def update_numberOfBases(self):
"""
Updates the numberOfBases in the PM while a resize handle is being
dragged.
@see: self.getCursorText() where it is called.
"""
#@Note: originally (before 2008-04-05, it was called in
#DnaStrand_ResizeHandle.on_drag() but that 'may' have some bugs
#(not verified) also see self.getCursorText() to know why it is
#called there (basically a workaround for bug 2729
if self.grabbedHandle is None:
return
currentPosition = self.grabbedHandle.currentPosition
resize_end = self.grabbedHandle.origin
new_duplexLength = vlen( currentPosition - resize_end )
numberOfBasePairs_to_change = getNumberOfBasePairsFromDuplexLength('B-DNA',
new_duplexLength)
original_numberOfBases = self.struct.getNumberOfBases()
#If the dot product of handle direction and the direction in which it
#is dragged is negative, this means we need to subtract bases
direction_of_drag = norm(currentPosition - resize_end)
if dot(self.grabbedHandle.direction, direction_of_drag ) < 0:
total_number_of_bases = original_numberOfBases - numberOfBasePairs_to_change
self.propMgr.numberOfBasesSpinBox.setValue(total_number_of_bases)
else:
total_number_of_bases = original_numberOfBases + numberOfBasePairs_to_change
self.propMgr.numberOfBasesSpinBox.setValue(total_number_of_bases - 1)
def getCursorText(self, endPoint1, endPoint2):
"""
This is used as a callback method in DnaLine mode
@see: DnaLineMode.setParams, DnaLineMode_GM.Draw
"""
text = ""
textColor = env.prefs[cursorTextColor_prefs_key]
if endPoint1 is None or endPoint2 is None:
return text, textColor
if not env.prefs[dnaDuplexEditCommand_showCursorTextCheckBox_prefs_key]:
return text, textColor
numberOfBasePairsString = ""
numberOfTurnsString = ""
duplexLengthString = ""
thetaString = ""
duplexLength = vlen(endPoint2 - endPoint1)
numberOfBasePairs = getNumberOfBasePairsFromDuplexLength("B-DNA", duplexLength, duplexRise=self.duplexRise)
numberOfBasePairsString = self._getCursorText_numberOfBasePairs(numberOfBasePairs)
numberOfTurnsString = self._getCursorText_numberOfTurns(numberOfBasePairs)
duplexLengthString = self._getCursorText_length(duplexLength)
if env.prefs[dnaDuplexEditCommand_cursorTextCheckBox_angle_prefs_key]:
vec = endPoint2 - endPoint1
theta = self.glpane.get_angle_made_with_screen_right(vec)
thetaString = "%5.2f deg" % theta
commaString = ", "
text = numberOfBasePairsString
if text and numberOfTurnsString:
text += commaString
text += numberOfTurnsString
if text and duplexLengthString:
text += commaString
text += duplexLengthString
if text and thetaString:
text += commaString
text += thetaString
# @TODO: The following updates the PM as the cursor moves.
# Need to rename this method so that you that it also does more things
# than just to return a textString -- Ninad 2007-12-20
self.propMgr.numberOfBasePairsSpinBox.setValue(numberOfBasePairs)
return text, textColor
def createStructure(self, showPropMgr = True):
"""
Overrides superclass method. Creates the structure (DnaSegment)
"""
assert self.propMgr is not None
if self.struct is not None:
self.struct = None
self.win.assy.part.ensure_toplevel_group()
self.propMgr.endPoint1 = self.mouseClickPoints[0]
self.propMgr.endPoint2 = self.mouseClickPoints[1]
duplexLength = vlen(self.mouseClickPoints[0] - self.mouseClickPoints[1])
numberOfBasePairs = \
getNumberOfBasePairsFromDuplexLength(
'B-DNA',
duplexLength,
duplexRise = self.duplexRise)
self.propMgr.numberOfBasePairsSpinBox.setValue(numberOfBasePairs)
self.preview_or_finalize_structure(previewing = True)
#Unpick the dna segments (while this command was still
#running. ) This is necessary , so that when you strat drawing
#rubberband line, it matches the display style of the glpane.
#If something was selected, and while in DnaLineMode you changed the
#display style, it will be applied only to the selected chunk.
#(and the glpane's display style will not change. This , in turn
#won't change the display of the rubberband line being drawn.
#Another bug: What if something else in the glpane is selected?
