Package psidev.psi.mi.jami.factory.options

Class MIDataSourceOptions

  • Direct Known Subclasses:
    MIFileDataSourceOptions
    public class MIDataSourceOptions
extends Object
    Class that lists all possible options for MIDataSource
    Since:
    05/12/13
    Version:
    $Id$
    Author:
    Marine Dumousseau (marine@ebi.ac.uk)

    • Field Detail

      • INTERACTION_CATEGORY_OPTION_KEY

        public static final String INTERACTION_CATEGORY_OPTION_KEY
        The option to describe the type of interaction object we want to return. It has to be an enum of type InteractionCategory (evidence, modelled, basic, complex, mixed). If this option is not provided, the default value will vary depending on the type of the datasource. Some datasources such as PSI-MI XML 3.0 files do not need this option as it can read a mix of interaction evidences and modelled
        See Also:
        Constant Field Values

      • COMPLEX_TYPE_OPTION_KEY

        public static final String COMPLEX_TYPE_OPTION_KEY
        The option to describe the complex type of interaction object we want to return. It has to be an enum of type ComplexType (binary,n-ary, self). If this option is not provided, the default value will be n-ary. Usually, two values can be provided for this option : - n-ary : we want to have interactions with a list of participants. They can have only two participants and so be binary but they should all implement Interaction interface - binary : we want to have interactions with only two participants and implementing BinaryInteraction interface. When the datasources provide n-ary interactions, it is up to them to expand the complexes in several binary interactions so only binary interactions are returned. When COMPLEX_TYPE_OPTION_KEY is binary, the option COMPLEX_EXPANSION_OPTION_KEY should be used to specify the complex expansion in case n-ary interactions need to be expanded - the other complex types such a self_inter and self_intra are equivalent to n-ary. It should return interactions implementing Interaction interface but not always BinaryInteraction
        See Also:
        Constant Field Values

      • COMPLEX_EXPANSION_OPTION_KEY

        public static final String COMPLEX_EXPANSION_OPTION_KEY
        The option to provide a complex expansion method to expand n-ary interactions in binary interactions. It has to be an object instance which implements the ComplexExpansionMethod interface This option make sense in case of datasources that may provide n-ary interactions but will not be recognized by datasources providing only binary interactions.
        See Also:
        Constant Field Values

      • STREAMING_OPTION_KEY

        public static final String STREAMING_OPTION_KEY
        The option to indicates if we want a datasource only providing an Iterator of interactions (streaming) or if we want a datasource that can return the all collection of interactions (not streaming). It has to be a boolean value. If this option is not provided, it will be true by default
        See Also:
        Constant Field Values

      • INPUT_TYPE_OPTION_KEY

        public static final String INPUT_TYPE_OPTION_KEY
        The input type (for instance psi25_xml, mitab). It must be a String. This option must always be provided to the MIDataSourceFactory to select the adapted datasource implementation that can read the datasource.
        See Also:
        Constant Field Values

      • INTERACTOR_FACTORY_OPTION_KEY

        public static final String INTERACTOR_FACTORY_OPTION_KEY
        The interactor factory used to create the proper interactor instance based on the interactor type and/or xrefs It must be an instance of InteractorFactory. If this option is not specified, it will create a new DefaultInteractorFactory to create the interactors or use another factory depending on the data source implementations.
        See Also:
        Constant Field Values

    • Constructor Detail

      • MIDataSourceOptions

        public MIDataSourceOptions()