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SparseIntVect now in c++

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This commit is contained in:
Greg Landrum
2007-09-23 06:53:43 +00:00
parent 1fa8cd321b
commit de0657caaa
6 changed files with 70 additions and 74 deletions
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118
Python/DataStructs/SparseIntVect.py
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@@ -5,7 +5,8 @@
#
import copy
class SparseIntVect(object):
class pySparseIntVect(object):
""" this class is pretty much obsolete (it's in C++ now) """
size=0
container={}
def __init__(self,size):
@@ -14,7 +15,7 @@ class SparseIntVect(object):
def UpdateFromSequence(self,seq):
"""
>>> c1=SparseIntVect(10)
>>> c1=pySparseIntVect(10)
>>> c1.UpdateFromSequence((0,1,1,5))
>>> [x for x in c1]
[(0, 1), (1, 2), (5, 1)]
@@ -27,7 +28,7 @@ class SparseIntVect(object):
self[v] += 1
def InitFromSequence(self,seq):
"""
>>> c1=SparseIntVect(10)
>>> c1=pySparseIntVect(10)
>>> c1.InitFromSequence((0,1,1,5))
>>> [x for x in c1]
[(0, 1), (1, 2), (5, 1)]
@@ -38,7 +39,7 @@ class SparseIntVect(object):
def Sum(self,useAbs=False):
"""
>>> c1=SparseIntVect(10)
>>> c1=pySparseIntVect(10)
>>> c1[0] = 3
>>> c1[2] = 2
>>> c1[4] = 5
@@ -62,11 +63,11 @@ class SparseIntVect(object):
def __eq__(self,other):
"""
>>> c1=SparseIntVect(10)
>>> c1=pySparseIntVect(10)
>>> c1[0] = 3
>>> c1[2] = 2
>>> c1[4] = 5
>>> c2=SparseIntVect(10)
>>> c2=pySparseIntVect(10)
>>> c2[0] = 3
>>> c2[2] = 2
>>> c1 == c2
@@ -74,7 +75,7 @@ class SparseIntVect(object):
>>> c1 == c1
True
"""
if not isinstance(other,SparseIntVect):
if not isinstance(other,pySparseIntVect):
raise TypeError
if self.size != other.size:
return 0
@@ -83,11 +84,11 @@ class SparseIntVect(object):
def __iand__(self,other):
"""
>>> c1=SparseIntVect(10)
>>> c1=pySparseIntVect(10)
>>> c1[0] = 3
>>> c1[2] = 2
>>> c1[4] = 5
>>> c2=SparseIntVect(10)
>>> c2=pySparseIntVect(10)
>>> c2[0] = 2
>>> c2[2] = -2
>>> c2[5] = 6
@@ -96,7 +97,7 @@ class SparseIntVect(object):
[(0, 2), (2, -2)]
"""
if not isinstance(other,SparseIntVect):
if not isinstance(other,pySparseIntVect):
raise TypeError
if self.size != other.size:
raise ValueError
@@ -113,11 +114,11 @@ class SparseIntVect(object):
return self
def __ior__(self,other):
"""
>>> c1=SparseIntVect(10)
>>> c1=pySparseIntVect(10)
>>> c1[0] = 3
>>> c1[2] = 2
>>> c1[4] = 5
>>> c2=SparseIntVect(10)
>>> c2=pySparseIntVect(10)
>>> c2[0] = 2
>>> c2[2] = -2
>>> c2[5] = 6
@@ -126,7 +127,7 @@ class SparseIntVect(object):
[(0, 3), (2, 2), (4, 5), (5, 6)]
"""
if not isinstance(other,SparseIntVect):
if not isinstance(other,pySparseIntVect):
raise TypeError
if self.size != other.size:
raise ValueError
@@ -146,11 +147,11 @@ class SparseIntVect(object):
def __iadd__(self,other):
"""
>>> c1=SparseIntVect(10)
>>> c1=pySparseIntVect(10)
>>> c1[0] = 3
>>> c1[2] = 2
>>> c1[4] = 5
>>> c2=SparseIntVect(10)
>>> c2=pySparseIntVect(10)
>>> c2[0] = 2
>>> c2[2] = -2
>>> c2[5] = 6
@@ -159,7 +160,7 @@ class SparseIntVect(object):
[(0, 5), (4, 5), (5, 6)]
"""
if not isinstance(other,SparseIntVect):
if not isinstance(other,pySparseIntVect):
raise TypeError
if self.size != other.size:
raise ValueError
@@ -178,11 +179,11 @@ class SparseIntVect(object):
def __isub__(self,other):
"""
>>> c1=SparseIntVect(10)
>>> c1=pySparseIntVect(10)
>>> c1[0] = 3
>>> c1[2] = 2
>>> c1[4] = 5
>>> c2=SparseIntVect(10)
>>> c2=pySparseIntVect(10)
>>> c2[0] = 2
>>> c2[2] = 2
>>> c2[5] = 6
@@ -191,7 +192,7 @@ class SparseIntVect(object):
[(0, 1), (4, 5), (5, -6)]
"""
if not isinstance(other,SparseIntVect):
if not isinstance(other,pySparseIntVect):
raise TypeError
if self.size != other.size:
raise ValueError
@@ -210,10 +211,10 @@ class SparseIntVect(object):
def __imul__(self,other):
"""
>>> c1=SparseIntVect(10)
>>> c1=pySparseIntVect(10)
>>> c1[0] = 3
>>> c1[4] = 5
>>> c2=SparseIntVect(10)
>>> c2=pySparseIntVect(10)
>>> c2[0] = 2
>>> c2[5] = 6
>>> c1 *= c2
@@ -221,7 +222,7 @@ class SparseIntVect(object):
[(0, 6)]
"""
if not isinstance(other,SparseIntVect):
if not isinstance(other,pySparseIntVect):
raise TypeError
if self.size != other.size:
raise ValueError
@@ -235,10 +236,10 @@ class SparseIntVect(object):
def __add__(self,other):
"""
>>> c1=SparseIntVect(10)
>>> c1=pySparseIntVect(10)
>>> c1[0] = 3
>>> c1[4] = 5
>>> c2=SparseIntVect(10)
>>> c2=pySparseIntVect(10)
>>> c2[0] = 2
>>> c2[5] = 6
>>> c3 = c2+c1
@@ -246,17 +247,17 @@ class SparseIntVect(object):
[(0, 5), (4, 5), (5, 6)]
"""
res = SparseIntVect(self.size)
res = pySparseIntVect(self.size)
res.container = copy.deepcopy(self.container)
res += other
return res
def __sub__(self,other):
"""
>>> c1=SparseIntVect(10)
>>> c1=pySparseIntVect(10)
>>> c1[0] = 3
>>> c1[2] = 2
>>> c1[4] = 5
>>> c2=SparseIntVect(10)
>>> c2=pySparseIntVect(10)
>>> c2[0] = 2
>>> c2[2] = 2
>>> c2[5] = 6
@@ -267,16 +268,16 @@ class SparseIntVect(object):
[(0, 3), (2, 2), (4, 5)]
"""
res = SparseIntVect(self.size)
res = pySparseIntVect(self.size)
res.container = copy.deepcopy(self.container)
res -= other
return res
def __mul__(self,other):
"""
>>> c1=SparseIntVect(10)
>>> c1=pySparseIntVect(10)
>>> c1[0] = 3
>>> c1[4] = 5
>>> c2=SparseIntVect(10)
>>> c2=pySparseIntVect(10)
>>> c2[0] = 2
>>> c2[5] = 6
>>> c3 = c1*c2
@@ -286,17 +287,17 @@ class SparseIntVect(object):
[(0, 3), (4, 5)]
"""
res = SparseIntVect(self.size)
res = pySparseIntVect(self.size)
res.container = copy.deepcopy(self.container)
res *= other
return res
def __and__(self,other):
"""
>>> c1=SparseIntVect(10)
>>> c1=pySparseIntVect(10)
>>> c1[0] = 3
>>> c1[2] = 2
>>> c1[4] = 5
