Function PrintEventList has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

def PrintEventList(events,out_list):
  '''print out events.  recurse if the list actually has another list
  in it'''
  if type(events) == type(""):
    if len(events) > 0:

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Function MakeNewick has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

def MakeNewick(res,node_link,frac):
    ''' generate the newick string '''

    node1 = res['node1']
    node2 = res['node2']

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Function GetPaths has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

def GetPaths(root_node,this_node,root_lca,this_lca,path_dict,output_f):
  last_stop = True
  if this_lca.AreRelated(root_lca):
    for kid in this_node.kid_nodes:
      kid_lca = this_node.lca_map[this_lca][kid]

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Function __init__ has 28 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def __init__(self,raw_name,arbre):
        # remove any leading angled brackets
        raw_name = raw_name.lstrip(">")

        # handle mixed underscore and dot environment

Function GetSibDists has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

    def GetSibDists(self,species_tree):
        '''get distances between all siblings on the tree'''
        parent_dict = {}
        dist_list = []
        for leaf in self.leaf_dict.values():

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Function EventGuideAdjust has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

def EventGuideAdjust(event_list,event_guide,model):
    ''' provide score adjustment based on event guide '''
    score_adjust = 0.0
    for event in event_list:
        if event in event_guide:

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Function GetChildLeaves has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

    def GetChildLeaves(this_node,parent_node,other_nodes):

        merge_list = []
        for kid_node in other_nodes:
            if parent_node in this_node.leaf_dict:

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Function GetNodeLinkDict has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

    def GetNodeLinkDict(this_node,node_link_dict):

        this_node.link_dict_visited = True
        leaf_dict = this_node.leaf_dict

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Function UnrootedLeaving has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

    def UnrootedLeaving(this_node):

        other_nodes = this_node.GetOtherNodes()
        for parent_node in other_nodes:
            child_nodes = list(set(other_nodes).difference(set([parent_node])))

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Avoid deeply nested control flow statements.

Open

                    if model.luca == "Root" or model.special == "hr":
                        if ancestor is not species_tree.root:
                            sscore = self.max_float

Function treePrint has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def treePrint(self,newickString):

    count = 0
        # implement sorting so that you can compare trees in a quick
        # and dirty way

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Avoid deeply nested control flow statements.

Open

                    if node_pair[0].name == model.outgroup:
                        node_link.TryRoot(node_pair)
                    if node_pair[1].name == model.outgroup:

Avoid deeply nested control flow statements.

Open

                    if len(raw_los_list) > 0:
                        sscore = node_link.max_float

                    # make sure losses only percolated down, not up
                    for ind in range(len(los_list)):

Avoid deeply nested control flow statements.

Open

                    if sscore >= node_link.best_score:
                        continue
                else:

Avoid deeply nested control flow statements.

Open

                    if num_dups > 0:
                        # need to deal w/ situation where dups erase
                        # information about ranges, which leads to
                        # problems when you're trying to prevent time
                        # paradoxes.  see notes from 05.25.10.

Avoid deeply nested control flow statements.

Open

                    if node_relation == 1:
                        this_paradox.append([hgt_str,accep_list])
        else:

Function TryTransfer has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

def TryTransfer(parent1,parent2,node1,node2,node_link,lca_tables):

Avoid deeply nested control flow statements.

Open

                    if ancestor in cur_lca_scores:
                        if sscore > cur_lca_scores[ancestor]:
                            continue

                # results datastructure

Avoid deeply nested control flow statements.

Open

                    for event in event0:
                        if 'hgt' in event:
                            hgt_parts = event.split(' --> ')
                            hgt_list.append(hgt_parts[1])

Avoid deeply nested control flow statements.

Open

                    if node_pair[1].name == model.outgroup:
                        node_link.TryRoot(node_pair)
                else: