IMP  2.0.0
The Integrative Modeling Platform
kmeans/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 2.0.8
3 #
4 # Do not make changes to this file unless you know what you are doing--modify
5 # the SWIG interface file instead.
6 
7 
8 
9 from sys import version_info
10 if version_info >= (2,6,0):
11  def swig_import_helper():
12  from os.path import dirname
13  import imp
14  fp = None
15  try:
16  fp, pathname, description = imp.find_module('_IMP_kmeans', [dirname(__file__)])
17  except ImportError:
18  import _IMP_kmeans
19  return _IMP_kmeans
20  if fp is not None:
21  try:
22  _mod = imp.load_module('_IMP_kmeans', fp, pathname, description)
23  finally:
24  fp.close()
25  return _mod
26  _IMP_kmeans = swig_import_helper()
27  del swig_import_helper
28 else:
29  import _IMP_kmeans
30 del version_info
31 try:
32  _swig_property = property
33 except NameError:
34  pass # Python < 2.2 doesn't have 'property'.
35 def _swig_setattr_nondynamic(self,class_type,name,value,static=1):
36  if (name == "thisown"): return self.this.own(value)
37  if (name == "this"):
38  if type(value).__name__ == 'SwigPyObject':
39  self.__dict__[name] = value
40  return
41  method = class_type.__swig_setmethods__.get(name,None)
42  if method: return method(self,value)
43  if (not static):
44  self.__dict__[name] = value
45  else:
46  raise AttributeError("You cannot add attributes to %s" % self)
47 
48 def _swig_setattr(self,class_type,name,value):
49  return _swig_setattr_nondynamic(self,class_type,name,value,0)
50 
51 def _swig_getattr(self,class_type,name):
52  if (name == "thisown"): return self.this.own()
53  method = class_type.__swig_getmethods__.get(name,None)
54  if method: return method(self)
55  raise AttributeError(name)
56 
57 def _swig_repr(self):
58  try: strthis = "proxy of " + self.this.__repr__()
59  except: strthis = ""
60  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
61 
62 try:
63  _object = object
64  _newclass = 1
65 except AttributeError:
66  class _object : pass
67  _newclass = 0
68 
69 
70 try:
71  import weakref
72  weakref_proxy = weakref.proxy
73 except:
74  weakref_proxy = lambda x: x
75 
76 
77 class IMP_KMEANS_SwigPyIterator(_object):
78  """Proxy of C++ swig::IMP_KMEANS_SwigPyIterator class"""
79  __swig_setmethods__ = {}
80  __setattr__ = lambda self, name, value: _swig_setattr(self, IMP_KMEANS_SwigPyIterator, name, value)
81  __swig_getmethods__ = {}
82  __getattr__ = lambda self, name: _swig_getattr(self, IMP_KMEANS_SwigPyIterator, name)
83  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
84  __repr__ = _swig_repr
85  __swig_destroy__ = _IMP_kmeans.delete_IMP_KMEANS_SwigPyIterator
86  __del__ = lambda self : None;
87  def value(self):
88  """value(IMP_KMEANS_SwigPyIterator self) -> PyObject *"""
89  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_value(self)
90 
91  def incr(self, n=1):
92  """
93  incr(IMP_KMEANS_SwigPyIterator self, size_t n=1) -> IMP_KMEANS_SwigPyIterator
94  incr(IMP_KMEANS_SwigPyIterator self) -> IMP_KMEANS_SwigPyIterator
95  """
96  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_incr(self, n)
97 
98  def decr(self, n=1):
99  """
100  decr(IMP_KMEANS_SwigPyIterator self, size_t n=1) -> IMP_KMEANS_SwigPyIterator
101  decr(IMP_KMEANS_SwigPyIterator self) -> IMP_KMEANS_SwigPyIterator
102  """
103  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_decr(self, n)
104 
105  def distance(self, *args):
106  """distance(IMP_KMEANS_SwigPyIterator self, IMP_KMEANS_SwigPyIterator x) -> ptrdiff_t"""
107  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_distance(self, *args)
108 
109  def equal(self, *args):
110  """equal(IMP_KMEANS_SwigPyIterator self, IMP_KMEANS_SwigPyIterator x) -> bool"""
111  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_equal(self, *args)
