Ejemplos de VirtualHelix en Python

Ejemplo n.º 1

Archivo: slicehelix.py Proyecto: REC17/cadnano2

 def createOrAddBasesToVirtualHelix(self, addBases=False,\
                                          addToScaffold=False):
     coord = (self._row, self._col)
     vh = self.virtualHelix()
     index = self.part().activeSlice()
     if not vh:
         vh = VirtualHelix()
         self.part().setVirtualHelixAt(coord, vh)
         vh.basesModified.connect(self.update)
     if addBases and addToScaffold:
         vh.connectStrand(StrandType.Scaffold, index - 1, index + 1)
     elif addBases and not addToScaffold:
         vh.connectStrand(StrandType.Staple, index - 1, index + 1)

Ejemplo n.º 2

Archivo: slicehelix.py Proyecto: MatthewMcAteer/cadnano2

 def createOrAddBasesToVirtualHelix(self, addBases=False,\
                                          addToScaffold=False):
     coord = (self._row, self._col)
     vh = self.virtualHelix()
     index = self.part().activeSlice()
     undoStack = self.part().undoStack()
     if not vh:
         undoStack.beginMacro("Add helix")
         vh = VirtualHelix(numBases=self.part().crossSectionStep())
         self.part().addVirtualHelixAt(coord, vh)
         vh.basesModified.connect(self.update)
     else:
         undoStack.beginMacro("Connect segment")
     if addBases and addToScaffold:
         vh.connectStrand(StrandType.Scaffold, index - 1, index + 1)
     elif addBases and not addToScaffold:
         vh.connectStrand(StrandType.Staple, index - 1, index + 1)
     self.undoStack().endMacro()

Ejemplo n.º 3

Archivo: unittests.py Proyecto: MatthewMcAteer/cadnano2

 def testAutoDragToBoundary(self):
     """docstring for testDrag"""
     vh0 = VirtualHelix(numBases=42, idnum=0)
     vh0.connectStrand(StrandType.Scaffold, 20, 22)
     str0 = "0 Scaffold: _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,> <,> <,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_\n0 Staple:   _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_"
     self.assertEqual(repr(vh0), str0)
     vh0.autoDragToBoundary(StrandType.Scaffold, 20)
     str1 = "0 Scaffold: _,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_\n0 Staple:   _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_"
     self.assertEqual(repr(vh0), str1)
     vh0.autoDragToBoundary(StrandType.Scaffold, 22)
     str2 = "0 Scaffold: _,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,> <,_\n0 Staple:   _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_"
     self.assertEqual(repr(vh0), str2)

Ejemplo n.º 4

Archivo: virtualhelix_tutorial.py Proyecto: REC17/cadnano2

#!/usr/bin/python
from model.virtualhelix import VirtualHelix
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)

Ejemplo n.º 5

Archivo: modeltests.py Proyecto: 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:   _,_ _,_ _,_ _,_ _,_ _,_ _,_ _,_')

Ejemplo n.º 6

Archivo: modeltests.py Proyecto: 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()

Ejemplo n.º 7

Archivo: modeltests.py Proyecto: 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:   _,_ _,_ _,_ _,_ _,_')

Ejemplo n.º 8

Archivo: virtualhelix_tutorial.py Proyecto: MatthewMcAteer/cadnano2

#!/usr/bin/python
import sys
sys.path.insert(0,'..')
from cadnano import app
from model.virtualhelix import VirtualHelix
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)"