx_k10[]) = "Free Failed in BitSet, bitset.pyx\n";
+
 static void __pyx_f_6bitset_6BitSet___dealloc__(PyObject *__pyx_v_self); /*proto*/
 static void __pyx_f_6bitset_6BitSet___dealloc__(PyObject *__pyx_v_self) {
+  int __pyx_1;
+  PyObject *__pyx_2 = 0;
+  PyObject *__pyx_3 = 0;
+  PyObject *__pyx_4 = 0;
   Py_INCREF(__pyx_v_self);
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/bitset.pyx":78 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/bitset.pyx":81 */
+  __pyx_1 = (((struct __pyx_obj_6bitset_BitSet *)__pyx_v_self)->bits == 0);
+  if (__pyx_1) {
+
+    /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/bitset.pyx":82 */
+    __pyx_2 = __Pyx_GetName(__pyx_b, __pyx_n_sys); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; goto __pyx_L1;}
+    __pyx_3 = PyObject_GetAttr(__pyx_2, __pyx_n_stderr); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; goto __pyx_L1;}
+    Py_DECREF(__pyx_2); __pyx_2 = 0;
+    __pyx_2 = PyObject_GetAttr(__pyx_3, __pyx_n_write); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; goto __pyx_L1;}
+    Py_DECREF(__pyx_3); __pyx_3 = 0;
+    __pyx_3 = PyTuple_New(1); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; goto __pyx_L1;}
+    Py_INCREF(__pyx_k9p);
+    PyTuple_SET_ITEM(__pyx_3, 0, __pyx_k9p);
+    __pyx_4 = PyObject_CallObject(__pyx_2, __pyx_3); if (!__pyx_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; goto __pyx_L1;}
+    Py_DECREF(__pyx_2); __pyx_2 = 0;
+    Py_DECREF(__pyx_3); __pyx_3 = 0;
+    Py_DECREF(__pyx_4); __pyx_4 = 0;
+
+    /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/bitset.pyx":82 */
+    __pyx_2 = __Pyx_GetName(__pyx_b, __pyx_n_sys); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; goto __pyx_L1;}
+    __pyx_3 = PyObject_GetAttr(__pyx_2, __pyx_n_stderr); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; goto __pyx_L1;}
+    Py_DECREF(__pyx_2); __pyx_2 = 0;
+    __pyx_4 = PyObject_GetAttr(__pyx_3, __pyx_n_flush); if (!__pyx_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; goto __pyx_L1;}
+    Py_DECREF(__pyx_3); __pyx_3 = 0;
+    __pyx_2 = PyTuple_New(0); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; goto __pyx_L1;}
+    __pyx_3 = PyObject_CallObject(__pyx_4, __pyx_2); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; goto __pyx_L1;}
+    Py_DECREF(__pyx_4); __pyx_4 = 0;
+    Py_DECREF(__pyx_2); __pyx_2 = 0;
+    Py_DECREF(__pyx_3); __pyx_3 = 0;
+
+    /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/bitset.pyx":83 */
+    __Pyx_Raise(__pyx_k10p, 0, 0);
+    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; goto __pyx_L1;}
+    goto __pyx_L2;
+  }
+  __pyx_L2:;
+
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/bitset.pyx":84 */
   bitFree((&((struct __pyx_obj_6bitset_BitSet *)__pyx_v_self)->bits));
 
+  goto __pyx_L0;
+  __pyx_L1:;
+  Py_XDECREF(__pyx_2);
+  Py_XDECREF(__pyx_3);
+  Py_XDECREF(__pyx_4);
+  __Pyx_AddTraceback("bitset.BitSet.__dealloc__");
+  __pyx_L0:;
   Py_DECREF(__pyx_v_self);
 }
 
   PyObject *__pyx_1 = 0;
   Py_INCREF(__pyx_v_self);
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/bitset.pyx":87 */
-  __pyx_1 = PyInt_FromLong(((struct __pyx_obj_6bitset_BitSet *)__pyx_v_self)->bitCount); if (!__pyx_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; goto __pyx_L1;}
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/bitset.pyx":93 */
+  __pyx_1 = PyInt_FromLong(((struct __pyx_obj_6bitset_BitSet *)__pyx_v_self)->bitCount); if (!__pyx_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 93; goto __pyx_L1;}
   __pyx_r = __pyx_1;
   __pyx_1 = 0;
   goto __pyx_L0;
 
-  __pyx_r = Py_None; Py_INCREF(Py_None);
+  __pyx_r = Py_None; Py_INCREF(__pyx_r);
   goto __pyx_L0;
   __pyx_L1:;
   Py_XDECREF(__pyx_1);
   Py_INCREF(__pyx_v_self);
   Py_INCREF(__pyx_v_index);
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/bitset.pyx":90 */
-  __pyx_1 = PyInt_AsLong(__pyx_v_index); if (PyErr_Occurred()) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 90; goto __pyx_L1;}
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/bitset.pyx":96 */
+  __pyx_1 = PyInt_AsLong(__pyx_v_index); if (PyErr_Occurred()) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 96; goto __pyx_L1;}
   bitSetOne(((struct __pyx_obj_6bitset_BitSet *)__pyx_v_self)->bits,__pyx_1);
 
-  __pyx_r = Py_None; Py_INCREF(Py_None);
+  __pyx_r = Py_None; Py_INCREF(__pyx_r);
   goto __pyx_L0;
   __pyx_L1:;
   __Pyx_AddTraceback("bitset.BitSet.set");
   Py_INCREF(__pyx_v_self);
   Py_INCREF(__pyx_v_index);
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/bitset.pyx":93 */
-  __pyx_1 = PyInt_AsLong(__pyx_v_index); if (PyErr_Occurred()) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 93; goto __pyx_L1;}
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/bitset.pyx":99 */
+  __pyx_1 = PyInt_AsLong(__pyx_v_index); if (PyErr_Occurred()) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 99; goto __pyx_L1;}
   bitClearOne(((struct __pyx_obj_6bitset_BitSet *)__pyx_v_self)->bits,__pyx_1);
 
-  __pyx_r = Py_None; Py_INCREF(Py_None);
+  __pyx_r = Py_None; Py_INCREF(__pyx_r);
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-  __pyx_v_other = Py_None; Py_INCREF(Py_None);
+  __pyx_v_other = Py_None; Py_INCREF(__pyx_v_other);
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/bitset.pyx":96 */
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-  __pyx_2 = PyTuple_New(1); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 96; goto __pyx_L1;}
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/bitset.pyx":102 */
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+  __pyx_1 = PyObject_CallObject(((PyObject*)__pyx_ptype_6bitset_BitSet), __pyx_2); if (!__pyx_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 102; goto __pyx_L1;}
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-  __pyx_1 = PyTuple_New(1); if (!__pyx_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 97; goto __pyx_L1;}
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/bitset.pyx":103 */
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+  __pyx_3 = PyObject_CallObject(__pyx_2, __pyx_1); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 103; goto __pyx_L1;}
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   Py_DECREF(__pyx_3); __pyx_3 = 0;
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/bitset.pyx":98 */
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/bitset.pyx":104 */
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   __pyx_r = __pyx_v_other;
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-  __pyx_r = Py_None; Py_INCREF(Py_None);
+  __pyx_r = Py_None; Py_INCREF(__pyx_r);
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-  __pyx_2 = PyInt_AsLong(__pyx_v_count); if (PyErr_Occurred()) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 101; goto __pyx_L1;}
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/bitset.pyx":107 */
+  __pyx_1 = PyInt_AsLong(__pyx_v_start); if (PyErr_Occurred()) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 107; goto __pyx_L1;}
+  __pyx_2 = PyInt_AsLong(__pyx_v_count); if (PyErr_Occurred()) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 107; goto __pyx_L1;}
   bitSetRange(((struct __pyx_obj_6bitset_BitSet *)__pyx_v_self)->bits,__pyx_1,__pyx_2);
 
-  __pyx_r = Py_None; Py_INCREF(Py_None);
+  __pyx_r = Py_None; Py_INCREF(__pyx_r);
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-  __pyx_2 = PyInt_FromLong(bitReadOne(((struct __pyx_obj_6bitset_BitSet *)__pyx_v_self)->bits,__pyx_1)); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 104; goto __pyx_L1;}
+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/bitset.pyx":110 */
+  __pyx_1 = PyInt_AsLong(__pyx_v_index); if (PyErr_Occurred()) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; goto __pyx_L1;}
+  __pyx_2 = PyInt_FromLong(bitReadOne(((struct __pyx_obj_6bitset_BitSet *)__pyx_v_self)->bits,__pyx_1)); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; goto __pyx_L1;}
   __pyx_r = __pyx_2;
   __pyx_2 = 0;
   goto __pyx_L0;
 
-  __pyx_r = Py_None; Py_INCREF(Py_None);
+  __pyx_r = Py_None; Py_INCREF(__pyx_r);
   goto __pyx_L0;
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   Py_XDECREF(__pyx_2);
   Py_INCREF(__pyx_v_start);
   Py_INCREF(__pyx_v_count);
 
-  /* "/Users/james/projects/bx-python-trunk/lib/bx/bitset.pyx":107 */
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+  /* "/afs/bx.psu.edu/home/radhesh/bx_code/svnroot/trunk/lib/bx/bitset.pyx":113 */
+  if (PyObject_Cmp(__pyx_v_count, Py_None, &__pyx_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 113; goto __pyx_L1;}
   __pyx_1 = __pyx_1 == 0;
   if (__pyx_1) {
-    __pyx_2 = PyInt_FromLong(((struct __pyx_obj_6bitset_BitSet *)__pyx_v_self)->bitCount); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 107; goto __pyx_L1;}
+    __pyx_2 = PyInt_FromLong(((struct __pyx_obj_6bitset_BitSet *)__pyx_v_self)->bitCount); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 113; goto __pyx_L1;}
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