DataStructs.SparseIntVect

Package DataStructs :: Module SparseIntVect |
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# Source Code for Module DataStructs.SparseIntVect

      1  # $Id: SparseIntVect.py 746 2008-07-07 13:21:24Z 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 -  def GetTotalVal(self,useAbs=False):
     63      return self.Sum(useAbs=useAbs)
     64
     65
     66 -  def __eq__(self,other):
     67      """
     68      >>> c1=pySparseIntVect(10)
     69      >>> c1[0] = 3
     70      >>> c1[2] = 2
     71      >>> c1[4] = 5
     72      >>> c2=pySparseIntVect(10)
     73      >>> c2[0] = 3
     74      >>> c2[2] = 2
     75      >>> c1 == c2
     76      False
     77      >>> c1 == c1
     78      True
     79      """
     80      if not isinstance(other,pySparseIntVect):
     81        raise TypeError
     82      if self.size != other.size:
     83        return 0
     84      return self.container==other.container
     85
     86
     87 -  def __iand__(self,other):
     88      """
     89      >>> c1=pySparseIntVect(10)
     90      >>> c1[0] = 3
     91      >>> c1[2] = 2
     92      >>> c1[4] = 5
     93      >>> c2=pySparseIntVect(10)
     94      >>> c2[0] = 2
     95      >>> c2[2] = -2
     96      >>> c2[5] = 6
     97      >>> c1 &= c2
     98      >>> [x for x in c1]
     99      [(0, 2), (2, -2)]
    100
    101      """
    102      if not isinstance(other,pySparseIntVect):
    103        raise TypeError
    104      if self.size != other.size:
    105        raise ValueError
    106
    107      newC = {}
    108      for idx,v in self.container.iteritems():
    109        ov = other.container.get(idx,0)
    110        if ov:
    111          if v<ov:
    112            newC[idx]=v
    113          else:
    114            newC[idx]=ov
    115      self.container=newC
    116      return self
    117 -  def __ior__(self,other):
    118      """
    119      >>> c1=pySparseIntVect(10)
    120      >>> c1[0] = 3
    121      >>> c1[2] = 2
    122      >>> c1[4] = 5
    123      >>> c2=pySparseIntVect(10)
    124      >>> c2[0] = 2
    125      >>> c2[2] = -2
    126      >>> c2[5] = 6
    127      >>> c1 |= c2
    128      >>> [x for x in c1]
    129      [(0, 3), (2, 2), (4, 5), (5, 6)]
    130
    131      """
    132      if not isinstance(other,pySparseIntVect):
    133        raise TypeError
    134      if self.size != other.size:
    135        raise ValueError
    136
    137      newC = {}
    138      for idx,v in self.container.iteritems():
    139        ov = other.container.get(idx,0)
    140        if v<ov:
    141          newC[idx]=ov
    142        else:
    143          newC[idx]=v
    144      for k,v in other.container.iteritems():
    145        if not newC.has_key(k):
    146          newC[k]=v
    147      self.container=newC
    148      return self
    149
    150 -  def __iadd__(self,other):
    151      """
    152      >>> c1=pySparseIntVect(10)
    153      >>> c1[0] = 3
    154      >>> c1[2] = 2
    155      >>> c1[4] = 5
    156      >>> c2=pySparseIntVect(10)
    157      >>> c2[0] = 2
    158      >>> c2[2] = -2
    159      >>> c2[5] = 6
    160      >>> c1 += c2
    161      >>> [x for x in c1]
    162      [(0, 5), (4, 5), (5, 6)]
    163
    164      """
    165      if not isinstance(other,pySparseIntVect):
    166        raise TypeError
    167      if self.size != other.size:
    168        raise ValueError
    169      seen={}
    170      for idx in self.container.keys():
    171        seen[idx]=1
    172        v = self.container[idx]+other[idx]
    173        if v:
    174          self.container[idx]=v
    175        else:
    176          del self.container[idx]
    177      for idx,v in other:
    178        if not seen.has_key(idx):
    179          self.container[idx]=v
    180      return self
    181
    182 -  def __isub__(self,other):
    183      """
    184      >>> c1=pySparseIntVect(10)
    185      >>> c1[0] = 3
    186      >>> c1[2] = 2
    187      >>> c1[4] = 5
    188      >>> c2=pySparseIntVect(10)
    189      >>> c2[0] = 2
    190      >>> c2[2] = 2
    191      >>> c2[5] = 6
    192      >>> c1 -= c2
    193      >>> [x for x in c1]
    194      [(0, 1), (4, 5), (5, -6)]
    195
    196      """
    197      if not isinstance(other,pySparseIntVect):
    198        raise TypeError
    199      if self.size != other.size:
    200        raise ValueError
    201      seen={}
    202      for idx in self.container.keys():
    203        seen[idx]=1
    204        v = self.container[idx]-other[idx]
    205        if v:
    206          self.container[idx]=v
    207        else:
    208          del self.container[idx]
    209      for idx,v in other:
    210        if not seen.has_key(idx):
    211          self.container[idx]=-v
    212      return self
    213
    214 -  def __imul__(self,other):
    215      """
    216      >>> c1=pySparseIntVect(10)
    217      >>> c1[0] = 3
    218      >>> c1[4] = 5
    219      >>> c2=pySparseIntVect(10)
    220      >>> c2[0] = 2
    221      >>> c2[5] = 6
    222      >>> c1 *= c2
    223      >>> [x for x in c1]
    224      [(0, 6)]
    225
    226      """
    227      if not isinstance(other,pySparseIntVect):
    228        raise TypeError
    229      if self.size != other.size:
    230        raise ValueError
    231      for idx in self.container.keys():
    232        v = self.container[idx]*other[idx]
    233        if v:
    234          self.container[idx]=v
    235        else:
    236          del self.container[idx]
    237      return self
    238
    239 -  def __add__(self,other):
    240      """
    241      >>> c1=pySparseIntVect(10)
    242      >>> c1[0] = 3
    243      >>> c1[4] = 5
    244      >>> c2=pySparseIntVect(10)
    245      >>> c2[0] = 2
    246      >>> c2[5] = 6
    247      >>> c3 = c2+c1
    248      >>> [x for x in c3]
    249      [(0, 5), (4, 5), (5, 6)]
    250
    251      """
    252      res = pySparseIntVect(self.size)
    253      res.container = copy.deepcopy(self.container)
    254      res += other
    255      return res
    256 -  def __sub__(self,other):
    257      """
    258      >>> c1=pySparseIntVect(10)
    259      >>> c1[0] = 3
    260      >>> c1[2] = 2
    261      >>> c1[4] = 5
    262      >>> c2=pySparseIntVect(10)
    263      >>> c2[0] = 2
    264      >>> c2[2] = 2
    265      >>> c2[5] = 6
    266      >>> c3 = c1-c2
    267      >>> [x for x in c3]
    268      [(0, 1), (4, 5), (5, -6)]
    269      >>> [x for x in c1]
    270      [(0, 3), (2, 2), (4, 5)]
    271
    272      """
    273      res = pySparseIntVect(self.size)
    274      res.container = copy.deepcopy(self.container)
    275      res -= other
    276      return res
    277 -  def __mul__(self,other):
    278      """
    279      >>> c1=pySparseIntVect(10)
    280      >>> c1[0] = 3
    281      >>> c1[4] = 5
    282      >>> c2=pySparseIntVect(10)
    283      >>> c2[0] = 2
    284      >>> c2[5] = 6
    285      >>> c3 = c1*c2
    286      >>> [x for x in c3]
    287      [(0, 6)]
    288      >>> [x for x in c1]
    289      [(0, 3), (4, 5)]
    290
    291      """
    292      res = pySparseIntVect(self.size)
    293      res.container = copy.deepcopy(self.container)
    294      res *= other
    295      return res
    296 -  def __and__(self,other):
    297      """
    298      >>> c1=pySparseIntVect(10)
    299      >>> c1[0] = 3
    300      >>> c1[2] = 2
    301      >>> c1[4] = 5
    302      >>> c2=pySparseIntVect(10)
    303      >>> c2[0] = 2
    304      >>> c2[2] = -2
    305      >>> c2[5] = 6
    306      >>> c3 = c1 & c2
    307      >>> [x for x in c3]
    308      [(0, 2), (2, -2)]
    309      >>> [x for x in c1]
    310      [(0, 3), (2, 2), (4, 5)]
    311
    312      """
    313      res = pySparseIntVect(self.size)
    314      res.container = copy.deepcopy(self.container)
    315      res &= other
    316      return res
    317 -  def __or__(self,other):
    318      """
    319      >>> c1=pySparseIntVect(10)
    320      >>> c1[0] = 3
    321      >>> c1[2] = 2
    322      >>> c1[4] = 5
    323      >>> c2=pySparseIntVect(10)
    324      >>> c2[0] = 2
    325      >>> c2[2] = -2
    326      >>> c2[5] = 6
    327      >>> c3 = c1 | c2
    328      >>> [x for x in c3]
    329      [(0, 3), (2, 2), (4, 5), (5, 6)]
    330      >>> [x for x in c1]
    331      [(0, 3), (2, 2), (4, 5)]
    332
    333      """
    334      res = pySparseIntVect(self.size)
    335      res.container = copy.deepcopy(self.container)
    336      res |= other
    337      return res
    338
    339 -  def __len__(self):
    340      return self.size
    341 -  def __getitem__(self,which):
    342      """
    343      >>> c1=pySparseIntVect(10)
    344      >>> c1[0] = 3
    345      >>> c1[4] = 5
    346      >>> c1[0]
    347      3
    348      >>> c1[1]
    349      0
    350
    351      """
    352      if abs(which)>=self.size:
    353        raise IndexError,which
    354      if which<0:
    355        which = self.size-which
    356      return self.container.get(which,0)
    357 -  def __setitem__(self,which,val):
    358      if abs(which)>=self.size:
    359        raise IndexError,which
    360      val = int(val)
    361      if which<0:
    362        which = self.size-which
    363      self.container[which]=val
    364 -  def __iter__(self):
    365      """
    366      >>> c=pySparseIntVect(10)
    367      >>> c[0] = 3
    368      >>> c[4] = 5
    369      >>> c[7] = -1
    370      >>> for idx,v in c:
    371      ...  print idx,v
    372      0 3
    373      4 5
    374      7 -1
    375
    376      """
    377      return self.container.iteritems()
    378
    379
    380  import DataStructs
    381  DiceSimilarity=DataStructs.DiceSimilarity
    382 -def pyDiceSimilarity(v1,v2,bounds=None,useAbs=False):
    383    """ Implements the DICE similarity metric.
    384
    385    >>> v1 = DataStructs.IntSparseIntVect(10)
    386    >>> v2 = DataStructs.IntSparseIntVect(10)
    387    >>> v1.UpdateFromSequence((1,2,3))
    388    >>> v2.UpdateFromSequence((1,2,3))
    389    >>> DiceSimilarity(v1,v2)
    390    1.0
    391
    392    >>> v2 = DataStructs.IntSparseIntVect(10)
    393    >>> v2.UpdateFromSequence((5,6))
    394    >>> DiceSimilarity(v1,v2)
    395    0.0
    396
    397    >>> v1 = DataStructs.IntSparseIntVect(10)
    398    >>> v2 = DataStructs.IntSparseIntVect(10)
    399    >>> v1.UpdateFromSequence((1,2,3,4))
    400    >>> v2.UpdateFromSequence((1,3,5,7))
    401    >>> DiceSimilarity(v1,v2)
    402    0.5
    403
    404    >>> v1 = DataStructs.IntSparseIntVect(10)
    405    >>> v2 = DataStructs.IntSparseIntVect(10)
    406    >>> v1.UpdateFromSequence((1,2,3,4,5,6))
    407    >>> v2.UpdateFromSequence((1,3))
    408    >>> DiceSimilarity(v1,v2)
    409    0.5
    410
    411    """
    412    denom = 1.0*(v1.GetTotalVal(useAbs=useAbs)+v2.GetTotalVal(useAbs=useAbs))
    413    if not denom:
    414      res = 0.0
    415    else:
    416      if bounds and (min(len(v1),len(v2))/denom) < bounds:
    417        numer = 0.0
    418      else:
    419        numer=0.0
    420        v3=v1&v2
    421        numer=v3.GetTotalVal(useAbs=useAbs)
    422      res = 2.*numer/denom
    423
    424    return res
    425
    426 -def DotProduct(bv1,bv2):
    427    res = 0.0
    428    for k,v in bv1.GetNonzeroElements().iteritems():
    429      res += v*bv2[k]
    430    return res
    431
    432  #------------------------------------
    433  #
    434  #  doctest boilerplate
    435  #
    436 -def _test():
    437    import doctest,sys
    438    return doctest.testmod(sys.modules["__main__"])
    439
    440  if __name__ == '__main__':
    441    import sys
    442    failed,tried = _test()
    443    sys.exit(failed)
    444