cls.StaticRTree.CStaticRTree Class Reference

1D static R-tree. More...

Classes
class	_CIntv
	Test class. More...

Public Member Functions
def	__init__ (s)
def	__str__ (s)
def	Initialize (s, intervals)
	Feed the object with interval data. More...
def	IntersectPoint (s, pos)
	Query which intervals intersect with a given point. More...
def	IntersectInterval (s, begin, end)
	Query which intervals intersect with a given closed interval. More...
def	ClosestInterval (s, pos)
	Get the closest interval to a position. More...

Static Public Attributes
	mode
	tree = CStaticRTree();
	i1
	i2 = _CIntv("i2", 5, 12);
	i3 = _CIntv("i3", 14,17);
def	rslt = tree.IntersectInterval(16, 1000);
	g = CHSEnsgenes(CPaths());
list	onChr

Detailed Description

1D static R-tree.

Tree is constructed once from a set of intervals. No insert or delete
functions are available. Based on ideas presented by Martin Davis at
http://lin-ear-th-inking.blogspot.it/2007/06/packed-1-dimensional-r-tree.html

Constructor & Destructor Documentation

__init__()

def cls.StaticRTree.CStaticRTree.__init__

(

s

)

Member Function Documentation

__str__()

def cls.StaticRTree.CStaticRTree.__str__

(

s

)

ClosestInterval()

def cls.StaticRTree.CStaticRTree.ClosestInterval	(		s,
			pos
	)

Get the closest interval to a position.

    This method is the most generic query that can be done on an
    interval. It also has the most possible outcomes: If the query
    position is contained in interval(s), they will be reported. If it is
    outside any interval, the closest will be reported. However, if there
    are two or more closest intervals, all of them will reported.
    @param pos  Position to be queried.
    @return @c List of @c Tuples (@c interval, @c distance). The @c
    interval is the data item itself as supplied to the @ref Initialize
    method and @c distance is the (unsigned) distance from @c pos to the
    interval border. If it is set to 0, the interval covers the point.

Initialize()

def cls.StaticRTree.CStaticRTree.Initialize	(		s,
			intervals
	)

Feed the object with interval data.

    This function is used to import data into the tree. The method should
    be called only once, as there is no update process for the static
    R-tree.
    @param  intervals @c List of objects with interval-like
    properties. Each object is required to have a @c GetBegin() and a
    @c GetEnd() method in order to determine its borders.

IntersectInterval()

def cls.StaticRTree.CStaticRTree.IntersectInterval	(		s,
			begin,
			end
	)

Query which intervals intersect with a given closed interval.

    @param begin  Start position of query interval.
    @param end  End position (inclusive) of the query interval.
    @return @c List of intervals that intersect with the query interval.

IntersectPoint()

def cls.StaticRTree.CStaticRTree.IntersectPoint	(		s,
			pos
	)

Query which intervals intersect with a given point.

    @param pos  Position to be queried.
    @return @c List of intervals that include this position.

Member Data Documentation

g

cls.StaticRTree.CStaticRTree.g = CHSEnsgenes(CPaths());

static

i1

cls.StaticRTree.CStaticRTree.i1

static

i2

cls.StaticRTree.CStaticRTree.i2 = _CIntv("i2", 5, 12);

static

i3

cls.StaticRTree.CStaticRTree.i3 = _CIntv("i3", 14,17);

static

mode

cls.StaticRTree.CStaticRTree.mode

static

onChr

list cls.StaticRTree.CStaticRTree.onChr

static

Initial value:

=  [x for x in g.values() if x.Chrom=="22" and \
                 x.Biotype=="protein_coding"];

rslt

def cls.StaticRTree.CStaticRTree.rslt = tree.IntersectInterval(16, 1000);

static

tree

cls.StaticRTree.CStaticRTree.tree = CStaticRTree();

static

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The documentation for this class was generated from the following file:

• cls/StaticRTree.py