#complete fix would be to call unpick_all_in_the_glpane. But
#that itself is undesirable. Okay for now -- Ninad 2008-02-20
#UPDATE 2008-02-21: The following code is commented out. Don't
#change the selection state of the
##if self._fallbackDnaGroup is not None:
##for segment in self._fallbackDnaGroup.members:
##segment.unpick()
#Now append this dnaSegment to self._segmentList
self._segmentList.append(self.struct)
#clear the mouseClickPoints list
self.mouseClickPoints = []
self.graphicsMode.resetVariables()
self.win.win_update() #fixes bug 2810
def createStructure(self):
"""
Overrides superclass method. Creates the structure (DnaSegment)
"""
assert self.propMgr is not None
if self.struct is not None:
self.struct = None
self.win.assy.part.ensure_toplevel_group()
self.propMgr.endPoint1 = self.mouseClickPoints[0]
self.propMgr.endPoint2 = self.mouseClickPoints[1]
duplexLength = vlen(self.mouseClickPoints[0] -
self.mouseClickPoints[1])
numberOfBasePairs = \
getNumberOfBasePairsFromDuplexLength(
'B-DNA',
duplexLength,
duplexRise = self.duplexRise)
self.propMgr.numberOfBasePairsSpinBox.setValue(numberOfBasePairs)
self.preview_or_finalize_structure(previewing=True)
#Unpick the dna segments (while this command was still
#running. ) This is necessary , so that when you strat drawing
#rubberband line, it matches the display style of the glpane.
#If something was selected, and while in DnaLineMode you changed the
#display style, it will be applied only to the selected chunk.
#(and the glpane's display style will not change. This , in turn
#won't change the display of the rubberband line being drawn.
#Another bug: What if something else in the glpane is selected?
#complete fix would be to call unpick_all_in_the_glpane. But
#that itself is undesirable. Okay for now -- Ninad 2008-02-20
#UPDATE 2008-02-21: The following code is commented out. Don't
#change the selection state of the
##if self._fallbackDnaGroup is not None:
##for segment in self._fallbackDnaGroup.members:
##segment.unpick()
#Now append this dnaSegment to self._segmentList
self._segmentList.append(self.struct)
#clear the mouseClickPoints list
self.mouseClickPoints = []
self.graphicsMode.resetVariables()
self.win.win_update() #fixes bug 2810
def _determine_numberOfBasePairs_to_change(self):
"""
"""
duplexRise = self.struct.getDuplexRise()
numberOfBasesToAddOrRemove = 0
# Following helps fixing bugs like 2904 and 2906 see also self.getCursorText()
# and TODO items in that method. Also note that the grabbed handle case
# is similar to the one in MultipleDnaSegmentResize_EditCommand.
# needs refactoring and overall cleanup.
if self.grabbedHandle is not None:
currentPosition = self.grabbedHandle.currentPosition
fixedEndOfStructure = self.grabbedHandle.fixedEndOfStructure
changedLength = vlen(currentPosition - self.grabbedHandle.origin)
direction_of_drag = norm(self.grabbedHandle.currentPosition - self.grabbedHandle.origin)
# Even when the direction of drag is negative (i.e. the basepairs being
# removed), make sure not to remove base pairs for very small movement
# of the grabbed handle
if changedLength < 0.2 * duplexRise:
return 0
# This check quickly determines if the grabbed handle moved by a distance
# more than the duplexRise and avoids further computations
# This condition is applicable only when the direction of drag is
# positive..i.e. bases bing added to the segment.
if changedLength < duplexRise and dot(self.grabbedHandle.direction, direction_of_drag) > 0:
return 0
# If the segment is being shortened (determined by checking the
# direction of drag)
numberOfBasesToAddOrRemove = getNumberOfBasePairsFromDuplexLength(
"B-DNA", changedLength, duplexRise=duplexRise
)
if dot(self.grabbedHandle.direction, direction_of_drag) < 0:
numberOfBasesToAddOrRemove = -numberOfBasesToAddOrRemove
if numberOfBasesToAddOrRemove > 0:
# dna.modify will remove the first base pair it creates
# (that basepair will only be used for proper alignment of the
# duplex with the existing structure) So we need to compensate for
# this basepair by adding 1 to the new number of base pairs.
# UPDATE 2008-05-14: The following commented out code
# i.e. "##numberOfBasesToAddOrRemove += 1" is not required in this
# class , because the way we compute the number of base pairs to
# be added is different than than how its done at the moment in the
# superclass. In this method, we compute bases to be added from
# the resize end and that computation INCLUDES the resize end.
# so the number that it returns is already one more than the actual
# bases to be added. so commenting out the following line
# -- Ninad 2008-05-14
##numberOfBasesToAddOrRemove += 1
pass
else:
# The Property manager will be showing the current number
# of base pairs (w. May be we can use that number directly here?
# The following is safer to do so lets just recompute the
# number of base pairs. (if it turns out to be slow, we will consider
# using the already computed calue from the property manager
new_numberOfBasePairs = self.propMgr.numberOfBasePairsSpinBox.value()
endPoint1, endPoint2 = self.struct.getAxisEndPoints()
if endPoint1 is None or endPoint2 is None:
return 0
original_duplex_length = vlen(endPoint1 - endPoint2)
original_numberOfBasePairs = self.struct.getNumberOfBasePairs()
numberOfBasesToAddOrRemove = new_numberOfBasePairs - original_numberOfBasePairs
if numberOfBasesToAddOrRemove > 0:
# dna.modify will remove the first base pair it creates
# (that basepair will only be used for proper alignment of the
# duplex with the existing structure) So we need to compensate for
# this basepair by adding 1 to the new number of base pairs.
numberOfBasesToAddOrRemove += 1
return numberOfBasesToAddOrRemove
def _determine_numberOfBasePairs_to_change(self):
"""
Overrides superclass method
@TODO: This is significantly different (and perhaps better)
than the superclass method. See how to incorporate changes in
this method in superclass.
@see: self.getDnaRibbonParams()
"""
currentPosition = self.grabbedHandle.currentPosition
fixedEndOfStructure = self.grabbedHandle.fixedEndOfStructure
duplexRise = self.struct.getDuplexRise()
changedLength = vlen(currentPosition - self.grabbedHandle.origin)
direction_of_drag = norm(self.grabbedHandle.currentPosition - \
self.grabbedHandle.origin)
#Even when the direction of drag is negative (i.e. the basepairs being
#removed), make sure not to remove base pairs for very small movement
#of the grabbed handle
if changedLength < 0.2*duplexRise:
return 0
#This check quickly determines if the grabbed handle moved by a distance
#more than the duplexRise and avoids further computations
#This condition is applicable only when the direction of drag is
#positive..i.e. bases bing added to the segment.
if changedLength < duplexRise and \
dot(self.grabbedHandle.direction, direction_of_drag) > 0:
return 0
#If the segment is being shortened (determined by checking the
#direction of drag)
numberOfBasesToAddOrRemove = \
getNumberOfBasePairsFromDuplexLength(
'B-DNA',
changedLength,
duplexRise = duplexRise)
if dot(self.grabbedHandle.direction, direction_of_drag) < 0:
numberOfBasesToAddOrRemove = - numberOfBasesToAddOrRemove
if numberOfBasesToAddOrRemove > 0:
#dna.modify will remove the first base pair it creates
#(that basepair will only be used for proper alignment of the
#duplex with the existing structure) So we need to compensate for
#this basepair by adding 1 to the new number of base pairs.
#UPDATE 2008-05-14: The following commented out code
#i.e. "##numberOfBasesToAddOrRemove += 1" is not required in this
#class , because the way we compute the number of base pairs to
#be added is different than than how its done at the moment in the
#superclass. In this method, we compute bases to be added from
#the resize end and that computation INCLUDES the resize end.
#so the number that it returns is already one more than the actual
#bases to be added. so commenting out the following line
# -- Ninad 2008-05-14
##numberOfBasesToAddOrRemove += 1
##print "*** numberOfBasesToAddOrRemove = ", numberOfBasesToAddOrRemove
##print "**** changedLength =", changedLength
pass
###UPDATE 2008-06-26: for some reason, when the number of base pairs
###to be added (i.e. value of numberOfBasesToAddOrRemove) is 1 more
###than the actual number of base pairs to be added. So subtract 1
###from this number. Cause not debugged. -- Ninad
##if numberOfBasesToAddOrRemove > 1:
##numberOfBasesToAddOrRemove -= 1
#UPDATE 2008-08-20: Note that DnaSegment_EditCommand.getCursorText()
#does the job of removing the extra basepair from numberOfBasesToAddOrRemove
#It(subtracting 1 basePair) is not done here as
#self._modifyStructure() needs it without the subtraction. This is
#prone to bugs and need to be cleaned up. -- Ninad
return numberOfBasesToAddOrRemove
def _determine_numberOfBasePairs_to_change(self):
"""
"""
duplexRise = self.struct.getDuplexRise()
numberOfBasesToAddOrRemove = 0
#Following helps fixing bugs like 2904 and 2906 see also self.getCursorText()
#and TODO items in that method. Also note that the grabbed handle case
#is similar to the one in MultipleDnaSegmentResize_EditCommand.
