def __init__(self, model, parent=None): AbstractMetaAnalysisWizard.__init__(self, model=model, meta_f_str=None, parent=parent) self.analysis_label = "Phylogenetic Meta Analysis" self.setWindowTitle(self.analysis_label) # Refine studies page self.removePage(Page_RefineStudies) self.refine_studies_page = RefineStudiesPage(model=model, need_species=True) self.setPage(Page_RefineStudies, self.refine_studies_page) # Tree selection page self.tree_page = TreePage() self.setPage(Page_TreePage, self.tree_page) # phylogenetic model design page self.phylo_model_design_page = PhyloModelDesignPage() self.setPage(Page_PhyloModelDesignPage, self.phylo_model_design_page) # data location page and parameters page self.parameters_page = PhyloAnalysisDetailsPage(model=model, default_method="ML") self.setPage(Page_Parameters, self.parameters_page)
class PhyloMAWizard(AbstractMetaAnalysisWizard): def __init__(self, model, parent=None): AbstractMetaAnalysisWizard.__init__(self, model=model, meta_f_str=None, parent=parent) self.analysis_label = "Phylogenetic Meta Analysis" self.setWindowTitle(self.analysis_label) # Refine studies page self.removePage(Page_RefineStudies) self.refine_studies_page = RefineStudiesPage(model=model, need_species=True) self.setPage(Page_RefineStudies, self.refine_studies_page) # Tree selection page self.tree_page = TreePage() self.setPage(Page_TreePage, self.tree_page) # phylogenetic model design page self.phylo_model_design_page = PhyloModelDesignPage() self.setPage(Page_PhyloModelDesignPage, self.phylo_model_design_page) # data location page and parameters page self.parameters_page = PhyloAnalysisDetailsPage(model=model, default_method="REML") self.setPage(Page_Parameters, self.parameters_page) def nextId_helper(self, page_id): if page_id == Page_ChooseEffectSize: return Page_Parameters elif page_id == Page_Parameters: return Page_RefineStudies elif page_id == Page_RefineStudies: return Page_TreePage elif page_id == Page_TreePage: return Page_PhyloModelDesignPage elif page_id == Page_PhyloModelDesignPage: return Page_Summary elif page_id == Page_Summary: return -1 # Summary Page def get_summary(self): ''' Make a summary string to show the user at the end of the wizard summarizing most of the user selections ''' return wizard_summary(wizard=self, next_id_helper=self.nextId_helper, summary_page_id=Page_Summary, analysis_label=self.analysis_label) ##### getters ##### def get_tree_and_filename(self): return self.tree_page.get_tree_and_filename() def get_tree(self): tree = self.get_tree_and_filename()['tree'] return tree ### Phylo Model Design Page #### def get_phylo_model_type(self): # BM or OU return self.phylo_model_design_page.get_phylo_model_type() def get_lambda(self): return self.phylo_model_design_page.get_lambda() def get_alpha(self): return self.phylo_model_design_page.get_alpha() def get_randomly_resolve_polytomies(self): return self.phylo_model_design_page.get_randomly_resolve_polytomies() ### phylo meta-analysis details page #### def get_data_location(self): return self.parameters_page.get_data_location() def get_random_effects_method(self): return self.parameters_page.get_random_effects_method() def get_conf_level(self): return self.parameters_page.get_conf_level() def get_include_species_as_random_factor(self): return self.parameters_page.get_include_species_as_random_factor() def get_plot_params(self): return self.parameters_page.get_plot_params()