model_details.i
/**********************************************/
/* BEGIN interface for model details */
/**********************************************/
%{
#include <sstream>
%}
/* scripting language access through 'md' instead of 'vrna_md_t' */
%rename (md) vrna_md_t;
%nodefaultctor vrna_md_t;
%nodefaultdtor vrna_md_t;
/* hide all attributes, except for some trivial ones */
typedef struct {
double temperature;
double betaScale;
int pf_smooth;
int dangles;
int special_hp;
int noLP;
int noGU;
int noGUclosure;
int logML;
int circ;
int gquad;
int uniq_ML;
int energy_set;
int backtrack;
char backtrack_type;
int compute_bpp;
char nonstandards[64];
int max_bp_span;
int min_loop_size;
int window_size;
int oldAliEn;
int ribo;
double cv_fact;
double nc_fact;
double sfact;
const int rtype[8];
const short alias[MAXALPHA+1];
const int const pair[MAXALPHA+1][MAXALPHA+1];
double salt;
int saltMLLower;
int saltMLUpper;
int saltDPXInit;
float saltDPXInitFact;
float helical_rise;
float backbone_length;
} vrna_md_t;
/* make a nice object oriented interface to vrna_md_t */
%extend vrna_md_t {
#ifdef SWIGPYTHON
%feature("autodoc")vrna_md_t::vrna_md_t;
%feature("kwargs")vrna_md_t::vrna_md_t;
#endif
/* Default constructor */
vrna_md_t(
const double temperature = vrna_md_defaults_temperature_get(),
const double betaScale = vrna_md_defaults_betaScale_get(),
const int pf_smooth = vrna_md_defaults_pf_smooth_get(),
const int dangles = vrna_md_defaults_dangles_get(),
const int special_hp = vrna_md_defaults_special_hp_get(),
const int noLP = vrna_md_defaults_noLP_get(),
const int noGU = vrna_md_defaults_noGU_get(),
const int noGUclosure = vrna_md_defaults_noGUclosure_get(),
const int logML = vrna_md_defaults_logML_get(),
const int circ = vrna_md_defaults_circ_get(),
const int gquad = vrna_md_defaults_gquad_get(),
const int uniq_ML = vrna_md_defaults_uniq_ML_get(),
const int energy_set = vrna_md_defaults_energy_set_get(),
const int backtrack = vrna_md_defaults_backtrack_get(),
const char backtrack_type = vrna_md_defaults_backtrack_type_get(),
const int compute_bpp = vrna_md_defaults_compute_bpp_get(),
const int max_bp_span = vrna_md_defaults_max_bp_span_get(),
const int min_loop_size = vrna_md_defaults_min_loop_size_get(),
const int window_size = vrna_md_defaults_window_size_get(),
const int oldAliEn = vrna_md_defaults_oldAliEn_get(),
const int ribo = vrna_md_defaults_ribo_get(),
const double cv_fact = vrna_md_defaults_cv_fact_get(),
const double nc_fact = vrna_md_defaults_nc_fact_get(),
const double sfact = vrna_md_defaults_sfact_get(),
const double salt = vrna_md_defaults_salt_get(),
const int saltMLLower = vrna_md_defaults_saltMLLower_get(),
const int saltMLUpper = vrna_md_defaults_saltMLUpper_get(),
const int saltDPXInit = vrna_md_defaults_saltDPXInit_get(),
const float saltDPXInitFact = vrna_md_defaults_saltDPXInitFact_get(),
const float helical_rise = vrna_md_defaults_helical_rise_get(),
const float backbone_length = vrna_md_defaults_backbone_length_get())
{
vrna_md_t *md = (vrna_md_t *)vrna_alloc(sizeof(vrna_md_t));
md->temperature = temperature;
md->betaScale = betaScale;
md->pf_smooth = pf_smooth;
md->dangles = dangles;
md->special_hp = special_hp;
md->noLP = noLP;
md->noGU = noGU;
md->noGUclosure = noGUclosure;
md->logML = logML;
md->circ = circ;
md->gquad = gquad;
md->uniq_ML = uniq_ML;
md->energy_set = energy_set;
