1
2
3
4
5
6
7 import _cstringkernel
8 import new
9 new_instancemethod = new.instancemethod
10 try:
11 _swig_property = property
12 except NameError:
13 pass
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
28 return _swig_setattr_nondynamic(self,class_type,name,value,0)
29
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
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:
47 _newclass = 0
48 del types
49
50
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__ = _cstringkernel.delete_PySwigIterator
59 __del__ = lambda self : None;
60 - def value(*args): return _cstringkernel.PySwigIterator_value(*args)
61 - def incr(*args): return _cstringkernel.PySwigIterator_incr(*args)
62 - def decr(*args): return _cstringkernel.PySwigIterator_decr(*args)
63 - def distance(*args): return _cstringkernel.PySwigIterator_distance(*args)
64 - def equal(*args): return _cstringkernel.PySwigIterator_equal(*args)
65 - def copy(*args): return _cstringkernel.PySwigIterator_copy(*args)
66 - def next(*args): return _cstringkernel.PySwigIterator_next(*args)
67 - def previous(*args): return _cstringkernel.PySwigIterator_previous(*args)
68 - def advance(*args): return _cstringkernel.PySwigIterator_advance(*args)
69 - def __eq__(*args): return _cstringkernel.PySwigIterator___eq__(*args)
70 - def __ne__(*args): return _cstringkernel.PySwigIterator___ne__(*args)
71 - def __iadd__(*args): return _cstringkernel.PySwigIterator___iadd__(*args)
72 - def __isub__(*args): return _cstringkernel.PySwigIterator___isub__(*args)
73 - def __add__(*args): return _cstringkernel.PySwigIterator___add__(*args)
74 - def __sub__(*args): return _cstringkernel.PySwigIterator___sub__(*args)
76 PySwigIterator_swigregister = _cstringkernel.PySwigIterator_swigregister
77 PySwigIterator_swigregister(PySwigIterator)
78
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 _cstringkernel.IntVector_iterator(*args)
87 - def __nonzero__(*args): return _cstringkernel.IntVector___nonzero__(*args)
88 - def __len__(*args): return _cstringkernel.IntVector___len__(*args)
89 - def pop(*args): return _cstringkernel.IntVector_pop(*args)
90 - def __getslice__(*args): return _cstringkernel.IntVector___getslice__(*args)
91 - def __setslice__(*args): return _cstringkernel.IntVector___setslice__(*args)
92 - def __delslice__(*args): return _cstringkernel.IntVector___delslice__(*args)
93 - def __delitem__(*args): return _cstringkernel.IntVector___delitem__(*args)
94 - def __getitem__(*args): return _cstringkernel.IntVector___getitem__(*args)
95 - def __setitem__(*args): return _cstringkernel.IntVector___setitem__(*args)
96 - def append(*args): return _cstringkernel.IntVector_append(*args)
97 - def empty(*args): return _cstringkernel.IntVector_empty(*args)
98 - def size(*args): return _cstringkernel.IntVector_size(*args)
99 - def clear(*args): return _cstringkernel.IntVector_clear(*args)
100 - def swap(*args): return _cstringkernel.IntVector_swap(*args)
101 - def get_allocator(*args): return _cstringkernel.IntVector_get_allocator(*args)
102 - def begin(*args): return _cstringkernel.IntVector_begin(*args)
103 - def end(*args): return _cstringkernel.IntVector_end(*args)
104 - def rbegin(*args): return _cstringkernel.IntVector_rbegin(*args)
105 - def rend(*args): return _cstringkernel.IntVector_rend(*args)
106 - def pop_back(*args): return _cstringkernel.IntVector_pop_back(*args)
107 - def erase(*args): return _cstringkernel.IntVector_erase(*args)
109 this = _cstringkernel.new_IntVector(*args)
110 try: self.this.append(this)
111 except: self.this = this
112 - def push_back(*args): return _cstringkernel.IntVector_push_back(*args)
113 - def front(*args): return _cstringkernel.IntVector_front(*args)
114 - def back(*args): return _cstringkernel.IntVector_back(*args)
115 - def assign(*args): return _cstringkernel.IntVector_assign(*args)
116 - def resize(*args): return _cstringkernel.IntVector_resize(*args)
117 - def insert(*args): return _cstringkernel.IntVector_insert(*args)
