# This file was automatically generated by SWIG (http://www.swig.org). # Version 1.3.40 # # Do not make changes to this file unless you know what you are doing--modify # the SWIG interface file instead. # This file is compatible with both classic and new-style classes. 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('_beagle', [dirname(__file__)]) except ImportError: import _beagle return _beagle if fp is not None: try: _mod = imp.load_module('_beagle', fp, pathname, description) finally: fp.close() return _mod _beagle = swig_import_helper() del swig_import_helper else: import _beagle 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) or hasattr(self,name): 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(): return _beagle.new_intp() new_intp = _beagle.new_intp def copy_intp(*args): return _beagle.copy_intp(*args) copy_intp = _beagle.copy_intp def delete_intp(*args): return _beagle.delete_intp(*args) delete_intp = _beagle.delete_intp def intp_assign(*args): return _beagle.intp_assign(*args) intp_assign = _beagle.intp_assign def intp_value(*args): return _beagle.intp_value(*args) intp_value = _beagle.intp_value def new_doublep(): return _beagle.new_doublep() new_doublep = _beagle.new_doublep def copy_doublep(*args): return _beagle.copy_doublep(*args) copy_doublep = _beagle.copy_doublep def delete_doublep(*args): return _beagle.delete_doublep(*args) delete_doublep = _beagle.delete_doublep def doublep_assign(*args): return _beagle.doublep_assign(*args) doublep_assign = _beagle.doublep_assign def doublep_value(*args): return _beagle.doublep_value(*args) doublep_value = _beagle.doublep_value def new_intArray(*args): return _beagle.new_intArray(*args) new_intArray = _beagle.new_intArray def delete_intArray(*args): return _beagle.delete_intArray(*args) delete_intArray = _beagle.delete_intArray def intArray_getitem(*args): return _beagle.intArray_getitem(*args) intArray_getitem = _beagle.intArray_getitem def intArray_setitem(*args): return _beagle.intArray_setitem(*args) intArray_setitem = _beagle.intArray_setitem def new_doubleArray(*args): return _beagle.new_doubleArray(*args) new_doubleArray = _beagle.new_doubleArray def delete_doubleArray(*args): return _beagle.delete_doubleArray(*args) delete_doubleArray = _beagle.delete_doubleArray def doubleArray_getitem(*args): return _beagle.doubleArray_getitem(*args) doubleArray_getitem = _beagle.doubleArray_getitem def doubleArray_setitem(*args): return _beagle.doubleArray_setitem(*args) doubleArray_setitem = _beagle.doubleArray_setitem BEAGLE_SUCCESS = _beagle.BEAGLE_SUCCESS BEAGLE_ERROR_GENERAL = _beagle.BEAGLE_ERROR_GENERAL BEAGLE_ERROR_OUT_OF_MEMORY = _beagle.BEAGLE_ERROR_OUT_OF_MEMORY BEAGLE_ERROR_UNIDENTIFIED_EXCEPTION = _beagle.BEAGLE_ERROR_UNIDENTIFIED_EXCEPTION BEAGLE_ERROR_UNINITIALIZED_INSTANCE = _beagle.BEAGLE_ERROR_UNINITIALIZED_INSTANCE BEAGLE_ERROR_OUT_OF_RANGE = _beagle.BEAGLE_ERROR_OUT_OF_RANGE BEAGLE_ERROR_NO_RESOURCE = _beagle.BEAGLE_ERROR_NO_RESOURCE BEAGLE_ERROR_NO_IMPLEMENTATION = _beagle.BEAGLE_ERROR_NO_IMPLEMENTATION BEAGLE_ERROR_FLOATING_POINT = _beagle.BEAGLE_ERROR_FLOATING_POINT BEAGLE_FLAG_PRECISION_SINGLE = _beagle.BEAGLE_FLAG_PRECISION_SINGLE BEAGLE_FLAG_PRECISION_DOUBLE = _beagle.BEAGLE_FLAG_PRECISION_DOUBLE BEAGLE_FLAG_COMPUTATION_SYNCH = _beagle.BEAGLE_FLAG_COMPUTATION_SYNCH BEAGLE_FLAG_COMPUTATION_ASYNCH = _beagle.BEAGLE_FLAG_COMPUTATION_ASYNCH BEAGLE_FLAG_EIGEN_REAL = _beagle.BEAGLE_FLAG_EIGEN_REAL BEAGLE_FLAG_EIGEN_COMPLEX = _beagle.BEAGLE_FLAG_EIGEN_COMPLEX BEAGLE_FLAG_SCALING_MANUAL = _beagle.BEAGLE_FLAG_SCALING_MANUAL BEAGLE_FLAG_SCALING_AUTO = _beagle.BEAGLE_FLAG_SCALING_AUTO BEAGLE_FLAG_SCALING_ALWAYS = _beagle.BEAGLE_FLAG_SCALING_ALWAYS BEAGLE_FLAG_SCALING_DYNAMIC = _beagle.BEAGLE_FLAG_SCALING_DYNAMIC BEAGLE_FLAG_SCALERS_RAW = _beagle.BEAGLE_FLAG_SCALERS_RAW BEAGLE_FLAG_SCALERS_LOG = _beagle.BEAGLE_FLAG_SCALERS_LOG BEAGLE_FLAG_INVEVEC_STANDARD = _beagle.BEAGLE_FLAG_INVEVEC_STANDARD BEAGLE_FLAG_INVEVEC_TRANSPOSED = _beagle.BEAGLE_FLAG_INVEVEC_TRANSPOSED BEAGLE_FLAG_VECTOR_SSE = _beagle.BEAGLE_FLAG_VECTOR_SSE BEAGLE_FLAG_VECTOR_NONE = _beagle.BEAGLE_FLAG_VECTOR_NONE BEAGLE_FLAG_THREADING_OPENMP = _beagle.BEAGLE_FLAG_THREADING_OPENMP BEAGLE_FLAG_THREADING_NONE = _beagle.BEAGLE_FLAG_THREADING_NONE BEAGLE_FLAG_PROCESSOR_CPU = _beagle.BEAGLE_FLAG_PROCESSOR_CPU BEAGLE_FLAG_PROCESSOR_GPU = _beagle.BEAGLE_FLAG_PROCESSOR_GPU BEAGLE_FLAG_PROCESSOR_FPGA = _beagle.BEAGLE_FLAG_PROCESSOR_FPGA BEAGLE_FLAG_PROCESSOR_CELL = _beagle.BEAGLE_FLAG_PROCESSOR_CELL BEAGLE_FLAG_FRAMEWORK_CUDA = _beagle.BEAGLE_FLAG_FRAMEWORK_CUDA BEAGLE_FLAG_FRAMEWORK_OPENCL = _beagle.BEAGLE_FLAG_FRAMEWORK_OPENCL BEAGLE_OP_COUNT = _beagle.BEAGLE_OP_COUNT BEAGLE_OP_NONE = _beagle.BEAGLE_OP_NONE class BeagleInstanceDetails(_object): __swig_setmethods__ = {} __setattr__ = lambda self, name, value: _swig_setattr(self, BeagleInstanceDetails, name, value) __swig_getmethods__ = {} __getattr__ = lambda self, name: _swig_getattr(self, BeagleInstanceDetails, name) __repr__ = _swig_repr __swig_setmethods__["resourceNumber"] = _beagle.BeagleInstanceDetails_resourceNumber_set __swig_getmethods__["resourceNumber"] = _beagle.BeagleInstanceDetails_resourceNumber_get if _newclass:resourceNumber = _swig_property(_beagle.BeagleInstanceDetails_resourceNumber_get, _beagle.BeagleInstanceDetails_resourceNumber_set) __swig_setmethods__["resourceName"] = _beagle.BeagleInstanceDetails_resourceName_set __swig_getmethods__["resourceName"] = _beagle.BeagleInstanceDetails_resourceName_get if _newclass:resourceName = _swig_property(_beagle.BeagleInstanceDetails_resourceName_get, _beagle.BeagleInstanceDetails_resourceName_set) __swig_setmethods__["implName"] = _beagle.BeagleInstanceDetails_implName_set __swig_getmethods__["implName"] = _beagle.BeagleInstanceDetails_implName_get if _newclass:implName = _swig_property(_beagle.BeagleInstanceDetails_implName_get, _beagle.BeagleInstanceDetails_implName_set) __swig_setmethods__["implDescription"] = _beagle.BeagleInstanceDetails_implDescription_set __swig_getmethods__["implDescription"] = _beagle.BeagleInstanceDetails_implDescription_get if _newclass:implDescription = _swig_property(_beagle.BeagleInstanceDetails_implDescription_get, _beagle.BeagleInstanceDetails_implDescription_set) __swig_setmethods__["flags"] = _beagle.BeagleInstanceDetails_flags_set __swig_getmethods__["flags"] = _beagle.BeagleInstanceDetails_flags_get if _newclass:flags = _swig_property(_beagle.BeagleInstanceDetails_flags_get, _beagle.BeagleInstanceDetails_flags_set) def __init__(self): this = _beagle.new_BeagleInstanceDetails() try: self.this.append(this) except: self.this = this __swig_destroy__ = _beagle.delete_BeagleInstanceDetails __del__ = lambda self : None; BeagleInstanceDetails_swigregister = _beagle.BeagleInstanceDetails_swigregister BeagleInstanceDetails_swigregister(BeagleInstanceDetails) class BeagleResource(_object): __swig_setmethods__ = {} __setattr__ = lambda self, name, value: _swig_setattr(self, BeagleResource, name, value) __swig_getmethods__ = {} __getattr__ = lambda self, name: _swig_getattr(self, BeagleResource, name) __repr__ = _swig_repr __swig_setmethods__["name"] = _beagle.BeagleResource_name_set __swig_getmethods__["name"] = _beagle.BeagleResource_name_get if _newclass:name = _swig_property(_beagle.BeagleResource_name_get, _beagle.BeagleResource_name_set) __swig_setmethods__["description"] = _beagle.BeagleResource_description_set __swig_getmethods__["description"] = _beagle.BeagleResource_description_get if _newclass:description = _swig_property(_beagle.BeagleResource_description_get, _beagle.BeagleResource_description_set) __swig_setmethods__["supportFlags"] = _beagle.BeagleResource_supportFlags_set __swig_getmethods__["supportFlags"] = _beagle.BeagleResource_supportFlags_get if _newclass:supportFlags = _swig_property(_beagle.BeagleResource_supportFlags_get, _beagle.BeagleResource_supportFlags_set) __swig_setmethods__["requiredFlags"] = _beagle.BeagleResource_requiredFlags_set __swig_getmethods__["requiredFlags"] = _beagle.BeagleResource_requiredFlags_get if _newclass:requiredFlags = _swig_property(_beagle.BeagleResource_requiredFlags_get, _beagle.BeagleResource_requiredFlags_set) def __init__(self): this = _beagle.new_BeagleResource() try: self.this.append(this) except: self.this = this __swig_destroy__ = _beagle.delete_BeagleResource __del__ = lambda self : None; BeagleResource_swigregister = _beagle.BeagleResource_swigregister BeagleResource_swigregister(BeagleResource) class BeagleResourceList(_object): __swig_setmethods__ = {} __setattr__ = lambda self, name, value: _swig_setattr(self, BeagleResourceList, name, value) __swig_getmethods__ = {} __getattr__ = lambda self, name: _swig_getattr(self, BeagleResourceList, name) __repr__ = _swig_repr __swig_setmethods__["list"] = _beagle.BeagleResourceList_list_set __swig_getmethods__["list"] = _beagle.BeagleResourceList_list_get if _newclass:list = _swig_property(_beagle.BeagleResourceList_list_get, _beagle.BeagleResourceList_list_set) __swig_setmethods__["length"] = _beagle.BeagleResourceList_length_set __swig_getmethods__["length"] = _beagle.BeagleResourceList_length_get if _newclass:length = _swig_property(_beagle.BeagleResourceList_length_get, _beagle.BeagleResourceList_length_set) def __init__(self): this = _beagle.new_BeagleResourceList() try: self.this.append(this) except: self.this = this __swig_destroy__ = _beagle.delete_BeagleResourceList __del__ = lambda self : None; BeagleResourceList_swigregister = _beagle.BeagleResourceList_swigregister BeagleResourceList_swigregister(BeagleResourceList) def beagleGetResourceList(): return _beagle.beagleGetResourceList() beagleGetResourceList = _beagle.beagleGetResourceList def beagleCreateInstance(*args): return _beagle.beagleCreateInstance(*args) beagleCreateInstance = _beagle.beagleCreateInstance def beagleFinalizeInstance(*args): return _beagle.beagleFinalizeInstance(*args) beagleFinalizeInstance = _beagle.beagleFinalizeInstance def beagleFinalize(): return _beagle.beagleFinalize() beagleFinalize = _beagle.beagleFinalize def beagleSetTipStates(*args): return _beagle.beagleSetTipStates(*args) beagleSetTipStates = _beagle.beagleSetTipStates def beagleSetTipPartials(*args): return _beagle.beagleSetTipPartials(*args) beagleSetTipPartials = _beagle.beagleSetTipPartials def beagleSetPartials(*args): return _beagle.beagleSetPartials(*args) beagleSetPartials = _beagle.beagleSetPartials def beagleGetPartials(*args): return _beagle.beagleGetPartials(*args) beagleGetPartials = _beagle.beagleGetPartials def beagleSetEigenDecomposition(*args): return _beagle.beagleSetEigenDecomposition(*args) beagleSetEigenDecomposition = _beagle.beagleSetEigenDecomposition def beagleSetStateFrequencies(*args): return _beagle.beagleSetStateFrequencies(*args) beagleSetStateFrequencies = _beagle.beagleSetStateFrequencies def beagleSetCategoryWeights(*args): return _beagle.beagleSetCategoryWeights(*args) beagleSetCategoryWeights = _beagle.beagleSetCategoryWeights def beagleSetCategoryRates(*args): return _beagle.beagleSetCategoryRates(*args) beagleSetCategoryRates = _beagle.beagleSetCategoryRates def beagleSetPatternWeights(*args): return _beagle.beagleSetPatternWeights(*args) beagleSetPatternWeights = _beagle.beagleSetPatternWeights def beagleUpdateTransitionMatrices(*args): return _beagle.beagleUpdateTransitionMatrices(*args) beagleUpdateTransitionMatrices = _beagle.beagleUpdateTransitionMatrices def beagleSetTransitionMatrix(*args): return _beagle.beagleSetTransitionMatrix(*args) beagleSetTransitionMatrix = _beagle.beagleSetTransitionMatrix def beagleGetTransitionMatrix(*args): return _beagle.beagleGetTransitionMatrix(*args) beagleGetTransitionMatrix = _beagle.beagleGetTransitionMatrix def beagleSetTransitionMatrices(*args): return _beagle.beagleSetTransitionMatrices(*args) beagleSetTransitionMatrices = _beagle.beagleSetTransitionMatrices class BeagleOperation(_object): __swig_setmethods__ = {} __setattr__ = lambda self, name, value: _swig_setattr(self, BeagleOperation, name, value) __swig_getmethods__ = {} __getattr__ = lambda self, name: _swig_getattr(self, BeagleOperation, name) __repr__ = _swig_repr __swig_setmethods__["destinationPartials"] = _beagle.BeagleOperation_destinationPartials_set __swig_getmethods__["destinationPartials"] = _beagle.BeagleOperation_destinationPartials_get if _newclass:destinationPartials = _swig_property(_beagle.BeagleOperation_destinationPartials_get, _beagle.BeagleOperation_destinationPartials_set) __swig_setmethods__["destinationScaleWrite"] = _beagle.BeagleOperation_destinationScaleWrite_set __swig_getmethods__["destinationScaleWrite"] = _beagle.BeagleOperation_destinationScaleWrite_get if _newclass:destinationScaleWrite = _swig_property(_beagle.BeagleOperation_destinationScaleWrite_get, _beagle.BeagleOperation_destinationScaleWrite_set) __swig_setmethods__["destinationScaleRead"] = _beagle.BeagleOperation_destinationScaleRead_set __swig_getmethods__["destinationScaleRead"] = _beagle.BeagleOperation_destinationScaleRead_get if _newclass:destinationScaleRead = _swig_property(_beagle.BeagleOperation_destinationScaleRead_get, _beagle.BeagleOperation_destinationScaleRead_set) __swig_setmethods__["child1Partials"] = _beagle.BeagleOperation_child1Partials_set __swig_getmethods__["child1Partials"] = _beagle.BeagleOperation_child1Partials_get if _newclass:child1Partials = _swig_property(_beagle.BeagleOperation_child1Partials_get, _beagle.BeagleOperation_child1Partials_set) __swig_setmethods__["child1TransitionMatrix"] = _beagle.BeagleOperation_child1TransitionMatrix_set __swig_getmethods__["child1TransitionMatrix"] = _beagle.BeagleOperation_child1TransitionMatrix_get if _newclass:child1TransitionMatrix = _swig_property(_beagle.BeagleOperation_child1TransitionMatrix_get, _beagle.BeagleOperation_child1TransitionMatrix_set) __swig_setmethods__["child2Partials"] = _beagle.BeagleOperation_child2Partials_set __swig_getmethods__["child2Partials"] = _beagle.BeagleOperation_child2Partials_get if _newclass:child2Partials = _swig_property(_beagle.BeagleOperation_child2Partials_get, _beagle.BeagleOperation_child2Partials_set) __swig_setmethods__["child2TransitionMatrix"] = _beagle.BeagleOperation_child2TransitionMatrix_set __swig_getmethods__["child2TransitionMatrix"] = _beagle.BeagleOperation_child2TransitionMatrix_get if _newclass:child2TransitionMatrix = _swig_property(_beagle.BeagleOperation_child2TransitionMatrix_get, _beagle.BeagleOperation_child2TransitionMatrix_set) def __init__(self): this = _beagle.new_BeagleOperation() try: self.this.append(this) except: self.this = this __swig_destroy__ = _beagle.delete_BeagleOperation __del__ = lambda self : None; BeagleOperation_swigregister = _beagle.BeagleOperation_swigregister BeagleOperation_swigregister(BeagleOperation) def beagleUpdatePartials(*args): return _beagle.beagleUpdatePartials(*args) beagleUpdatePartials = _beagle.beagleUpdatePartials def beagleWaitForPartials(*args): return _beagle.beagleWaitForPartials(*args) beagleWaitForPartials = _beagle.beagleWaitForPartials def beagleAccumulateScaleFactors(*args): return _beagle.beagleAccumulateScaleFactors(*args) beagleAccumulateScaleFactors = _beagle.beagleAccumulateScaleFactors def beagleRemoveScaleFactors(*args): return _beagle.beagleRemoveScaleFactors(*args) beagleRemoveScaleFactors = _beagle.beagleRemoveScaleFactors def beagleResetScaleFactors(*args): return _beagle.beagleResetScaleFactors(*args) beagleResetScaleFactors = _beagle.beagleResetScaleFactors def beagleCopyScaleFactors(*args): return _beagle.beagleCopyScaleFactors(*args) beagleCopyScaleFactors = _beagle.beagleCopyScaleFactors def beagleCalculateRootLogLikelihoods(*args): return _beagle.beagleCalculateRootLogLikelihoods(*args) beagleCalculateRootLogLikelihoods = _beagle.beagleCalculateRootLogLikelihoods def beagleCalculateEdgeLogLikelihoods(*args): return _beagle.beagleCalculateEdgeLogLikelihoods(*args) beagleCalculateEdgeLogLikelihoods = _beagle.beagleCalculateEdgeLogLikelihoods def beagleGetSiteLogLikelihoods(*args): return _beagle.beagleGetSiteLogLikelihoods(*args) beagleGetSiteLogLikelihoods = _beagle.beagleGetSiteLogLikelihoods def beagleGetSiteDerivatives(*args): return _beagle.beagleGetSiteDerivatives(*args) beagleGetSiteDerivatives = _beagle.beagleGetSiteDerivatives def new_BeagleOperationArray(*args): return _beagle.new_BeagleOperationArray(*args) new_BeagleOperationArray = _beagle.new_BeagleOperationArray def delete_BeagleOperationArray(*args): return _beagle.delete_BeagleOperationArray(*args) delete_BeagleOperationArray = _beagle.delete_BeagleOperationArray def BeagleOperationArray_getitem(*args): return _beagle.BeagleOperationArray_getitem(*args) BeagleOperationArray_getitem = _beagle.BeagleOperationArray_getitem def BeagleOperationArray_setitem(*args): return _beagle.BeagleOperationArray_setitem(*args) BeagleOperationArray_setitem = _beagle.BeagleOperationArray_setitem def createStates(st,ttab): states = new_intArray(len(st)) for i in range(0,len(st)): intArray_setitem(states,i,ttab[st[i]]) return states def make_intarray(ia): result = new_intArray(len(ia)) for i in range(0,len(ia)): intArray_setitem(result,i,ia[i]) return result def make_doublearray(da): result = new_doubleArray(len(da)) for i in range(0,len(da)): doubleArray_setitem(result,i,da[i]) return result def make_operation(arg): o = BeagleOperation() o.destinationPartials = arg[0] o.destinationScaleWrite = arg[1] o.destinationScaleRead = arg[2] o.child1Partials = arg[3] o.child1TransitionMatrix = arg[4] o.child2Partials = arg[5] o.child2TransitionMatrix = arg[6] return o def createPatternWeights(wts): weights = new_doubleArray(len(wts)) for i in range(0,len(wts)): doubleArray_setitem(weights,i,wts[i]) return weights