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openbsd-ports/biology/py-biopython/patches/patch-Bio_Cluster_clustermodule_c
alek 1d6d4168a4 Update to 1.41
2005-12-03 22:34:52 +00:00

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$OpenBSD: patch-Bio_Cluster_clustermodule_c,v 1.1 2005/12/03 22:34:52 alek Exp $
--- Bio/Cluster/clustermodule.c.orig Wed Apr 27 10:09:08 2005
+++ Bio/Cluster/clustermodule.c Mon Nov 21 21:06:54 2005
@@ -111,7 +111,7 @@ parse_mask (PyObject* object, PyArrayObj
return mask;
}
if(!PyArray_Check (object)) /* Try to convert object to a 2D double array */
- { *array = (PyArrayObject*) PyArray_FromObject(object, PyArray_LONG, 2, 2);
+ { *array = (PyArrayObject*) PyArray_FromObject(object, PyArray_INT, 2, 2);
if (!(*array))
{ strcpy (message, "mask cannot be converted to needed array");
PyErr_SetString(ErrorObject, buffer);
@@ -121,8 +121,8 @@ parse_mask (PyObject* object, PyArrayObj
else /* User passed an array */
{ *array = (PyArrayObject*) object;
Py_INCREF(object);
- if ((*array)->descr->type_num != PyArray_LONG)
- { PyArrayObject* av = (PyArrayObject*) PyArray_Cast (*array, PyArray_LONG);
+ if ((*array)->descr->type_num != PyArray_INT)
+ { PyArrayObject* av = (PyArrayObject*) PyArray_Cast (*array, PyArray_INT);
Py_DECREF((PyObject*) *array);
*array = av;
if (!(*array))
@@ -281,7 +281,7 @@ parse_initialid(PyObject* object, int* n
PyArrayObject* array;
/* -- First we create the clusterid variable ------------------------ */
PyArrayObject* clusterid =
- (PyArrayObject*) PyArray_FromDims(1, &nitems, PyArray_LONG);
+ (PyArrayObject*) PyArray_FromDims(1, &nitems, PyArray_INT);
if (!clusterid)
{ strcpy(message, "Could not create clusterid array -- too big?");
PyErr_SetString (ErrorObject, buffer);
@@ -291,7 +291,7 @@ parse_initialid(PyObject* object, int* n
if (object==NULL) return clusterid;
/* -- Check if the specified object is an array --------------------- */
if(!PyArray_Check (object))
- { array = (PyArrayObject*) PyArray_FromObject(object, PyArray_LONG,1,1);
+ { array = (PyArrayObject*) PyArray_FromObject(object, PyArray_INT,1,1);
if (!array)
{ strcpy (message, "initialid cannot be converted to needed array.");
PyErr_SetString(ErrorObject, buffer);
@@ -304,8 +304,8 @@ parse_initialid(PyObject* object, int* n
Py_INCREF(object);
}
/* -- Check if the array contains integers -------------------------- */
- if (array->descr->type_num != PyArray_LONG)
- { PyArrayObject* av = (PyArrayObject*) PyArray_Cast(array, PyArray_LONG);
+ if (array->descr->type_num != PyArray_INT)
+ { PyArrayObject* av = (PyArrayObject*) PyArray_Cast(array, PyArray_INT);
Py_DECREF((PyObject*) array);
array = av;
if (!array)
@@ -394,7 +394,7 @@ parse_clusterid(PyObject* object, PyArra
}
/* -- The user specified something. Let's see if it is an array ----- */
if(!PyArray_Check (object))
- { *array = (PyArrayObject*) PyArray_FromObject(object, PyArray_LONG,1,1);
+ { *array = (PyArrayObject*) PyArray_FromObject(object, PyArray_INT,1,1);
if (!(*array))
{ strcpy (message, "clusterid cannot be converted to needed array.");
