path = ['Import', 'Sequence features', 'gff annotations']
tooltip = 'Import feature annotations from a general feature format file.'
@classmethod
def applicable(cls, target, coord=None):
if target.msaview_classname == 'data.msa':
return cls(target.features)
if target.msaview_classname == 'data.sequence_features':
return cls(target)
def run(self):
gff = open(self.params['location'])
features = []
for annotation in iter_gff_annotations(gff):
annotation.sequence_index = get_id_index(self.target.msa.ids, annotation.sequence_id)
if annotation.sequence_index is None:
continue
annotation.mapping = map_region_to_msa(annotation.region, self.target.msa.msa_positions[annotation.sequence_index])
if annotation.mapping is None:
continue
features.append(annotation)
self.target.add_features(features)
def get_options(self):
path = ''
if self.target and self.target.msa.path:
path = self.target.msa.path + '.gff'
return [Option(propname='location', default=path, value=path, nick='Location', tooltip='Where to read the GFF annotations from.')]
register_action(ImportGFFAnnotations)
@classmethod
def applicable(cls, target, coord=None):
cm = target.get_compute_manager()
if not cm:
return
a = cls(target, coord)
if not cm.computing():
a.path = list(cls.path)
a.path[-1] += ' (nothing to do)'
return a
def run(self):
self.target.get_compute_manager().compute_all()
register_action(ComputeAll)
class AbortAllComputations(Action):
action_name = "abort-all-computations"
path = ['Computation', 'Abort all computations']
tooltip = "Abort all running background tasks."
@classmethod
def applicable(cls, target, coord=None):
cm = target.get_compute_manager()
if not (cm and cm.computing()):
return
return cls(target, coord)
def run(self):
self.target.get_compute_manager().abort_all()
action_name = 'open-fasta-alignment'
path = ['Open', 'Fasta alignment']
tooltip = 'Read a gapped fasta alignment file.'
@classmethod
def applicable(cls, target=None, coord=None):
if target.msaview_classname == 'data.msa':
return cls(target)
def get_options(self):
return [Option(propname='location', default='', value='', nick='Location', tooltip='The alignment file to read.')]
def run(self):
self.target.read_fasta(open(self.params['location']))
register_action(ReadFasta)
class SaveFasta(Action):
action_name = 'save-fasta-alignment'
path = ['Save', 'Fasta alignment']
tooltip = 'Save alignment in gapped fasta format.'
@classmethod
def applicable(cls, target=None, coord=None):
if target.msaview_classname == 'data.msa':
return cls(target)
def get_options(self):
try:
path = os.path.splitext(self.target.path)[0] + '.gfasta'
except:
