Package PyML :: Package containers :: Package ext :: Module csequencedata
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Source Code for Module PyML.containers.ext.csequencedata

  1  # This file was automatically generated by SWIG (http://www.swig.org). 
  2  # Version 1.3.31 
  3  # 
  4  # Don't modify this file, modify the SWIG interface instead. 
  5  # This file is compatible with both classic and new-style classes. 
  6   
  7  import _csequencedata 
  8  import new 
  9  new_instancemethod = new.instancemethod 
 10  try: 
 11      _swig_property = property 
 12  except NameError: 
 13      pass # Python < 2.2 doesn't have 'property'. 
14 -def _swig_setattr_nondynamic(self,class_type,name,value,static=1):
15 if (name == "thisown"): return self.this.own(value) 16 if (name == "this"): 17 if type(value).__name__ == 'PySwigObject': 18 self.__dict__[name] = value 19 return 20 method = class_type.__swig_setmethods__.get(name,None) 21 if method: return method(self,value) 22 if (not static) or hasattr(self,name): 23 self.__dict__[name] = value 24 else: 25 raise AttributeError("You cannot add attributes to %s" % self)
26
27 -def _swig_setattr(self,class_type,name,value):
28 return _swig_setattr_nondynamic(self,class_type,name,value,0)
29
30 -def _swig_getattr(self,class_type,name):
31 if (name == "thisown"): return self.this.own() 32 method = class_type.__swig_getmethods__.get(name,None) 33 if method: return method(self) 34 raise AttributeError,name
35
36 -def _swig_repr(self):
37 try: strthis = "proxy of " + self.this.__repr__() 38 except: strthis = "" 39 return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
40 41 import types 42 try: 43 _object = types.ObjectType 44 _newclass = 1 45 except AttributeError:
46 - class _object : pass
47 _newclass = 0 48 del types 49 50
51 -class PySwigIterator(_object):
52 __swig_setmethods__ = {} 53 __setattr__ = lambda self, name, value: _swig_setattr(self, PySwigIterator, name, value) 54 __swig_getmethods__ = {} 55 __getattr__ = lambda self, name: _swig_getattr(self, PySwigIterator, name)
56 - def __init__(self): raise AttributeError, "No constructor defined"
57 __repr__ = _swig_repr 58 __swig_destroy__ = _csequencedata.delete_PySwigIterator 59 __del__ = lambda self : None;
60 - def value(*args): return _csequencedata.PySwigIterator_value(*args)
61 - def incr(*args): return _csequencedata.PySwigIterator_incr(*args)
62 - def decr(*args): return _csequencedata.PySwigIterator_decr(*args)
63 - def distance(*args): return _csequencedata.PySwigIterator_distance(*args)
64 - def equal(*args): return _csequencedata.PySwigIterator_equal(*args)
65 - def copy(*args): return _csequencedata.PySwigIterator_copy(*args)
66 - def next(*args): return _csequencedata.PySwigIterator_next(*args)
67 - def previous(*args): return _csequencedata.PySwigIterator_previous(*args)
68 - def advance(*args): return _csequencedata.PySwigIterator_advance(*args)
69 - def __eq__(*args): return _csequencedata.PySwigIterator___eq__(*args)
70 - def __ne__(*args): return _csequencedata.PySwigIterator___ne__(*args)
71 - def __iadd__(*args): return _csequencedata.PySwigIterator___iadd__(*args)
72 - def __isub__(*args): return _csequencedata.PySwigIterator___isub__(*args)
73 - def __add__(*args): return _csequencedata.PySwigIterator___add__(*args)
74 - def __sub__(*args): return _csequencedata.PySwigIterator___sub__(*args)
75 - def __iter__(self): return self
76 PySwigIterator_swigregister = _csequencedata.PySwigIterator_swigregister 77 PySwigIterator_swigregister(PySwigIterator) 78