112 
113  def copy(self):
114  """copy(IMP_KMEANS_SwigPyIterator self) -> IMP_KMEANS_SwigPyIterator"""
115  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_copy(self)
116 
117  def next(self):
118  """next(IMP_KMEANS_SwigPyIterator self) -> PyObject *"""
119  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_next(self)
120 
121  def __next__(self):
122  """__next__(IMP_KMEANS_SwigPyIterator self) -> PyObject *"""
123  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator___next__(self)
124 
125  def previous(self):
126  """previous(IMP_KMEANS_SwigPyIterator self) -> PyObject *"""
127  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_previous(self)
128 
129  def advance(self, *args):
130  """advance(IMP_KMEANS_SwigPyIterator self, ptrdiff_t n) -> IMP_KMEANS_SwigPyIterator"""
131  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_advance(self, *args)
132 
133  def __eq__(self, *args):
134  """__eq__(IMP_KMEANS_SwigPyIterator self, IMP_KMEANS_SwigPyIterator x) -> bool"""
135  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator___eq__(self, *args)
136 
137  def __ne__(self, *args):
138  """__ne__(IMP_KMEANS_SwigPyIterator self, IMP_KMEANS_SwigPyIterator x) -> bool"""
139  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator___ne__(self, *args)
140 
141  def __iadd__(self, *args):
142  """__iadd__(IMP_KMEANS_SwigPyIterator self, ptrdiff_t n) -> IMP_KMEANS_SwigPyIterator"""
143  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator___iadd__(self, *args)
144 
145  def __isub__(self, *args):
146  """__isub__(IMP_KMEANS_SwigPyIterator self, ptrdiff_t n) -> IMP_KMEANS_SwigPyIterator"""
147  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator___isub__(self, *args)
148 
149  def __add__(self, *args):
150  """__add__(IMP_KMEANS_SwigPyIterator self, ptrdiff_t n) -> IMP_KMEANS_SwigPyIterator"""
151  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator___add__(self, *args)
152 
153  def __sub__(self, *args):
154  """
155  __sub__(IMP_KMEANS_SwigPyIterator self, ptrdiff_t n) -> IMP_KMEANS_SwigPyIterator
156  __sub__(IMP_KMEANS_SwigPyIterator self, IMP_KMEANS_SwigPyIterator x) -> ptrdiff_t
157  """
158  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator___sub__(self, *args)
159 
160  def __iter__(self): return self
161 IMP_KMEANS_SwigPyIterator_swigregister = _IMP_kmeans.IMP_KMEANS_SwigPyIterator_swigregister
162 IMP_KMEANS_SwigPyIterator_swigregister(IMP_KMEANS_SwigPyIterator)
163 
164 _value_types=[]
165 _object_types=[]
166 _raii_types=[]
167 _plural_types=[]
168 
169 IMP_HAS_DEPRECATED = _IMP_kmeans.IMP_HAS_DEPRECATED
170 IMP_DEBUG = _IMP_kmeans.IMP_DEBUG
171 IMP_RELEASE = _IMP_kmeans.IMP_RELEASE
172 IMP_SILENT = _IMP_kmeans.IMP_SILENT
173 IMP_PROGRESS = _IMP_kmeans.IMP_PROGRESS
174 IMP_TERSE = _IMP_kmeans.IMP_TERSE
175 IMP_VERBOSE = _IMP_kmeans.IMP_VERBOSE
176 IMP_NONE = _IMP_kmeans.IMP_NONE
177 IMP_USAGE = _IMP_kmeans.IMP_USAGE
178 IMP_INTERNAL = _IMP_kmeans.IMP_INTERNAL
179 IMP_COMPILER_HAS_AUTO = _IMP_kmeans.IMP_COMPILER_HAS_AUTO
180 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_kmeans.IMP_COMPILER_HAS_DEBUG_VECTOR
181 IMP_COMPILER_HAS_NULLPTR = _IMP_kmeans.IMP_COMPILER_HAS_NULLPTR
182 IMP_BASE_HAS_BOOST_RANDOM = _IMP_kmeans.IMP_BASE_HAS_BOOST_RANDOM
183 IMP_BASE_HAS_GPERFTOOLS = _IMP_kmeans.IMP_BASE_HAS_GPERFTOOLS
184 IMP_BASE_HAS_LOG4CXX = _IMP_kmeans.IMP_BASE_HAS_LOG4CXX
185 IMP_BASE_HAS_TCMALLOC_HEAPCHECKER = _IMP_kmeans.IMP_BASE_HAS_TCMALLOC_HEAPCHECKER
186 IMP_BASE_HAS_TCMALLOC_HEAPPROFILER = _IMP_kmeans.IMP_BASE_HAS_TCMALLOC_HEAPPROFILER
187 import sys
188 class _DirectorObjects(object):
189  """@internal Simple class to keep references to director objects
190  to prevent premature deletion."""
191  def __init__(self):
192  self._objects = []
193  def register(self, obj):
194  """Take a reference to a director object; will only work for
195  refcounted C++ classes"""
196  if hasattr(obj, 'get_ref_count'):
197  self._objects.append(obj)
198  def cleanup(self):
199  """Only drop our reference and allow cleanup by Python if no other
200  Python references exist (we hold 3 references: one in self._objects,
201  one in x, and one in the argument list for getrefcount) *and* no
202  other C++ references exist (the Python object always holds one)"""
203  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
204  or x.get_ref_count() > 1]
205 
206 
207  self._objects = objs
208  def get_object_count(self):
209  """Get number of director objects (useful for testing only)"""
210  return len(self._objects)
211 _director_objects = _DirectorObjects()
212 
213 DEFAULT_CHECK = _IMP_kmeans.DEFAULT_CHECK
214 NONE = _IMP_kmeans.NONE
215 USAGE = _IMP_kmeans.USAGE
216 USAGE_AND_INTERNAL = _IMP_kmeans.USAGE_AND_INTERNAL
217 
218 def set_check_level(*args):
219  """set_check_level(IMP::base::CheckLevel tf)"""
220  return _IMP_kmeans.set_check_level(*args)
221 
222 def get_check_level():
223  """get_check_level() -> IMP::base::CheckLevel"""
224  return _IMP_kmeans.get_check_level()
225 class _ostream(_object):
226  """Proxy of C++ std::ostream class"""
227  __swig_setmethods__ = {}
228  __setattr__ = lambda self, name, value: _swig_setattr(self, _ostream, name, value)
229  __swig_getmethods__ = {}
230  __getattr__ = lambda self, name: _swig_getattr(self, _ostream, name)
231  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined")
232  __repr__ = _swig_repr
233  def write(self, *args):
234  """write(_ostream self, char const * osa_buf)"""
235  return _IMP_kmeans._ostream_write(self, *args)
236 
237 _ostream_swigregister = _IMP_kmeans._ostream_swigregister
238 _ostream_swigregister(_ostream)
239 
240 IMP_COMPILER_HAS_OVERRIDE = _IMP_kmeans.IMP_COMPILER_HAS_OVERRIDE
241 IMP_COMPILER_HAS_FINAL = _IMP_kmeans.IMP_COMPILER_HAS_FINAL
242 import IMP.base
243 IMP_KMEANS_HAS_BOOST_FILESYSTEM = _IMP_kmeans.IMP_KMEANS_HAS_BOOST_FILESYSTEM
244 IMP_KMEANS_HAS_BOOST_PROGRAMOPTIONS = _IMP_kmeans.IMP_KMEANS_HAS_BOOST_PROGRAMOPTIONS
245 IMP_KMEANS_HAS_BOOST_RANDOM = _IMP_kmeans.IMP_KMEANS_HAS_BOOST_RANDOM
246 IMP_KMEANS_HAS_BOOST_SYSTEM = _IMP_kmeans.IMP_KMEANS_HAS_BOOST_SYSTEM
247 _object_types.append("KMeans")
248 
249 
250 def _object_cast_to_KMeans(*args):
251  """_object_cast_to_KMeans(Object o) -> KMeans"""
252  return _IMP_kmeans._object_cast_to_KMeans(*args)
253 KM_LLOYDS = _IMP_kmeans.KM_LLOYDS
254 KM_LOCAL_SWAP = _IMP_kmeans.KM_LOCAL_SWAP
255 KM_LOCAL_EZ_HYBRID = _IMP_kmeans.KM_LOCAL_EZ_HYBRID
256 KM_HYBRID = _IMP_kmeans.KM_HYBRID
257 class KMeans(IMP.base.Object):
258  """Proxy of C++ IMP::kmeans::KMeans class"""
259  __swig_setmethods__ = {}
260  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
261  __setattr__ = lambda self, name, value: _swig_setattr(self, KMeans, name, value)
262  __swig_getmethods__ = {}
263  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
264  __getattr__ = lambda self, name: _swig_getattr(self, KMeans, name)
265  def __init__(self, *args):
266  """
