Python VirtualHelix.clearStrand Examples

Programming Language: Python

Namespace/Package Name: model.virtualhelix

Class/Type: VirtualHelix

Method/Function: clearStrand

Examples at hotexamples.com: 5

Python VirtualHelix.clearStrand - 5 examples found. These are the top rated real world Python examples of model.virtualhelix.VirtualHelix.clearStrand extracted from open source projects. You can rate examples to help us improve the quality of examples.

Frequently Used Methods

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connectStrand(7)

clearStrand(5)

undoStack(4)

installXoverFrom3To5(3)

autoDragToBoundary(1)

connect3To5(1)

Example #1

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File: modeltests.py Project: MatthewMcAteer/cadnano2

    def testVH(self):
        """
        Perform the VirtualHelix tutorial and make sure that the
        expected changes occur to the sample VirtualHelix
        """
        vh = VirtualHelix(numBases=8, idnum=0)
        self.assertEqual(repr(vh), '0 Scaffold: _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_\n0 Staple:   _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_')

        vh.connectStrand(StrandType.Scaffold, 2, 6)
        vh.connectStrand(StrandType.Staple, 0, 7)
        self.assertEqual(repr(vh), '0 Scaffold: _,_ _,_ _,> <,> <,> <,> <,_ _,_\n0 Staple:   _,> <,> <,> <,> <,> <,> <,> <,_')

        vh.clearStrand(StrandType.Scaffold, 3.5, 4.5)
        vh.clearStrand(StrandType.Staple, 2.5, 5.5)
        self.assertEqual(repr(vh), '0 Scaffold: _,_ _,_ _,> <,_ _,> <,> <,_ _,_\n0 Staple:   _,> <,> <,_ _,_ _,_ _,> <,> <,_')

        vh1 = VirtualHelix(numBases=5, idnum=1)
        vh1.connectStrand(StrandType.Staple, 0, 4)
        self.assertEqual(repr(vh), '0 Scaffold: _,_ _,_ _,> <,_ _,> <,> <,_ _,_\n0 Staple:   _,> <,> <,_ _,_ _,_ _,> <,> <,_')
        self.assertEqual(repr(vh1), '1 Scaffold: _,_ _,_ _,_ _,_ _,_\n1 Staple:   _,> <,> <,> <,> <,_')

        vh.installXoverFrom3To5(StrandType.Staple, 2, vh1, 2)
        self.assertEqual(repr(vh), '0 Scaffold: _,_ _,_ _,> <,_ _,> <,> <,_ _,_\n0 Staple:   _,> <,_ 1:2,> <,_ _,_ _,> <,> <,_')
        self.assertEqual(repr(vh1), '1 Scaffold: _,_ _,_ _,_ _,_ _,_\n1 Staple:   _,> <,_ 0:2,> <,> <,_')

        vh.undoStack().undo()
        self.assertEqual(repr(vh), '0 Scaffold: _,_ _,_ _,> <,_ _,> <,> <,_ _,_\n0 Staple:   _,> <,> <,_ _,_ _,_ _,> <,> <,_')
        self.assertEqual(repr(vh1), '1 Scaffold: _,_ _,_ _,_ _,_ _,_\n1 Staple:   _,> <,> <,> <,> <,_')

        vh1.undoStack().undo()
        self.assertEqual(repr(vh), '0 Scaffold: _,_ _,_ _,> <,_ _,> <,> <,_ _,_\n0 Staple:   _,> <,> <,_ _,_ _,_ _,> <,> <,_')
        self.assertEqual(repr(vh1), '1 Scaffold: _,_ _,_ _,_ _,_ _,_\n1 Staple:   _,_ _,_ _,_ _,_ _,_')

        vh.undoStack().undo()
        self.assertEqual(repr(vh), '0 Scaffold: _,_ _,_ _,> <,_ _,> <,> <,_ _,_\n0 Staple:   _,> <,> <,> <,> <,> <,> <,> <,_')