#needs refactoring and overall cleanup.
if self.grabbedHandle is not None:
currentPosition = self.grabbedHandle.currentPosition
fixedEndOfStructure = self.grabbedHandle.fixedEndOfStructure
changedLength = vlen(currentPosition - self.grabbedHandle.origin)
direction_of_drag = norm(self.grabbedHandle.currentPosition - \
self.grabbedHandle.origin)
#Even when the direction of drag is negative (i.e. the basepairs being
#removed), make sure not to remove base pairs for very small movement
#of the grabbed handle
if changedLength < 0.2 * duplexRise:
return 0
#This check quickly determines if the grabbed handle moved by a distance
#more than the duplexRise and avoids further computations
#This condition is applicable only when the direction of drag is
#positive..i.e. bases bing added to the segment.
if changedLength < duplexRise and \
dot(self.grabbedHandle.direction, direction_of_drag) > 0:
return 0
#If the segment is being shortened (determined by checking the
#direction of drag)
numberOfBasesToAddOrRemove = \
getNumberOfBasePairsFromDuplexLength(
'B-DNA',
changedLength,
duplexRise = duplexRise)
if dot(self.grabbedHandle.direction, direction_of_drag) < 0:
numberOfBasesToAddOrRemove = -numberOfBasesToAddOrRemove
if numberOfBasesToAddOrRemove > 0:
#dna.modify will remove the first base pair it creates
#(that basepair will only be used for proper alignment of the
#duplex with the existing structure) So we need to compensate for
#this basepair by adding 1 to the new number of base pairs.
#UPDATE 2008-05-14: The following commented out code
#i.e. "##numberOfBasesToAddOrRemove += 1" is not required in this
#class , because the way we compute the number of base pairs to
#be added is different than than how its done at the moment in the
#superclass. In this method, we compute bases to be added from
#the resize end and that computation INCLUDES the resize end.
#so the number that it returns is already one more than the actual
#bases to be added. so commenting out the following line
# -- Ninad 2008-05-14
##numberOfBasesToAddOrRemove += 1
pass
else:
#The Property manager will be showing the current number
#of base pairs (w. May be we can use that number directly here?
#The following is safer to do so lets just recompute the
#number of base pairs. (if it turns out to be slow, we will consider
#using the already computed calue from the property manager
new_numberOfBasePairs = self.propMgr.numberOfBasePairsSpinBox.value(
)
endPoint1, endPoint2 = self.struct.getAxisEndPoints()
if endPoint1 is None or endPoint2 is None:
return 0
original_duplex_length = vlen(endPoint1 - endPoint2)
original_numberOfBasePairs = self.struct.getNumberOfBasePairs()
numberOfBasesToAddOrRemove = new_numberOfBasePairs - original_numberOfBasePairs
if numberOfBasesToAddOrRemove > 0:
#dna.modify will remove the first base pair it creates
#(that basepair will only be used for proper alignment of the
#duplex with the existing structure) So we need to compensate for
#this basepair by adding 1 to the new number of base pairs.
numberOfBasesToAddOrRemove += 1
return numberOfBasesToAddOrRemove
def _determine_numberOfBasePairs_to_change(self):
"""
Overrides superclass method
@TODO: This is significantly different (and perhaps better)
than the superclass method. See how to incorporate changes in
this method in superclass.