118 - def reserve(*args): return _cstringkernel.IntVector_reserve(*args)
119 - def capacity(*args): return _cstringkernel.IntVector_capacity(*args)
120 __swig_destroy__ = _cstringkernel.delete_IntVector
121 __del__ = lambda self : None;
122 IntVector_swigregister = _cstringkernel.IntVector_swigregister
123 IntVector_swigregister(IntVector)
124
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 _cstringkernel.DoubleVector_iterator(*args)
133 - def __nonzero__(*args): return _cstringkernel.DoubleVector___nonzero__(*args)
134 - def __len__(*args): return _cstringkernel.DoubleVector___len__(*args)
135 - def pop(*args): return _cstringkernel.DoubleVector_pop(*args)
136 - def __getslice__(*args): return _cstringkernel.DoubleVector___getslice__(*args)
137 - def __setslice__(*args): return _cstringkernel.DoubleVector___setslice__(*args)
138 - def __delslice__(*args): return _cstringkernel.DoubleVector___delslice__(*args)
139 - def __delitem__(*args): return _cstringkernel.DoubleVector___delitem__(*args)
140 - def __getitem__(*args): return _cstringkernel.DoubleVector___getitem__(*args)
141 - def __setitem__(*args): return _cstringkernel.DoubleVector___setitem__(*args)
142 - def append(*args): return _cstringkernel.DoubleVector_append(*args)
143 - def empty(*args): return _cstringkernel.DoubleVector_empty(*args)
144 - def size(*args): return _cstringkernel.DoubleVector_size(*args)
145 - def clear(*args): return _cstringkernel.DoubleVector_clear(*args)
146 - def swap(*args): return _cstringkernel.DoubleVector_swap(*args)
147 - def get_allocator(*args): return _cstringkernel.DoubleVector_get_allocator(*args)
148 - def begin(*args): return _cstringkernel.DoubleVector_begin(*args)
149 - def end(*args): return _cstringkernel.DoubleVector_end(*args)
150 - def rbegin(*args): return _cstringkernel.DoubleVector_rbegin(*args)
151 - def rend(*args): return _cstringkernel.DoubleVector_rend(*args)
152 - def pop_back(*args): return _cstringkernel.DoubleVector_pop_back(*args)
153 - def erase(*args): return _cstringkernel.DoubleVector_erase(*args)
155 this = _cstringkernel.new_DoubleVector(*args)
156 try: self.this.append(this)
157 except: self.this = this
158 - def push_back(*args): return _cstringkernel.DoubleVector_push_back(*args)
159 - def front(*args): return _cstringkernel.DoubleVector_front(*args)
160 - def back(*args): return _cstringkernel.DoubleVector_back(*args)
161 - def assign(*args): return _cstringkernel.DoubleVector_assign(*args)
162 - def resize(*args): return _cstringkernel.DoubleVector_resize(*args)
163 - def insert(*args): return _cstringkernel.DoubleVector_insert(*args)
164 - def reserve(*args): return _cstringkernel.DoubleVector_reserve(*args)
165 - def capacity(*args): return _cstringkernel.DoubleVector_capacity(*args)
166 __swig_destroy__ = _cstringkernel.delete_DoubleVector
167 __del__ = lambda self : None;
168 DoubleVector_swigregister = _cstringkernel.DoubleVector_swigregister
169 DoubleVector_swigregister(DoubleVector)
170
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 _cstringkernel.StringVector_iterator(*args)
179 - def __nonzero__(*args): return _cstringkernel.StringVector___nonzero__(*args)
180 - def __len__(*args): return _cstringkernel.StringVector___len__(*args)
181 - def pop(*args): return _cstringkernel.StringVector_pop(*args)
182 - def __getslice__(*args): return _cstringkernel.StringVector___getslice__(*args)
183 - def __setslice__(*args): return _cstringkernel.StringVector___setslice__(*args)
184 - def __delslice__(*args): return _cstringkernel.StringVector___delslice__(*args)
185 - def __delitem__(*args): return _cstringkernel.StringVector___delitem__(*args)
186 - def __getitem__(*args): return _cstringkernel.StringVector___getitem__(*args)
187 - def __setitem__(*args): return _cstringkernel.StringVector___setitem__(*args)
188 - def append(*args): return _cstringkernel.StringVector_append(*args)
189 - def empty(*args): return _cstringkernel.StringVector_empty(*args)
