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}