001 /** 002 * Copyright (C) 2010 The Roslin Institute <contact andy.law@roslin.ed.ac.uk> 003 * 004 * This file is part of the Ensembl Java API demonstration project developed by the 005 * Bioinformatics Group at The Roslin Institute, The Royal (Dick) School of 006 * Veterinary Studies, University of Edinburgh. 007 * 008 * This is free software: you can redistribute it and/or modify 009 * it under the terms of the GNU General Public License (version 3) as published by 010 * the Free Software Foundation. 011 * 012 * This software is distributed in the hope that it will be useful, 013 * but WITHOUT ANY WARRANTY; without even the implied warranty of 014 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 015 * GNU General Public License for more details. 016 * 017 * You should have received a copy of the GNU General Public License 018 * in this software distribution. If not, see <http://www.gnu.org/licenses/gpl-3.0.html/>. 019 */ 020 021 package uk.ac.roslin.ensembl.datasourceaware.core; 022 023 import uk.ac.roslin.ensembl.model.core.CoordSystemType; 024 import uk.ac.roslin.ensembl.model.core.CoordinateSystem; 025 import uk.ac.roslin.ensembl.config.EnsemblCoordSystemType; 026 027 /** 028 * 029 * @author paterson 030 */ 031 public class DACoordinateSystem implements CoordinateSystem { 032 033 protected Integer id = null; 034 protected Integer speciesID = null; 035 protected EnsemblCoordSystemType type; 036 protected Integer rank; 037 protected String version; 038 protected Boolean defaultVersion = false; 039 protected Boolean sequenceLevel = false; 040 041 public DACoordinateSystem() { 042 043 } 044 045 @Override 046 public Boolean isTopLevel() { 047 048 return (rank !=null) ? this.rank.equals(1) : false; 049 } 050 051 /** 052 * Get the value of speciesID 053 * 054 * @return the value of speciesID 055 */ 056 @Override 057 public Integer getSpeciesID() { 058 return speciesID; 059 } 060 061 /** 062 * Set the value of speciesID 063 * 064 * @param speciesID new value of speciesID 065 */ 066 @Override 067 public void setSpeciesID(Integer speciesID) { 068 this.speciesID = speciesID; 069 } 070 071 072 /** 073 * Get the value of id 074 * 075 * @return the value of id 076 */ 077 @Override 078 public Integer getId() { 079 return id; 080 } 081 082 /** 083 * Set the value of id 084 * 085 * @param id new value of id 086 */ 087 @Override 088 public void setId(Integer id) { 089 this.id = id; 090 } 091 092 /** 093 * Get the value of type 094 * 095 * @return the value of type 096 */ 097 @Override 098 public EnsemblCoordSystemType getType() { 099 return type; 100 } 101 102 /** 103 * Set the value of type 104 * 105 * @param type new value of type 106 */ 107 @Override 108 public void setType(CoordSystemType type) { 109 this.type = (EnsemblCoordSystemType) type; 110 } 111 /** 112 * Get the value of version 113 * 114 * @return the value of version 115 */ 116 @Override 117 public String getVersion() { 118 return version; 119 } 120 121 /** 122 * Set the value of version 123 * 124 * @param version new value of version 125 */ 126 @Override 127 public void setVersion(String version) { 128 this.version = version; 129 } 130 131 /** 132 * Get the value of rank 133 * 134 * @return the value of rank 135 */ 136 @Override 137 public Integer getRank() { 138 return rank; 139 } 140 141 /** 142 * Set the value of rank 143 * 144 * @param rank new value of rank 145 */ 146 @Override 147 public void setRank(Integer rank) { 148 this.rank = rank; 149 } 150 151 @Override 152 public Boolean isDefaultVersion() { 153 return defaultVersion; 154 } 155 156 @Override 157 public void setDefaultVersion(Boolean defaultVersion) { 158 this.defaultVersion = defaultVersion; 159 } 160 161 @Override 162 public Boolean isSequenceLevel() { 163 return sequenceLevel; 164 } 165 166 @Override 167 public void setSequenceLevel(Boolean sequenceLevel) { 168 this.sequenceLevel = sequenceLevel; 169 } 170 171 }