        vh.undoStack().undo()
        self.assertEqual(repr(vh), '0 Scaffold: _,_ _,_ _,> <,> <,> <,> <,_ _,_\n0 Staple:   _,> <,> <,> <,> <,> <,> <,> <,_')

        vh.undoStack().undo()
        self.assertEqual(repr(vh), '0 Scaffold: _,_ _,_ _,> <,> <,> <,> <,_ _,_\n0 Staple:   _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_')

        vh.undoStack().undo()
        self.assertEqual(repr(vh), '0 Scaffold: _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_\n0 Staple:   _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_')

        vh.connectStrand(StrandType.Scaffold, 2, 4)
        vh.connectStrand(StrandType.Scaffold, 0, 7)
        vh.undoStack().undo()
        self.assertEqual(repr(vh), '0 Scaffold: _,_ _,_ _,> <,> <,_ _,_ _,_ _,_\n0 Staple:   _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_')

Example #2

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File: modeltests.py Project: MatthewMcAteer/cadnano2

 def testClearCrossovers(self):
     vh = VirtualHelix(numBases=8, idnum=0)
     vh.connectStrand(StrandType.Staple, 0, 7)
     vh1 = VirtualHelix(numBases=5, idnum=1)
     vh1.connectStrand(StrandType.Staple, 0, 5)
     vh1.installXoverFrom3To5(StrandType.Staple, 3, vh, 2)
     self.assertEqual(repr(vh), '0 Scaffold: _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_\n0 Staple:   _,> <,> <,1:3 _,> <,> <,> <,> <,_')
     self.assertEqual(repr(vh1), '1 Scaffold: _,_ _,_ _,_ _,_ _,_\n1 Staple:   _,> <,> <,> <,0:2 _,_')
     vh1.clearStrand(StrandType.Staple, 0, 5)
     self.assertEqual(repr(vh), '0 Scaffold: _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_\n0 Staple:   _,> <,> <,_ _,> <,> <,> <,> <,_')
     self.assertEqual(repr(vh1), '1 Scaffold: _,_ _,_ _,_ _,_ _,_\n1 Staple:   _,_ _,_ _,_ _,_ _,_')
     vh1.undoStack().undo()
     vh1.undoStack().undo()
     self.assertEqual(repr(vh), '0 Scaffold: _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_\n0 Staple:   _,> <,> <,> <,> <,> <,> <,> <,_')
     self.assertEqual(repr(vh1), '1 Scaffold: _,_ _,_ _,_ _,_ _,_\n1 Staple:   _,> <,> <,> <,> <,_')
     vh.installXoverFrom3To5(StrandType.Staple, 2, vh1, 3)
     self.assertEqual(repr(vh), '0 Scaffold: _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_\n0 Staple:   _,> <,_ 1:3,> <,> <,> <,> <,> <,_')
     self.assertEqual(repr(vh1), '1 Scaffold: _,_ _,_ _,_ _,_ _,_\n1 Staple:   _,> <,> <,_ 0:2,> <,_')
     vh1.clearStrand(StrandType.Staple, 0, 5)
     self.assertEqual(repr(vh), '0 Scaffold: _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_\n0 Staple:   _,> <,_ _,> <,> <,> <,> <,> <,_')
     self.assertEqual(repr(vh1), '1 Scaffold: _,_ _,_ _,_ _,_ _,_\n1 Staple:   _,_ _,_ _,_ _,_ _,_')

