def handle_msa_change(self, msa, change):
if change.has_changed('sequences'):
self.clear()
self.update()
def integrate(self, ancestor, name=None):
msa = integrate_ancestor_msa(self, ancestor)
self.msaview_name = Component.integrate(self, msa, name)
self.msa = msa
return self.msaview_name
class CScoreSetting(ComponentSetting):
component_class = CScore
presets.register_component_defaults(CScoreSetting)
presets.add_builtin('gradient:cscore_default',
Gradient.from_colorstops((0.0, presets.get_value('color:clustalx_red')),
(1.0, presets.get_value('color:clustalx_yellow')),
(1.0, Color.from_str("#8ae3d4850000"))))
class CScoreRenderer(Renderer):
__gproperties__ = dict(
gradient = (
gobject.TYPE_PYOBJECT,
'gradient',
'the colors for different bar heights in the plot',
gobject.PARAM_READWRITE),
cscore = (
gobject.TYPE_PYOBJECT,
def integrate(self, ancestor, name=None):
self.msaview_name = Labeler.integrate(self, ancestor, name)
msa = integrate_ancestor_msa(self, ancestor)
self.sequence_information = msa.sequence_information
return self.msaview_name
class GeneLocationRendererSetting(ComponentSetting):
component_class = GeneLocationRenderer
setting_types = dict(alpha=FloatSetting,
color=ColorSetting,
font=FontSetting,
transform_labels=BoolSetting,
resize_seqview_to_fit=BoolSetting)
presets.register_component_defaults(GeneLocationRendererSetting)
class FindEnsemblIDsForUniprotSequences(Action):
action_name = 'find-ensembl-ids'
path = ['Import', 'Sequence information', 'Find Ensembl links']
tooltip = 'Extract Ensembl links from already imported UniProtKB XML data.'
@classmethod
def applicable(cls, target, coord=None):
if target.msaview_classname != 'data.msa':
return
etree_category = target.sequence_information.categories.get('uniprot-etree', [None])
try:
(e for e in etree_category if (e and e.root) is not None).next()
except StopIteration:
return
