001package org.biopax.paxtools.model.level2; 002 003import java.util.Set; 004 005/** 006 * This class represents a discrete biological unit used when describing 007 * pathways. This is the root class for all biological concepts in the ontology, 008 * which include pathways, interactions and physical entities. As the most 009 * abstract class in the ontology, instances of the entity class should never be 010 * created. Instead, more specific classes should be used. Synonyms: thing, 011 * object, bioentity. 012 */ 013public interface entity 014 extends Level2Element, XReferrable, InteractionParticipant 015{ 016// -------------------------- OTHER METHODS -------------------------- 017 018 /** 019 * This method adds the given text to the avaialability set. 020 * 021 * @param AVAILABILITY_TEXT a string describing the availability of this data 022 * (e.g. a copyright statement). 023 */ 024 public void addAVAILABILITY(String AVAILABILITY_TEXT); 025 026 /** 027 * This method adds the given value to the DATA_SOURCE set. 028 * 029 * @param DATA_SOURCE_INST a free text description of the source of this data, 030 * e.g. a database or person name. 031 */ 032 public void addDATA_SOURCE(dataSource DATA_SOURCE_INST); 033 034 /** 035 * This method adds the given value to the SYNONYMS set. 036 * 037 * @param SYNONYMS_TEXT a new name to be added 038 */ 039 public void addSYNONYMS(String SYNONYMS_TEXT); 040// --------------------- ACCESORS and MUTATORS--------------------- 041 042 /** 043 * The contents of this set can be modified but semantic consistency is not 044 * guaranteed. Using {@link #addAVAILABILITY(String)} and {@link 045 * #removeAVAILABILITY(String)} is recommended. 046 * 047 * @return a set of strings describing the availability of this data (e.g. a 048 * copyright statement). 049 */ 050 051 public Set<String> getAVAILABILITY(); 052 053 054 /** 055 * This method returns a set of free text descriptions of the source of this 056 * data, e.g. a database or person name. This property should be used to 057 * describe the source of the data. This is meant to be used by databases that 058 * export their data to the BioPAX format or by systems that are integrating 059 * data from multiple sources. The granularity of use (specifying the data 060 * source in many or few instances) is up to the user. It is intended that this 061 * property report the last data source, not all data sources that the data has 062 * passed through from creation. 063 * 064 * The contents of this set can be modified but semantic consistency is not 065 * guaranteed. Using {@link #addDATA_SOURCE} and {@link #removeDATA_SOURCE} is 066 * recommended. 067 * 068 * @return a set of free text descriptions of the source of this data, e.g. a 069 * database or person name. 070 */ 071 public Set<dataSource> getDATA_SOURCE(); 072 073 074 /** 075 * This method returns the preferred full name for this entity. 076 * 077 * @return preferred full name for this entity 078 */ 079 public String getNAME(); 080 081 /** 082 * This method sets an abbreviated name for this entity, preferably a name that 083 * is short enough to be used in a visualization application to label a 084 * graphical element that represents this entity. If no short name is 085 * available, an xref may be used for this purpose by the visualization 086 * application. 087 * 088 * @return an abbreviated name suitable for display. 089 */ 090 public String getSHORT_NAME(); 091 092 /** 093 * The contents of this set can be modified but semantic consistency is not 094 * guaranteed. Using {@link #addSYNONYMS} and {@link #removeSYNONYMS} is 095 * recommended. 096 * 097 * @return a set of synonyms for the name of this entity. This should include 098 * the values of the NAME and SHORT-NAME property so that it is easy to 099 * find all known names in one place. 100 */ 101 public Set<String> getSYNONYMS(); 102 103 /** 104 * This method removes the given text from the avaialability set. 105 * 106 * @param AVAILABILITY_TEXT a string describing the availability of this data 107 * (e.g. a copyright statement). 108 */ 109 public void removeAVAILABILITY(String AVAILABILITY_TEXT); 110 111 /** 112 * This method removes the given value from the DATA_SOURCE set. 113 * 114 * @param DATA_SOURCE_INST a free text description of the source of this data, 115 * e.g. a database or person name. 116 */ 117 public void removeDATA_SOURCE(dataSource DATA_SOURCE_INST); 118 119 /** 120 * This method removes the given value from the SYNONYMS set. 121 * 122 * @param SYNONYMS_TEXT a new name to be added 123 */ 124 public void removeSYNONYMS(String SYNONYMS_TEXT); 125 126 /** 127 * This method overrides existing set with the new set. If you want to append 128 * to the existing set, use {@link #addAVAILABILITY} instead. 129 * 130 * @param AVAILABILITY_TEXT a set of strings describing the availability of 131 * this data (e.g. a copyright statement). 132 */ 133 public void setAVAILABILITY(Set<String> AVAILABILITY_TEXT); 134 135 /** 136 * This method overrides existing set with the new set. If you want to append 137 * to the existing set, use {@link #addDATA_SOURCE} instead. 138 * 139 * @param DATA_SOURCE a set of free text descriptions of the source of this 140 * data, e.g. a database or person name. 141 */ 142 public void setDATA_SOURCE(Set<dataSource> DATA_SOURCE); 143 144 /** 145 * This method sets the preferred full name for this entity to the given 146 * value. 147 * 148 * @param NAME The preferred full name for this entity. 149 */ 150 public void setNAME(String NAME); 151 152 /** 153 * An abbreviated name for this entity, preferably a name that is short enough 154 * to be used in a visualization application to label a graphical element that 155 * represents this entity. If no short name is available, an xref may be used 156 * for this purpose by the visualization application. 157 * 158 * @param SHORT_NAME new short name 159 */ 160 public void setSHORT_NAME(String SHORT_NAME); 161 162 /** 163 * This method overrides existing set with the new set. If you want to append 164 * to the existing set, use {@link #addSYNONYMS} instead. 165 * 166 * @param SYNONYMS a set of names for this entity. 167 */ 168 public void setSYNONYMS(Set<String> SYNONYMS); 169}