--- /dev/null
+# This file was automatically generated by SWIG (http://www.swig.org).
+# Version 2.0.8
+#
+# Do not make changes to this file unless you know what you are doing--modify
+# the SWIG interface file instead.
+
+
+
+from sys import version_info
+if version_info >= (2,6,0):
+ def swig_import_helper():
+ from os.path import dirname
+ import imp
+ fp = None
+ try:
+ fp, pathname, description = imp.find_module('_RNA', [dirname(__file__)])
+ except ImportError:
+ import _RNA
+ return _RNA
+ if fp is not None:
+ try:
+ _mod = imp.load_module('_RNA', fp, pathname, description)
+ finally:
+ fp.close()
+ return _mod
+ _RNA = swig_import_helper()
+ del swig_import_helper
+else:
+ import _RNA
+del version_info
+try:
+ _swig_property = property
+except NameError:
+ pass # Python < 2.2 doesn't have 'property'.
+def _swig_setattr_nondynamic(self,class_type,name,value,static=1):
+ if (name == "thisown"): return self.this.own(value)
+ if (name == "this"):
+ if type(value).__name__ == 'SwigPyObject':
+ self.__dict__[name] = value
+ return
+ method = class_type.__swig_setmethods__.get(name,None)
+ if method: return method(self,value)
+ if (not static):
+ self.__dict__[name] = value
+ else:
+ raise AttributeError("You cannot add attributes to %s" % self)
+
+def _swig_setattr(self,class_type,name,value):
+ return _swig_setattr_nondynamic(self,class_type,name,value,0)
+
+def _swig_getattr(self,class_type,name):
+ if (name == "thisown"): return self.this.own()
+ method = class_type.__swig_getmethods__.get(name,None)
+ if method: return method(self)
+ raise AttributeError(name)
+
+def _swig_repr(self):
+ try: strthis = "proxy of " + self.this.__repr__()
+ except: strthis = ""
+ return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
+
+try:
+ _object = object
+ _newclass = 1
+except AttributeError:
+ class _object : pass
+ _newclass = 0
+
+
+
+def new_intP(*args):
+ return _RNA.new_intP(*args)
+new_intP = _RNA.new_intP
+
+def delete_intP(*args):
+ return _RNA.delete_intP(*args)
+delete_intP = _RNA.delete_intP
+
+def intP_getitem(*args):
+ return _RNA.intP_getitem(*args)
+intP_getitem = _RNA.intP_getitem
+
+def intP_setitem(*args):
+ return _RNA.intP_setitem(*args)
+intP_setitem = _RNA.intP_setitem
+class intArray(_object):
+ __swig_setmethods__ = {}
+ __setattr__ = lambda self, name, value: _swig_setattr(self, intArray, name, value)
+ __swig_getmethods__ = {}
+ __getattr__ = lambda self, name: _swig_getattr(self, intArray, name)
+ __repr__ = _swig_repr
+ def __init__(self, *args):
+ this = _RNA.new_intArray(*args)
+ try: self.this.append(this)
+ except: self.this = this
+ __swig_destroy__ = _RNA.delete_intArray
+ __del__ = lambda self : None;
+ def __getitem__(self, *args): return _RNA.intArray___getitem__(self, *args)
+ def __setitem__(self, *args): return _RNA.intArray___setitem__(self, *args)
+ def cast(self): return _RNA.intArray_cast(self)
+ __swig_getmethods__["frompointer"] = lambda x: _RNA.intArray_frompointer
+ if _newclass:frompointer = staticmethod(_RNA.intArray_frompointer)
+intArray_swigregister = _RNA.intArray_swigregister
+intArray_swigregister(intArray)
+
+def intArray_frompointer(*args):
+ return _RNA.intArray_frompointer(*args)
+intArray_frompointer = _RNA.intArray_frompointer
+
+
+def new_floatP(*args):
+ return _RNA.new_floatP(*args)
+new_floatP = _RNA.new_floatP
+
+def delete_floatP(*args):
+ return _RNA.delete_floatP(*args)
+delete_floatP = _RNA.delete_floatP
+
+def floatP_getitem(*args):
+ return _RNA.floatP_getitem(*args)
+floatP_getitem = _RNA.floatP_getitem
+
+def floatP_setitem(*args):
+ return _RNA.floatP_setitem(*args)
+floatP_setitem = _RNA.floatP_setitem
+class floatArray(_object):
+ __swig_setmethods__ = {}
+ __setattr__ = lambda self, name, value: _swig_setattr(self, floatArray, name, value)
+ __swig_getmethods__ = {}
+ __getattr__ = lambda self, name: _swig_getattr(self, floatArray, name)
+ __repr__ = _swig_repr
+ def __init__(self, *args):
+ this = _RNA.new_floatArray(*args)
+ try: self.this.append(this)
+ except: self.this = this
+ __swig_destroy__ = _RNA.delete_floatArray
+ __del__ = lambda self : None;