@see: self.getDnaRibbonParams()
"""
currentPosition = self.grabbedHandle.currentPosition
fixedEndOfStructure = self.grabbedHandle.fixedEndOfStructure
duplexRise = self.struct.getDuplexRise()
changedLength = vlen(currentPosition - self.grabbedHandle.origin)
direction_of_drag = norm(self.grabbedHandle.currentPosition - \
self.grabbedHandle.origin)
#Even when the direction of drag is negative (i.e. the basepairs being
#removed), make sure not to remove base pairs for very small movement
#of the grabbed handle
if changedLength < 0.2 * duplexRise:
return 0
#This check quickly determines if the grabbed handle moved by a distance
#more than the duplexRise and avoids further computations
#This condition is applicable only when the direction of drag is
#positive..i.e. bases bing added to the segment.
if changedLength < duplexRise and \
dot(self.grabbedHandle.direction, direction_of_drag) > 0:
return 0
#If the segment is being shortened (determined by checking the
#direction of drag)
numberOfBasesToAddOrRemove = \
getNumberOfBasePairsFromDuplexLength(
'B-DNA',
changedLength,
duplexRise = duplexRise)
if dot(self.grabbedHandle.direction, direction_of_drag) < 0:
numberOfBasesToAddOrRemove = -numberOfBasesToAddOrRemove
if numberOfBasesToAddOrRemove > 0:
#dna.modify will remove the first base pair it creates
#(that basepair will only be used for proper alignment of the
#duplex with the existing structure) So we need to compensate for
#this basepair by adding 1 to the new number of base pairs.
#UPDATE 2008-05-14: The following commented out code
#i.e. "##numberOfBasesToAddOrRemove += 1" is not required in this
#class , because the way we compute the number of base pairs to
#be added is different than than how its done at the moment in the
#superclass. In this method, we compute bases to be added from
#the resize end and that computation INCLUDES the resize end.
#so the number that it returns is already one more than the actual
#bases to be added. so commenting out the following line
# -- Ninad 2008-05-14
##numberOfBasesToAddOrRemove += 1
##print "*** numberOfBasesToAddOrRemove = ", numberOfBasesToAddOrRemove
##print "**** changedLength =", changedLength
pass
###UPDATE 2008-06-26: for some reason, when the number of base pairs
###to be added (i.e. value of numberOfBasesToAddOrRemove) is 1 more
###than the actual number of base pairs to be added. So subtract 1
###from this number. Cause not debugged. -- Ninad
##if numberOfBasesToAddOrRemove > 1:
##numberOfBasesToAddOrRemove -= 1
#UPDATE 2008-08-20: Note that DnaSegment_EditCommand.getCursorText()
#does the job of removing the extra basepair from numberOfBasesToAddOrRemove
#It(subtracting 1 basePair) is not done here as
#self._modifyStructure() needs it without the subtraction. This is
#prone to bugs and need to be cleaned up. -- Ninad
return numberOfBasesToAddOrRemove
def _determine_numberOfBasePairs_to_change(self):
"""
Overrides superclass method
@TODO: This is significantly different (and perhaps better)
than the superclass method. See how to incorporate changes in
this method in superclass.
@see: self.getDnaRibbonParams()
"""
currentPosition = self.grabbedHandle.currentPosition
fixedEndOfStructure = self.grabbedHandle.fixedEndOfStructure
duplexRise = self.struct.getDuplexRise()
changedLength = vlen(currentPosition - self.grabbedHandle.origin)
direction_of_drag = norm(self.grabbedHandle.currentPosition - \
self.grabbedHandle.origin)
#Even when the direction of drag is negative (i.e. the basepairs being
#removed), make sure not to remove base pairs for very small movement
#of the grabbed handle
if changedLength < 0.2 * duplexRise:
return 0
#This check quickly determines if the grabbed handle moved by a distance
#more than the duplexRise and avoids further computations
#This condition is applicable only when the direction of drag is
#positive..i.e. bases bing added to the segment.
if changedLength < duplexRise and \
dot(self.grabbedHandle.direction, direction_of_drag) > 0:
return 0
#If the segment is being shortened (determined by checking the
#direction of drag)
numberOfBasesToAddOrRemove = \
getNumberOfBasePairsFromDuplexLength(
'B-DNA',
changedLength,
duplexRise = duplexRise)
if dot(self.grabbedHandle.direction, direction_of_drag) < 0:
numberOfBasesToAddOrRemove = -numberOfBasesToAddOrRemove
if numberOfBasesToAddOrRemove > 0:
#dna.modify will remove the first base pair it creates
#(that basepair will only be used for proper alignment of the
#duplex with the existing structure) So we need to compensate for
#this basepair by adding 1 to the new number of base pairs.
#UPDATE 2008-05-14: The following is not required in this particular
#class , because the way we compute the number of base pairs to
#be added is different than than how its done at the moment in the
#superclass. In this method, we compute bases to be added from
#the resize end and that computation INCLUDES the resize end.
