Class | Description |
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ClusterByShortPath |
Dialog of function clustering by oriented shortest paths
Launch the task of creating clusters
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ClusterByShortPathTask |
Task of creating networks from clusters by copy of nodes and edges from the current network
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CreateConnectionsBetweenNests |
Create edges between nests from a reference network
Delete all old edges between nests
Search if every edge of reference network belongs to different network nest
Several edges having same interaction type become one edge (left and right are got as same)
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CreateNestNetwork |
Create a new network composed of nests from networks selected in a list by NestUtils.selectNetworks
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DestroyUnusedNetworksAsNest |
Propose a list of unused networks by the active nest network
After selecting networks to be destroyed, ask confirmation
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DestroyUnusedNetworksAsNestTask |
Destroy networks of the list
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FindCommonNodes |
Create an belonging matrix for every node in module
Complete it by node size and frequency in modules
Delete and create intersection edges containing number of common nodes
Put number of nodes in node attribute
Put number of common nodes in edge attributes
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InteractionGraph |
Put the graph from Cytoscape network in practical data structure
Compute degrees and put them in a structure which can be sorted by several ways
Compute the shortest path matrix used in clustering by breadth first search
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InterOf2SelectedNests |
Create networks from intersection of 2 nest networks (nodes and edges)
Delete edges and nodes of intersection in 2 networks
Dialog of confirmation displaying nodes to bet deleted
Transfer positions to created intersection network
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ListComponents |
List component in current network and nests from species described as BiNoM syntax
Network generally converted from a CellDesigner file or URL
Species are identified by attribute CELLDESIGNER_SPECIES
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ListNodesByNest |
List nodes in current network inside nest or not
Result in a text box
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MergeSelectedNests |
Merge selected nests using NestMerging
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ModuleVisualStyle |
Create a style to visualize nest networks
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NestInNodeAttribute |
Create a node attribute containing nest name where it is in the current network
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NestMerging |
Merge several nests and create merged networks
Replace selected nodes by one merged and delete edges in nest network
Transfer positions to created network
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NestUtils |
Class gathering useful functions shared by several classes of nest manager:
- Access by different structure to list of nodes or edges
- Edges linking nodes
- Reconnection between 2 nodes by copy an edge from a reference network
- Create network made of nests
- Pack part of network in nest keeping connections
- Transfer positions, delete edges
- Dialog to select one or several networks
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PackInNestNode |
Pack nodes inside selected networks in nest pointing to these networks
Position of nest are the mean position of nodes
Edges are recreated between nests and nodes with the same attributes
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RecreateLostConnectionsInsideNests |
Create edges inside nested network from a reference network
Delete all old edges of nested network
Search edges which nodes belong to the nested network
Copy edges attributes included from the reference network to every nested network
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RecreateLostConnectionsInsideNestsTask |
Task of updating edges inside all nests
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ShortPathClustering |
Algorithm of clustering based on
a distance computed by minimum linkage of the oriented shortest path
when shortest paths are equal, the bigger number of links is get as minimum
The ceiling size of cluster and the max length of shortest paths are parameters
the condition to stop clustering is the
- the maximal length of shortest paths is reached
- the number of clusters remaining in the queue is less than 2
When the size of an union of clusters exceed the ceiling size, it is not created and
the biggest is out of the queue and kept apart
the start list of nodes is sorted by in degree, so sources are first
every created cluster is placed at the end of the queue to slow the increasing of size
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