+ def __getitem__(self, *args): return _RNA.floatArray___getitem__(self, *args)
+ def __setitem__(self, *args): return _RNA.floatArray___setitem__(self, *args)
+ def cast(self): return _RNA.floatArray_cast(self)
+ __swig_getmethods__["frompointer"] = lambda x: _RNA.floatArray_frompointer
+ if _newclass:frompointer = staticmethod(_RNA.floatArray_frompointer)
+floatArray_swigregister = _RNA.floatArray_swigregister
+floatArray_swigregister(floatArray)
+
+def floatArray_frompointer(*args):
+ return _RNA.floatArray_frompointer(*args)
+floatArray_frompointer = _RNA.floatArray_frompointer
+
+
+def new_doubleP(*args):
+ return _RNA.new_doubleP(*args)
+new_doubleP = _RNA.new_doubleP
+
+def delete_doubleP(*args):
+ return _RNA.delete_doubleP(*args)
+delete_doubleP = _RNA.delete_doubleP
+
+def doubleP_getitem(*args):
+ return _RNA.doubleP_getitem(*args)
+doubleP_getitem = _RNA.doubleP_getitem
+
+def doubleP_setitem(*args):
+ return _RNA.doubleP_setitem(*args)
+doubleP_setitem = _RNA.doubleP_setitem
+class doubleArray(_object):
+ __swig_setmethods__ = {}
+ __setattr__ = lambda self, name, value: _swig_setattr(self, doubleArray, name, value)
+ __swig_getmethods__ = {}
+ __getattr__ = lambda self, name: _swig_getattr(self, doubleArray, name)
+ __repr__ = _swig_repr
+ def __init__(self, *args):
+ this = _RNA.new_doubleArray(*args)
+ try: self.this.append(this)
+ except: self.this = this
+ __swig_destroy__ = _RNA.delete_doubleArray
+ __del__ = lambda self : None;
+ def __getitem__(self, *args): return _RNA.doubleArray___getitem__(self, *args)
+ def __setitem__(self, *args): return _RNA.doubleArray___setitem__(self, *args)
+ def cast(self): return _RNA.doubleArray_cast(self)
+ __swig_getmethods__["frompointer"] = lambda x: _RNA.doubleArray_frompointer
+ if _newclass:frompointer = staticmethod(_RNA.doubleArray_frompointer)
+doubleArray_swigregister = _RNA.doubleArray_swigregister
+doubleArray_swigregister(doubleArray)
+
+def doubleArray_frompointer(*args):
+ return _RNA.doubleArray_frompointer(*args)
+doubleArray_frompointer = _RNA.doubleArray_frompointer
+
+
+def new_ushortP(*args):
+ return _RNA.new_ushortP(*args)
+new_ushortP = _RNA.new_ushortP
+
+def delete_ushortP(*args):
+ return _RNA.delete_ushortP(*args)
+delete_ushortP = _RNA.delete_ushortP
+
+def ushortP_getitem(*args):
+ return _RNA.ushortP_getitem(*args)
+ushortP_getitem = _RNA.ushortP_getitem
+
+def ushortP_setitem(*args):
+ return _RNA.ushortP_setitem(*args)
+ushortP_setitem = _RNA.ushortP_setitem
+
+def new_shortP(*args):
+ return _RNA.new_shortP(*args)
+new_shortP = _RNA.new_shortP
+
+def delete_shortP(*args):
+ return _RNA.delete_shortP(*args)
+delete_shortP = _RNA.delete_shortP
+
+def shortP_getitem(*args):
+ return _RNA.shortP_getitem(*args)
+shortP_getitem = _RNA.shortP_getitem
+
+def shortP_setitem(*args):
+ return _RNA.shortP_setitem(*args)
+shortP_setitem = _RNA.shortP_setitem
+
+def cdata(*args):
+ return _RNA.cdata(*args)
+cdata = _RNA.cdata
+
+def memmove(*args):
+ return _RNA.memmove(*args)
+memmove = _RNA.memmove
+VERSION = _RNA.VERSION
+
+def fold(*args):
+ return _RNA.fold(*args)
+fold = _RNA.fold
+
+def fold_par(*args):
+ return _RNA.fold_par(*args)
+fold_par = _RNA.fold_par
+
+def circfold(*args):
+ return _RNA.circfold(*args)
+circfold = _RNA.circfold
+
+def energy_of_structure(*args):
+ return _RNA.energy_of_structure(*args)
+energy_of_structure = _RNA.energy_of_structure
+
+def energy_of_struct_par(*args):
+ return _RNA.energy_of_struct_par(*args)
+energy_of_struct_par = _RNA.energy_of_struct_par
+
+def energy_of_circ_structure(*args):
+ return _RNA.energy_of_circ_structure(*args)
+energy_of_circ_structure = _RNA.energy_of_circ_structure
+
+def energy_of_circ_struct_par(*args):
+ return _RNA.energy_of_circ_struct_par(*args)
+energy_of_circ_struct_par = _RNA.energy_of_circ_struct_par
+
+def energy_of_gquad_structure(*args):
+ return _RNA.energy_of_gquad_structure(*args)
+energy_of_gquad_structure = _RNA.energy_of_gquad_structure
+
+def energy_of_structure_pt(*args):
+ return _RNA.energy_of_structure_pt(*args)
+energy_of_structure_pt = _RNA.energy_of_structure_pt
+
