jalviewX
File SequenceFeaturesPojo.java
Coverage histogram
0% of files have more coverage
Classes
| Class | Line # | Actions | ||||
|---|---|---|---|---|---|---|
| SequenceFeaturesPojo | 28 | 21 | 22 | 3 |
Contributing tests
This file is covered by 2 tests.
.
Source view
| 1 | /* | |
| 2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
| 3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
| 4 | * | |
| 5 | * This file is part of Jalview. | |
| 6 | * | |
| 7 | * Jalview is free software: you can redistribute it and/or | |
| 8 | * modify it under the terms of the GNU General Public License | |
| 9 | * as published by the Free Software Foundation, either version 3 | |
| 10 | * of the License, or (at your option) any later version. | |
| 11 | * | |
| 12 | * Jalview is distributed in the hope that it will be useful, but | |
| 13 | * WITHOUT ANY WARRANTY; without even the implied warranty | |
| 14 | * of MERCHANTABILITY or FITNESS FOR A PARTICULAR | |
| 15 | * PURPOSE. See the GNU General Public License for more details. | |
| 16 | * | |
| 17 | * You should have received a copy of the GNU General Public License | |
| 18 | * along with Jalview. If not, see <http://www.gnu.org/licenses/>. | |
| 19 | * The Jalview Authors are detailed in the 'AUTHORS' file. | |
| 20 | */ | |
| 21 | package jalview.json.binding.biojson.v1; | |
| 22 | ||
| 23 | import java.util.Map; | |
| 24 | import java.util.Vector; | |
| 25 | ||
| 26 | import com.github.reinert.jjschema.Attributes; | |
| 27 | ||
| 28 | public class SequenceFeaturesPojo | |
| 29 | { | |
| 30 | @Attributes( | |
| 31 | required = true, | |
| 32 | description = "Start residue position for the sequence feature") | |
| 33 | private int xStart; | |
| 34 | ||
| 35 | @Attributes( | |
| 36 | required = true, | |
| 37 | description = "End residue position for the sequence feature") | |
| 38 | private int xEnd; | |
| 39 | ||
| 40 | @Attributes( | |
| 41 | required = true, | |
| 42 | minItems = 1, | |
| 43 | maxItems = 2147483647, | |
| 44 | description = "Reference to the sequence in the alignment<br> (more like a foreign key)") | |
| 45 | private String sequenceRef; | |
| 46 | ||
| 47 | @Attributes( | |
| 48 | required = true, | |
| 49 | description = "The name or type of the SequenceFeature") | |
| 50 | private String type; | |
| 51 | ||
| 52 | @Attributes(required = false, description = "Score") | |
| 53 | private Float score; | |
| 54 | ||
| 55 | @Attributes(required = false, description = "Description for the feature") | |
| 56 | private String description; | |
| 57 | ||
| 58 | @Attributes( | |
| 59 | required = false, | |
| 60 | description = "Additional metadata for the feature") | |
| 61 | private Map<String, Object> otherDetails; | |
| 62 | ||
| 63 | @Attributes(required = false, description = "Fill colour") | |
| 64 | private String fillColor; | |
| 65 | ||
| 66 | @Attributes(required = true, description = "Feature group") | |
| 67 | private String featureGroup; | |
| 68 | ||
| 69 | @Attributes( | |
| 70 | required = false, | |
| 71 | description = "URL links associated to the feature") | |
| 72 | private Vector<String> links; | |
| 73 | ||
| 74 | 0 |  public SequenceFeaturesPojo() |
| 75 | { | |
| 76 | } | |
| 77 | ||
| 78 | 12 | public SequenceFeaturesPojo(String sequenceRef) |
| 79 | { | |
| 80 | 12 | this.sequenceRef = sequenceRef; |
| 81 | } | |
| 82 | ||
| 83 | 12 | public String getFillColor() |
| 84 | { | |
| 85 | 12 | return "#" + fillColor; |
| 86 | } | |
| 87 | ||
| 88 | 12 | public void setFillColor(String fillColor) |
| 89 | { | |
| 90 | 12 | this.fillColor = fillColor; |
| 91 | } | |
| 92 | ||
| 93 | 12 | public int getXstart() |
| 94 | { | |
| 95 | 12 | return xStart; |
| 96 | } | |
| 97 | ||
| 98 | 12 | public void setXstart(int xStart) |
| 99 | { | |
| 100 | 12 | this.xStart = xStart; |
| 101 | } | |
| 102 | ||
| 103 | 12 | public int getXend() |
| 104 | { | |
| 105 | 12 | return xEnd; |
| 106 | } | |
| 107 | ||
| 108 | 12 | public void setXend(int xend) |
| 109 | { | |
| 110 | 12 | this.xEnd = xend; |
| 111 | } | |
| 112 | ||
| 113 | 12 | public String getType() |
| 114 | { | |
| 115 | 12 | return type; |
| 116 | } | |
| 117 | ||
| 118 | 12 | public void setType(String type) |
| 119 | { | |
| 120 | 12 | this.type = type; |
| 121 | } | |
| 122 | ||
| 123 | 12 | public Float getScore() |
| 124 | { | |
| 125 | 12 | return score; |
| 126 | } | |
| 127 | ||
| 128 | 12 | public void setScore(Float score) |
| 129 | { | |
| 130 | 12 | this.score = score; |
| 131 | } | |
| 132 | ||
| 133 | 12 | public String getDescription() |
| 134 | { | |
| 135 | 12 | return description; |
| 136 | } | |
| 137 | ||
| 138 | 12 | public void setDescription(String description) |
| 139 | { | |
| 140 | 12 | this.description = description; |
| 141 | } | |
| 142 | ||
| 143 | 12 | public Map<String, Object> getOtherDetails() |
| 144 | { | |
| 145 | 12 | return otherDetails; |
| 146 | } | |
| 147 | ||
| 148 | 12 | public void setOtherDetails(Map<String, Object> otherDetails) |
| 149 | { | |
| 150 | 12 | this.otherDetails = otherDetails; |
| 151 | } | |
| 152 | ||
| 153 | 12 | public Vector<String> getLinks() |
| 154 | { | |
| 155 | 12 | return links; |
| 156 | } | |
| 157 | ||
| 158 | 12 | public void setLinks(Vector<String> links) |
| 159 | { | |
| 160 | 12 | this.links = links; |
| 161 | } | |
| 162 | ||
| 163 | 12 | public String getFeatureGroup() |
| 164 | { | |
| 165 | 12 | return featureGroup; |
| 166 | } | |
| 167 | ||
| 168 | 12 | public void setFeatureGroup(String featureGroup) |
| 169 | { | |
| 170 | 12 | this.featureGroup = featureGroup; |
| 171 | } | |
| 172 | ||
| 173 | 12 | public String getSequenceRef() |
| 174 | { | |
| 175 | 12 | return sequenceRef; |
| 176 | } | |
| 177 | ||
| 178 | 0 | public void setSequenceRef(String sequenceRef) |
| 179 | { | |
| 180 | 0 | this.sequenceRef = sequenceRef; |
| 181 | } | |
| 182 | ||
| 183 | } |