def _reverseSequence(self, itemIndex):
"""
Reverse the strand sequence and update the StrandTextEdit widgets.
This is used when the 'strand direction' combobox item changes.
Example: If the sequence direction option is 5' to 3' then while
adding the bases, those get added to extend the 3' end.
Changing the direction (3' to 5') reverses the existing sequence in
the text edit (which was meant to be for 5' to 3')
@param itemIndex: currentIndex of combobox
@type itemIndex: int
@see self._determine_complementSequence() and bug 2787
"""
sequence = str(self.getPlainSequence())
complementSequence = str(self.sequenceTextEdit_mate.toPlainText())
reverseSequence = getReverseSequence(sequence)
#Important to reverse the complement sequence separately
#see bug 2787 for implementation notes.
#@see self._determine_complementSequence()
reverseComplementSequence = getReverseSequence(complementSequence)
self._setComplementSequence(reverseComplementSequence)
self._setSequence(reverseSequence)
return
def _reverseSequence(self, itemIndex):
"""
Reverse the strand sequence and update the StrandTextEdit widgets.
This is used when the 'strand direction' combobox item changes.
Example: If the sequence direction option is 5' to 3' then while
adding the bases, those get added to extend the 3' end.
Changing the direction (3' to 5') reverses the existing sequence in
the text edit (which was meant to be for 5' to 3')
@param itemIndex: currentIndex of combobox
@type itemIndex: int
@see self._determine_complementSequence() and bug 2787
"""
sequence = str(self.getPlainSequence())
complementSequence = str(self.sequenceTextEdit_mate.toPlainText())
reverseSequence = getReverseSequence(sequence)
#Important to reverse the complement sequence separately
#see bug 2787 for implementation notes.
#@see self._determine_complementSequence()
reverseComplementSequence = getReverseSequence(complementSequence)
self._setComplementSequence(reverseComplementSequence)
self._setSequence(reverseSequence)
return
def invokeAction(self, inActionName):
"""
Applies an action on the current sequence displayed in the PM.
@param inActionName: The action name.
@type inActionName: str
@return: The sequence after the action has been applied.
@rtype: str
"""
sequence, allKnown = self._getSequence()
outResult = ""
if inActionName == self._action_Complement:
outResult = getComplementSequence(sequence)
elif inActionName == self._action_Reverse:
outResult = getReverseSequence(sequence)
elif inActionName == self._action_ConvertUnrecognized:
outResult = replaceUnrecognized(sequence, replaceBase='N')
self.setSequence(outResult)
elif inActionName == self._action_RemoveUnrecognized:
outResult = replaceUnrecognized(sequence, replaceBase='')
self.setSequence(outResult)
return
def invokeAction( self, inActionName ):
"""
Applies an action on the current sequence displayed in the PM.
@param inActionName: The action name.
@type inActionName: str
@return: The sequence after the action has been applied.
@rtype: str
"""
sequence, allKnown = self._getSequence()
outResult = ""
if inActionName == self._action_Complement:
outResult = getComplementSequence(sequence)
elif inActionName == self._action_Reverse:
outResult = getReverseSequence(sequence)
elif inActionName == self._action_ConvertUnrecognized:
outResult = replaceUnrecognized(sequence, replaceBase = 'N')
self.setSequence( outResult )
elif inActionName == self._action_RemoveUnrecognized:
outResult = replaceUnrecognized(sequence, replaceBase = '')
self.setSequence( outResult )
return
def _getSequence( self,
reverse = False,
complement = False,
resolve_random = False,
cdict = {} ):
"""
Get the current DNA sequence from the Property Manager.
This method is not fully private. It's used repeatedly to get the
same sequence when making the DNA (which means its return value
should be deterministic, even when making sequences with randomly
chosen bases [nim]), and it's also called from class
DnaGeneratorPropertyManager to return data to be stored back into the
Property Manager, for implementing the reverse and complement actions.
(Ideally it would preserve whitespace and capitalization when used
that way, but it doesn't.)
@param reverse: If true, returns the reverse sequence.
@type reverse: bool
@param complement: If true, returns the complement sequence.
@type complement: bool
@param resolve_random:
@type resolve_random: True
@param cdict:
@type cdict: dictionary
@return: (sequence, allKnown) where I{sequence} is a string in which
each letter describes one base of the sequence currently
described by the UI, as modified by the passed reverse,
complement, and resolve_random flags, and I{allKnown} is a
boolean which says whether every base in the return value
has a known identity.
@rtype: tuple
@note: All punctuation/symbols are purged from the sequence and
any bogus/unknown bases are substituted as 'N' (unknown).
"""
sequence = ''
allKnown = True
cdict = basesDict
# (Note: I think this code implies that it can no longer be a
# number of bases. [bruce 070518 comment])
currentSequence = str(self.getPlainSequence(inOmitSymbols = True))
for ch in currentSequence:
if ch in cdict.keys(): #'CGATN':
properties = cdict[ch]
if ch == 'N': ###e soon: or any other letter indicating a random base
if resolve_random: #bruce 070518 new feature
i = len(sequence)
data = self._random_data_for_index(i)
# a random int in range(12), in a lazily extended cache
ch = list(cdict)[data%4]
# modulus must agree with number of valid entries in
# cdict.
else:
allKnown = False
if complement:
try:
ch = properties['Complement']
except (KeyError):
raise KeyError("DNA dictionary doesn't have a \
'Complement' key for '%r'." % ch)
ch = 'N'
elif ch in self.validSymbols: #'\ \t\r\n':
ch = ''
else:
allKnown = False
sequence += ch
if reverse:
sequence = getReverseSequence(sequence)
return (sequence, allKnown)