190 - def size(*args): return _cstringkernel.StringVector_size(*args)
191 - def clear(*args): return _cstringkernel.StringVector_clear(*args)
192 - def swap(*args): return _cstringkernel.StringVector_swap(*args)
193 - def get_allocator(*args): return _cstringkernel.StringVector_get_allocator(*args)
194 - def begin(*args): return _cstringkernel.StringVector_begin(*args)
195 - def end(*args): return _cstringkernel.StringVector_end(*args)
196 - def rbegin(*args): return _cstringkernel.StringVector_rbegin(*args)
197 - def rend(*args): return _cstringkernel.StringVector_rend(*args)
198 - def pop_back(*args): return _cstringkernel.StringVector_pop_back(*args)
199 - def erase(*args): return _cstringkernel.StringVector_erase(*args)
201 this = _cstringkernel.new_StringVector(*args)
202 try: self.this.append(this)
203 except: self.this = this
204 - def push_back(*args): return _cstringkernel.StringVector_push_back(*args)
205 - def front(*args): return _cstringkernel.StringVector_front(*args)
206 - def back(*args): return _cstringkernel.StringVector_back(*args)
207 - def assign(*args): return _cstringkernel.StringVector_assign(*args)
208 - def resize(*args): return _cstringkernel.StringVector_resize(*args)
209 - def insert(*args): return _cstringkernel.StringVector_insert(*args)
210 - def reserve(*args): return _cstringkernel.StringVector_reserve(*args)
211 - def capacity(*args): return _cstringkernel.StringVector_capacity(*args)
212 __swig_destroy__ = _cstringkernel.delete_StringVector
213 __del__ = lambda self : None;
214 StringVector_swigregister = _cstringkernel.StringVector_swigregister
215 StringVector_swigregister(StringVector)
216
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 _cstringkernel.LongVector_iterator(*args)
225 - def __nonzero__(*args): return _cstringkernel.LongVector___nonzero__(*args)
226 - def __len__(*args): return _cstringkernel.LongVector___len__(*args)
227 - def pop(*args): return _cstringkernel.LongVector_pop(*args)
228 - def __getslice__(*args): return _cstringkernel.LongVector___getslice__(*args)
229 - def __setslice__(*args): return _cstringkernel.LongVector___setslice__(*args)
230 - def __delslice__(*args): return _cstringkernel.LongVector___delslice__(*args)
231 - def __delitem__(*args): return _cstringkernel.LongVector___delitem__(*args)
232 - def __getitem__(*args): return _cstringkernel.LongVector___getitem__(*args)
233 - def __setitem__(*args): return _cstringkernel.LongVector___setitem__(*args)
234 - def append(*args): return _cstringkernel.LongVector_append(*args)
235 - def empty(*args): return _cstringkernel.LongVector_empty(*args)
236 - def size(*args): return _cstringkernel.LongVector_size(*args)
237 - def clear(*args): return _cstringkernel.LongVector_clear(*args)
238 - def swap(*args): return _cstringkernel.LongVector_swap(*args)
239 - def get_allocator(*args): return _cstringkernel.LongVector_get_allocator(*args)
240 - def begin(*args): return _cstringkernel.LongVector_begin(*args)
241 - def end(*args): return _cstringkernel.LongVector_end(*args)
242 - def rbegin(*args): return _cstringkernel.LongVector_rbegin(*args)
243 - def rend(*args): return _cstringkernel.LongVector_rend(*args)
244 - def pop_back(*args): return _cstringkernel.LongVector_pop_back(*args)
245 - def erase(*args): return _cstringkernel.LongVector_erase(*args)
247 this = _cstringkernel.new_LongVector(*args)
248 try: self.this.append(this)
249 except: self.this = this
250 - def push_back(*args): return _cstringkernel.LongVector_push_back(*args)
251 - def front(*args): return _cstringkernel.LongVector_front(*args)
252 - def back(*args): return _cstringkernel.LongVector_back(*args)
253 - def assign(*args): return _cstringkernel.LongVector_assign(*args)
254 - def resize(*args): return _cstringkernel.LongVector_resize(*args)
255 - def insert(*args): return _cstringkernel.LongVector_insert(*args)
256 - def reserve(*args): return _cstringkernel.LongVector_reserve(*args)
