Sure, sorry...
This is the function that is visible from python and the one that the
python code calls:
static PyObject * IMFind (PyObject *self, PyObject *args, PyObject
*kwargs) {
//Array for the detection of the parameters coming from Python
static char *kwlist[] =
{"shareInt","root","prefix","lowerLimit",NULL};
//Root protein code
char *root;
//Pefix for the output file
char *prefix;
//Incoming Python object
PyObject *shareIntPy;
//Number of proteins at level two from the root, that will appear in
the iMotifs' proteins
int *pSize = new int;
//Maximum number of common interactors
int *max = new int;
//Set relating each protein (integer) with their interactors...
set<unsigned int>** shareInt;
//Lower limit for iMotif search
int lowLim;
//Vector for the seed iMotifs from an specific threshold
vector<iMotif> IMseed;
//Vector of all the working iMotifs during the identification process
vector<iMotif> IMarray;
//Receiving data from python
if (!PyArg_ParseTupleAndKeywords(args, kwargs, "Ossi", kwlist,
&shareIntPy, &root, &prefix,&lowLim)) {
cerr << "Error in parameter transference from python to iMotif
C++
module"<<endl;
return Py_BuildValue("");
}
//The position of the name in the vector corresponds to the number by
which it is represented
//Here we take the info coming from python and transform it
into a vector (will allow us to work with numbers instead of
// strings) and shareInt which is an array of sets (form
std::set)
vector<string> translator = string2int
(shareIntPy,root,shareInt,pSize,max);
//Loop for iMotif search at threshold thr till the specified lower
limit
for (int thr = *max; thr >= lowLim; thr--) {
cout << "Checking threshold " << thr << endl;
//Specifying the output file name
stringstream filename;
filename << prefix << "." << thr;
//Getting the seed iMotifs for this threshold
IMseed = getSeedIM(shareInt,*pSize,thr);
//Adding the new seeds (if any) to those obtained from previous
rounds...
if (!IMseed.size()) {
IMseed.clear();
vector<iMotif>().swap(IMseed); //This is how I try to
free them
now, size & capacity gets to 0, but the
// memory is
not freed...
} else {
IMarray.insert(IMarray.end(),IMseed.begin(),IMseed.end());
IMseed.clear();
vector<iMotif>().swap(IMseed);
}
//Fuse those iMotifs sharing thr interactors
// It also deletes the IMarray before giving it the
new data in the same way as I use here for IMseed
processIMVector(IMarray,thr);
writeIMVector(IMarray,translator,filename.str());
}
return Py_BuildValue("");
}
The object iMotif used here is composed by 2 sets and 3 strings just
like this: (the access is done by setters and getters)
class iMotif {
private:
//Set of the proteins that shares the iMotif with the root
set<unsigned int> proteins;
//Set of the proteins to which the iMotifs interacts
set<unsigned int> interactors;
//iMotifs interactors signature
string MD5Interactor;
//iMotifs proteins signature
string MD5Proteins;
//Real MD5 according to the sequences names
string signature;
...
}
and I specified the destructor as:
iMotif::~iMotif() {
this->proteins.clear();
set<unsigned int>().swap(this->proteins);
this->interactors.clear();
set<unsigned int>().swap(this->proteins);
}
The call to the function from python goes like this:
iMotifs.IMFind(shareInt=intersections_dict,
root=options.protein_problem, prefix=prefixOutFile, lowerLimit=1);
where intersections_dict is a dictionary and options.protein_problem
and prefixOutFile are strings. There is nothing to return from C++ to
python, the result is directly printed into several files.
Thanks,
J
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