def changeInstanceProperty(self, part_instance: ObjectInstance,
view: str,
key: str,
value: Any,
use_undostack: bool = True):
c = ChangeInstancePropertyCommand(self, part_instance, view, key, value)
util.doCmd(self, c, use_undostack=use_undostack)
def splitStrand(self,
strand: StrandT,
base_idx: int,
update_sequence: bool = True,
use_undostack: bool = True) -> bool:
"""Break strand into two strands. Reapply sequence by default.
Args:
strand: the :class:`Strand`
base_idx: the index
update_sequence (optional): whether to emit signal, default=``True``
use_undostack (optional): default=``True``
Returns:
``True`` if successful, ``False`` otherwise
TODO consider return strands instead
"""
if self.strandCanBeSplit(strand, base_idx):
if self.isStrandInSet(strand):
c = SplitCommand(strand, base_idx, update_sequence)
util.doCmd(self, c, use_undostack=use_undostack)
return True
else:
return False
else:
return False
def mergeStrands(self,
priority_strand: StrandT,
other_strand: StrandT,
use_undostack: bool = True) -> bool:
"""Merge the priority_strand and other_strand into a single new strand.
The oligo of priority should be propagated to the other and all of
its connections.
Args:
priority_strand: priority strand
other_strand: other strand
use_undostack (optional): default=``True``
Returns:
``True`` if strands were merged, ``False`` otherwise
"""
low_and_high_strands = self.strandsCanBeMerged(priority_strand,
other_strand)
if low_and_high_strands:
strand_low, strand_high = low_and_high_strands
if self.isStrandInSet(strand_low):
c = MergeCommand(strand_low, strand_high, priority_strand)
util.doCmd(self, c, use_undostack=use_undostack)
return True
else:
return False
def splitStrand(self,
strand,
base_idx,
update_sequence=True,
use_undostack=True):
"""Break strand into two strands. Reapply sequence by default.
Args:
strand (Strand): the :class:`Strand`
base_idx (int): the index
update_sequence (:obj:`bool`, optional): whether to emit signal, default=True
use_undostack (:obj:`bool`, optional): default=True
Returns:
bool: True if successful, False otherwise
TODO consider return strands instead
"""
if self.strandCanBeSplit(strand, base_idx):
if self.isStrandInSet(strand):
c = SplitCommand(strand, base_idx, update_sequence)
util.doCmd(self, c, use_undostack=use_undostack)
return True
else:
return False
else:
return False
def removeMods(self, document: DocT, mod_id: str, idx: int, use_undostack: bool = True):
"""Used to add mods during a merge operation."""
idx_low, idx_high = self.idxs()
print("attempting to remove")
if idx_low == idx or idx == idx_high:
print("removing a modification at {}".format(idx))
c = RemoveModsCommand(document, self, idx, mod_id)
util.doCmd(self, c, use_undostack=use_undostack)
def removeMods(self, document, mod_id, idx, use_undostack=True):
"""Used to add mods during a merge operation."""
