Package org.cytoscape.filter.transformers

Interface Transformers

public interface Transformers
Identifiers of the Transformers supplied by the core. Details of the tunable parameters for each Transformer are specified here as well.

Module: filter-api

To use this in your app, include the following dependency in your POM:

<dependency>
    <groupId>org.cytoscape</groupId>
    <artifactId>filter-api</artifactId>
</dependency>

Cytoscape Backwards Compatibility (API Interface): We expect that this interface will be used but not implemented by developers using this interface. As such, we reserve the right to add methods to the interface as part of minor version upgrades. We will not remove methods for any changes other than major version upgrades.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final String
    ADJACENCY_TRANSFORMER
    The id of the core Adjacency Transformer, which finds adjacent nodes and edges based on how they are connected to the input nodes.
    static final String
    COLUMN_FILTER
    The id of the core Column Filter, which finds nodes and edges based on their column values.
    static final String
    DEGREE_FILTER
    The id of the core Degree Filter, which finds nodes based on their degree.
    static final String
    INTERACTION_TRANSFORMER
    The id of the core Interaction Transformer, which finds nodes based on how they are connected to the input edges.
    static final String
    TOPOLOGY_FILTER
    The id of the core Topology Filter, which finds nodes based on the size of their neighborhood.

  • Field Details

    • COLUMN_FILTER

      static final String COLUMN_FILTER
      The id of the core Column Filter, which finds nodes and edges based on their column values.
      Tunable parameters:
      type
      Determines what type of objects will be matched. Must be one of the following Strings:
      • nodes
      • edges
      • nodes+edges
      caseSensitive
      Applicable only to String columns. Set this to true if the predicate should be applied to the criterion in a case-sensitive way, or false, otherwise.
      columnName
      The name of the column the predicate will be applied to.
      criterion
      When used as with a binary Predicate, this value is passed as the second argument. In the case of a ternary predicate (e.g. Predicate.BETWEEN), this should be a 2-element Number array containing the second and third arguments.
      predicate
      The Predicate used to test the column's cell value, which is passed as the first argument to the predicate.
      See Also:

    • DEGREE_FILTER

      static final String DEGREE_FILTER
      The id of the core Degree Filter, which finds nodes based on their degree.
      Tunable parameters:
      edgeType
      Determines which edges to follow when computing the degree.
      criterion
      When used as with a binary Predicate, this value is passed as the second argument. In the case of a ternary predicate (e.g. Predicate.BETWEEN), this should be a 2-element Number array containing the second and third arguments.
      predicate
      The Predicate used to test against the node degree, which is passed as the first argument to the predicate.
      See Also:

    • TOPOLOGY_FILTER

      static final String TOPOLOGY_FILTER
      The id of the core Topology Filter, which finds nodes based on the size of their neighborhood. In particular, this filter picks nodes with a particular number of neighbors within a given distance.
      Tunable parameters:
      distance
      The maximum distance to consider when computing the size of a node's neighborhood.
      threshold
      This value is passed as the second argument to the Predicate.
      predicate
      The binary Predicate used to test against the node neighborhood size, which is passed as the first argument to the predicate.
      See Also:

    • INTERACTION_TRANSFORMER

      static final String INTERACTION_TRANSFORMER
      The id of the core Interaction Transformer, which finds nodes based on how they are connected to the input edges.
      Tunable parameters:
      selectSource
      When true, adds the source nodes of the input edges to the TransformerSink.
      selectTarget
      When true, adds the target nodes of the input edges to the TransformerSink.
      See Also:

    • ADJACENCY_TRANSFORMER

      static final String ADJACENCY_TRANSFORMER
      The id of the core Adjacency Transformer, which finds adjacent nodes and edges based on how they are connected to the input nodes.
      Tunable parameters:
      action
      ADD - Output adjacent nodes/edges (as determined by the 'output' parameter) and also output all the nodes/edges that are in the input.
      REPLACE - Only output adjacent nodes/edges (as determined by the 'output' parameter).
      output
      NODES - Only output adjacent nodes.
      EDGES - Only output adjacent edges.
      NODES_AND_EDGES - Output adjacent nodes/edges.
      edgesAre
      INCOMING - Only consider adjacent nodes/edges when the adjacent edges are incoming.
      OUTGOING - Only consider adjacent nodes/edges when the adjacent edges are outgoing.
      INCOMING_AND_OUTGOING - Consider all adjacent nodes/edges.
      filterTarget
      NODES - Only apply nested sub-filter to adjacent nodes.
      EDGES - Only apply nested sub-filter to adjacent nodes.
      NODES_AND_EDGES - Apply nested sub-filter to the adjacent node and edge. Note, the filter will only pass if it is an OR filter that has separate column filters for nodes and edges.
      See Also: