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IMP Reference Guide
2.22.0
The Integrative Modeling Platform
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A class to represent a node in a spatiotemporal process. More...
A class to represent a node in a spatiotemporal process.
Each graphNode contains a list of it's component subcoplexes, an array of scores, a time index and a list of pointers to nodes to which edges coming from this node point.
Definition at line 12 of file graphNode.py.
Public Member Functions | |
| def | __init__ |
| Initialize a node. More... | |
| def | __repr__ |
| String representation of a graphNode. More... | |
| def | add_edge |
| Add a directed edge to the node. More... | |
| def | add_score |
| Update the score list by appending score. More... | |
| def | get_edges |
| Return the list of edges for this node. More... | |
| def | get_index |
| Return the node's index. More... | |
| def | get_label |
| Return the node's index. More... | |
| def | get_scores |
| Return the scores array. More... | |
| def | get_subcomplex_components |
| Return a list of subcomplexes in this node's representation. More... | |
| def | get_time |
| Return the time associated with this node. More... | |
| def | get_weight |
| Return the weight of the node. More... | |
| def | init_graphNode |
| Function that initiates a graph node with specific time, label, and expected_subcomplexes. More... | |
| def | set_expected_subcomplexes |
| Set the list of possible subcomplex components. More... | |
| def | set_index |
| Set an index to label node's identity. More... | |
| def | set_label |
| Set an index to label node's identity. More... | |
| def | set_scores |
| Set the score data for this node. More... | |
| def | set_subcomplex_components |
| Set the list of subcomplex components. More... | |
| def | set_time |
| Set the time. More... | |
| def IMP.spatiotemporal.graphNode.graphNode.__init__ | ( | self | ) |
Initialize a node.
Definition at line 17 of file graphNode.py.
| def IMP.spatiotemporal.graphNode.graphNode.__repr__ | ( | self | ) |
String representation of a graphNode.
Definition at line 29 of file graphNode.py.
| def IMP.spatiotemporal.graphNode.graphNode.add_edge | ( | self, | |
| edge | |||
| ) |
Add a directed edge to the node.
Expects a graphNode object.
Definition at line 127 of file graphNode.py.
| def IMP.spatiotemporal.graphNode.graphNode.add_score | ( | self, | |
| score | |||
| ) |
Update the score list by appending score.
Definition at line 161 of file graphNode.py.
| def IMP.spatiotemporal.graphNode.graphNode.get_edges | ( | self | ) |
Return the list of edges for this node.
Definition at line 139 of file graphNode.py.
| def IMP.spatiotemporal.graphNode.graphNode.get_index | ( | self | ) |
Return the node's index.
Definition at line 81 of file graphNode.py.
| def IMP.spatiotemporal.graphNode.graphNode.get_label | ( | self | ) |
Return the node's index.
Definition at line 92 of file graphNode.py.
| def IMP.spatiotemporal.graphNode.graphNode.get_scores | ( | self | ) |
Return the scores array.
Definition at line 171 of file graphNode.py.
| def IMP.spatiotemporal.graphNode.graphNode.get_subcomplex_components | ( | self | ) |
Return a list of subcomplexes in this node's representation.
Definition at line 103 of file graphNode.py.
| def IMP.spatiotemporal.graphNode.graphNode.get_time | ( | self | ) |
Return the time associated with this node.
Definition at line 149 of file graphNode.py.
| def IMP.spatiotemporal.graphNode.graphNode.get_weight | ( | self | ) |
Return the weight of the node.
A weight refers in this case to the sum score of the scores list.
Definition at line 97 of file graphNode.py.
| def IMP.spatiotemporal.graphNode.graphNode.init_graphNode | ( | self, | |
| time, | |||
| label, | |||
| scorestr, | |||
| subcomplexstr, | |||
| expected_subcomplexes | |||
| ) |
Function that initiates a graph node with specific time, label, and expected_subcomplexes.
Scores and components are extracted from files named scorestr and subcomplexstr respectively. Returns a single graphNode object.
| time | string, time point in the stepwise temporal process |
| label | string, a number label for the graphNode |
| scorestr | string, trailing characters at the end of the file with scores for each stage of the spatiotemporal model |
| subcomplexstr | string, trailing characters after the subcomplex file, which is a list of subcomplexes included in the given label/time |
| expected_subcomplexes | list of all possible subcomplex strings in the model |
Definition at line 45 of file graphNode.py.
| def IMP.spatiotemporal.graphNode.graphNode.set_expected_subcomplexes | ( | self, | |
| expected_subcomplexes | |||
| ) |
Set the list of possible subcomplex components.
Should include all possible components across the entire spatiotemporal model
Definition at line 120 of file graphNode.py.
| def IMP.spatiotemporal.graphNode.graphNode.set_index | ( | self, | |
| index | |||
| ) |
Set an index to label node's identity.
Definition at line 76 of file graphNode.py.
| def IMP.spatiotemporal.graphNode.graphNode.set_label | ( | self, | |
| label | |||
| ) |
Set an index to label node's identity.
Definition at line 87 of file graphNode.py.
| def IMP.spatiotemporal.graphNode.graphNode.set_scores | ( | self, | |
| scores | |||
| ) |
Set the score data for this node.
Expects an list of floats which represent the total score array.
Definition at line 154 of file graphNode.py.
| def IMP.spatiotemporal.graphNode.graphNode.set_subcomplex_components | ( | self, | |
| scs, | |||
| fn | |||
| ) |
Set the list of subcomplex components.
Should be one of the standard used components.
Definition at line 108 of file graphNode.py.
| def IMP.spatiotemporal.graphNode.graphNode.set_time | ( | self, | |
| time | |||
| ) |
Set the time.
Definition at line 144 of file graphNode.py.