Source Code for Module DataStructs.SparseIntVect

  1  # $Id: SparseIntVect.py 363 2007-10-04 05:37:14Z glandrum $ 
  2  # 
  3  #  Copyright (C) 2007 Greg Landrum 
  4  #   All Rights Reserved 
  5  # 
  6  import copy 
  7   
  8 -class pySparseIntVect(object): 
  9    """ this class is pretty much obsolete (it's in C++ now) """ 
 10    size=0 
 11    container={} 
 12 -  def __init__(self,size): 
 13      self.size=size 
 14      self.container={} 
 15   
 16 -  def UpdateFromSequence(self,seq): 
 17      """ 
 18      >>> c1=pySparseIntVect(10) 
 19      >>> c1.UpdateFromSequence((0,1,1,5)) 
 20      >>> [x for x in c1] 
 21      [(0, 1), (1, 2), (5, 1)] 
 22      >>> c1.UpdateFromSequence((0,3)) 
 23      >>> [x for x in c1] 
 24      [(0, 2), (1, 2), (3, 1), (5, 1)] 
 25   
 26      """ 
 27      for v in seq: 
 28        self[v] += 1 
 29 -  def InitFromSequence(self,seq): 
 30      """ 
 31      >>> c1=pySparseIntVect(10) 
 32      >>> c1.InitFromSequence((0,1,1,5)) 
 33      >>> [x for x in c1] 
 34      [(0, 1), (1, 2), (5, 1)] 
 35   
 36      """ 
 37      self.container={} 
 38      self.UpdateFromSequence(seq) 
 39         
 40 -  def Sum(self,useAbs=False): 
 41      """ 
 42      >>> c1=pySparseIntVect(10) 
 43      >>> c1[0] = 3 
 44      >>> c1[2] = 2 
 45      >>> c1[4] = 5 
 46      >>> c1.Sum() 
 47      10 
 48   
 49      >>> c1[2] = -2 
 50      >>> c1.Sum() 
 51      6 
 52      >>> c1.Sum(useAbs=True) 
 53      10 
 54      """ 
 55      res=0 
 56      for v in self.container.values(): 
 57        if not useAbs: 
 58          res+=v 
 59        else: 
 60          res+=abs(v) 
 61      return res 
 62     
 63   
 64 -  def __eq__(self,other): 
 65      """ 
 66      >>> c1=pySparseIntVect(10) 
 67      >>> c1[0] = 3 
 68      >>> c1[2] = 2 
 69      >>> c1[4] = 5 
 70      >>> c2=pySparseIntVect(10) 
 71      >>> c2[0] = 3 
 72      >>> c2[2] = 2 
 73      >>> c1 == c2 
 74      False 
 75      >>> c1 == c1 
 76      True 
 77      """ 
 78      if not isinstance(other,pySparseIntVect): 
 79        raise TypeError 
 80      if self.size != other.size: 
 81        return 0 
 82      return self.container==other.container 
 83       
 84   
 85 -  def __iand__(self,other): 
 86      """ 
 87      >>> c1=pySparseIntVect(10) 
 88      >>> c1[0] = 3 
 89      >>> c1[2] = 2 
 90      >>> c1[4] = 5 
 91      >>> c2=pySparseIntVect(10) 
 92      >>> c2[0] = 2 
 93      >>> c2[2] = -2 
 94      >>> c2[5] = 6 
 95      >>> c1 &= c2 
 96      >>> [x for x in c1] 
 97      [(0, 2), (2, -2)] 
 98   
 99      """ 
100      if not isinstance(other,pySparseIntVect): 
101        raise TypeError 
102      if self.size != other.size: 
103        raise ValueError 
104   
105      newC = {} 
106      for idx,v in self.container.iteritems(): 
107        ov = other.container.get(idx,0) 
108        if ov: 
109          if v<ov: 
110            newC[idx]=v 
111          else: 
112            newC[idx]=ov 
113      self.container=newC 
114      return self 
115 -  def __ior__(self,other): 
116      """ 
117      >>> c1=pySparseIntVect(10) 
118      >>> c1[0] = 3 
119      >>> c1[2] = 2 
120      >>> c1[4] = 5 
121      >>> c2=pySparseIntVect(10) 
122      >>> c2[0] = 2 
123      >>> c2[2] = -2 
124      >>> c2[5] = 6 
125      >>> c1 |= c2 
126      >>> [x for x in c1] 
127      [(0, 3), (2, 2), (4, 5), (5, 6)] 
128   
129      """ 
130      if not isinstance(other,pySparseIntVect): 
131        raise TypeError 
132      if self.size != other.size: 
133        raise ValueError 
134   
135      newC = {} 
136      for idx,v in self.container.iteritems(): 
137        ov = other.container.get(idx,0) 
138        if v<ov: 
139          newC[idx]=ov 
140        else: 
141          newC[idx]=v 
142      for k,v in other.container.iteritems(): 
143        if not newC.has_key(k): 
144          newC[k]=v 
145      self.container=newC 
146      return self 
147     
148 -  def __iadd__(self,other): 
149      """ 
150      >>> c1=pySparseIntVect(10) 
151      >>> c1[0] = 3 
152      >>> c1[2] = 2 
153      >>> c1[4] = 5 
154      >>> c2=pySparseIntVect(10) 
155      >>> c2[0] = 2 
156      >>> c2[2] = -2 
157      >>> c2[5] = 6 
158      >>> c1 += c2 
159      >>> [x for x in c1] 
160      [(0, 5), (4, 5), (5, 6)] 
161   
162      """ 
163      if not isinstance(other,pySparseIntVect): 
164        raise TypeError 
165      if self.size != other.size: 
166        raise ValueError 
167      seen={} 
168      for idx in self.container.keys(): 
169        seen[idx]=1 
170        v = self.container[idx]+other[idx] 
171        if v: 
172          self.container[idx]=v 
173        else: 
174          del self.container[idx] 
175      for idx,v in other: 
176        if not seen.has_key(idx): 
177          self.container[idx]=v 
178      return self 
179     
180 -  def __isub__(self,other): 
181      """ 
182      >>> c1=pySparseIntVect(10) 
183      >>> c1[0] = 3 
184      >>> c1[2] = 2 
185      >>> c1[4] = 5 
186      >>> c2=pySparseIntVect(10) 
187      >>> c2[0] = 2 
188      >>> c2[2] = 2 
189      >>> c2[5] = 6 
190      >>> c1 -= c2 
191      >>> [x for x in c1] 
192      [(0, 1), (4, 5), (5, -6)] 
193   
194      """ 
195      if not isinstance(other,pySparseIntVect): 
196        raise TypeError 
197      if self.size != other.size: 
198        raise ValueError 
199      seen={} 
200      for idx in self.container.keys(): 
201        seen[idx]=1 
202        v = self.container[idx]-other[idx] 
203        if v: 
204          self.container[idx]=v 
205        else: 
206          del self.container[idx] 
207      for idx,v in other: 
208        if not seen.has_key(idx): 
209          self.container[idx]=-v 
210      return self 
211   
212 -  def __imul__(self,other): 
213      """ 
214      >>> c1=pySparseIntVect(10) 
215      >>> c1[0] = 3 
216      >>> c1[4] = 5 
217      >>> c2=pySparseIntVect(10) 
218      >>> c2[0] = 2 
219      >>> c2[5] = 6 
220      >>> c1 *= c2 
221      >>> [x for x in c1] 
222      [(0, 6)] 
223   
224      """ 
225      if not isinstance(other,pySparseIntVect): 
226        raise TypeError 
227      if self.size != other.size: 
228        raise ValueError 
229      for idx in self.container.keys(): 
230        v = self.container[idx]*other[idx] 
231        if v: 
232          self.container[idx]=v 
233        else: 
234          del self.container[idx] 
235      return self 
236     
237 -  def __add__(self,other): 
238      """ 
239      >>> c1=pySparseIntVect(10) 
240      >>> c1[0] = 3 
241      >>> c1[4] = 5 
242      >>> c2=pySparseIntVect(10) 
243      >>> c2[0] = 2 
244      >>> c2[5] = 6 
245      >>> c3 = c2+c1 
246      >>> [x for x in c3] 
247      [(0, 5), (4, 5), (5, 6)] 
248   
249      """ 
250      res = pySparseIntVect(self.size) 
251      res.container = copy.deepcopy(self.container) 
252      res += other 
253      return res 
254 -  def __sub__(self,other): 
255      """ 
256      >>> c1=pySparseIntVect(10) 
257      >>> c1[0] = 3 
258      >>> c1[2] = 2 
259      >>> c1[4] = 5 
260      >>> c2=pySparseIntVect(10) 
261      >>> c2[0] = 2 
262      >>> c2[2] = 2 
263      >>> c2[5] = 6 
264      >>> c3 = c1-c2 
265      >>> [x for x in c3] 
266      [(0, 1), (4, 5), (5, -6)] 
267      >>> [x for x in c1] 
268      [(0, 3), (2, 2), (4, 5)] 
269   
270      """ 
271      res = pySparseIntVect(self.size) 
272      res.container = copy.deepcopy(self.container) 
273      res -= other 
274      return res 
275 -  def __mul__(self,other): 
276      """ 
277      >>> c1=pySparseIntVect(10) 
278      >>> c1[0] = 3 
279      >>> c1[4] = 5 
280      >>> c2=pySparseIntVect(10) 
281      >>> c2[0] = 2 
282      >>> c2[5] = 6 
283      >>> c3 = c1*c2 
284      >>> [x for x in c3] 
285      [(0, 6)] 
286      >>> [x for x in c1] 
287      [(0, 3), (4, 5)] 
288   
289      """ 
290      res = pySparseIntVect(self.size) 
291      res.container = copy.deepcopy(self.container) 
292      res *= other 