79 -class IntVector(_object):
80 __swig_setmethods__ = {} 81 __setattr__ = lambda self, name, value: _swig_setattr(self, IntVector, name, value) 82 __swig_getmethods__ = {} 83 __getattr__ = lambda self, name: _swig_getattr(self, IntVector, name) 84 __repr__ = _swig_repr
85 - def iterator(*args): return _csequencedata.IntVector_iterator(*args)
86 - def __iter__(self): return self.iterator()
87 - def __nonzero__(*args): return _csequencedata.IntVector___nonzero__(*args)
88 - def __len__(*args): return _csequencedata.IntVector___len__(*args)
89 - def pop(*args): return _csequencedata.IntVector_pop(*args)
90 - def __getslice__(*args): return _csequencedata.IntVector___getslice__(*args)
91 - def __setslice__(*args): return _csequencedata.IntVector___setslice__(*args)
92 - def __delslice__(*args): return _csequencedata.IntVector___delslice__(*args)
93 - def __delitem__(*args): return _csequencedata.IntVector___delitem__(*args)
94 - def __getitem__(*args): return _csequencedata.IntVector___getitem__(*args)
95 - def __setitem__(*args): return _csequencedata.IntVector___setitem__(*args)
96 - def append(*args): return _csequencedata.IntVector_append(*args)
97 - def empty(*args): return _csequencedata.IntVector_empty(*args)
98 - def size(*args): return _csequencedata.IntVector_size(*args)
99 - def clear(*args): return _csequencedata.IntVector_clear(*args)
100 - def swap(*args): return _csequencedata.IntVector_swap(*args)
101 - def get_allocator(*args): return _csequencedata.IntVector_get_allocator(*args)
102 - def begin(*args): return _csequencedata.IntVector_begin(*args)
103 - def end(*args): return _csequencedata.IntVector_end(*args)
104 - def rbegin(*args): return _csequencedata.IntVector_rbegin(*args)
105 - def rend(*args): return _csequencedata.IntVector_rend(*args)
106 - def pop_back(*args): return _csequencedata.IntVector_pop_back(*args)
107 - def erase(*args): return _csequencedata.IntVector_erase(*args)
108 - def __init__(self, *args):
109 this = _csequencedata.new_IntVector(*args) 110 try: self.this.append(this) 111 except: self.this = this
112 - def push_back(*args): return _csequencedata.IntVector_push_back(*args)
113 - def front(*args): return _csequencedata.IntVector_front(*args)
114 - def back(*args): return _csequencedata.IntVector_back(*args)
115 - def assign(*args): return _csequencedata.IntVector_assign(*args)
116 - def resize(*args): return _csequencedata.IntVector_resize(*args)
117 - def insert(*args): return _csequencedata.IntVector_insert(*args)
118 - def reserve(*args): return _csequencedata.IntVector_reserve(*args)
119 - def capacity(*args): return _csequencedata.IntVector_capacity(*args)
120 __swig_destroy__ = _csequencedata.delete_IntVector 121 __del__ = lambda self : None; 122 IntVector_swigregister = _csequencedata.IntVector_swigregister 123 IntVector_swigregister(IntVector) 124
125 -class DoubleVector(_object):
126 __swig_setmethods__ = {} 127 __setattr__ = lambda self, name, value: _swig_setattr(self, DoubleVector, name, value) 128 __swig_getmethods__ = {} 129 __getattr__ = lambda self, name: _swig_getattr(self, DoubleVector, name) 130 __repr__ = _swig_repr
131 - def iterator(*args): return _csequencedata.DoubleVector_iterator(*args)
132 - def __iter__(self): return self.iterator()
133 - def __nonzero__(*args): return _csequencedata.DoubleVector___nonzero__(*args)
134 - def __len__(*args): return _csequencedata.DoubleVector___len__(*args)
