FloatOption(self, 'width', hint_digits=2),
FloatOption(self, 'height', hint_digits=2),
IntOption(self, 'max_width', hint_maximum=300),
IntOption(self, 'max_height', hint_maximum=300)]
class LocatorSetting(ComponentSetting):
component_class = Locator
setting_types = dict(alpha=FloatSetting,
always_show=BoolSetting,
height=FloatSetting,
max_height=IntSetting,
max_width=IntSetting,
timeout=FloatSetting,
width=FloatSetting)
presets.register_component_defaults(LocatorSetting)
# TODO: Selection appearance settings.
class SelectionOverlay(Overlay):
__gproperties__ = dict(
area_dash = (
gobject.TYPE_PYOBJECT,
'area dash',
'edge dash for area selections',
gobject.PARAM_READWRITE),
area_fill = (
gobject.TYPE_PYOBJECT,
'area fill',
'background fill for area selections',
gobject.PARAM_READWRITE),
for i, f in enumerate(feature_list):
if feature == f:
break
if feature.mapping.start < f.mapping.start:
feature_list.insert(i, feature)
break
else:
feature_list.append(feature)
new_features.append(feature)
if new_features:
self.emit('changed', Change('features', 'added', new_features))
class SequenceFeatureRegistrySetting(ComponentSetting):
component_class = SequenceFeatureRegistry
presets.register_component_defaults(SequenceFeatureRegistrySetting)
# Actions:
def iter_gff_annotations(gff_file, filter=None):
for line in gff_file:
line = line.strip()
if not line or line.startswith('#'):
continue
yield GFFFeature.from_gff_line(line)
class ImportGFFAnnotations(Action):
action_name = 'import-gff-annotations'
path = ['Import', 'Sequence features', 'gff annotations']
tooltip = 'Import feature annotations from a general feature format file.'
self.categories[category][sequence_index] = None
removed_entries.append(old_entry)
changed_categories.add(category)
if removed_entries:
self.emit('changed', Change(changed_categories, 'removed', removed_entries))
def get_entry(self, category, sequence_index):
c = self.categories.get(category, None)
if c:
return c[sequence_index]
def clear(self):
self.categories = {}
self.emit('changed', Change())
def integrate(self, ancestor, name=None):
msa = ancestor.find_descendant('data.msa')
if msa is None:
msa = ancestor.integrate_descendant('data.msa')
if msa is None:
raise TypeError('no suitable parent')
self.msaview_name = msa.add(self, name)
self.msa = msa
return self.msaview_name
class SequenceInformationRegistrySetting(ComponentSetting):
component_class = SequenceInformationRegistry
presets.register_component_defaults(SequenceInformationRegistrySetting)
pos_region = self.get_position_region(pos_start, pos_end, sequence_index)
areas.append(Area(pos_region, Region(sequence_index, 1)))
return areas
def integrate(self, ancestor, name=None):
self.msaview_name = ancestor.add(self, name)
m = ancestor.find_ancestor('root')
m.descendants.register(self.features, self.features.msaview_name)
m.descendants.register(self.sequence_information, self.sequence_information.msaview_name)
return self.msaview_name
class MSASetting(ComponentSetting):
component_class = MSA
presets.register_component_defaults(MSASetting)
# Actions
class ReadFasta(Action):
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.')]