PyErr_SetString(ErrorObject, buffer);
@@ -406,8 +406,8 @@ parse_clusterid(PyObject* object, PyArra
Py_INCREF(object);
}
/* -- Check if the array contains integers -------------------------- */
- if ((*array)->descr->type_num != PyArray_LONG)
- { PyArrayObject* av = (PyArrayObject*) PyArray_Cast(*array, PyArray_LONG);
+ if ((*array)->descr->type_num != PyArray_INT)
+ { PyArrayObject* av = (PyArrayObject*) PyArray_Cast(*array, PyArray_INT);
Py_DECREF((PyObject*) (*array));
*array = av;
if (!(*array))
@@ -663,7 +663,7 @@ parse_index(PyObject* object, PyArrayObj
/* Check if the user specified an array */
if(!PyArray_Check (object)) /* Try to convert to an array of type long */
{ *array = (PyArrayObject*)
- PyArray_ContiguousFromObject(object, PyArray_LONG, 1, 1);
+ PyArray_ContiguousFromObject(object, PyArray_INT, 1, 1);
if (!(*array))
{ strcpy(message, "index argument cannot be converted to needed type.");
PyErr_SetString (ErrorObject, buffer);
@@ -672,7 +672,7 @@ parse_index(PyObject* object, PyArrayObj
}
}
/* If an array, make sure it contains integers */
- else if ((*array)->descr->type_num == PyArray_LONG)
+ else if ((*array)->descr->type_num == PyArray_INT)
{ *array = (PyArrayObject*) object;
Py_INCREF(object);
}
@@ -697,7 +697,7 @@ parse_index(PyObject* object, PyArrayObj
}
if (!(*array)->flags & CONTIGUOUS)
{ PyObject* av =
- PyArray_ContiguousFromObject((PyObject*) array, PyArray_LONG, 0, 0);
+ PyArray_ContiguousFromObject((PyObject*) array, PyArray_INT, 0, 0);
Py_DECREF(object); /* can only happen if *array==(PyArrayObject*)object */
if(!av)
{ strcpy(message, "Failed making argument index contiguous.");
@@ -800,7 +800,7 @@ py_kcluster (PyObject* self, PyObject* a
"dist",
"initialid",
NULL };
- if(!PyArg_ParseTupleAndKeywords(args, keywords, "O|lOOllccO", kwlist,
+ if(!PyArg_ParseTupleAndKeywords(args, keywords, "O|iOOiiccO", kwlist,
&DATA,
&NCLUSTERS,
&MASK,
@@ -899,7 +899,7 @@ py_kcluster (PyObject* self, PyObject* a
free_weight(aWEIGHT, weight);
/* --------------------------------------------------------------------- */
- return Py_BuildValue("Ndl", aCLUSTERID, ERROR, IFOUND);
+ return Py_BuildValue("Ndi", aCLUSTERID, ERROR, IFOUND);
}
/* end of wrapper for kcluster */
@@ -1015,7 +1015,7 @@ py_kmedoids (PyObject* self, PyObject* a
strcpy(message, "Unknown error in kmedoids");
return NULL;
}
- return Py_BuildValue("Ndl",aCLUSTERID, ERROR, IFOUND);
+ return Py_BuildValue("Ndi",aCLUSTERID, ERROR, IFOUND);
}
/* end of wrapper for kmedoids */
@@ -1091,7 +1091,7 @@ py_treecluster (PyObject* self, PyObject
"dist",
"distancematrix",
NULL };
- if(!PyArg_ParseTupleAndKeywords(args, keywords, "|OOOlccO", kwlist,
+ if(!PyArg_ParseTupleAndKeywords(args, keywords, "|OOOiccO", kwlist,
&DATA,
&MASK,
&WEIGHT,
@@ -1165,7 +1165,7 @@ py_treecluster (PyObject* self, PyObject
/* -- Create the output variable tree ---------------------------------- */
shape[0] = nnodes;
shape[1] = 2;
- aRESULT = (PyArrayObject*) PyArray_FromDims(2, shape, PyArray_LONG);
+ aRESULT = (PyArrayObject*) PyArray_FromDims(2, shape, PyArray_INT);
