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/****************************************/
/* Iterator of all the mers in a string */
/****************************************/
#ifdef SWIGPYTHON
%exception __next__ {
$action;
if(!result) {
PyErr_SetString(PyExc_StopIteration, "Done");
SWIG_fail;
}
}
%exception next {
$action;
if(!result) {
PyErr_SetString(PyExc_StopIteration, "Done");
SWIG_fail;
}
}
#endif
%{
class StringMers {
#ifdef SWIGPYTHON
const char* const m_str;
#endif
const char* m_current;
const char* const m_last;
const bool m_canonical;
MerDNA m_m, m_rcm;
unsigned int m_filled;
public:
StringMers(const char* str, int len, bool canonical)
#ifdef SWIGPYTHON
: m_str(strndup(str, len)) // In Python, duplicate the string! Can this be improved?
, m_current(m_str)
#else
: m_current(str)
#endif
, m_last(m_current + len)
, m_canonical(canonical)
, m_filled(0)
{ }
#ifdef SWIGPYTHON
~StringMers() {
free((void*)m_str);
}
#endif
bool next_mer() {
if(m_current == m_last)
return false;
do {
int code = jellyfish::mer_dna::code(*m_current);
++m_current;
if(code >= 0) {
m_m.shift_left(code);
if(m_canonical)
m_rcm.shift_right(m_rcm.complement(code));
m_filled = std::min(m_filled + 1, m_m.k());
} else
m_filled = 0;
} while(m_filled < m_m.k() && m_current != m_last);
return m_filled == m_m.k();
}
const MerDNA* mer() const { return !m_canonical || m_m < m_rcm ? &m_m : &m_rcm; }
const MerDNA* next_mer__() {
return next_mer() ? mer() : nullptr;
}
#ifdef SWIGRUBY
void each() {
if(!rb_block_given_p()) return;
while(next_mer()) {
auto m = SWIG_NewPointerObj(const_cast<MerDNA*>(mer()), SWIGTYPE_p_MerDNA, 0);
rb_yield(m);
}
}
#endif
#ifdef SWIGPYTHON
StringMers* __iter__() { return this; }
const MerDNA* __next__() { return next_mer__(); }
const MerDNA* next() { return next_mer__(); }
#endif
#ifdef SWIGPERL
const MerDNA* each() { return next_mer__(); }
#endif
};
StringMers* string_mers(char* str, int length) { return new StringMers(str, length, false); }
StringMers* string_canonicals(char* str, int length) { return new StringMers(str, length, true); }
%}
%apply (char *STRING, int LENGTH) { (char* str, int length) };
%newobject string_mers;
%newobject string_canonicals;
%feature("autodoc", "Get an iterator to the mers in the string");
StringMers* string_mers(char* str, int length);
%feature("autodoc", "Get an iterator to the canonical mers in the string");
StringMers* string_canonicals(char* str, int length);
#ifdef SWIGRUBY
%mixin StringMers "Enumerable";
%init %{
rb_eval_string("class String\n"
" def mers(&b); it = Jellyfish::string_mers(self); b ? it.each(&b) : it; end\n"
" def canonicals(&b); it = Jellyfish::string_canonicals(self, &b); b ? it.each(&b) : it; end\n"
"end");
%}
#endif
/* #ifdef SWIGPERL */
/* // For perl, return an empty array at end of iterator */
/* %typemap(out) const MerDNA* { */
/* if($1) { */
/* SWIG_Object m = SWIG_NewPointerObj(const_cast<MerDNA*>($1), SWIGTYPE_p_MerDNA, 0); */
/* %append_output(m); */
/* } */
/* } */
/* #endif */
%feature("autodoc", "Extract k-mers from a sequence string");
class StringMers {
public:
%feature("autodoc", "Create a k-mers parser from a string. Pass true as a second argument to get canonical mers");
StringMers(const char* str, int len, bool canonical);
%feature("autodoc", "Get the next mer. Return false if reached the end of the string.");
bool next_mer();
%feature("autodoc", "Return the current mer (or its canonical representation)");
const MerDNA* mer() const;
#ifdef SWIGRUBY
%feature("autodoc", "Iterate through all the mers in the string");
void each();
#endif
#ifdef SWIGPYTHON
StringMers* __iter__();
const MerDNA* __next__();
const MerDNA* next();
#endif
#ifdef SWIGPERL
MerDNA* each();
#endif
};
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