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()