+def energy_of_struct_pt_par(*args):
+ return _RNA.energy_of_struct_pt_par(*args)
+energy_of_struct_pt_par = _RNA.energy_of_struct_pt_par
+
+def free_arrays():
+ return _RNA.free_arrays()
+free_arrays = _RNA.free_arrays
+
+def parenthesis_structure(*args):
+ return _RNA.parenthesis_structure(*args)
+parenthesis_structure = _RNA.parenthesis_structure
+
+def parenthesis_zuker(*args):
+ return _RNA.parenthesis_zuker(*args)
+parenthesis_zuker = _RNA.parenthesis_zuker
+
+def letter_structure(*args):
+ return _RNA.letter_structure(*args)
+letter_structure = _RNA.letter_structure
+
+def update_fold_params():
+ return _RNA.update_fold_params()
+update_fold_params = _RNA.update_fold_params
+
+def update_fold_params_par(*args):
+ return _RNA.update_fold_params_par(*args)
+update_fold_params_par = _RNA.update_fold_params_par
+
+def backtrack_fold_from_pair(*args):
+ return _RNA.backtrack_fold_from_pair(*args)
+backtrack_fold_from_pair = _RNA.backtrack_fold_from_pair
+
+def energy_of_move(*args):
+ return _RNA.energy_of_move(*args)
+energy_of_move = _RNA.energy_of_move
+
+def energy_of_move_pt(*args):
+ return _RNA.energy_of_move_pt(*args)
+energy_of_move_pt = _RNA.energy_of_move_pt
+
+def loop_energy(*args):
+ return _RNA.loop_energy(*args)
+loop_energy = _RNA.loop_energy
+
+def export_fold_arrays(*args):
+ return _RNA.export_fold_arrays(*args)
+export_fold_arrays = _RNA.export_fold_arrays
+
+def export_fold_arrays_par(*args):
+ return _RNA.export_fold_arrays_par(*args)
+export_fold_arrays_par = _RNA.export_fold_arrays_par
+
+def export_circfold_arrays(*args):
+ return _RNA.export_circfold_arrays(*args)
+export_circfold_arrays = _RNA.export_circfold_arrays
+
+def export_circfold_arrays_par(*args):
+ return _RNA.export_circfold_arrays_par(*args)
+export_circfold_arrays_par = _RNA.export_circfold_arrays_par
+
+def assign_plist_from_db(*args):
+ return _RNA.assign_plist_from_db(*args)
+assign_plist_from_db = _RNA.assign_plist_from_db
+
+def LoopEnergy(*args):
+ return _RNA.LoopEnergy(*args)
+LoopEnergy = _RNA.LoopEnergy
+
+def HairpinE(*args):
+ return _RNA.HairpinE(*args)
+HairpinE = _RNA.HairpinE
+
+def initialize_fold(*args):
+ return _RNA.initialize_fold(*args)
+initialize_fold = _RNA.initialize_fold
+
+def energy_of_struct(*args):
+ return _RNA.energy_of_struct(*args)
+energy_of_struct = _RNA.energy_of_struct
+
+def energy_of_struct_pt(*args):
+ return _RNA.energy_of_struct_pt(*args)
+energy_of_struct_pt = _RNA.energy_of_struct_pt
+
+def energy_of_circ_struct(*args):
+ return _RNA.energy_of_circ_struct(*args)
+energy_of_circ_struct = _RNA.energy_of_circ_struct
+
+def cofold(*args):
+ return _RNA.cofold(*args)
+cofold = _RNA.cofold
+
+def cofold_par(*args):
+ return _RNA.cofold_par(*args)
+cofold_par = _RNA.cofold_par
+
+def free_co_arrays():
+ return _RNA.free_co_arrays()
+free_co_arrays = _RNA.free_co_arrays
+
+def update_cofold_params():
+ return _RNA.update_cofold_params()
+update_cofold_params = _RNA.update_cofold_params
+
+def update_cofold_params_par(*args):
+ return _RNA.update_cofold_params_par(*args)
+update_cofold_params_par = _RNA.update_cofold_params_par
+
+def export_cofold_arrays_gq(*args):
+ return _RNA.export_cofold_arrays_gq(*args)
+export_cofold_arrays_gq = _RNA.export_cofold_arrays_gq
+
+def export_cofold_arrays(*args):
+ return _RNA.export_cofold_arrays(*args)
+export_cofold_arrays = _RNA.export_cofold_arrays
+
+def zukersubopt(*args):
+ return _RNA.zukersubopt(*args)
+zukersubopt = _RNA.zukersubopt
+
+def zukersubopt_par(*args):
+ return _RNA.zukersubopt_par(*args)
+zukersubopt_par = _RNA.zukersubopt_par
+
+def get_monomere_mfes(*args):
+ return _RNA.get_monomere_mfes(*args)
+get_monomere_mfes = _RNA.get_monomere_mfes
+
+def initialize_cofold(*args):
+ return _RNA.initialize_cofold(*args)
+initialize_cofold = _RNA.initialize_cofold
+
+def pf_fold(*args):
+ return _RNA.pf_fold(*args)
+pf_fold = _RNA.pf_fold
+
+def pf_fold_par(*args):
+ return _RNA.pf_fold_par(*args)
+pf_fold_par = _RNA.pf_fold_par
+
+def pf_circ_fold(*args):
+ return _RNA.pf_circ_fold(*args)
+pf_circ_fold = _RNA.pf_circ_fold
+
+def pbacktrack(*args):
+ return _RNA.pbacktrack(*args)
+pbacktrack = _RNA.pbacktrack
+
+def pbacktrack_circ(*args):
+ return _RNA.pbacktrack_circ(*args)
+pbacktrack_circ = _RNA.pbacktrack_circ
+
+def free_pf_arrays():
+ return _RNA.free_pf_arrays()
+free_pf_arrays = _RNA.free_pf_arrays
+
+def update_pf_params(*args):
+ return _RNA.update_pf_params(*args)
+update_pf_params = _RNA.update_pf_params
+
+def update_pf_params_par(*args):
+ return _RNA.update_pf_params_par(*args)
+update_pf_params_par = _RNA.update_pf_params_par
+
+def export_bppm():
+ return _RNA.export_bppm()
+export_bppm = _RNA.export_bppm
+
+def assign_plist_from_pr(*args):
+ return _RNA.assign_plist_from_pr(*args)
+assign_plist_from_pr = _RNA.assign_plist_from_pr
+
+def assign_plist_gquad_from_pr(*args):
+ return _RNA.assign_plist_gquad_from_pr(*args)
+assign_plist_gquad_from_pr = _RNA.assign_plist_gquad_from_pr
+
+def get_centroid_struct_gquad_pr(*args):
+ return _RNA.get_centroid_struct_gquad_pr(*args)
+get_centroid_struct_gquad_pr = _RNA.get_centroid_struct_gquad_pr
+
+def get_pf_arrays(*args):
+ return _RNA.get_pf_arrays(*args)
+get_pf_arrays = _RNA.get_pf_arrays
+
+def get_subseq_F(*args):
+ return _RNA.get_subseq_F(*args)
+get_subseq_F = _RNA.get_subseq_F
+
+def get_centroid_struct_pl(*args):
+ return _RNA.get_centroid_struct_pl(*args)
+get_centroid_struct_pl = _RNA.get_centroid_struct_pl
+
+def get_centroid_struct_pr(*args):
+ return _RNA.get_centroid_struct_pr(*args)
+get_centroid_struct_pr = _RNA.get_centroid_struct_pr
+
+def mean_bp_distance(*args):
+ return _RNA.mean_bp_distance(*args)
+mean_bp_distance = _RNA.mean_bp_distance
+
+def mean_bp_distance_pr(*args):
+ return _RNA.mean_bp_distance_pr(*args)
+mean_bp_distance_pr = _RNA.mean_bp_distance_pr
+
+def bppm_to_structure(*args):
+ return _RNA.bppm_to_structure(*args)
+bppm_to_structure = _RNA.bppm_to_structure
+
+def stackProb(*args):
+ return _RNA.stackProb(*args)
+stackProb = _RNA.stackProb
+
+def bppm_symbol(*args):
+ return _RNA.bppm_symbol(*args)
+bppm_symbol = _RNA.bppm_symbol
+
+def init_pf_fold(*args):
+ return _RNA.init_pf_fold(*args)
+init_pf_fold = _RNA.init_pf_fold
+
+def centroid(*args):
+ return _RNA.centroid(*args)
+centroid = _RNA.centroid
+
+def mean_bp_dist(*args):
+ return _RNA.mean_bp_dist(*args)
+mean_bp_dist = _RNA.mean_bp_dist
+
+def expLoopEnergy(*args):
+ return _RNA.expLoopEnergy(*args)
+expLoopEnergy = _RNA.expLoopEnergy
+
+def expHairpinEnergy(*args):
+ return _RNA.expHairpinEnergy(*args)
+expHairpinEnergy = _RNA.expHairpinEnergy
+
+def co_pf_fold(*args):
+ return _RNA.co_pf_fold(*args)
+co_pf_fold = _RNA.co_pf_fold
+
+def co_pf_fold_par(*args):
+ return _RNA.co_pf_fold_par(*args)
+co_pf_fold_par = _RNA.co_pf_fold_par
+
+def export_co_bppm():
+ return _RNA.export_co_bppm()
+export_co_bppm = _RNA.export_co_bppm
+
+def free_co_pf_arrays():
+ return _RNA.free_co_pf_arrays()
+free_co_pf_arrays = _RNA.free_co_pf_arrays
+
+def update_co_pf_params(*args):
+ return _RNA.update_co_pf_params(*args)
+update_co_pf_params = _RNA.update_co_pf_params
+
+def update_co_pf_params_par(*args):
+ return _RNA.update_co_pf_params_par(*args)
+update_co_pf_params_par = _RNA.update_co_pf_params_par
+
+def get_concentrations(*args):
+ return _RNA.get_concentrations(*args)
+get_concentrations = _RNA.get_concentrations
+
+def inverse_fold(*args):
+ return _RNA.inverse_fold(*args)
+inverse_fold = _RNA.inverse_fold
+
+def inverse_pf_fold(*args):
+ return _RNA.inverse_pf_fold(*args)
+inverse_pf_fold = _RNA.inverse_pf_fold
+
+def option_string():
+ return _RNA.option_string()
+option_string = _RNA.option_string
+
+def set_model_details(*args):
+ return _RNA.set_model_details(*args)
+set_model_details = _RNA.set_model_details
+
+def update_alifold_params():
+ return _RNA.update_alifold_params()
+update_alifold_params = _RNA.update_alifold_params
+
+def circalifold(*args):
+ return _RNA.circalifold(*args)
+circalifold = _RNA.circalifold
+
+def free_alifold_arrays():
+ return _RNA.free_alifold_arrays()
+free_alifold_arrays = _RNA.free_alifold_arrays
+
+def get_mpi(*args):
+ return _RNA.get_mpi(*args)
+get_mpi = _RNA.get_mpi
+
+def readribosum(*args):
