SWIG use typemaps to convert C++ to python and vice verca.
This howto shows you, with some example, how to use them. The
conecept of this syntax is well explained in the SWIG documentation.
http://www.swig.org/Doc1.3/Typemaps.html


1. How to convert a list of integer from pyhton to C++?

//python integer list -> int array
	%typemap(in) (int len, int *value) //int len and int* value are the name of the arguments from the c++
																		 //funciton, $1 refers to int len and $2 to *value
	{
		int i;
		if (!PyList_Check($input))
		{
		  PyErr_SetString(PyExc_ValueError, "Expecting a list");
		  return NULL;
		}
		$1 = PyList_Size($input); //get size of the list
		$2 = (int*) malloc(($1+1)*sizeof(int)); //allocate memory with the correct size
		for (i = 0; i < $1; i++)
		{
		  PyObject *s = PyList_GetItem($input,i);
		  if (!PyInt_Check(s))
			{
		      free($2);
		      PyErr_SetString(PyExc_ValueError, "List items must be integers");
		      return NULL;
		  }
		  $2[i] = (int)PyInt_AS_LONG(s); //put the value into the array
		}
		$2[i] = 0;
	}

To avoid memory leaks, we have to release the allocate memory at the end of the C++ function
	%typemap(freearg) (int len, int *value) 
	{
		 if ($2) free($2);
	}
//////////////////////////////////////////////////////////////////////////////////////////////////////////

2. String array or list of strings in python
//same as above but with some small changes
%typemap(in) (int amount, char **needles)
	{
  /* Check if is a list */

  if (PyList_Check($input))
	{
    int i;
    $1 = PyList_Size($input);
    $2 = (char **) malloc(($1+1)*sizeof(char *));
    for (i = 0; i < $1; i++) 
		{
      PyObject *o = PyList_GetItem($input,i);
      if (PyString_Check(o))
				$2[i] = PyString_AsString(PyList_GetItem($input,i));
      else 
			{
				PyErr_SetString(PyExc_TypeError,"list must contain strings");
				free($2);
				return NULL;
      }
    }
    $2[i] = 0;
	}
	else 
	{
    PyErr_SetString(PyExc_TypeError,"not a list");
    return NULL;
  }
}

%typemap(freearg) (int amount, char **needles) {
   if ($2) free((char*)$2);
}
/////////////////////////////////////////////////////////////////////////////////////////////////////////////

3. How to set a default value for an argument?

	%typemap(default) unsigned int dia2 
	{
		 $1 = 0;
	}

Be careful, if you set a default value for one argument you have to guaranty that the following arguments also have a default value. 
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4. How to return a value into an argument -> multiple results?
This is done by using the Keyword argout. First initialise a dummy value which tells SWIG not to consider this argument to be filled in python.

//(here for a int value)
	%typemap(in,numinputs=0)int& scoreAlignment(int temp)
	{
		$1=&temp;
	}
//here for a list of strings
	%typemap(in,numinputs=0) char** str1(char* temp) 
	{
		$1 = (char **) malloc((strlen(temp)+1)*sizeof(char *));
	}
//list of integer
	%typemap(in,numinputs=0) int** scoreMatrix(int* temp)
	{
		  $1 = (int **) malloc((sizeof(temp)+1)*sizeof(int *));
	}
//for pointer to a struct
	%typemap(in,numinputs=0)_Pattern<seqan::String<seqan::Dna5> >& pattern()
	{
		$1=new _Pattern<seqan::String<seqan::Dna5> >();
	}

We saved the result into one argument how we represent them now to python?

//e.g by a tupel: if we have to report two solutions

	%typemap(argout)int& scoreAlignment
	{    
		PyObject *o, *o2, *o3; 
    o = PyInt_FromLong(*$1); //$1 -> value which has to be convert to python
    if ((!$result) || ($result == Py_None))  //check if already exist a result if not set the actual result
		{
			$result = o;
    }
		else
		{
      if(!PyTuple_Check($result)) //build a tuple 
			 {
            PyObject *o2 = $result;
            $result = PyTuple_New(1);
            PyTuple_SetItem($result,0,o2);
        }
				o3 = PyTuple_New(1);
        PyTuple_SetItem(o3,0,o);
        o2 = $result;
        $result = PySequence_Concat(o2,o3);
        Py_DECREF(o2);
        Py_DECREF(o3);
    }
	}

//by returning a string list
	%typemap(argout)char** str1
	{
		$result=SWIG_Python_AppendOutput($result, PyString_FromStringAndSize(*$1,strlen(*$1)));
	}


//by returning a integer list

	%typemap(argout) (int** scoreMatrix, int& aSize)
	{
  	int i;
  	$result = PyList_New(*$2); //build a list with the the size aSize
  	for (i = 0; i < *$2; i++)
	 {
    	PyObject *o =PyInt_FromLong(*(*$1+i));
    	PyList_SetItem($result,i,o);
  	}
	}

//don't forget to release the pre allocated memory

	%typemap(freearg) char ** 
	{
		free((char *) $1);
	}

	%typemap(freearg) int ** 
	{
		free((int *) $1);
	}

	%typemap(freearg) _Pattern<seqan::String<seqan::Dna5> >& 
	{
		delete $1;
	}

/////////////////////////////////////////////////////////////////////////////////////

What about templates?

SWIG does not wrapping any kind of template function, unless you have specified the type via %template command
e.g %template(alignDna)seqan::alignSequence<seqan::Dna5>;. 
This command tells SWIG to build a function alignDna with the specified type, after that the function can be called in python. 

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