Package psidev.psi.mi.jami.xml.model.extension.factory.options

Class PsiXmlWriterOptions

  • public class PsiXmlWriterOptions
extends InteractionWriterOptions
    Class that lists all possible options for PsiXml Writer. The options listed in InteractionWriterOptions are also valid for a PsiXml Writer
    Since:
    05/12/13
    Version:
    $Id$
    Author:
    Marine Dumousseau (marine@ebi.ac.uk)

    • Field Detail

      • ELEMENT_WITH_ID_CACHE_OPTION

        public static final String ELEMENT_WITH_ID_CACHE_OPTION
        The object instance implementing the PsiXmlObjectCache interface. This object will be used to index MI objects which will be referenced in several places and to assign unique ids. If this option is not provided, it will use a InMemoryIdentityObjectCache by default for compact Xml writers and it will use a InMemoryLightIdentityObjectCache by default for expanded XML writers.
        See Also:
        Constant Field Values

      • XML_TYPE_OPTION

        public static final String XML_TYPE_OPTION
        The PSI-XML flavour which has to be an enum of type PsiXmlType (compact or expanded) If this option is not provided, it will write expanded XML files.
        See Also:
        Constant Field Values

      • XML_ENTRY_ATTRIBUTES_OPTION

        public static final String XML_ENTRY_ATTRIBUTES_OPTION
        The option to provide a collection of annotations to write in each entry. If this option is not provided, it will not write any attributes in each entry.
        See Also:
        Constant Field Values

      • XML_EXTENDED_OPTION

        public static final String XML_EXTENDED_OPTION
        The option to select specialised XML writers using specific object instances such as expanded interactions, participants, features, confidences, parameters, host organisms, xrefs. It has to be a boolean value. If this option is not provided, it will be set to false by default.
        See Also:
        Constant Field Values

      • XML_NAMES_OPTION

        public static final String XML_NAMES_OPTION
        The option to select XML writers that will write shortLabel, fullName and aliases for named experiments, named interactions, named participants and named features. It has to be a boolean value. If this option is not provided, it will be set to false by default.
        See Also:
        Constant Field Values

      • XML_VERSION_OPTION

        public static final String XML_VERSION_OPTION
        The option to choose the PSI-XML version. It has to be an enum of type PsiXmlVersion. If this option is not provided, it will write PSI-XML
        See Also:
        Constant Field Values

      • COMPACT_XML_EXPERIMENT_SET_OPTION

        public static final String COMPACT_XML_EXPERIMENT_SET_OPTION
        The option to provide a set of experiment that will be used to list all unique experiments in a compact xml file.. If this option is not provided, it will use a default identity set that will be based on object equality.
        See Also:
        Constant Field Values

      • COMPACT_XML_INTERACTOR_SET_OPTION

        public static final String COMPACT_XML_INTERACTOR_SET_OPTION
        The option to provide a set of interactors that will be used to list all unique interactors in a compact xml file.. If this option is not provided, it will use a default identity set that will be based on object equality.
        See Also:
        Constant Field Values

      • COMPACT_XML_AVAILABILITY_SET_OPTION

        public static final String COMPACT_XML_AVAILABILITY_SET_OPTION
        The option to provide a set of String that will be used to list all unique availabilities in a compact xml file.. If this option is not provided, it will use a default HashSet that will be based on object hashcode.
        See Also:
        Constant Field Values

      • XML_INTERACTION_SET_OPTION

        public static final String XML_INTERACTION_SET_OPTION
        The option to provide a set of interactions that will be used to list all unique interactions in a compact xml file.. If this option is not provided, it will use a default identity set that will be based on object equality.
        See Also:
        Constant Field Values

      • DEFAULT_RELEASE_DATE_OPTION

        public static final String DEFAULT_RELEASE_DATE_OPTION
        The option to provide a default release date for each entry source. If this option is not provided, it will use the current date as the release date.
        See Also:
        Constant Field Values

      • DEFAULT_SOURCE_OPTION

        public static final String DEFAULT_SOURCE_OPTION
        The option to provide a default source for each entry source in case the interactions do not have a source. If this option is not provided, it will use an unknown source with the default release date.
        See Also:
        Constant Field Values

      • WRITE_COMPLEX_AS_INTERACTOR_OPTION

        public static final String WRITE_COMPLEX_AS_INTERACTOR_OPTION
        The option to write complexes as interactions (false) or as interactors (true) when a participant is in fact a sub-complex. It is a boolean value. If this option is not provided, it will be set to false by default (complexes written as interactions).
        See Also:
        Constant Field Values

    • Constructor Detail

      • PsiXmlWriterOptions

        public PsiXmlWriterOptions()