Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/util/simplegraph.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 """ |
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2 Fencepost-simple graph structure implementation. |
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3 """ |
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4 # Currently (2013.7.12) only used in easing the parsing of graph datatype data. |
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5 |
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6 |
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7 class SimpleGraphNode: |
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8 """ |
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9 Node representation. |
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10 """ |
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11 |
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12 def __init__(self, index, **data): |
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13 """ |
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14 :param index: index of this node in some parent list |
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15 :type index: int |
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16 :param data: any extra data that needs to be saved |
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17 :type data: (variadic dictionary) |
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18 """ |
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19 # a bit application specific (could be 'id') |
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20 self.index = index |
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21 self.data = data |
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22 |
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23 |
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24 class SimpleGraphEdge: |
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25 """ |
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26 Edge representation. |
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27 """ |
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28 |
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29 def __init__(self, source_index, target_index, **data): |
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30 """ |
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31 :param source_index: index of the edge's source node in some parent list |
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32 :type source_index: int |
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33 :param target_index: index of the edge's target node in some parent list |
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34 :type target_index: int |
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35 :param data: any extra data that needs to be saved |
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36 :type data: (variadic dictionary) |
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37 """ |
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38 self.source_index = source_index |
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39 self.target_index = target_index |
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40 self.data = data |
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41 |
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42 |
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43 class SimpleGraph: |
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44 """ |
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45 Each node is unique (by id) and stores its own index in the node list/odict. |
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46 Each edge is represented as two indeces into the node list/odict. |
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47 Both nodes and edges allow storing extra information if needed. |
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48 |
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49 Allows: |
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50 multiple edges between two nodes |
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51 self referential edges (an edge from a node to itself) |
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52 |
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53 These graphs are not specifically directed but since source and targets on the |
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54 edges are listed - it could easily be used that way. |
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55 """ |
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56 |
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57 def __init__(self, nodes=None, edges=None): |
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58 # use an odict so that edge indeces actually match the final node list indeces |
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59 self.nodes = nodes or {} |
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60 self.edges = edges or [] |
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61 |
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62 def add_node(self, node_id, **data): |
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63 """ |
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64 Adds a new node only if it doesn't already exist. |
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65 :param node_id: some unique identifier |
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66 :type node_id: (hashable) |
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67 :param data: any extra data that needs to be saved |
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68 :type data: (variadic dictionary) |
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69 :returns: the new node |
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70 """ |
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71 if node_id in self.nodes: |
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72 return self.nodes[node_id] |
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73 node_index = len(self.nodes) |
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74 new_node = SimpleGraphNode(node_index, **data) |
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75 self.nodes[node_id] = new_node |
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76 return new_node |
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77 |
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78 def add_edge(self, source_id, target_id, **data): |
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79 """ |
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80 Adds a new node only if it doesn't already exist. |
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81 :param source_id: the id of the source node |
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82 :type source_id: (hashable) |
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83 :param target_id: the id of the target node |
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84 :type target_id: (hashable) |
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85 :param data: any extra data that needs to be saved for the edge |
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86 :type data: (variadic dictionary) |
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87 :returns: the new node |
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88 |
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89 ..note: that, although this will create new nodes if necessary, there's |
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90 no way to pass `data` to them - so if you need to assoc. more data with |
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91 the nodes, use `add_node` first. |
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92 """ |
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93 # adds target_id to source_id's edge list |
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94 # adding source_id and/or target_id to nodes if not there already |
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95 if source_id not in self.nodes: |
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96 self.add_node(source_id) |
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97 if target_id not in self.nodes: |
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98 self.add_node(target_id) |
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99 new_edge = SimpleGraphEdge(self.nodes[source_id].index, self.nodes[target_id].index, **data) |
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100 self.edges.append(new_edge) |
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101 return new_edge |
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102 |
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103 def gen_node_dicts(self): |
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104 """ |
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105 Returns a generator that yields node dictionaries in the form: |
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106 { 'id': <the nodes unique id>, 'data': <any additional node data> } |
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107 """ |
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108 for node_id, node in self.nodes.items(): |
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109 yield {'id': node_id, 'data': node.data} |
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110 |
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111 def gen_edge_dicts(self): |
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112 """ |
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113 Returns a generator that yields node dictionaries in the form:: |
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114 |
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115 { |
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116 'source': <the index of the source node in the graph's node list>, |
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117 'target': <the index of the target node in the graph's node list>, |
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118 'data' : <any additional edge data> |
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119 } |
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120 """ |
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121 for edge in self.edges: |
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122 yield {'source': edge.source_index, 'target': edge.target_index, 'data': edge.data} |
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123 |
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124 def as_dict(self): |
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125 """ |
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126 Returns a dictionary of the form:: |
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127 |
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128 { 'nodes': <a list of node dictionaries>, 'edges': <a list of node dictionaries> } |
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129 """ |
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130 return {'nodes': list(self.gen_node_dicts()), 'edges': list(self.gen_edge_dicts())} |