+ return _RNA.readribosum(*args)
+readribosum = _RNA.readribosum
+
+def energy_of_alistruct(*args):
+ return _RNA.energy_of_alistruct(*args)
+energy_of_alistruct = _RNA.energy_of_alistruct
+
+def energy_of_ali_gquad_structure(*args):
+ return _RNA.energy_of_ali_gquad_structure(*args)
+energy_of_ali_gquad_structure = _RNA.energy_of_ali_gquad_structure
+
+def encode_ali_sequence(*args):
+ return _RNA.encode_ali_sequence(*args)
+encode_ali_sequence = _RNA.encode_ali_sequence
+
+def alloc_sequence_arrays(*args):
+ return _RNA.alloc_sequence_arrays(*args)
+alloc_sequence_arrays = _RNA.alloc_sequence_arrays
+
+def free_sequence_arrays(*args):
+ return _RNA.free_sequence_arrays(*args)
+free_sequence_arrays = _RNA.free_sequence_arrays
+
+def alipf_fold_par(*args):
+ return _RNA.alipf_fold_par(*args)
+alipf_fold_par = _RNA.alipf_fold_par
+
+def alipf_fold(*args):
+ return _RNA.alipf_fold(*args)
+alipf_fold = _RNA.alipf_fold
+
+def alipf_circ_fold(*args):
+ return _RNA.alipf_circ_fold(*args)
+alipf_circ_fold = _RNA.alipf_circ_fold
+
+def export_ali_bppm():
+ return _RNA.export_ali_bppm()
+export_ali_bppm = _RNA.export_ali_bppm
+
+def free_alipf_arrays():
+ return _RNA.free_alipf_arrays()
+free_alipf_arrays = _RNA.free_alipf_arrays
+
+def alipbacktrack(*args):
+ return _RNA.alipbacktrack(*args)
+alipbacktrack = _RNA.alipbacktrack
+
+def get_alipf_arrays(*args):
+ return _RNA.get_alipf_arrays(*args)
+get_alipf_arrays = _RNA.get_alipf_arrays
+
+def alifold(*args):
+ return _RNA.alifold(*args)
+alifold = _RNA.alifold
+
+def consensus(*args):
+ return _RNA.consensus(*args)
+consensus = _RNA.consensus
+
+def consens_mis(*args):
+ return _RNA.consens_mis(*args)
+consens_mis = _RNA.consens_mis
+class COORDINATE(_object):
+ __swig_setmethods__ = {}
+ __setattr__ = lambda self, name, value: _swig_setattr(self, COORDINATE, name, value)
+ __swig_getmethods__ = {}
+ __getattr__ = lambda self, name: _swig_getattr(self, COORDINATE, name)
+ __repr__ = _swig_repr
+ __swig_setmethods__["X"] = _RNA.COORDINATE_X_set
+ __swig_getmethods__["X"] = _RNA.COORDINATE_X_get
+ if _newclass:X = _swig_property(_RNA.COORDINATE_X_get, _RNA.COORDINATE_X_set)
+ __swig_setmethods__["Y"] = _RNA.COORDINATE_Y_set
+ __swig_getmethods__["Y"] = _RNA.COORDINATE_Y_get
+ if _newclass:Y = _swig_property(_RNA.COORDINATE_Y_get, _RNA.COORDINATE_Y_set)
+ def get(self, *args): return _RNA.COORDINATE_get(self, *args)
+ def __init__(self):
+ this = _RNA.new_COORDINATE()
+ try: self.this.append(this)
+ except: self.this = this
+ __swig_destroy__ = _RNA.delete_COORDINATE
+ __del__ = lambda self : None;
+COORDINATE_swigregister = _RNA.COORDINATE_swigregister
+COORDINATE_swigregister(COORDINATE)
+cvar = _RNA.cvar
+
+
+def get_xy_coordinates(*args):
+ return _RNA.get_xy_coordinates(*args)
+get_xy_coordinates = _RNA.get_xy_coordinates
+class SOLUTION(_object):
+ __swig_setmethods__ = {}
+ __setattr__ = lambda self, name, value: _swig_setattr(self, SOLUTION, name, value)
+ __swig_getmethods__ = {}
+ __getattr__ = lambda self, name: _swig_getattr(self, SOLUTION, name)
+ __repr__ = _swig_repr
+ __swig_setmethods__["energy"] = _RNA.SOLUTION_energy_set
+ __swig_getmethods__["energy"] = _RNA.SOLUTION_energy_get
+ if _newclass:energy = _swig_property(_RNA.SOLUTION_energy_get, _RNA.SOLUTION_energy_set)
+ __swig_setmethods__["structure"] = _RNA.SOLUTION_structure_set
+ __swig_getmethods__["structure"] = _RNA.SOLUTION_structure_get
+ if _newclass:structure = _swig_property(_RNA.SOLUTION_structure_get, _RNA.SOLUTION_structure_set)
+ def get(self, *args): return _RNA.SOLUTION_get(self, *args)
+ def size(self): return _RNA.SOLUTION_size(self)
+ __swig_destroy__ = _RNA.delete_SOLUTION
+ __del__ = lambda self : None;
+ def __init__(self):
+ this = _RNA.new_SOLUTION()
+ try: self.this.append(this)
+ except: self.this = this
+SOLUTION_swigregister = _RNA.SOLUTION_swigregister
+SOLUTION_swigregister(SOLUTION)
+
+
+def subopt(*args):
+ return _RNA.subopt(*args)
+subopt = _RNA.subopt
+
+def get_pr(*args):
+ return _RNA.get_pr(*args)
+get_pr = _RNA.get_pr
+
+def b2HIT(*args):
+ return _RNA.b2HIT(*args)
+b2HIT = _RNA.b2HIT
