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src/c/o/cogent-1.5.3/cogent/parse/cigar.py   cogent(Download)
 
import re
from cogent.core.location import LostSpan, Span, Map, _LostSpan
from cogent import DNA, LoadSeqs
 
 
        if c == 'M':
            spans.append(Span(posn, posn+n))
            posn += n
        else:

src/p/y/pycogent-HEAD/cogent/parse/cigar.py   pycogent(Download)
 
import re
from cogent.core.location import LostSpan, Span, Map, _LostSpan
from cogent import DNA, LoadSeqs
 
 
        if c == 'M':
            spans.append(Span(posn, posn+n))
            posn += n
        else:

src/p/y/pycogent-HEAD/tests/test_core/test_location.py   pycogent(Download)
"""
from cogent.util.unit_test import TestCase, main
from cogent.core.location import Span, Range, Point, RangeFromString, Map
 
__author__ = "Rob Knight"
    def setUp(self):
        """Define some standard Spans"""
        self.empty = Span(0, 0)
        self.full = Span(35, 30)    #will convert to (30, 35) internally
        self.overlapping = Span(32, 36)
        self.inside = Span(31, 32)

src/c/o/cogent-1.5.3/tests/test_core/test_location.py   cogent(Download)
"""
from cogent.util.unit_test import TestCase, main
from cogent.core.location import Span, Range, Point, RangeFromString
 
__author__ = "Rob Knight"
    def setUp(self):
        """Define some standard Spans"""
        self.empty = Span(0, 0)
        self.full = Span(35, 30)    #will convert to (30, 35) internally
        self.overlapping = Span(32, 36)
        self.inside = Span(31, 32)

src/p/y/pycogent-HEAD/tests/test_core/test_annotation.py   pycogent(Download)
from cogent import DNA, LoadSeqs
from cogent.core.annotation import Feature, Variable, _Feature
from cogent.core.location import Map, Span, as_map
 
__author__ = "Gavin Huttley"
    def test_span(self):
        length = 100
        forward = Span(20, 30)
        reverse = Span(70, 80, Reverse=True)
        assert forward.reversedRelativeTo(100) == reverse
    def test_map(self):
        """reversing a map with multiple spans should preserve span relative
        order"""
        forward = [Span(20,30), Span(40,50)]
        fmap = Map(spans=forward, parent_length=100)

src/c/o/cogent-1.5.3/cogent/draw/linear.py   cogent(Download)
import copy
import warnings
from cogent.core.location import Map, Span, _norm_slice
from cogent.core.moltype import DNA
 

src/p/y/pycogent-HEAD/cogent/draw/linear.py   pycogent(Download)
import copy
import warnings
from cogent.core.location import Map, Span, _norm_slice
from cogent.core.moltype import DNA
 

src/c/o/cogent-1.5.3/tests/test_core/test_annotation.py   cogent(Download)
from cogent import DNA, LoadSeqs
from cogent.core.annotation import Feature, Variable
from cogent.core.location import Map, Span
 
__author__ = "Gavin Huttley"
    def test_span(self):
        length = 100
        forward = Span(20, 30)
        reverse = Span(70, 80, Reverse=True)
        assert forward.reversedRelativeTo(100) == reverse
    def test_map(self):
        """reversing a map with multiple spans should preserve span relative
        order"""
        forward = [Span(20,30), Span(40,50)]
        fmap = Map(spans=forward, parent_length=100)

src/c/o/cogent-1.5.3/cogent/motif/util.py   cogent(Download)
from __future__ import division
from cogent.core.alignment import Alignment
from cogent.core.location import Span
 
__author__ = "Jeremy Widmann"
class Location(Span):
    """Object that stores location information for a module
 
    -Sequence refers to the original sequence the module came from
    -SeqId is the key of the sequence in the alignment

src/p/y/pycogent-HEAD/cogent/motif/util.py   pycogent(Download)
from __future__ import division
from cogent.core.alignment import Alignment
from cogent.core.location import Span
 
__author__ = "Jeremy Widmann"
class Location(Span):
    """Object that stores location information for a module
 
    -Sequence refers to the original sequence the module came from
    -SeqId is the key of the sequence in the alignment

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