267  __init__(IMP::kmeans::KMeans self, std::string const & fname_data, int dim, unsigned int max_nPts) -> KMeans
268  __init__(IMP::kmeans::KMeans self) -> KMeans
269  """
270  this = _IMP_kmeans.new_KMeans(*args)
271  try: self.this.append(this)
272  except: self.this = this
273  def get_version_info(self):
274  """get_version_info(KMeans self) -> VersionInfo"""
275  return _IMP_kmeans.KMeans_get_version_info(self)
276 
277  __swig_destroy__ = _IMP_kmeans.delete_KMeans
278  __del__ = lambda self : None;
279  def execute(self, *args):
280  """
281  execute(KMeans self, unsigned int k, IMP::kmeans::KM_ALG_TYPE alg_type=KM_LLOYDS, int stages=100)
282  execute(KMeans self, unsigned int k, IMP::kmeans::KM_ALG_TYPE alg_type=KM_LLOYDS)
283  execute(KMeans self, unsigned int k)
284  """
285  return _IMP_kmeans.KMeans_execute(self, *args)
286 
287  def add_data_pt(self, *args):
288  """add_data_pt(KMeans self, IMP::Floats const & p)"""
289  return _IMP_kmeans.KMeans_add_data_pt(self, *args)
290 
291  def clear_data(self):
292  """clear_data(KMeans self)"""
293  return _IMP_kmeans.KMeans_clear_data(self)
294 
295  def get_data_point(self, *args):
296  """get_data_point(KMeans self, unsigned int i) -> IMP::Floats const &"""
297  return _IMP_kmeans.KMeans_get_data_point(self, *args)
298 
299  def get_number_of_data_points(self):
300  """get_number_of_data_points(KMeans self) -> unsigned int"""
301  return _IMP_kmeans.KMeans_get_number_of_data_points(self)
302 
303  def print_centers(self):
304  """print_centers(KMeans self)"""
305  return _IMP_kmeans.KMeans_print_centers(self)
306 
307  def get_center(self, *args):
308  """get_center(KMeans self, unsigned int i) -> IMP::Floats"""
309  return _IMP_kmeans.KMeans_get_center(self, *args)
310 
311  def get_assignments(self):
312  """get_assignments(KMeans self) -> IMP::Ints"""
313  return _IMP_kmeans.KMeans_get_assignments(self)
314 
315  def get_squared_distance_to_centers(self):
316  """get_squared_distance_to_centers(KMeans self) -> IMP::Floats"""
317  return _IMP_kmeans.KMeans_get_squared_distance_to_centers(self)
318 
319  def get_number_of_centers(self):
320  """get_number_of_centers(KMeans self) -> unsigned int"""
321  return _IMP_kmeans.KMeans_get_number_of_centers(self)
322 
323  def __str__(self):
324  """__str__(KMeans self) -> std::string"""
325  return _IMP_kmeans.KMeans___str__(self)
326 
327  def __repr__(self):
328  """__repr__(KMeans self) -> std::string"""
329  return _IMP_kmeans.KMeans___repr__(self)
330 
331  def get_from(o):
332  return _object_cast_to_KMeans(o)
333  get_from = staticmethod(get_from)
334 
335 KMeans_swigregister = _IMP_kmeans.KMeans_swigregister
336 KMeans_swigregister(KMeans)
337 
338 
339 def get_module_version():
340  """get_module_version() -> std::string const"""
341  return _IMP_kmeans.get_module_version()
342 
343 def get_example_path(*args):
344  """get_example_path(std::string fname) -> std::string"""
345  return _IMP_kmeans.get_example_path(*args)
346 
347 def get_data_path(*args):
348  """get_data_path(std::string fname) -> std::string"""
349  return _IMP_kmeans.get_data_path(*args)
350 import _version_check
351 _version_check.check_version(get_module_version())
352 
353 # This file is compatible with both classic and new-style classes.
354 
355