001/**
002 * Copyright (C) 2010-2015 The Roslin Institute <contact andy.law@roslin.ed.ac.uk>
003 *
004 * This file is part of JEnsembl: a Java API to Ensembl data sources developed by the
005 * Bioinformatics Group at The Roslin Institute, The Royal (Dick) School of
006 * Veterinary Studies, University of Edinburgh.
007 *
008 * Project hosted at: http://jensembl.sourceforge.net
009 *
010 * This is free software: you can redistribute it and/or modify
011 * it under the terms of the GNU General Public License (version 3) as published by
012 * the Free Software Foundation.
013 *
014 * This software is distributed in the hope that it will be useful,
015 * but WITHOUT ANY WARRANTY; without even the implied warranty of
016 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
017 * GNU General Public License for more details.
018 *
019 * You should have received a copy of the GNU General Public License
020 * in this software distribution. If not, see: http://opensource.org/licenses/gpl-3.0.html
021 */
022package uk.ac.roslin.ensembl.model.compara;
023
024import java.io.Serializable;
025import uk.ac.roslin.ensembl.model.Coordinate;
026
027
028/**
029 * Utility class used to hold properties of an aligned homology object (gene)
030 * in a HomologyPairRelationship. The compara database doesnt hold enough info 
031 * to instantiate objects fully.
032 * Because a DAHomologyPairRelationship is typically instantiated from the
033 * compara databases - the target gene in particular is likely to not
034 * be a core-datasource aware object, and therefore species & and mapping details
035 * are only simple fields grabbed from compara: these are held in properties
036 * objects
037 * @author tpaterso
038 */
039public class HomologyAlignmentProperties implements Serializable {
040
041    private String cigarLine = null;
042    private String peptideID = null;
043    private String geneID = null;
044    private String speciesName = 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
052
053    public String getCigarLine() {
054        return cigarLine;
055    }
056
057    public void setCigarLine(String cigarLine) {
058        this.cigarLine = cigarLine;
059    }
060
061    public String getGeneID() {
062        return geneID;
063    }
064
065    public void setGeneID(String geneID) {
066        this.geneID = geneID;
067    }
068
069    public String getPeptideID() {
070        return peptideID;
071    }
072
073    public void setPeptideID(String peptideID) {
074        this.peptideID = peptideID;
075    }
076
077    public Integer getPercentCovered() {
078        return percentCovered;
079    }
080
081    public void setPercentCovered(Integer percentCovered) {
082        this.percentCovered = percentCovered;
083    }
084
085    public Integer getPercentIdentity() {
086        return percentIdentity;
087    }
088
089    public void setPercentIdentity(Integer percentIdentity) {
090        this.percentIdentity = percentIdentity;
091    }
092
093    public Integer getPercentSimilar() {
094        return percentSimilar;
095    }
096
097    public void setPercentSimilar(Integer percentSimilar) {
098        this.percentSimilar = percentSimilar;
099    }
100
101    public String getSpeciesName() {
102        return speciesName;
103    }
104
105    public void setSpeciesName(String speciesName) {
106        this.speciesName = speciesName;
107    }
108
109    public String getSequenceName() {
110        return sequenceName;
111    }
112
113    public void setSequenceName(String seqName) {
114        this.sequenceName = seqName;
115    }
116
117    public Coordinate getCoords() {
118        return coords;
119    }
120
121    public void setCoords(Coordinate coords) {
122        this.coords = coords;
123    }
124
125
126}