Example #3

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File: modeltests.py Project: MatthewMcAteer/cadnano2

    def testFractionalClearStrandCommand(self):
        """
        The new API for clearStrand allows fractional values for
        base indices (see docs/virtualhelix.pdf). This tets them.
        """
        vh = VirtualHelix(numBases=8, idnum=0)
        self.assertEqual(repr(vh), '0 Scaffold: _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_\n0 Staple:   _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_')

        vh.connectStrand(StrandType.Scaffold, 2, 6)
        vh.connectStrand(StrandType.Staple, 0, 7)
        self.assertEqual(repr(vh), '0 Scaffold: _,_ _,_ _,> <,> <,> <,> <,_ _,_\n0 Staple:   _,> <,> <,> <,> <,> <,> <,> <,_')

        vh.clearStrand(StrandType.Scaffold, 4, 4)
        vh.clearStrand(StrandType.Staple, 3, 5)
        self.assertEqual(repr(vh), '0 Scaffold: _,_ _,_ _,> <,> <,> <,> <,_ _,_\n0 Staple:   _,> <,> <,_ _,_ _,_ _,> <,> <,_')

        vh.undoStack().undo()
        vh.undoStack().undo()
        self.assertEqual(repr(vh), '0 Scaffold: _,_ _,_ _,> <,> <,> <,> <,_ _,_\n0 Staple:   _,> <,> <,> <,> <,> <,> <,> <,_')

        vh.undoStack().undo()

Example #4

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File: virtualhelix_tutorial.py Project: REC17/cadnano2

from model.enum import StrandType
from code import interact

print "vh = VirtualHelix(numBases=8, idnum=0)"
vh = VirtualHelix(numBases=8, idnum=0)
print str(vh) + "\n\n"

print "vh.connectStrand(StrandType.Scaffold,2,6)"
print "vh.connectStrand(StrandType.Staple,0,7)"
vh.connectStrand(StrandType.Scaffold,2,6)
vh.connectStrand(StrandType.Staple,0,7)
print str(vh) + "\n\n"

print "vh.clearStrand(StrandType.Scaffold,4,4)"
print "vh.clearStrand(StrandType.Staple,3,5)"
vh.clearStrand(StrandType.Scaffold,4,4)
vh.clearStrand(StrandType.Staple,3,5)
print str(vh) + "\n\n"

print "vh1 = VirtualHelix(numBases=5, idnum=1)"
print "vh1.connectStrand(StrandType.Staple, 0, 4)"
vh1 = VirtualHelix(numBases=5, idnum=1)
vh1.connectStrand(StrandType.Staple, 0, 4)
print str(vh)
print str(vh1) + "\n\n"

print "vh.connect3To5(StrandType.Staple, 2, vh1, 3)"
vh.connect3To5(StrandType.Staple, 2, vh1, 2)
print str(vh)
print str(vh1)
interact(local=locals())

Example #5

Show file

File: virtualhelix_tutorial.py Project: MatthewMcAteer/cadnano2

from model.enum import StrandType
from code import interact

print "vh = VirtualHelix(numBases=8, idnum=0)"
vh = VirtualHelix(numBases=8, idnum=0)
print repr(repr(vh)) + "\n\n"

print "vh.connectStrand(StrandType.Scaffold,2,6)"
print "vh.connectStrand(StrandType.Staple,0,7)"
vh.connectStrand(StrandType.Scaffold,2,6)
vh.connectStrand(StrandType.Staple,0,7)
print repr(repr(vh)) + "\n\n"

print "vh.clearStrand(StrandType.Scaffold, 3.5, 4.5)"
print "vh.clearStrand(StrandType.Staple, 2.5, 5.5)"
vh.clearStrand(StrandType.Scaffold, 3.5, 4.5)
vh.clearStrand(StrandType.Staple, 2.5, 5.5)
print repr(repr(vh))
print "vh.undoStack().undo()"
vh.undoStack().undo()
print repr(repr(vh))
print "vh.clearStrand(StrandType.Staple, 3, 5)"
vh.clearStrand(StrandType.Staple, 3, 5)
print repr(repr(vh)) + "\n\n"

print "vh1 = VirtualHelix(numBases=5, idnum=1)"
print "vh1.connectStrand(StrandType.Staple, 0, 4)"
vh1 = VirtualHelix(numBases=5, idnum=1)
vh1.connectStrand(StrandType.Staple, 0, 4)
print repr(repr(vh))
print repr(repr(vh1)) + "\n\n"