135 - def pop(*args): return _csequencedata.DoubleVector_pop(*args)
136 - def __getslice__(*args): return _csequencedata.DoubleVector___getslice__(*args)
137 - def __setslice__(*args): return _csequencedata.DoubleVector___setslice__(*args)
138 - def __delslice__(*args): return _csequencedata.DoubleVector___delslice__(*args)
139 - def __delitem__(*args): return _csequencedata.DoubleVector___delitem__(*args)
140 - def __getitem__(*args): return _csequencedata.DoubleVector___getitem__(*args)
141 - def __setitem__(*args): return _csequencedata.DoubleVector___setitem__(*args)
142 - def append(*args): return _csequencedata.DoubleVector_append(*args)
143 - def empty(*args): return _csequencedata.DoubleVector_empty(*args)
144 - def size(*args): return _csequencedata.DoubleVector_size(*args)
145 - def clear(*args): return _csequencedata.DoubleVector_clear(*args)
146 - def swap(*args): return _csequencedata.DoubleVector_swap(*args)
147 - def get_allocator(*args): return _csequencedata.DoubleVector_get_allocator(*args)
148 - def begin(*args): return _csequencedata.DoubleVector_begin(*args)
149 - def end(*args): return _csequencedata.DoubleVector_end(*args)
150 - def rbegin(*args): return _csequencedata.DoubleVector_rbegin(*args)
151 - def rend(*args): return _csequencedata.DoubleVector_rend(*args)
152 - def pop_back(*args): return _csequencedata.DoubleVector_pop_back(*args)
153 - def erase(*args): return _csequencedata.DoubleVector_erase(*args)
154 - def __init__(self, *args):
155 this = _csequencedata.new_DoubleVector(*args) 156 try: self.this.append(this) 157 except: self.this = this
158 - def push_back(*args): return _csequencedata.DoubleVector_push_back(*args)
159 - def front(*args): return _csequencedata.DoubleVector_front(*args)
160 - def back(*args): return _csequencedata.DoubleVector_back(*args)
161 - def assign(*args): return _csequencedata.DoubleVector_assign(*args)
162 - def resize(*args): return _csequencedata.DoubleVector_resize(*args)
163 - def insert(*args): return _csequencedata.DoubleVector_insert(*args)
164 - def reserve(*args): return _csequencedata.DoubleVector_reserve(*args)
165 - def capacity(*args): return _csequencedata.DoubleVector_capacity(*args)
166 __swig_destroy__ = _csequencedata.delete_DoubleVector 167 __del__ = lambda self : None; 168 DoubleVector_swigregister = _csequencedata.DoubleVector_swigregister 169 DoubleVector_swigregister(DoubleVector) 170
171 -class StringVector(_object):
172 __swig_setmethods__ = {} 173 __setattr__ = lambda self, name, value: _swig_setattr(self, StringVector, name, value) 174 __swig_getmethods__ = {} 175 __getattr__ = lambda self, name: _swig_getattr(self, StringVector, name) 176 __repr__ = _swig_repr
177 - def iterator(*args): return _csequencedata.StringVector_iterator(*args)
178 - def __iter__(self): return self.iterator()
179 - def __nonzero__(*args): return _csequencedata.StringVector___nonzero__(*args)
180 - def __len__(*args): return _csequencedata.StringVector___len__(*args)
181 - def pop(*args): return _csequencedata.StringVector_pop(*args)
182 - def __getslice__(*args): return _csequencedata.StringVector___getslice__(*args)
183 - def __setslice__(*args): return _csequencedata.StringVector___setslice__(*args)
184 - def __delslice__(*args): return _csequencedata.StringVector___delslice__(*args)
185 - def __delitem__(*args): return _csequencedata.StringVector___delitem__(*args)
186 - def __getitem__(*args): return _csequencedata.StringVector___getitem__(*args)
187 - def __setitem__(*args): return _csequencedata.StringVector___setitem__(*args)
