Remove trailing spaces
git-svn-id: https://bucket.mit.edu/svn/nilm/nilmdb@10824 ddd99763-3ecb-0310-9145-efcb8ce7c51f
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@ -1,3 +1,4 @@
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# cython: profile=True
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# This is from bx-python 554:07aca5a9f6fc (BSD licensed), modified to
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# store interval ranges as doubles rather than 32-bit integers.
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@ -63,9 +64,9 @@ cdef float nlog = -1.0 / log(0.5)
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cdef class IntervalNode:
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"""
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A single node of an `IntervalTree`.
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NOTE: Unless you really know what you are doing, you probably should us
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`IntervalTree` rather than using this directly.
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`IntervalTree` rather than using this directly.
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"""
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cdef float priority
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cdef public object interval
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@ -82,7 +83,7 @@ cdef class IntervalNode:
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property root_node:
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def __get__(self):
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return self.croot if self.croot is not EmptyNode else None
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def __repr__(self):
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return "IntervalNode(%g, %g)" % (self.start, self.end)
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@ -101,7 +102,7 @@ cdef class IntervalNode:
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self.cleft = EmptyNode
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self.cright = EmptyNode
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self.croot = EmptyNode
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cpdef IntervalNode insert(IntervalNode self, double start, double end, object interval):
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"""
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Insert a new IntervalNode into the tree of which this node is
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@ -114,7 +115,7 @@ cdef class IntervalNode:
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cdef double decision_endpoint = start
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if start == self.start:
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decision_endpoint = end
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if decision_endpoint > self.start:
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# insert to cright tree
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if self.cright is not EmptyNode:
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@ -133,7 +134,7 @@ cdef class IntervalNode:
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# rebalance tree
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if self.priority < self.cleft.priority:
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croot = self.rotate_right()
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croot.set_ends()
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self.cleft.croot = croot
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self.cright.croot = croot
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@ -154,7 +155,7 @@ cdef class IntervalNode:
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return croot
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cdef inline void set_ends(IntervalNode self):
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if self.cright is not EmptyNode and self.cleft is not EmptyNode:
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if self.cright is not EmptyNode and self.cleft is not EmptyNode:
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self.maxend = dmax3(self.end, self.cright.maxend, self.cleft.maxend)
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self.minend = dmin3(self.end, self.cright.minend, self.cleft.minend)
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self.minstart = dmin3(self.start, self.cright.minstart, self.cleft.minstart)
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@ -166,7 +167,7 @@ cdef class IntervalNode:
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self.maxend = dmax2(self.end, self.cleft.maxend)
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self.minend = dmin2(self.end, self.cleft.minend)
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self.minstart = dmin2(self.start, self.cleft.minstart)
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def intersect( self, double start, double end, sort=True ):
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"""
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@ -180,7 +181,7 @@ cdef class IntervalNode:
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return results
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find = intersect
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cdef void _intersect( IntervalNode self, double start, double end, list results):
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# Left subtree
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if self.cleft is not EmptyNode and self.cleft.maxend > start:
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@ -191,7 +192,7 @@ cdef class IntervalNode:
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# Right subtree
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if self.cright is not EmptyNode and self.start < end:
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self.cright._intersect( start, end, results )
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cdef void _seek_left(IntervalNode self, double position, list results, int n, double max_dist):
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# we know we can bail in these 2 cases.
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@ -213,7 +214,7 @@ cdef class IntervalNode:
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self.cleft._seek_left(position, results, n, max_dist)
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cdef void _seek_right(IntervalNode self, double position, list results, int n, double max_dist):
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# we know we can bail in these 2 cases.
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if self.maxend < position: return
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@ -223,7 +224,7 @@ cdef class IntervalNode:
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# the ordering of these 3 blocks makes it so the results are
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# ordered nearest to farest from the query position
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if self.cleft is not EmptyNode:
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if self.cleft is not EmptyNode:
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self.cleft._seek_right(position, results, n, max_dist)
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if -1 < self.start - position < max_dist:
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@ -232,7 +233,7 @@ cdef class IntervalNode:
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if self.cright is not EmptyNode:
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self.cright._seek_right(position, results, n, max_dist)
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cpdef left(self, position, int n=1, double max_dist=2500):
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"""
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find n features with a start > than `position`
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@ -330,49 +331,49 @@ cdef class Interval:
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cdef class IntervalTree:
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"""
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Data structure for performing window intersect queries on a set of
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Data structure for performing window intersect queries on a set of
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of possibly overlapping 1d intervals.
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Usage
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=====
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Create an empty IntervalTree
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>>> from bx.intervals.intersection import Interval, IntervalTree
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>>> intersecter = IntervalTree()
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An interval is a start and end position and a value (possibly None).
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You can add any object as an interval:
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>>> intersecter.insert( 0, 10, "food" )
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>>> intersecter.insert( 3, 7, dict(foo='bar') )
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>>> intersecter.find( 2, 5 )
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['food', {'foo': 'bar'}]
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If the object has start and end attributes (like the Interval class) there
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is are some shortcuts:
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>>> intersecter = IntervalTree()
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>>> intersecter.insert_interval( Interval( 0, 10 ) )
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>>> intersecter.insert_interval( Interval( 3, 7 ) )
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>>> intersecter.insert_interval( Interval( 3, 40 ) )
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>>> intersecter.insert_interval( Interval( 13, 50 ) )
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>>> intersecter.find( 30, 50 )
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[Interval(3, 40), Interval(13, 50)]
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>>> intersecter.find( 100, 200 )
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[]
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Before/after for intervals
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>>> intersecter.before_interval( Interval( 10, 20 ) )
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[Interval(3, 7)]
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>>> intersecter.before_interval( Interval( 5, 20 ) )
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[]
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Upstream/downstream
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>>> intersecter.upstream_of_interval(Interval(11, 12))
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[Interval(0, 10)]
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>>> intersecter.upstream_of_interval(Interval(11, 12, strand="-"))
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@ -381,16 +382,16 @@ cdef class IntervalTree:
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>>> intersecter.upstream_of_interval(Interval(1, 2, strand="-"), num_intervals=3)
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[Interval(3, 7), Interval(3, 40), Interval(13, 50)]
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"""
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cdef IntervalNode root
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def __cinit__( self ):
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root = None
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# ---- Position based interfaces -----------------------------------------
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def insert( self, double start, double end, object value=None ):
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"""
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Insert the interval [start,end) associated with value `value`.
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@ -399,7 +400,7 @@ cdef class IntervalTree:
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self.root = IntervalNode( start, end, value )
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else:
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self.root = self.root.insert( start, end, value )
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add = insert
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@ -410,7 +411,7 @@ cdef class IntervalTree:
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if self.root is None:
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return []
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return self.root.find( start, end )
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def before( self, position, num_intervals=1, max_dist=2500 ):
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"""
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Find `num_intervals` intervals that lie before `position` and are no
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@ -481,7 +482,7 @@ cdef class IntervalTree:
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return self.root.left( interval.start, num_intervals, max_dist )
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else:
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return self.root.right( interval.end, num_intervals, max_dist )
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def traverse(self):
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"""
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iterator that traverses the tree
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