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 }