188 - def append(*args): return _csequencedata.StringVector_append(*args)
189 - def empty(*args): return _csequencedata.StringVector_empty(*args)
190 - def size(*args): return _csequencedata.StringVector_size(*args)
191 - def clear(*args): return _csequencedata.StringVector_clear(*args)
192 - def swap(*args): return _csequencedata.StringVector_swap(*args)
193 - def get_allocator(*args): return _csequencedata.StringVector_get_allocator(*args)
194 - def begin(*args): return _csequencedata.StringVector_begin(*args)
195 - def end(*args): return _csequencedata.StringVector_end(*args)
196 - def rbegin(*args): return _csequencedata.StringVector_rbegin(*args)
197 - def rend(*args): return _csequencedata.StringVector_rend(*args)
198 - def pop_back(*args): return _csequencedata.StringVector_pop_back(*args)
199 - def erase(*args): return _csequencedata.StringVector_erase(*args)
200 - def __init__(self, *args):
201 this = _csequencedata.new_StringVector(*args) 202 try: self.this.append(this) 203 except: self.this = this
204 - def push_back(*args): return _csequencedata.StringVector_push_back(*args)
205 - def front(*args): return _csequencedata.StringVector_front(*args)
206 - def back(*args): return _csequencedata.StringVector_back(*args)
207 - def assign(*args): return _csequencedata.StringVector_assign(*args)
208 - def resize(*args): return _csequencedata.StringVector_resize(*args)
209 - def insert(*args): return _csequencedata.StringVector_insert(*args)
210 - def reserve(*args): return _csequencedata.StringVector_reserve(*args)
211 - def capacity(*args): return _csequencedata.StringVector_capacity(*args)
212 __swig_destroy__ = _csequencedata.delete_StringVector 213 __del__ = lambda self : None; 214 StringVector_swigregister = _csequencedata.StringVector_swigregister 215 StringVector_swigregister(StringVector) 216
217 -class LongVector(_object):
218 __swig_setmethods__ = {} 219 __setattr__ = lambda self, name, value: _swig_setattr(self, LongVector, name, value) 220 __swig_getmethods__ = {} 221 __getattr__ = lambda self, name: _swig_getattr(self, LongVector, name) 222 __repr__ = _swig_repr
223 - def iterator(*args): return _csequencedata.LongVector_iterator(*args)
224 - def __iter__(self): return self.iterator()
225 - def __nonzero__(*args): return _csequencedata.LongVector___nonzero__(*args)
226 - def __len__(*args): return _csequencedata.LongVector___len__(*args)
227 - def pop(*args): return _csequencedata.LongVector_pop(*args)
228 - def __getslice__(*args): return _csequencedata.LongVector___getslice__(*args)
229 - def __setslice__(*args): return _csequencedata.LongVector___setslice__(*args)
230 - def __delslice__(*args): return _csequencedata.LongVector___delslice__(*args)
231 - def __delitem__(*args): return _csequencedata.LongVector___delitem__(*args)
232 - def __getitem__(*args): return _csequencedata.LongVector___getitem__(*args)
233 - def __setitem__(*args): return _csequencedata.LongVector___setitem__(*args)
234 - def append(*args): return _csequencedata.LongVector_append(*args)
235 - def empty(*args): return _csequencedata.LongVector_empty(*args)
236 - def size(*args): return _csequencedata.LongVector_size(*args)
237 - def clear(*args): return _csequencedata.LongVector_clear(*args)
238 - def swap(*args): return _csequencedata.LongVector_swap(*args)
239 - def get_allocator(*args): return _csequencedata.LongVector_get_allocator(*args)
240 - def begin(*args): return _csequencedata.LongVector_begin(*args)
