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/* Copyright 2005 by Frank Kauff. All rights reserved.
*
* This file is part of the Biopython distribution and governed by your
* choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
* Please see the LICENSE file that should have been included as part of this
* package.
*
* cnexus.c
*
* Parse input strings, cut out (nested) comments, deal with quoted text.
* Input lines terminated with ; are separated by ASCII code 7 (something
* that naturally doesn't occur in plain NEXUS files).
*
* Used by Nexus.py
*/
#include <Python.h>
#include <string.h>
static PyObject * cnexus_scanfile(PyObject *self, PyObject *args)
{
PyObject *cleaninput;
const char *input;
char *scanned, *scanned_start;
char t, quotelevel;
int speciallevel, commlevel;
quotelevel=0;
speciallevel=0;
commlevel=0;
if (!PyArg_ParseTuple(args, "s", &input))
return NULL;
if (!(scanned=PyMem_RawMalloc(strlen(input)+1)))
PyErr_NoMemory();
scanned_start=scanned;
for(t=*input;(t=*input);input++)
{
/* end of standard quote */
if (!(commlevel || speciallevel) && t==quotelevel)
quotelevel=0;
/* start of standard quote */
else if (!quotelevel && !(commlevel || speciallevel) && (t=='\'' || t=='"'))
quotelevel=t;
/* start of comment outside quote */
else if (!quotelevel && t=='[')
{
/* check for special comments */
/*if ((*(input+1)=='!' || *(input+1)=='&' || *(input+1)=='%' ||
*(input+1)=='/' || *(input+1)=='\\' || *(input+1)=='@')
&& !(commlevel || speciallevel))
speciallevel=1;
*/
if ((*(input+1)=='&') && !(commlevel || speciallevel))
speciallevel=1;
else /* standard comment */
commlevel++;
}
else if (!quotelevel && t==']')
{
/* does it end a special comment? */
if (speciallevel)
speciallevel=0;
else
{
commlevel--;
if (commlevel<0) /* error: unmatched ] */
{
PyMem_RawFree(scanned_start);
return Py_BuildValue("s","]");
}
continue;
}
}
if (!commlevel)
{
/* we replace the ; at the end of command lines with special
* character to make subsequent parsing of blocks easier */
if (t==';' && !(quotelevel || speciallevel))
/* need an ascii code that's not part of a nexus file, used as
* separator */
*(scanned++)=7;
else
*(scanned++)=t;
}
/* printf("t %c, commlevel %d, speciallevel %d, quotelevel '%c', scanned %d\n",
* t,commlevel,speciallevel,quotelevel,scanned);
*/
}
if (commlevel>0)
{
/* error: unmatched [ */
PyMem_RawFree(scanned_start);
return Py_BuildValue("s","[");
}
else
{
*scanned=0; /* end of string */
cleaninput= Py_BuildValue("s",scanned_start);
PyMem_RawFree(scanned_start);
return cleaninput;
}
}
static PyMethodDef cNexusMethods[]=
{
{"scanfile",cnexus_scanfile,METH_VARARGS,"Scan file and deal with comments and quotes."},
{NULL,NULL,0,NULL}
};
static struct PyModuleDef moduledef = {
PyModuleDef_HEAD_INIT,
"cnexus",
NULL,
-1,
cNexusMethods,
NULL,
NULL,
NULL,
NULL
};
PyObject *
PyInit_cnexus(void)
{
return PyModule_Create(&moduledef);
}
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