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

    • Field Detail

      • 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:
        Constant Field Values

      • 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:
        Constant Field Values

      • 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:
        Constant Field Values

      • 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:
        Constant Field Values

      • 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:
        Constant Field Values