#so the number that it returns is already one more than the actual
#bases to be added. so commenting out the following line
# -- Ninad 2008-05-14
##numberOfBasesToAddOrRemove += 1
pass
return numberOfBasesToAddOrRemove
def getCursorText(self, endPoint1, endPoint2):
"""
This is used as a callback method in DnaLine mode
@see: DnaLineMode.setParams, DnaLineMode_GM.Draw
"""
text = ''
textColor = env.prefs[cursorTextColor_prefs_key]
if endPoint1 is None or endPoint2 is None:
return text, textColor
if not env.prefs[dnaDuplexEditCommand_showCursorTextCheckBox_prefs_key]:
return text, textColor
numberOfBasePairsString = ''
numberOfTurnsString = ''
duplexLengthString = ''
thetaString = ''
duplexLength = vlen(endPoint2 - endPoint1)
numberOfBasePairs = getNumberOfBasePairsFromDuplexLength(
'B-DNA', duplexLength, duplexRise=self.duplexRise)
numberOfBasePairsString = self._getCursorText_numberOfBasePairs(
numberOfBasePairs)
numberOfTurnsString = self._getCursorText_numberOfTurns(
numberOfBasePairs)
duplexLengthString = self._getCursorText_length(duplexLength)
if env.prefs[dnaDuplexEditCommand_cursorTextCheckBox_angle_prefs_key]:
vec = endPoint2 - endPoint1
theta = self.glpane.get_angle_made_with_screen_right(vec)
thetaString = "%5.2f deg" % theta
commaString = ", "
text = numberOfBasePairsString
if text and numberOfTurnsString:
text += commaString
text += numberOfTurnsString
if text and duplexLengthString:
text += commaString
text += duplexLengthString
if text and thetaString:
text += commaString
text += thetaString
#@TODO: The following updates the PM as the cursor moves.
#Need to rename this method so that you that it also does more things
#than just to return a textString -- Ninad 2007-12-20
self.propMgr.numberOfBasePairsSpinBox.setValue(numberOfBasePairs)
return text, textColor
def _determine_numberOfBasePairs_to_change(self):
"""
Overrides superclass method
@TODO: This is significantly different (and perhaps better)
than the superclass method. See how to incorporate changes in
this method in superclass.
@see: self.getDnaRibbonParams()
"""
currentPosition = self.grabbedHandle.currentPosition
fixedEndOfStructure = self.grabbedHandle.fixedEndOfStructure
duplexRise = self.struct.getDuplexRise()
changedLength = vlen(currentPosition - self.grabbedHandle.origin)
direction_of_drag = norm(self.grabbedHandle.currentPosition - \
self.grabbedHandle.origin)
#Even when the direction of drag is negative (i.e. the basepairs being
#removed), make sure not to remove base pairs for very small movement
#of the grabbed handle
if changedLength < 0.2*duplexRise:
return 0
#This check quickly determines if the grabbed handle moved by a distance
#more than the duplexRise and avoids further computations
#This condition is applicable only when the direction of drag is
#positive..i.e. bases bing added to the segment.
if changedLength < duplexRise and \
dot(self.grabbedHandle.direction, direction_of_drag) > 0:
return 0
#If the segment is being shortened (determined by checking the
#direction of drag)
numberOfBasesToAddOrRemove = \
getNumberOfBasePairsFromDuplexLength(
'B-DNA',
changedLength,
duplexRise = duplexRise)
if dot(self.grabbedHandle.direction, direction_of_drag) < 0:
numberOfBasesToAddOrRemove = - numberOfBasesToAddOrRemove
if numberOfBasesToAddOrRemove > 0:
#dna.modify will remove the first base pair it creates
#(that basepair will only be used for proper alignment of the
#duplex with the existing structure) So we need to compensate for
#this basepair by adding 1 to the new number of base pairs.
#UPDATE 2008-05-14: The following is not required in this particular
#class , because the way we compute the number of base pairs to
#be added is different than than how its done at the moment in the
#superclass. In this method, we compute bases to be added from
#the resize end and that computation INCLUDES the resize end.
#so the number that it returns is already one more than the actual
#bases to be added. so commenting out the following line
# -- Ninad 2008-05-14
##numberOfBasesToAddOrRemove += 1
pass
return numberOfBasesToAddOrRemove