diff --git a/dnaplotlib2/__init__.py b/dnaplotlib2/__init__.py index a620523..7d2b5fc 100644 --- a/dnaplotlib2/__init__.py +++ b/dnaplotlib2/__init__.py @@ -8,4 +8,4 @@ # """ # paraSBOLv # """ -from .parasbolv import * +# from .parasbolv import * diff --git a/dnaplotlib2/dnaplotlib2.py b/dnaplotlib2/dnaplotlib2.py index 5e79a9c..1ecd60f 100644 --- a/dnaplotlib2/dnaplotlib2.py +++ b/dnaplotlib2/dnaplotlib2.py @@ -327,7 +327,7 @@ def dfs(self, obj): if isinstance(self.node, sbol3.Component): self.visited.add(self.node) - + # print(f"node display id ->>> {self.node.display_id}, roles ->> {self.node.roles}, instance of ->> {self.node.instance_of}") # if object doesn't contain subcomponents features, get its attributes if self.node.features == []: @@ -395,10 +395,7 @@ def bio_render(self, biodesign): mol_pos = (50,50) self.biodesign = biodesign - # print(f'biodesign backbones len : {len(self.biodesign.backbones)}') - ## draw molecular species - # print(f"self.biodesgin.molecular_species {self.biodesign.molecular_species}") if len(self.biodesign.molecular_species) != 0: for mol in self.biodesign.molecular_species: bound, end_point = self.renderer.draw_glyph(ax, mol['molecular_species_type'], position=mol_pos) @@ -426,70 +423,4 @@ def bio_render(self, biodesign): plt.show() - # def draw_construct(self, biodesign, part_list=[]): - # import parasbolv as psv - # import matplotlib.pyplot as plt - - # # Draw construct - # self.biodesign = biodesign - # self.part_list = part_list - - # i = 0 - - # for b in self.biodesign.backbones: - - # for part in b: - # self.part_list.append(list(part.values())) - - # self.part_dict[i] = self.part_list - # i = i + 1 - - # # print(self.part_list) - # self.part_list = [] - # # print(self.part_list) - - # # from collections import namedtuple - # self.interaction_dict = {} - # interaction_list = [] - # # interaction = namedtuple('interaction', ['starting_glyph', 'ending_glyph', 'interaction_type', 'interaction_parameters']) - - # i = 0 - - # for interaction in self.biodesign.interaction: - # print('part_dict - > ',self.part_dict) - # print('interaction - >', interaction) - - - # interaction['start_object'] = list(interaction['start_object'].values()) - # interaction['end_object'] = list(interaction['end_object'].values()) - - # # interaction[] - # interaction_list.append([interaction['start_object'], interaction['end_object'], interaction['interaction_type'], - # {'color': (0.75,0,0)}]) - # # interaction_list.append(interaction(part_list[2], part_list[4], 'control', {'color': (0, 0.75, 0), - # # 'direction':'reverse'})) - # self.interaction_dict[i] = interaction_list - # i = i + 1 - # interaction_list = [] - # print('part_dict - > ',self.part_dict) - # print('interaction_list -> ',interaction_list) - # print('self.interaction_dict - > ', self.interaction_dict) - - - # # todo- create a loop to draw a list of backbones - - # construct = psv.Construct(self.part_dict[0], self.renderer, interaction_list=self.interaction_dict[0]) - - # fig, ax, baseline_start, baseline_end, bounds = construct.draw() - # ax.plot([baseline_start[0], baseline_end[0]], [baseline_start[1], baseline_end[1]], color=(0,0,0), linewidth=1.5, zorder=0) - - # construct2 = psv.Construct(self.part_dict[1], self.renderer, interaction_list=self.interaction_dict[1], - # fig=fig, ax=ax, start_position=(0,60), additional_bounds_list=[bounds]) - # construct2.update_bounds() - # fig, ax, baseline_start, baseline_end, bounds = construct2.draw() - # ax.plot([baseline_start[0], baseline_end[0]], [baseline_start[1], baseline_end[1]], color=(0,0,0), linewidth=1.5, zorder=0) - - # plt.show() - - - # # def draw_construct(self, biodesign, part_list): + \ No newline at end of file