001package org.biopax.paxtools.model.level3; 002 003/** 004 * Tagger interface for protein, dna and rna entities 005 */ 006public interface SequenceEntityReference extends EntityReference 007{ 008 009 /** 010 * An organism, e.g. 'Homo sapiens'. This is the organism that the entity is found in. Pathways may 011 * not have an organism associated with them, for instance, reference pathways from KEGG. 012 * Sequence-based entities (DNA, protein, RNA) may contain an xref to a sequence database that 013 * contains organism information, in which case the information should be consistent with the value 014 * for ORGANISM. 015 * 016 * @return the organism for this gene. 017 */ 018 BioSource getOrganism(); 019 020 /** 021 * An organism, e.g. 'Homo sapiens'. This is the organism that the entity is found in. Pathways may 022 * not have an organism associated with them, for instance, reference pathways from KEGG. 023 * Sequence-based entities (DNA, protein, RNA) may contain an xref to a sequence database that 024 * contains organism information, in which case the information should be consistent with the value 025 * for ORGANISM. 026 * 027 * @param source new organism for this gene 028 */ 029 void setOrganism(BioSource source); 030 031 /** 032 * Polymer sequence in uppercase letters. For DNA, usually A,C,G,T letters representing the 033 * nucleosides of adenine, cytosine, guanine and thymine, respectively; for RNA, usually A, C, U, 034 * G; for protein, usually the letters corresponding to the 20 letter IUPAC amino acid code. 035 * @return sequence - primary structure of a biopolymer. 036 */ 037 String getSequence(); 038 039 /** 040 * Polymer sequence in uppercase letters. For DNA, usually A,C,G,T letters representing the 041 * nucleosides of adenine, cytosine, guanine and thymine, respectively; for RNA, usually A, C, U, 042 * G; for protein, usually the letters corresponding to the 20 letter IUPAC amino acid code. 043 * @param sequence Polymer sequence in uppercase letters. 044 */ 045 void setSequence(String sequence); 046 047 048}