md->backtrack = backtrack;
md->backtrack_type = backtrack_type;
md->compute_bpp = compute_bpp;
md->max_bp_span = max_bp_span;
md->min_loop_size = min_loop_size;
md->window_size = window_size;
md->oldAliEn = oldAliEn;
md->ribo = ribo;
md->cv_fact = cv_fact;
md->nc_fact = nc_fact;
md->sfact = sfact;
md->salt = salt;
md->saltMLLower = saltMLLower;
md->saltMLUpper = saltMLUpper;
md->saltDPXInit = saltDPXInit;
md->saltDPXInitFact = saltDPXInitFact;
md->helical_rise = helical_rise;
md->backbone_length = backbone_length;
vrna_md_update(md);
return md;
}
~vrna_md_t()
{
free($self);
}
void
reset()
{
vrna_md_set_default($self);
}
void
set_from_globals()
{
set_model_details($self);
}
char *
option_string()
{
return vrna_md_option_string($self);
}
#ifdef SWIGPYTHON
std::string
__str__()
{
std::ostringstream out;
out << "{ temperature: " << $self->temperature ;
out << ", dangles: " << $self->dangles;
out << ", betaScale: " << $self->betaScale ;
out << ", pf_smooth: " << $self->pf_smooth ;
out << ", special_hp: " << $self->special_hp ;
out << ", noLP: " << $self->noLP ;
out << ", noGU: " << $self->noGU ;
out << ", noGUclosure: " << $self->noGUclosure ;
out << ", logML: " << $self->logML ;
out << ", circ: " << $self->circ ;
out << ", gquad: " << $self->gquad ;
out << ", uniq_ML: " << $self->uniq_ML ;
out << ", energy_set: " << $self->energy_set ;
out << ", backtrack: " << $self->backtrack ;
out << ", backtrack_type: " << $self->backtrack_type ;
out << ", compute_bpp: " << $self->compute_bpp ;
out << ", max_bp_span: " << $self->max_bp_span ;
out << ", min_loop_size: " << $self->min_loop_size;
out << ", window_size: " << $self->window_size ;
out << ", oldAliEn: " << $self->oldAliEn;
out << ", ribo: " << $self->ribo;
out << ", cv_fact: " << $self->cv_fact ;
out << ", nc_fact: " << $self->nc_fact ;
out << ", sfact: " << $self->sfact ;
out << ", salt: " << $self->salt ;
out << ", saltMLLower: " << $self->saltMLLower ;
out << ", saltMLUpper: " << $self->saltMLUpper ;
out << ", saltDPXInit: " << $self->saltDPXInit ;
out << ", saltDPXInitFact: " << $self->saltDPXInitFact ;
out << ", helical_rise: " << $self->helical_rise ;
out << ", backbone_length: " << $self->backbone_length ;
out << " }";
return std::string(out.str());
}
%pythoncode %{
def __repr__(self):
# reformat string representation (self.__str__()) to something
# that looks like a constructor argument list
strthis = self.__str__().replace(": ", "=").replace("{ ", "").replace(" }", "")
return "%s.%s(%s)" % (self.__class__.__module__, self.__class__.__name__, strthis)
%}
#endif
}
/*
* Hide the entire interface
*/
%ignore set_model_details;
%ignore option_string;
/*
* Include typemaps for augmenting reading and assignment of
* global variables with their corresponding getter/setter
* functions in the library
*/
%include globals-md.i
/* these two global variables will be handled by getter/setter methods */
%ignore helical_rise;
%ignore backbone_length;
/*
* The list of available global variables in the scripting
* interface. Access to these variables is defined in the
* typemap definition file above
*/
extern double temperature;
extern int dangles;
extern double betaScale;
extern int pf_smooth;
extern int tetra_loop; /* this is an alias of special_hp */
extern int special_hp;
extern int noLonelyPairs; /* this is an alias of noLP */
extern int noLP;