257 - def capacity(*args): return _cstringkernel.LongVector_capacity(*args)
258 __swig_destroy__ = _cstringkernel.delete_LongVector
259 __del__ = lambda self : None;
260 LongVector_swigregister = _cstringkernel.LongVector_swigregister
261 LongVector_swigregister(LongVector)
262
275 StringKernel_swigregister = _cstringkernel.StringKernel_swigregister
276 StringKernel_swigregister(StringKernel)
277
279 __swig_setmethods__ = {}
280 for _s in [StringKernel]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
281 __setattr__ = lambda self, name, value: _swig_setattr(self, PositionalKmer, name, value)
282 __swig_getmethods__ = {}
283 for _s in [StringKernel]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
284 __getattr__ = lambda self, name: _swig_getattr(self, PositionalKmer, name)
285 __repr__ = _swig_repr
287 this = _cstringkernel.new_PositionalKmer(*args)
288 try: self.this.append(this)
289 except: self.this = this
290 __swig_destroy__ = _cstringkernel.delete_PositionalKmer
291 __del__ = lambda self : None;
292 __swig_setmethods__["mink"] = _cstringkernel.PositionalKmer_mink_set
293 __swig_getmethods__["mink"] = _cstringkernel.PositionalKmer_mink_get
294 if _newclass:mink = _swig_property(_cstringkernel.PositionalKmer_mink_get, _cstringkernel.PositionalKmer_mink_set)
295 __swig_setmethods__["maxk"] = _cstringkernel.PositionalKmer_maxk_set
296 __swig_getmethods__["maxk"] = _cstringkernel.PositionalKmer_maxk_get
297 if _newclass:maxk = _swig_property(_cstringkernel.PositionalKmer_maxk_get, _cstringkernel.PositionalKmer_maxk_set)
298 __swig_setmethods__["maxShift"] = _cstringkernel.PositionalKmer_maxShift_set
299 __swig_getmethods__["maxShift"] = _cstringkernel.PositionalKmer_maxShift_get
300 if _newclass:maxShift = _swig_property(_cstringkernel.PositionalKmer_maxShift_get, _cstringkernel.PositionalKmer_maxShift_set)
301 __swig_setmethods__["noShiftStart"] = _cstringkernel.PositionalKmer_noShiftStart_set
302 __swig_getmethods__["noShiftStart"] = _cstringkernel.PositionalKmer_noShiftStart_get
303 if _newclass:noShiftStart = _swig_property(_cstringkernel.PositionalKmer_noShiftStart_get, _cstringkernel.PositionalKmer_noShiftStart_set)
304 __swig_setmethods__["noShiftEnd"] = _cstringkernel.PositionalKmer_noShiftEnd_set
305 __swig_getmethods__["noShiftEnd"] = _cstringkernel.PositionalKmer_noShiftEnd_get
306 if _newclass:noShiftEnd = _swig_property(_cstringkernel.PositionalKmer_noShiftEnd_get, _cstringkernel.PositionalKmer_noShiftEnd_set)
307 __swig_setmethods__["mismatches"] = _cstringkernel.PositionalKmer_mismatches_set
308 __swig_getmethods__["mismatches"] = _cstringkernel.PositionalKmer_mismatches_get
309 if _newclass:mismatches = _swig_property(_cstringkernel.PositionalKmer_mismatches_get, _cstringkernel.PositionalKmer_mismatches_set)
310 __swig_setmethods__["mismatchProfile"] = _cstringkernel.PositionalKmer_mismatchProfile_set
311 __swig_getmethods__["mismatchProfile"] = _cstringkernel.PositionalKmer_mismatchProfile_get
312 if _newclass:mismatchProfile = _swig_property(_cstringkernel.PositionalKmer_mismatchProfile_get, _cstringkernel.PositionalKmer_mismatchProfile_set)
313 __swig_setmethods__["shiftWeight"] = _cstringkernel.PositionalKmer_shiftWeight_set
314 __swig_getmethods__["shiftWeight"] = _cstringkernel.PositionalKmer_shiftWeight_get
315 if _newclass:shiftWeight = _swig_property(_cstringkernel.PositionalKmer_shiftWeight_get, _cstringkernel.PositionalKmer_shiftWeight_set)
316 - def setMismatchProfile(*args): return _cstringkernel.PositionalKmer_setMismatchProfile(*args)
317 - def duplicate(*args): return _cstringkernel.PositionalKmer_duplicate(*args)
318 - def castToBase(*args): return _cstringkernel.PositionalKmer_castToBase(*args)
319 - def eval(*args): return _cstringkernel.PositionalKmer_eval(*args)
320 - def shiftSize(*args): return _cstringkernel.PositionalKmer_shiftSize(*args)
321 PositionalKmer_swigregister = _cstringkernel.PositionalKmer_swigregister
322 PositionalKmer_swigregister(PositionalKmer)
323