293      return res 
294 -  def __and__(self,other): 
295      """ 
296      >>> c1=pySparseIntVect(10) 
297      >>> c1[0] = 3 
298      >>> c1[2] = 2 
299      >>> c1[4] = 5 
300      >>> c2=pySparseIntVect(10) 
301      >>> c2[0] = 2 
302      >>> c2[2] = -2 
303      >>> c2[5] = 6 
304      >>> c3 = c1 & c2 
305      >>> [x for x in c3] 
306      [(0, 2), (2, -2)] 
307      >>> [x for x in c1] 
308      [(0, 3), (2, 2), (4, 5)] 
309   
310      """ 
311      res = pySparseIntVect(self.size) 
312      res.container = copy.deepcopy(self.container) 
313      res &= other 
314      return res 
315 -  def __or__(self,other): 
316      """ 
317      >>> c1=pySparseIntVect(10) 
318      >>> c1[0] = 3 
319      >>> c1[2] = 2 
320      >>> c1[4] = 5 
321      >>> c2=pySparseIntVect(10) 
322      >>> c2[0] = 2 
323      >>> c2[2] = -2 
324      >>> c2[5] = 6 
325      >>> c3 = c1 | c2 
326      >>> [x for x in c3] 
327      [(0, 3), (2, 2), (4, 5), (5, 6)] 
328      >>> [x for x in c1] 
329      [(0, 3), (2, 2), (4, 5)] 
330   
331      """ 
332      res = pySparseIntVect(self.size) 
333      res.container = copy.deepcopy(self.container) 
334      res |= other 
335      return res 
336     
337 -  def __len__(self): 
338      return self.size 
339 -  def __getitem__(self,which): 
340      """ 
341      >>> c1=pySparseIntVect(10) 
342      >>> c1[0] = 3 
343      >>> c1[4] = 5 
344      >>> c1[0] 
345      3 
346      >>> c1[1] 
347      0 
348       
349      """ 
350      if abs(which)>=self.size: 
351        raise IndexError,which 
352      if which<0: 
353        which = self.size-which 
354      return self.container.get(which,0) 
355 -  def __setitem__(self,which,val): 
356      if abs(which)>=self.size: 
357        raise IndexError,which 
358      val = int(val) 
359      if which<0: 
360        which = self.size-which 
361      self.container[which]=val 
362 -  def __iter__(self): 
363      """ 
364      >>> c=pySparseIntVect(10) 
365      >>> c[0] = 3 
366      >>> c[4] = 5 
367      >>> c[7] = -1 
368      >>> for idx,v in c: 
369      ...  print idx,v 
370      0 3 
371      4 5 
372      7 -1 
373   
374      """ 
375      return self.container.iteritems() 
376   
377       
378  import DataStructs 
379  DiceSimilarity=DataStructs.DiceSimilarity 
380 -def pyDiceSimilarity(v1,v2,bounds=None,useAbs=False): 
381    """ Implements the DICE similarity metric. 
382   
383    >>> v1 = DataStructs.IntSparseIntVect(10) 
384    >>> v2 = DataStructs.IntSparseIntVect(10) 
385    >>> v1.UpdateFromSequence((1,2,3)) 
386    >>> v2.UpdateFromSequence((1,2,3)) 
387    >>> DiceSimilarity(v1,v2) 
388    1.0 
389   
390    >>> v2 = DataStructs.IntSparseIntVect(10) 
391    >>> v2.UpdateFromSequence((5,6)) 
392    >>> DiceSimilarity(v1,v2) 
393    0.0 
394   
395    >>> v1 = DataStructs.IntSparseIntVect(10) 
396    >>> v2 = DataStructs.IntSparseIntVect(10) 
397    >>> v1.UpdateFromSequence((1,2,3,4)) 
398    >>> v2.UpdateFromSequence((1,3,5,7)) 
399    >>> DiceSimilarity(v1,v2) 
400    0.5 
401   
402    >>> v1 = DataStructs.IntSparseIntVect(10) 
403    >>> v2 = DataStructs.IntSparseIntVect(10) 
404    >>> v1.UpdateFromSequence((1,2,3,4,5,6)) 
405    >>> v2.UpdateFromSequence((1,3)) 
406    >>> DiceSimilarity(v1,v2) 
407    0.5 
408   
409    """ 
410    denom = 1.0*(v1.GetTotalVal(useAbs=useAbs)+v2.GetTotalVal(useAbs=useAbs)) 
411    if not denom: 
412      res = 0.0 
413    else: 
414      if bounds and (min(len(v1),len(v2))/denom) < bounds: 
415        numer = 0.0 
416      else: 
417        numer=0.0 
418        v3=v1&v2 
419        numer=v3.GetTotalVal(useAbs=useAbs) 
420      res = 2.*numer/denom 
421   
422    return res 
423   
424  #------------------------------------ 
425  # 
426  #  doctest boilerplate 
427  # 
428 -def _test(): 
429    import doctest,sys 
430    return doctest.testmod(sys.modules["__main__"]) 
431   
432  if __name__ == '__main__': 
433    import sys 
434    failed,tried = _test() 
435    sys.exit(failed) 
436