idx_low, idx_high = self.idxs()
print("attempting to remove")
if idx_low == idx or idx == idx_high:
print("removing a modification at {}".format(idx))
c = RemoveModsCommand(document, self, idx, mod_id)
util.doCmd(self, c, use_undostack=use_undostack)
def createMod(self,
params: dict,
mid: str = None,
use_undostack: bool = True) -> Tuple[dict, str]:
"""Create a modification
Args:
params:
mid: optional, modification ID string
use_undostack: optional, default is ``True``
Returns:
tuple of :obj:`dict`, :obj:`str` of form::
(dictionary of modification paramemters, modification ID string)
Raises:
KeyError: Duplicate mod ID
"""
if mid is None:
mid = uuid4().hex
elif mid in self._mods:
raise KeyError("createMod: Duplicate mod id: {}".format(mid))
name = params.get('name', mid)
color = params.get('color', '#00FF00')
seq5p = params.get('seq5p', '')
seq3p = params.get('seq3p', '')
seqInt = params.get('seqInt', '')
note = params.get('note', '')
cmdparams = {
'props': {
'name': name,
'color': color,
'note': note,
'seq5p': seq5p,
'seq3p': seq3p,
'seqInt': seqInt,
},
'ext_locations':
set(), # external mods, mod belongs to idx outside of strand
'int_locations':
set() # internal mods, mod belongs between idx and idx + 1
}
item = {
'name': name,
'color': color,
'note': note,
'seq5p': seq5p,
'seq3p': seq3p,
'seqInt': seqInt
}
c = AddModCommand(self, cmdparams, mid)
util.doCmd(self, c, use_undostack=use_undostack)
return item, mid
def changeInstanceProperty(self,
part_instance,
view,
key,
value,
use_undostack=True):
c = ChangeInstancePropertyCommand(self, part_instance, view, key,
value)
util.doCmd(self, c, use_undostack=use_undostack)
def changeInstanceProperty(self,
part_instance: ObjectInstance,
view: str,
key: str,
value: Any,
use_undostack: bool = True):
c = ChangeInstancePropertyCommand(self, part_instance, view, key,
value)
util.doCmd(self, c, use_undostack=use_undostack)
def destroyMod(self, mid, use_undostack=True):
"""Destroy an existing modification
Args:
mid (str): optional, modification ID string
use_undostack (bool): optional, default is True
"""
if mid in self._mods:
c = RemoveModCommand(self, mid)
util.doCmd(self, c, use_undostack=use_undostack)
def destroyMod(self, mid: str, use_undostack: bool = True):
"""Destroy an existing modification
Args:
mid: optional, modification ID string
use_undostack: optional, default is ``True``
"""
if mid in self._mods:
c = RemoveModCommand(self, mid)
util.doCmd(self, c, use_undostack=use_undostack)
def modifyMod(self, params, mid, use_undostack=True):
"""Modify an existing modification
Args:
params (dict):
mid (str): optional, modification ID string
use_undostack (bool): optional, default is True
"""
if mid in self._mods:
c = ModifyModCommand(self, params, mid)
util.doCmd(self, c, use_undostack=use_undostack)
def modifyMod(self, params, mid, use_undostack=True):
"""Modify an existing modification
Args:
params (dict):
mid (str): optional, modification ID string
use_undostack (bool): optional, default is True
"""
if mid in self._mods:
c = ModifyModCommand(self, params, mid)
util.doCmd(self, c, use_undostack=use_undostack)
def modifyMod(self, params: dict, mid: str, use_undostack: bool = True):
"""Modify an existing modification
Args:
params:
mid: optional, modification ID string
use_undostack: optional, default is ``True``
"""
if mid in self._mods:
c = ModifyModCommand(self, params, mid)
util.doCmd(self, c, use_undostack=use_undostack)
def modifyMod(self, params: dict, mid: str, use_undostack: bool = True):
"""Modify an existing modification
Args:
params:
mid: optional, modification ID string
use_undostack: optional, default is ``True``
"""
if mid in self._mods:
c = ModifyModCommand(self, params, mid)
util.doCmd(self, c, use_undostack=use_undostack)
def createMod( self,
params: dict,
mid: str = None,
use_undostack: bool = True) -> Tuple[dict, str]:
"""Create a modification
Args:
params:
mid: optional, modification ID string
use_undostack: optional, default is ``True``
Returns:
tuple of :obj:`dict`, :obj:`str` of form::
(dictionary of modification paramemters, modification ID string)
Raises:
KeyError: Duplicate mod ID
"""
if mid is None:
mid = uuid4().hex
elif mid in self._mods:
raise KeyError("createMod: Duplicate mod id: {}".format(mid))
name = params.get('name', mid)
color = params.get('color', '#00FF00')
seq5p = params.get('seq5p', '')
seq3p = params.get('seq3p', '')
seqInt = params.get('seqInt', '')
note = params.get('note', '')
cmdparams = {
'props': {'name': name,
'color': color,
'note': note,
'seq5p': seq5p,
'seq3p': seq3p,
'seqInt': seqInt,
},
'ext_locations': set(), # external mods, mod belongs to idx outside of strand
'int_locations': set() # internal mods, mod belongs between idx and idx + 1
}
item = {'name': name,
'color': color,
'note': note,
'seq5p': seq5p,
'seq3p': seq3p,
'seqInt': seqInt
}
c = AddModCommand(self, cmdparams, mid)
util.doCmd(self, c, use_undostack=use_undostack)
return item, mid
def splitStrand(self, strand, base_idx, update_sequence=True, use_undostack=True):
"""Break strand into two strands. Reapply sequence by default.
