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    package uk.ac.roslin.ensembl.model.compara;
021    
022    import java.io.Serializable;
023    import uk.ac.roslin.ensembl.model.Coordinate;
024    
025    
026    /**
027     * Utility class used to hold properties of an aligned homology object (gene)
028     * in a HomologyPairRelationship. The compara database doesnt hold enough info 
029     * to instantiate objects fully.
030     * Because a DAHomologyPairRelationship is typically instantiated from the
031     * compara databases - the target gene in particular is likely to not
032     * be a core-datasource aware object, and therefore species & and mapping details
033     * are only simple fields grabbed from compara: these are held in properties
034     * objects
035     * @author tpaterso
036     */
037    public class HomologyAlignmentProperties implements Serializable {
038    
039        private String cigarLine = null;
040        private String peptideID = null;
041        private String geneID = null;
042        private String speciesName = null;
043        private Integer cigarStart = null;
044        private Integer cigarEnd = null;
045        private Integer percentCovered = null;
046        private Integer percentIdentity = null;
047        private Integer percentSimilar = null;
048        private Coordinate coords = null;
049        private String sequenceName = null;
050    
051        public Integer getCigarEnd() {
052            return cigarEnd;
053        }
054    
055        public void setCigarEnd(Integer cigarEnd) {
056            this.cigarEnd = cigarEnd;
057        }
058    
059        public String getCigarLine() {
060            return cigarLine;
061        }
062    
063        public void setCigarLine(String cigarLine) {
064            this.cigarLine = cigarLine;
065        }
066    
067        public Integer getCigarStart() {
068            return cigarStart;
069        }
070    
071        public void setCigarStart(Integer cigarStart) {
072            this.cigarStart = cigarStart;
073        }
074    
075        public String getGeneID() {
076            return geneID;
077        }
078    
079        public void setGeneID(String geneID) {
080            this.geneID = geneID;
081        }
082    
083        public String getPeptideID() {
084            return peptideID;
085        }
086    
087        public void setPeptideID(String peptideID) {
088            this.peptideID = peptideID;
089        }
090    
091        public Integer getPercentCovered() {
092            return percentCovered;
093        }
094    
095        public void setPercentCovered(Integer percentCovered) {
096            this.percentCovered = percentCovered;
097        }
098    
099        public Integer getPercentIdentity() {
100            return percentIdentity;
101        }
102    
103        public void setPercentIdentity(Integer percentIdentity) {
104            this.percentIdentity = percentIdentity;
105        }
106    
107        public Integer getPercentSimilar() {
108            return percentSimilar;
109        }
110    
111        public void setPercentSimilar(Integer percentSimilar) {
112            this.percentSimilar = percentSimilar;
113        }
114    
115        public String getSpeciesName() {
116            return speciesName;
117        }
118    
119        public void setSpeciesName(String speciesName) {
120            this.speciesName = speciesName;
121        }
122    
123        public String getSequenceName() {
124            return sequenceName;
125        }
126    
127        public void setSequenceName(String seqName) {
128            this.sequenceName = seqName;
129        }
130    
131        public Coordinate getCoords() {
132            return coords;
133        }
134    
135        public void setCoords(Coordinate coords) {
136            this.coords = coords;
137        }
138    
139    
140    }