241 - def end(*args): return _csequencedata.LongVector_end(*args)
242 - def rbegin(*args): return _csequencedata.LongVector_rbegin(*args)
243 - def rend(*args): return _csequencedata.LongVector_rend(*args)
244 - def pop_back(*args): return _csequencedata.LongVector_pop_back(*args)
245 - def erase(*args): return _csequencedata.LongVector_erase(*args)
246 - def __init__(self, *args):
247 this = _csequencedata.new_LongVector(*args) 248 try: self.this.append(this) 249 except: self.this = this
250 - def push_back(*args): return _csequencedata.LongVector_push_back(*args)
251 - def front(*args): return _csequencedata.LongVector_front(*args)
252 - def back(*args): return _csequencedata.LongVector_back(*args)
253 - def assign(*args): return _csequencedata.LongVector_assign(*args)
254 - def resize(*args): return _csequencedata.LongVector_resize(*args)
255 - def insert(*args): return _csequencedata.LongVector_insert(*args)
256 - def reserve(*args): return _csequencedata.LongVector_reserve(*args)
257 - def capacity(*args): return _csequencedata.LongVector_capacity(*args)
258 __swig_destroy__ = _csequencedata.delete_LongVector 259 __del__ = lambda self : None; 260 LongVector_swigregister = _csequencedata.LongVector_swigregister 261 LongVector_swigregister(LongVector) 262
263 -class DataSet(_object):
264 __swig_setmethods__ = {} 265 __setattr__ = lambda self, name, value: _swig_setattr(self, DataSet, name, value) 266 __swig_getmethods__ = {} 267 __getattr__ = lambda self, name: _swig_getattr(self, DataSet, name)
268 - def __init__(self): raise AttributeError, "No constructor defined"
269 __repr__ = _swig_repr 270 __swig_setmethods__["Y"] = _csequencedata.DataSet_Y_set 271 __swig_getmethods__["Y"] = _csequencedata.DataSet_Y_get 272 if _newclass:Y = _swig_property(_csequencedata.DataSet_Y_get, _csequencedata.DataSet_Y_set) 273 __swig_setmethods__["norms"] = _csequencedata.DataSet_norms_set 274 __swig_getmethods__["norms"] = _csequencedata.DataSet_norms_get 275 if _newclass:norms = _swig_property(_csequencedata.DataSet_norms_get, _csequencedata.DataSet_norms_set) 276 __swig_setmethods__["kernel"] = _csequencedata.DataSet_kernel_set 277 __swig_getmethods__["kernel"] = _csequencedata.DataSet_kernel_get 278 if _newclass:kernel = _swig_property(_csequencedata.DataSet_kernel_get, _csequencedata.DataSet_kernel_set)
279 - def setY(*args): return _csequencedata.DataSet_setY(*args)
280 - def computeNorms(*args): return _csequencedata.DataSet_computeNorms(*args)
281 - def setKernel(*args): return _csequencedata.DataSet_setKernel(*args)
282 - def attachKernel(*args): return _csequencedata.DataSet_attachKernel(*args)
283 - def getKernelMatrixAsVector(*args): return _csequencedata.DataSet_getKernelMatrixAsVector(*args)
284 - def size(*args): return _csequencedata.DataSet_size(*args)
285 - def dotProduct(*args): return _csequencedata.DataSet_dotProduct(*args)
286 - def duplicate(*args): return _csequencedata.DataSet_duplicate(*args)
287 - def castToBase(*args): return _csequencedata.DataSet_castToBase(*args)
288 - def show(*args): return _csequencedata.DataSet_show(*args)
289 __swig_destroy__ = _csequencedata.delete_DataSet 290 __del__ = lambda self : None;
291 DataSet_swigregister = _csequencedata.DataSet_swigregister 292 DataSet_swigregister(DataSet) 293
294 -class SequenceData(DataSet):