if (!aRESULT)
{ strcpy(message, "Could not create array for return value -- too big?");
PyErr_SetString(ErrorObject, buffer);
@@ -1228,7 +1228,7 @@ py_treecluster (PyObject* self, PyObject
/* -- Create the output variable tree ---------------------------------- */
shape[0] = nnodes;
shape[1] = 2;
- aRESULT = (PyArrayObject*) PyArray_FromDims(2, shape, PyArray_LONG);
+ aRESULT = (PyArrayObject*) PyArray_FromDims(2, shape, PyArray_INT);
if (!aRESULT)
{ strcpy(message, "Could not create array for return value -- too big?");
PyErr_SetString(ErrorObject, buffer);
@@ -1341,7 +1341,7 @@ py_somcluster (PyObject* self, PyObject*
"niter",
"dist",
NULL };
- if(!PyArg_ParseTupleAndKeywords(args, keywords, "O|OOllldlc", kwlist,
+ if(!PyArg_ParseTupleAndKeywords(args, keywords, "O|OOiiidic", kwlist,
&DATA,
&MASK,
&WEIGHT,
@@ -1403,7 +1403,7 @@ py_somcluster (PyObject* self, PyObject*
/* --------------------------------------------------------------------- */
shape[0] = nitems;
shape[1] = 2;
- aCLUSTERID = (PyArrayObject*) PyArray_FromDims(2, shape, PyArray_LONG);
+ aCLUSTERID = (PyArrayObject*) PyArray_FromDims(2, shape, PyArray_INT);
if (!aCLUSTERID)
{ strcpy(buffer, "somcluster: Could not create clusterid array -- too big?");
PyErr_SetString (ErrorObject, buffer);
@@ -1656,7 +1656,7 @@ py_clusterdistance (PyObject* self, PyOb
"dist",
"transpose",
NULL };
- if(!PyArg_ParseTupleAndKeywords(args, keywords, "O|OOOOccl", kwlist,
+ if(!PyArg_ParseTupleAndKeywords(args, keywords, "O|OOOOcci", kwlist,
&DATA,
&MASK,
&WEIGHT,
@@ -1826,7 +1826,7 @@ py_clustercentroid (PyObject* self, PyOb
for (i=0; i<shape[0]; i++)
cdata[i] = ((double*) (aCDATA->data)) + i*shape[1];
/* -- Create the centroid mask output variable ------------------------- */
- aCMASK = (PyArrayObject*) PyArray_FromDims(2, shape, PyArray_LONG);
+ aCMASK = (PyArrayObject*) PyArray_FromDims(2, shape, PyArray_INT);
if (!aCMASK)
{ strcpy(message, "Could not create centroids array -- too big?");
PyErr_SetString (ErrorObject, buffer);
@@ -1934,7 +1934,7 @@ py_distancematrix (PyObject* self, PyObj
"transpose",
"dist",
NULL };
- if(!PyArg_ParseTupleAndKeywords(args, keywords, "O|OOlc", kwlist,
+ if(!PyArg_ParseTupleAndKeywords(args, keywords, "O|OOic", kwlist,
&DATA,
&MASK,
&WEIGHT,
@@ -2056,7 +2056,7 @@ py_cuttree (PyObject* self, PyObject* ar
{ aTREE = (PyArrayObject*) TREE;
Py_INCREF((PyObject*) aTREE);
}
- if (aTREE->descr->type_num != PyArray_LONG)
+ if (aTREE->descr->type_num != PyArray_INT)
{ PyErr_SetString (ErrorObject,
"cuttree: Argument tree should contain integer values only");
return NULL;
@@ -2095,7 +2095,7 @@ py_cuttree (PyObject* self, PyObject* ar
return NULL;
}
/* -- Create the clusterid output variable ----------------------------- */
- aCLUSTERID = (PyArrayObject*) PyArray_FromDims(1, &NELEMENTS, PyArray_LONG);
+ aCLUSTERID = (PyArrayObject*) PyArray_FromDims(1, &NELEMENTS, PyArray_INT);
if (!aCLUSTERID) {
PyErr_SetString (ErrorObject,
"cuttree: Could not create array for return value -- too big?");
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