+
+def b2C(*args):
+ return _RNA.b2C(*args)
+b2C = _RNA.b2C
+
+def b2Shapiro(*args):
+ return _RNA.b2Shapiro(*args)
+b2Shapiro = _RNA.b2Shapiro
+
+def add_root(*args):
+ return _RNA.add_root(*args)
+add_root = _RNA.add_root
+
+def expand_Shapiro(*args):
+ return _RNA.expand_Shapiro(*args)
+expand_Shapiro = _RNA.expand_Shapiro
+
+def expand_Full(*args):
+ return _RNA.expand_Full(*args)
+expand_Full = _RNA.expand_Full
+
+def unexpand_Full(*args):
+ return _RNA.unexpand_Full(*args)
+unexpand_Full = _RNA.unexpand_Full
+
+def unweight(*args):
+ return _RNA.unweight(*args)
+unweight = _RNA.unweight
+
+def unexpand_aligned_F(*args):
+ return _RNA.unexpand_aligned_F(*args)
+unexpand_aligned_F = _RNA.unexpand_aligned_F
+
+def parse_structure(*args):
+ return _RNA.parse_structure(*args)
+parse_structure = _RNA.parse_structure
+
+def make_tree(*args):
+ return _RNA.make_tree(*args)
+make_tree = _RNA.make_tree
+
+def tree_edit_distance(*args):
+ return _RNA.tree_edit_distance(*args)
+tree_edit_distance = _RNA.tree_edit_distance
+
+def print_tree(*args):
+ return _RNA.print_tree(*args)
+print_tree = _RNA.print_tree
+
+def free_tree(*args):
+ return _RNA.free_tree(*args)
+free_tree = _RNA.free_tree
+
+def Make_swString(*args):
+ return _RNA.Make_swString(*args)
+Make_swString = _RNA.Make_swString
+
+def string_edit_distance(*args):
+ return _RNA.string_edit_distance(*args)
+string_edit_distance = _RNA.string_edit_distance
+
+def profile_edit_distance(*args):
+ return _RNA.profile_edit_distance(*args)
+profile_edit_distance = _RNA.profile_edit_distance
+
+def Make_bp_profile_bppm(*args):
+ return _RNA.Make_bp_profile_bppm(*args)
+Make_bp_profile_bppm = _RNA.Make_bp_profile_bppm
+
+def print_bppm(*args):
+ return _RNA.print_bppm(*args)
+print_bppm = _RNA.print_bppm
+
+def free_profile(*args):
+ return _RNA.free_profile(*args)
+free_profile = _RNA.free_profile
+
+def Make_bp_profile(*args):
+ return _RNA.Make_bp_profile(*args)
+Make_bp_profile = _RNA.Make_bp_profile
+VRNA_INPUT_ERROR = _RNA.VRNA_INPUT_ERROR
+VRNA_INPUT_QUIT = _RNA.VRNA_INPUT_QUIT
+VRNA_INPUT_MISC = _RNA.VRNA_INPUT_MISC
+VRNA_INPUT_FASTA_HEADER = _RNA.VRNA_INPUT_FASTA_HEADER
+VRNA_INPUT_SEQUENCE = _RNA.VRNA_INPUT_SEQUENCE
+VRNA_INPUT_CONSTRAINT = _RNA.VRNA_INPUT_CONSTRAINT
+VRNA_INPUT_NO_TRUNCATION = _RNA.VRNA_INPUT_NO_TRUNCATION
+VRNA_INPUT_NO_REST = _RNA.VRNA_INPUT_NO_REST
+VRNA_INPUT_NO_SPAN = _RNA.VRNA_INPUT_NO_SPAN
+VRNA_INPUT_NOSKIP_BLANK_LINES = _RNA.VRNA_INPUT_NOSKIP_BLANK_LINES
+VRNA_INPUT_BLANK_LINE = _RNA.VRNA_INPUT_BLANK_LINE
+VRNA_INPUT_NOSKIP_COMMENTS = _RNA.VRNA_INPUT_NOSKIP_COMMENTS
+VRNA_INPUT_COMMENT = _RNA.VRNA_INPUT_COMMENT
+VRNA_CONSTRAINT_PIPE = _RNA.VRNA_CONSTRAINT_PIPE
+VRNA_CONSTRAINT_DOT = _RNA.VRNA_CONSTRAINT_DOT
+VRNA_CONSTRAINT_X = _RNA.VRNA_CONSTRAINT_X
+VRNA_CONSTRAINT_ANG_BRACK = _RNA.VRNA_CONSTRAINT_ANG_BRACK
+VRNA_CONSTRAINT_RND_BRACK = _RNA.VRNA_CONSTRAINT_RND_BRACK
+VRNA_CONSTRAINT_MULTILINE = _RNA.VRNA_CONSTRAINT_MULTILINE
+VRNA_CONSTRAINT_NO_HEADER = _RNA.VRNA_CONSTRAINT_NO_HEADER
+VRNA_CONSTRAINT_ALL = _RNA.VRNA_CONSTRAINT_ALL
+VRNA_CONSTRAINT_G = _RNA.VRNA_CONSTRAINT_G
+VRNA_OPTION_MULTILINE = _RNA.VRNA_OPTION_MULTILINE
+FILENAME_MAX_LENGTH = _RNA.FILENAME_MAX_LENGTH
+FILENAME_ID_LENGTH = _RNA.FILENAME_ID_LENGTH
+
+def space(*args):
+ return _RNA.space(*args)
+space = _RNA.space
+
+def xrealloc(*args):
+ return _RNA.xrealloc(*args)
+xrealloc = _RNA.xrealloc
+
+def nrerror(*args):
+ return _RNA.nrerror(*args)
+nrerror = _RNA.nrerror
+
+def warn_user(*args):
+ return _RNA.warn_user(*args)
+warn_user = _RNA.warn_user
+
+def init_rand():
+ return _RNA.init_rand()
+init_rand = _RNA.init_rand
+
+def urn():
+ return _RNA.urn()
+urn = _RNA.urn
+
+def int_urn(*args):
+ return _RNA.int_urn(*args)
+int_urn = _RNA.int_urn
+
+def filecopy(*args):
+ return _RNA.filecopy(*args)
+filecopy = _RNA.filecopy
+
+def time_stamp():
+ return _RNA.time_stamp()
+time_stamp = _RNA.time_stamp
+
+def random_string(*args):
+ return _RNA.random_string(*args)
+random_string = _RNA.random_string
+
+def hamming(*args):
+ return _RNA.hamming(*args)
+hamming = _RNA.hamming
+