295 __swig_setmethods__ = {} 296 for _s in [DataSet]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{})) 297 __setattr__ = lambda self, name, value: _swig_setattr(self, SequenceData, name, value) 298 __swig_getmethods__ = {} 299 for _s in [DataSet]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{})) 300 __getattr__ = lambda self, name: _swig_getattr(self, SequenceData, name) 301 __repr__ = _swig_repr 302 __swig_setmethods__["X"] = _csequencedata.SequenceData_X_set 303 __swig_getmethods__["X"] = _csequencedata.SequenceData_X_get 304 if _newclass:X = _swig_property(_csequencedata.SequenceData_X_get, _csequencedata.SequenceData_X_set)
305 - def __init__(self, *args):
306 this = _csequencedata.new_SequenceData(*args) 307 try: self.this.append(this) 308 except: self.this = this
309 __swig_destroy__ = _csequencedata.delete_SequenceData 310 __del__ = lambda self : None; 311 __swig_setmethods__["stringKernel"] = _csequencedata.SequenceData_stringKernel_set 312 __swig_getmethods__["stringKernel"] = _csequencedata.SequenceData_stringKernel_get 313 if _newclass:stringKernel = _swig_property(_csequencedata.SequenceData_stringKernel_get, _csequencedata.SequenceData_stringKernel_set) 314 __swig_setmethods__["stringKernelType"] = _csequencedata.SequenceData_stringKernelType_set 315 __swig_getmethods__["stringKernelType"] = _csequencedata.SequenceData_stringKernelType_get 316 if _newclass:stringKernelType = _swig_property(_csequencedata.SequenceData_stringKernelType_get, _csequencedata.SequenceData_stringKernelType_set)
317 - def addPattern(*args): return _csequencedata.SequenceData_addPattern(*args)
318 - def getSequence(*args): return _csequencedata.SequenceData_getSequence(*args)
319 - def size(*args): return _csequencedata.SequenceData_size(*args)
320 - def castToBase(*args): return _csequencedata.SequenceData_castToBase(*args)
321 - def show(*args): return _csequencedata.SequenceData_show(*args)
322 - def duplicate(*args): return _csequencedata.SequenceData_duplicate(*args)
323 - def dotProduct(*args): return _csequencedata.SequenceData_dotProduct(*args)
324 __swig_setmethods__["minKmerLength"] = _csequencedata.SequenceData_minKmerLength_set 325 __swig_getmethods__["minKmerLength"] = _csequencedata.SequenceData_minKmerLength_get 326 if _newclass:minKmerLength = _swig_property(_csequencedata.SequenceData_minKmerLength_get, _csequencedata.SequenceData_minKmerLength_set) 327 __swig_setmethods__["maxKmerLength"] = _csequencedata.SequenceData_maxKmerLength_set 328 __swig_getmethods__["maxKmerLength"] = _csequencedata.SequenceData_maxKmerLength_get 329 if _newclass:maxKmerLength = _swig_property(_csequencedata.SequenceData_maxKmerLength_get, _csequencedata.SequenceData_maxKmerLength_set) 330 __swig_setmethods__["mismatches"] = _csequencedata.SequenceData_mismatches_set 331 __swig_getmethods__["mismatches"] = _csequencedata.SequenceData_mismatches_get 332 if _newclass:mismatches = _swig_property(_csequencedata.SequenceData_mismatches_get, _csequencedata.SequenceData_mismatches_set) 333 __swig_setmethods__["mismatchProfile"] = _csequencedata.SequenceData_mismatchProfile_set 334 __swig_getmethods__["mismatchProfile"] = _csequencedata.SequenceData_mismatchProfile_get 335 if _newclass:mismatchProfile = _swig_property(_csequencedata.SequenceData_mismatchProfile_get, _csequencedata.SequenceData_mismatchProfile_set)
336 - def setMismatchProfile(*args): return _csequencedata.SequenceData_setMismatchProfile(*args)
337 - def positionalKmerKernel(*args): return _csequencedata.SequenceData_positionalKmerKernel(*args)
338 SequenceData_swigregister = _csequencedata.SequenceData_swigregister 339 SequenceData_swigregister(SequenceData) 340