extern int noGU;
extern int no_closingGU; /* this is an alias of noGUclosure */
extern int noGUclosure;
extern int logML;
extern int circ;
extern int gquad;
extern int uniq_ML;
extern int energy_set;
extern int backtrack;
extern char backtrack_type; /* still needs implementation */
extern int do_backtrack; /* this is an alias of compute_bpp */
extern int compute_bpp;
extern int max_bp_span;
extern int min_loop_size;
extern int window_size;
extern int oldAliEn;
extern int ribo;
extern double cv_fact;
extern double nc_fact;
extern double sfact;
extern double salt;
extern int saltDPXInit;
extern double saltDPXInitFact;
extern double helical_rise;
extern double backbone_length;
%constant double MODEL_DEFAULT_TEMPERATURE = VRNA_MODEL_DEFAULT_TEMPERATURE;
%constant double MODEL_DEFAULT_PF_SCALE = VRNA_MODEL_DEFAULT_PF_SCALE;
%constant double MODEL_DEFAULT_BETA_SCALE = VRNA_MODEL_DEFAULT_BETA_SCALE;
%constant int MODEL_DEFAULT_DANGLES = VRNA_MODEL_DEFAULT_DANGLES;
%constant int MODEL_DEFAULT_SPECIAL_HP = VRNA_MODEL_DEFAULT_SPECIAL_HP;
%constant int MODEL_DEFAULT_NO_LP = VRNA_MODEL_DEFAULT_NO_LP;
%constant int MODEL_DEFAULT_NO_GU = VRNA_MODEL_DEFAULT_NO_GU;
%constant int MODEL_DEFAULT_NO_GU_CLOSURE = VRNA_MODEL_DEFAULT_NO_GU_CLOSURE;
%constant int MODEL_DEFAULT_CIRC = VRNA_MODEL_DEFAULT_CIRC;
%constant int MODEL_DEFAULT_GQUAD = VRNA_MODEL_DEFAULT_GQUAD;
%constant int MODEL_DEFAULT_UNIQ_ML = VRNA_MODEL_DEFAULT_UNIQ_ML;
%constant int MODEL_DEFAULT_ENERGY_SET = VRNA_MODEL_DEFAULT_ENERGY_SET;
%constant int MODEL_DEFAULT_BACKTRACK = VRNA_MODEL_DEFAULT_BACKTRACK;
%constant char MODEL_DEFAULT_BACKTRACK_TYPE = VRNA_MODEL_DEFAULT_BACKTRACK_TYPE;
%constant int MODEL_DEFAULT_COMPUTE_BPP = VRNA_MODEL_DEFAULT_COMPUTE_BPP;
%constant int MODEL_DEFAULT_MAX_BP_SPAN = VRNA_MODEL_DEFAULT_MAX_BP_SPAN;
%constant int MODEL_DEFAULT_WINDOW_SIZE = VRNA_MODEL_DEFAULT_WINDOW_SIZE;
%constant int MODEL_DEFAULT_LOG_ML = VRNA_MODEL_DEFAULT_LOG_ML;
%constant int MODEL_DEFAULT_ALI_OLD_EN = VRNA_MODEL_DEFAULT_ALI_OLD_EN;
%constant int MODEL_DEFAULT_ALI_RIBO = VRNA_MODEL_DEFAULT_ALI_RIBO;
%constant double MODEL_DEFAULT_ALI_CV_FACT = VRNA_MODEL_DEFAULT_ALI_CV_FACT;
%constant double MODEL_DEFAULT_ALI_NC_FACT = VRNA_MODEL_DEFAULT_ALI_NC_FACT;
%constant int MODEL_DEFAULT_PF_SMOOTH = VRNA_MODEL_DEFAULT_PF_SMOOTH;
%constant double MODEL_DEFAULT_SALT = VRNA_MODEL_DEFAULT_SALT;
%constant int MODEL_DEFAULT_SALT_MLLOWER = VRNA_MODEL_DEFAULT_SALT_MLLOWER;
%constant int MODEL_DEFAULT_SALT_MLUPPER = VRNA_MODEL_DEFAULT_SALT_MLUPPER;
%constant int MODEL_DEFAULT_SALT_DPXINIT = VRNA_MODEL_DEFAULT_SALT_DPXINIT;
%constant double MODEL_DEFAULT_SALT_DPXINIT_FACT = VRNA_MODEL_DEFAULT_SALT_DPXINIT_FACT;
%constant double MODEL_DEFAULT_HELICAL_RISE = VRNA_MODEL_DEFAULT_HELICAL_RISE;
%constant double MODEL_DEFAULT_BACKBONE_LENGTH = VRNA_MODEL_DEFAULT_BACKBONE_LENGTH;
%constant double MODEL_SALT_DPXINIT_FACT_RNA = VRNA_MODEL_SALT_DPXINIT_FACT_RNA;
%constant double MODEL_SALT_DPXINIT_FACT_DNA = VRNA_MODEL_SALT_DPXINIT_FACT_DNA;
%constant double MODEL_HELICAL_RISE_RNA = VRNA_MODEL_HELICAL_RISE_RNA;
%constant double MODEL_HELICAL_RISE_DNA = VRNA_MODEL_HELICAL_RISE_DNA;
%constant double MODEL_BACKBONE_LENGTH_RNA = VRNA_MODEL_BACKBONE_LENGTH_RNA;
%constant double MODEL_BACKBONE_LENGTH_DNA = VRNA_MODEL_BACKBONE_LENGTH_DNA;
%include <ViennaRNA/model.h>
