001/*
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 * created at 28 Jan 2014
021 * Author: ap3
022 */
023
024package org.biojava.nbio.genome.parsers.genename;
025
026import java.io.Serializable;
027import java.util.List;
028
029public class GeneChromosomePosition implements Comparable<GeneChromosomePosition>, Serializable{
030
031        private static final long serialVersionUID = -6886306238993367835L;
032        private String geneName;
033        private String genebankId;
034        private String chromosome;
035        private Character orientation;
036        private Integer transcriptionStart;
037        private Integer transcriptionEnd;
038        private Integer cdsStart;
039        private Integer cdsEnd;
040        int exonCount;
041        private List<Integer> exonStarts;
042        private List<Integer> exonEnds;
043
044        public String getGeneName() {
045                return geneName;
046        }
047
048
049        public void setGeneName(String geneName) {
050                this.geneName = geneName;
051        }
052
053
054        public String getGenebankId() {
055                return genebankId;
056        }
057
058
059        public void setGenebankId(String genebankId) {
060                this.genebankId = genebankId;
061        }
062
063
064        public String getChromosome() {
065                return chromosome;
066        }
067
068
069        public void setChromosome(String chromosome) {
070                this.chromosome = chromosome;
071        }
072
073
074        public Character getOrientation() {
075                return orientation;
076        }
077
078
079        public void setOrientation(Character orientation) {
080                this.orientation = orientation;
081        }
082
083
084        public Integer getTranscriptionStart() {
085                return transcriptionStart;
086        }
087
088
089        public void setTranscriptionStart(Integer transcriptionStart) {
090                this.transcriptionStart = transcriptionStart;
091        }
092
093
094        public Integer getTranscriptionEnd() {
095                return transcriptionEnd;
096        }
097
098
099        public void setTranscriptionEnd(Integer transcriptionEnd) {
100                this.transcriptionEnd = transcriptionEnd;
101        }
102
103
104        public Integer getCdsStart() {
105                return cdsStart;
106        }
107
108
109        public void setCdsStart(Integer cdsStart) {
110                this.cdsStart = cdsStart;
111        }
112
113
114        public Integer getCdsEnd() {
115                return cdsEnd;
116        }
117
118
119        public void setCdsEnd(Integer cdsEnd) {
120                this.cdsEnd = cdsEnd;
121        }
122
123
124        public int getExonCount() {
125                return exonCount;
126        }
127
128
129        public void setExonCount(int exonCount) {
130                this.exonCount = exonCount;
131        }
132
133
134        public List<Integer> getExonStarts() {
135                return exonStarts;
136        }
137
138
139        public void setExonStarts(List<Integer> exonStarts) {
140                this.exonStarts = exonStarts;
141        }
142
143
144        public List<Integer> getExonEnds() {
145                return exonEnds;
146        }
147
148
149        public void setExonEnds(List<Integer> exonEnds) {
150                this.exonEnds = exonEnds;
151        }
152
153
154        @Override
155        public int compareTo(GeneChromosomePosition o) {
156                return geneName.compareTo(o.getGeneName());
157        }
158
159
160        @Override
161        public String toString() {
162                return "GeneChromosomePosition [geneName=" + geneName + ", genebankId="
163                                + genebankId + ", chromosome=" + chromosome + ", orientation="
164                                + orientation + ", transcriptionStart=" + transcriptionStart
165                                + ", transcriptionEnd=" + transcriptionEnd + ", cdsStart="
166                                + cdsStart + ", cdsEnd=" + cdsEnd + ", exonCount=" + exonCount
167                                + ", exonStarts=" + exonStarts + ", exonEnds=" + exonEnds + "]";
168        }
169
170}