+def hamming_bound(*args):
+ return _RNA.hamming_bound(*args)
+hamming_bound = _RNA.hamming_bound
+
+def get_line(*args):
+ return _RNA.get_line(*args)
+get_line = _RNA.get_line
+
+def skip_comment_lines(*args):
+ return _RNA.skip_comment_lines(*args)
+skip_comment_lines = _RNA.skip_comment_lines
+
+def get_input_line(*args):
+ return _RNA.get_input_line(*args)
+get_input_line = _RNA.get_input_line
+
+def get_multi_input_line(*args):
+ return _RNA.get_multi_input_line(*args)
+get_multi_input_line = _RNA.get_multi_input_line
+
+def read_record(*args):
+ return _RNA.read_record(*args)
+read_record = _RNA.read_record
+
+def extract_record_rest_structure(*args):
+ return _RNA.extract_record_rest_structure(*args)
+extract_record_rest_structure = _RNA.extract_record_rest_structure
+
+def pack_structure(*args):
+ return _RNA.pack_structure(*args)
+pack_structure = _RNA.pack_structure
+
+def unpack_structure(*args):
+ return _RNA.unpack_structure(*args)
+unpack_structure = _RNA.unpack_structure
+
+def make_pair_table(*args):
+ return _RNA.make_pair_table(*args)
+make_pair_table = _RNA.make_pair_table
+
+def make_pair_table_pk(*args):
+ return _RNA.make_pair_table_pk(*args)
+make_pair_table_pk = _RNA.make_pair_table_pk
+
+def copy_pair_table(*args):
+ return _RNA.copy_pair_table(*args)
+copy_pair_table = _RNA.copy_pair_table
+
+def alimake_pair_table(*args):
+ return _RNA.alimake_pair_table(*args)
+alimake_pair_table = _RNA.alimake_pair_table
+
+def make_pair_table_snoop(*args):
+ return _RNA.make_pair_table_snoop(*args)
+make_pair_table_snoop = _RNA.make_pair_table_snoop
+
+def make_loop_index_pt(*args):
+ return _RNA.make_loop_index_pt(*args)
+make_loop_index_pt = _RNA.make_loop_index_pt
+
+def bp_distance(*args):
+ return _RNA.bp_distance(*args)
+bp_distance = _RNA.bp_distance
+
+def print_tty_input_seq():
+ return _RNA.print_tty_input_seq()
+print_tty_input_seq = _RNA.print_tty_input_seq
+
+def print_tty_input_seq_str(*args):
+ return _RNA.print_tty_input_seq_str(*args)
+print_tty_input_seq_str = _RNA.print_tty_input_seq_str
+
+def print_tty_constraint_full():
+ return _RNA.print_tty_constraint_full()
+print_tty_constraint_full = _RNA.print_tty_constraint_full
+
+def print_tty_constraint(*args):
+ return _RNA.print_tty_constraint(*args)
+print_tty_constraint = _RNA.print_tty_constraint
+
+def str_DNA2RNA(*args):
+ return _RNA.str_DNA2RNA(*args)
+str_DNA2RNA = _RNA.str_DNA2RNA
+
+def str_uppercase(*args):
+ return _RNA.str_uppercase(*args)
+str_uppercase = _RNA.str_uppercase
+
+def get_iindx(*args):
+ return _RNA.get_iindx(*args)
+get_iindx = _RNA.get_iindx
+
+def get_indx(*args):
+ return _RNA.get_indx(*args)
+get_indx = _RNA.get_indx
+
+def getConstraint(*args):
+ return _RNA.getConstraint(*args)
+getConstraint = _RNA.getConstraint
+
+def constrain_ptypes(*args):
+ return _RNA.constrain_ptypes(*args)
+constrain_ptypes = _RNA.constrain_ptypes
+
+def make_referenceBP_array(*args):
+ return _RNA.make_referenceBP_array(*args)
+make_referenceBP_array = _RNA.make_referenceBP_array
+
+def compute_BPdifferences(*args):
+ return _RNA.compute_BPdifferences(*args)
+compute_BPdifferences = _RNA.compute_BPdifferences
+
+def read_parameter_file(*args):
+ return _RNA.read_parameter_file(*args)
+read_parameter_file = _RNA.read_parameter_file
+
+def write_parameter_file(*args):
+ return _RNA.write_parameter_file(*args)
+write_parameter_file = _RNA.write_parameter_file
+
+def deref_any(*args):
+ return _RNA.deref_any(*args)
+deref_any = _RNA.deref_any
+
+def scale_parameters():
+ return _RNA.scale_parameters()
+scale_parameters = _RNA.scale_parameters
+
+def copy_parameters():
+ return _RNA.copy_parameters()
+copy_parameters = _RNA.copy_parameters
+
+def set_parameters(*args):
+ return _RNA.set_parameters(*args)
+set_parameters = _RNA.set_parameters
+
+def get_aligned_line(*args):
+ return _RNA.get_aligned_line(*args)
+get_aligned_line = _RNA.get_aligned_line
+
+def make_loop_index(*args):
+ return _RNA.make_loop_index(*args)
+make_loop_index = _RNA.make_loop_index
+class duplexT(_object):
+ __swig_setmethods__ = {}
+ __setattr__ = lambda self, name, value: _swig_setattr(self, duplexT, name, value)
+ __swig_getmethods__ = {}
+ __getattr__ = lambda self, name: _swig_getattr(self, duplexT, name)
+ __repr__ = _swig_repr
+ __swig_setmethods__["i"] = _RNA.duplexT_i_set
+ __swig_getmethods__["i"] = _RNA.duplexT_i_get
+ if _newclass:i = _swig_property(_RNA.duplexT_i_get, _RNA.duplexT_i_set)
+ __swig_setmethods__["j"] = _RNA.duplexT_j_set
+ __swig_getmethods__["j"] = _RNA.duplexT_j_get
+ if _newclass:j = _swig_property(_RNA.duplexT_j_get, _RNA.duplexT_j_set)
+ __swig_setmethods__["structure"] = _RNA.duplexT_structure_set
+ __swig_getmethods__["structure"] = _RNA.duplexT_structure_get
+ if _newclass:structure = _swig_property(_RNA.duplexT_structure_get, _RNA.duplexT_structure_set)
+ __swig_setmethods__["energy"] = _RNA.duplexT_energy_set
+ __swig_getmethods__["energy"] = _RNA.duplexT_energy_get
+ if _newclass:energy = _swig_property(_RNA.duplexT_energy_get, _RNA.duplexT_energy_set)
+ def __init__(self):
+ this = _RNA.new_duplexT()
+ try: self.this.append(this)
+ except: self.this = this
+ __swig_destroy__ = _RNA.delete_duplexT
+ __del__ = lambda self : None;
+duplexT_swigregister = _RNA.duplexT_swigregister
+duplexT_swigregister(duplexT)
+
+
+def duplexfold(*args):
+ return _RNA.duplexfold(*args)
+duplexfold = _RNA.duplexfold
+
+def aliduplexfold(*args):
+ return _RNA.aliduplexfold(*args)
+aliduplexfold = _RNA.aliduplexfold
+
+def encode_seq(*args):
+ return _RNA.encode_seq(*args)
+encode_seq = _RNA.encode_seq
+
+def Lfold(*args):
+ return _RNA.Lfold(*args)
+Lfold = _RNA.Lfold
+
+def Lfoldz(*args):
+ return _RNA.Lfoldz(*args)
+Lfoldz = _RNA.Lfoldz
+
+def aliLfold(*args):
+ return _RNA.aliLfold(*args)
+aliLfold = _RNA.aliLfold
+PI = _RNA.PI
+PIHALF = _RNA.PIHALF
+VRNA_PLOT_TYPE_SIMPLE = _RNA.VRNA_PLOT_TYPE_SIMPLE
+VRNA_PLOT_TYPE_NAVIEW = _RNA.VRNA_PLOT_TYPE_NAVIEW
+VRNA_PLOT_TYPE_CIRCULAR = _RNA.VRNA_PLOT_TYPE_CIRCULAR
+
+def simple_xy_coordinates(*args):
+ return _RNA.simple_xy_coordinates(*args)
+simple_xy_coordinates = _RNA.simple_xy_coordinates
+
+def simple_circplot_coordinates(*args):
+ return _RNA.simple_circplot_coordinates(*args)
+simple_circplot_coordinates = _RNA.simple_circplot_coordinates
+
+def PS_rna_plot_snoop_a(*args):
+ return _RNA.PS_rna_plot_snoop_a(*args)
+PS_rna_plot_snoop_a = _RNA.PS_rna_plot_snoop_a
+
+def PS_rna_plot(*args):
+ return _RNA.PS_rna_plot(*args)
+PS_rna_plot = _RNA.PS_rna_plot
+
+def PS_rna_plot_a(*args):
+ return _RNA.PS_rna_plot_a(*args)
+PS_rna_plot_a = _RNA.PS_rna_plot_a
+
+def PS_rna_plot_a_gquad(*args):
+ return _RNA.PS_rna_plot_a_gquad(*args)
+PS_rna_plot_a_gquad = _RNA.PS_rna_plot_a_gquad
+
+def gmlRNA(*args):
+ return _RNA.gmlRNA(*args)
+gmlRNA = _RNA.gmlRNA
+
+def ssv_rna_plot(*args):
+ return _RNA.ssv_rna_plot(*args)
+ssv_rna_plot = _RNA.ssv_rna_plot
+
+def svg_rna_plot(*args):
+ return _RNA.svg_rna_plot(*args)
+svg_rna_plot = _RNA.svg_rna_plot
+
+def xrna_plot(*args):
+ return _RNA.xrna_plot(*args)
+xrna_plot = _RNA.xrna_plot
+
+def PS_color_dot_plot(*args):
+ return _RNA.PS_color_dot_plot(*args)
+PS_color_dot_plot = _RNA.PS_color_dot_plot
+
+def PS_color_dot_plot_turn(*args):
+ return _RNA.PS_color_dot_plot_turn(*args)
+PS_color_dot_plot_turn = _RNA.PS_color_dot_plot_turn
+
+def PS_dot_plot_list(*args):
+ return _RNA.PS_dot_plot_list(*args)
+PS_dot_plot_list = _RNA.PS_dot_plot_list
+
+def PS_dot_plot_turn(*args):
+ return _RNA.PS_dot_plot_turn(*args)
+PS_dot_plot_turn = _RNA.PS_dot_plot_turn
+
+def PS_color_aln(*args):
+ return _RNA.PS_color_aln(*args)
+PS_color_aln = _RNA.PS_color_aln
+
+def aliPS_color_aln(*args):
+ return _RNA.aliPS_color_aln(*args)
+aliPS_color_aln = _RNA.aliPS_color_aln
+
+def PS_dot_plot(*args):
+ return _RNA.PS_dot_plot(*args)
+PS_dot_plot = _RNA.PS_dot_plot
+
+def find_saddle(*args):
+ return _RNA.find_saddle(*args)
+find_saddle = _RNA.find_saddle
+
+def get_path(*args):
+ return _RNA.get_path(*args)
+get_path = _RNA.get_path
+
+def free_path(*args):
+ return _RNA.free_path(*args)
+free_path = _RNA.free_path
+# This file is compatible with both classic and new-style classes.
+
+
git://source.jalview.org / jabaws.git / blobdiff