Args:
strand (Strand): the :class:`Strand`
base_idx (int): the index
update_sequence (:obj:`bool`, optional): whether to emit signal, default=True
use_undostack (:obj:`bool`, optional): default=True
Returns:
bool: True if successful, False otherwise
TODO consider return strands instead
"""
if self.strandCanBeSplit(strand, base_idx):
if self.isStrandInSet(strand):
c = SplitCommand(strand, base_idx, update_sequence)
util.doCmd(self, c, use_undostack=use_undostack)
return True
else:
return False
else:
return False
def mergeStrands(self, priority_strand, other_strand, use_undostack=True):
"""Merge the priority_strand and other_strand into a single new strand.
The oligo of priority should be propagated to the other and all of
its connections.
Args:
priority_strand (Strand): priority strand
other_strand (Strand): other strand
use_undostack (:obj:`bool`, optional): default=True
Returns:
bool: True if strands were merged, False otherwise
"""
low_and_high_strands = self.strandsCanBeMerged(priority_strand, other_strand)
if low_and_high_strands:
strand_low, strand_high = low_and_high_strands
if self.isStrandInSet(strand_low):
c = MergeCommand(strand_low, strand_high, priority_strand)
util.doCmd(self, c, use_undostack=use_undostack)
return True
else:
return False
def splitStrand(self, strand: StrandT, base_idx: int,
update_sequence: bool = True,
use_undostack: bool = True) -> bool:
"""Break strand into two strands. Reapply sequence by default.
Args:
strand: the :class:`Strand`
base_idx: the index
update_sequence (optional): whether to emit signal, default=``True``
use_undostack (optional): default=``True``
Returns:
``True`` if successful, ``False`` otherwise
TODO consider return strands instead
"""
if self.strandCanBeSplit(strand, base_idx):
if self.isStrandInSet(strand):
c = SplitCommand(strand, base_idx, update_sequence)
util.doCmd(self, c, use_undostack=use_undostack)
return True
else:
return False
else:
return False
def _addPart(self, part, use_undostack=True):
"""Add part to the document via AddInstanceCommand.
"""
c = AddInstanceCommand(self, part)
util.doCmd(self, c, use_undostack)
def remove(self, use_undostack=True):
c = RemoveOligoCommand(self)
util.doCmd(self, c, use_undostack=use_undostack)
def applyColor(self, color, use_undostack=True):
if color == self.getColor():
return # oligo already has this color
c = ApplyColorCommand(self, color)
util.doCmd(self, c, use_undostack=use_undostack)
def applySequence(self, sequence, use_undostack=True):
c = ApplySequenceCommand(self, sequence)
util.doCmd(self, c, use_undostack=use_undostack)
def changeInstanceProperty(self, part_instance, view, key, value, use_undostack=True):
c = ChangeInstancePropertyCommand(self, part_instance, view, key, value)
util.doCmd(self, c, use_undostack=use_undostack)
def applySequence(self, sequence, use_undostack=True):
c = ApplySequenceCommand(self, sequence)
util.doCmd(self, c, use_undostack=use_undostack)
def applyColor(self, color, use_undostack=True):
if color == self.getColor():
return # oligo already has this color
c = ApplyColorCommand(self, color)
util.doCmd(self, c, use_undostack=use_undostack)
def remove(self, use_undostack=True):
c = RemoveOligoCommand(self)
util.doCmd(self, c, use_undostack=use_undostack)
def _addPart(self, part: Part, use_undostack: bool = True):
"""Add part to the document via AddInstanceCommand.
"""
c = AddInstanceCommand(self, part)
util.doCmd(self, c, use_undostack)