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

Class InteractionWriterOptions

    • Field Detail

      • OUTPUT_OPTION_KEY

        public static final String OUTPUT_OPTION_KEY
        The option to select where to write the interactions. It is usually a String(path to a file), OutputStream, File or Writer but it can vary depending on the writers. Some specialised writers may not need this option (such as database writers).
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        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 writers that can only write binary interactions but it may not be recognized by writers that can write n-ary interactions.
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        Constant Field Values

      • OUTPUT_FORMAT_OPTION_KEY

        public static final String OUTPUT_FORMAT_OPTION_KEY
        The file format (for instance psi25_xml, mitab). It must be a String. This option must always be provided to the InteractionWriterFactory to select the adapted writer implementation that can write a specific file format. It may not be adapted to more specialised writers such as database writers.
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        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 write. It has to be an enum of type ComplexType (binary,n-ary, self). If this option is not provided, the default value will vary depending on the type of the datasource. Usually, two values can be provided for this option : - n-ary : we want to write interactions with a list of participants. They can have only two participants and so be binary but they should all implement Interaction interface. When the writer only write binary interactions,it is up to them to expand the complexes in several binary interactions so only binary interactions are written. 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 - binary : we want to write interactions with only two participants and implementing BinaryInteraction interface. - the other complex types such a self_inter and self_intra are equivalent to n-ary. It should write interactions implementing Interaction interface but not always BinaryInteraction so may need to be exapnded by the writer if it can only write binary interactions
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        Constant Field Values

      • INTERACTION_CATEGORY_OPTION_KEY

        public static final String INTERACTION_CATEGORY_OPTION_KEY
        The option to describe the type of interaction object we want to write. It has to be an enum of type InteractionCategory(mixed, modelled, evidence, complex, basic). If this option is not provided, the default value will vary depending on the type of the interaction writer. The PSI-MI XML 3.0 writer do not need this option.
        See Also:
        Constant Field Values

    • Constructor Detail

      • InteractionWriterOptions

        public InteractionWriterOptions()