001package org.biopax.paxtools.model.level3;
002
003import java.util.Set;
004
005
006public interface Pathway extends Process,Controller
007{
008// -------------------------- OTHER METHODS --------------------------
009
010        // Property PATHWAY-COMPONENTS
011
012        Set<Process> getPathwayComponent();
013
014        void addPathwayComponent(Process components);
015
016        void removePathwayComponent(Process components);
017
018
019
020        // Property PATHWAY-ORDER
021
022        Set<PathwayStep> getPathwayOrder();
023
024        void addPathwayOrder(PathwayStep order);
025
026        void removePathwayOrder(PathwayStep order);
027
028        
029
030        /**
031         * An organism, e.g. 'Homo sapiens'. This is the organism that the entity is found in. Pathways may
032         * not have an organism associated with them, for instance, reference pathways from KEGG.
033         * Sequence-based entities (DNA, protein, RNA) may contain an xref to a sequence database that
034         * contains organism information, in which case the information should be consistent with the value
035         * for ORGANISM.
036         *
037         * @return the organism for this gene.
038         */
039        BioSource getOrganism();
040
041        /**
042         * An organism, e.g. 'Homo sapiens'. This is the organism that the entity is found in. Pathways may
043         * not have an organism associated with them, for instance, reference pathways from KEGG.
044         * Sequence-based entities (DNA, protein, RNA) may contain an xref to a sequence database that
045         * contains organism information, in which case the information should be consistent with the value
046         * for ORGANISM.
047         *
048         * @param source new organism for this gene
049         */
050        void setOrganism(BioSource source);
051}