>>> c2=SparseIntVect(10)
>>> c2=pySparseIntVect(10)
>>> c2[0] = 2
>>> c2[2] = -2
>>> c2[5] = 6
@@ -307,17 +308,17 @@ class SparseIntVect(object):
[(0, 3), (2, 2), (4, 5)]
"""
res = SparseIntVect(self.size)
res = pySparseIntVect(self.size)
res.container = copy.deepcopy(self.container)
res &= other
return res
def __or__(self,other):
"""
>>> c1=SparseIntVect(10)
>>> c1=pySparseIntVect(10)
>>> c1[0] = 3
>>> c1[2] = 2
>>> c1[4] = 5
>>> c2=SparseIntVect(10)
>>> c2=pySparseIntVect(10)
>>> c2[0] = 2
>>> c2[2] = -2
>>> c2[5] = 6
@@ -328,7 +329,7 @@ class SparseIntVect(object):
[(0, 3), (2, 2), (4, 5)]
"""
res = SparseIntVect(self.size)
res = pySparseIntVect(self.size)
res.container = copy.deepcopy(self.container)
res |= other
return res
@@ -337,7 +338,7 @@ class SparseIntVect(object):
return self.size
def __getitem__(self,which):
"""
>>> c1=SparseIntVect(10)
>>> c1=pySparseIntVect(10)
>>> c1[0] = 3
>>> c1[4] = 5
>>> c1[0]
@@ -360,7 +361,7 @@ class SparseIntVect(object):
self.container[which]=val
def __iter__(self):
"""
>>> c=SparseIntVect(10)
>>> c=pySparseIntVect(10)
>>> c[0] = 3
>>> c[4] = 5
>>> c[7] = -1
@@ -374,50 +375,47 @@ class SparseIntVect(object):
return self.container.iteritems()
import DataStructs
def DiceSimilarity(v1,v2,bounds=None,useAbs=False):
""" Implements the DICE similarity metric.
>>> v1 = SparseIntVect(10)
>>> v2 = SparseIntVect(10)
>>> v1.InitFromSequence((1,2,3))
>>> v2.InitFromSequence((1,2,3))
>>> v1 = DataStructs.IntSparseIntVect(10)
>>> v2 = DataStructs.IntSparseIntVect(10)
>>> v1.UpdateFromSequence((1,2,3))
>>> v2.UpdateFromSequence((1,2,3))
>>> DiceSimilarity(v1,v2)
1.0
>>> v2.InitFromSequence((5,6))
>>> v2 = DataStructs.IntSparseIntVect(10)
>>> v2.UpdateFromSequence((5,6))
>>> DiceSimilarity(v1,v2)
0.0
>>> v1.InitFromSequence((1,2,3,4))
>>> v2.InitFromSequence((1,3,5,7))
>>> v1 = DataStructs.IntSparseIntVect(10)
>>> v2 = DataStructs.IntSparseIntVect(10)
>>> v1.UpdateFromSequence((1,2,3,4))
>>> v2.UpdateFromSequence((1,3,5,7))
>>> DiceSimilarity(v1,v2)
0.5
>>> v1.InitFromSequence((1,2,3,4,5,6))
>>> v2.InitFromSequence((1,3))
>>> v1 = DataStructs.IntSparseIntVect(10)
>>> v2 = DataStructs.IntSparseIntVect(10)
>>> v1.UpdateFromSequence((1,2,3,4,5,6))
>>> v2.UpdateFromSequence((1,3))
>>> DiceSimilarity(v1,v2)
0.5
"""
denom = 1.0*(v1.Sum(useAbs=useAbs)+v2.Sum(useAbs=useAbs))
denom = 1.0*(v1.GetTotalVal(useAbs=useAbs)+v2.GetTotalVal(useAbs=useAbs))
if not denom:
res = 0.0
else:
if bounds and (min(len(v1),len(v2))/denom) < bounds:
numer = 0.0
else:
#tv = v1&v2
#numer = 2.0*tv.Sum(useAbs=useAbs)
numer=0.0
v1C=v1.container
v2C=v2.container
for k in v1C.keys():
if v2C.has_key(k):
if useAbs:
numer+=min(abs(v1C[k]),abs(v2C[k]))
else:
numer+=min(v1C[k],v2C[k])
v3=v1&v2
numer=v3.GetTotalVal(useAbs=useAbs)
res = 2.*numer/denom
return res