jalviewX
File SequenceGrpPojo.java
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| Class | Line # | Actions | ||||
|---|---|---|---|---|---|---|
| SequenceGrpPojo | 27 | 20 | 20 | 2 |
Contributing tests
This file is covered by 2 tests.
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| 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.ArrayList; | |
| 24 | ||
| 25 | import com.github.reinert.jjschema.Attributes; | |
| 26 | ||
| 27 | public class SequenceGrpPojo | |
| 28 | { | |
| 29 | @Attributes( | |
| 30 | required = false, | |
| 31 | description = "The <a href=\"#colourScheme\">Colour Scheme</a> applied to the Sequence Group") | |
| 32 | private String colourScheme; | |
| 33 | ||
| 34 | @Attributes( | |
| 35 | required = true, | |
| 36 | description = "The name assigned to the seqGroup") | |
| 37 | private String groupName; | |
| 38 | ||
| 39 | @Attributes( | |
| 40 | required = false, | |
| 41 | description = "Serial version identifier for the <b>seqGroup</b> object model") | |
| 42 | private String description; | |
| 43 | ||
| 44 | @Attributes( | |
| 45 | required = false, | |
| 46 | description = "Determines if the seqGroup border should be visible or not") | |
| 47 | private boolean displayBoxes; | |
| 48 | ||
| 49 | @Attributes( | |
| 50 | required = false, | |
| 51 | description = "Determines if the texts of the group is displayed or not") | |
| 52 | private boolean displayText; | |
| 53 | ||
| 54 | @Attributes( | |
| 55 | required = false, | |
| 56 | description = "Determines if the residues text for the group is coloured") | |
| 57 | private boolean colourText; | |
| 58 | ||
| 59 | @Attributes( | |
| 60 | required = false, | |
| 61 | description = "Boolean value indicating whether residues should only be shown <br/>that are different from current reference or consensus sequence") | |
| 62 | private boolean showNonconserved; | |
| 63 | ||
| 64 | @Attributes( | |
| 65 | required = true, | |
| 66 | description = "The index of the group’s first residue in the alignment space") | |
| 67 | private int startRes; | |
| 68 | ||
| 69 | @Attributes( | |
| 70 | required = true, | |
| 71 | description = "The index of the group’s last residue in the alignment space") | |
| 72 | private int endRes; | |
| 73 | ||
| 74 | @Attributes( | |
| 75 | required = true, | |
| 76 | minItems = 1, | |
| 77 | uniqueItems = true, | |
| 78 | description = "An array of the unique id's for the sequences belonging to the group") | |
| 79 | private ArrayList<String> sequenceRefs = new ArrayList<String>(); | |
| 80 | ||
| 81 | 3 |  public String getColourScheme() |
| 82 | { | |
| 83 | 3 | return colourScheme; |
| 84 | } | |
| 85 | ||
| 86 | 3 | public void setColourScheme(String colourScheme) |
| 87 | { | |
| 88 | 3 | this.colourScheme = colourScheme; |
| 89 | } | |
| 90 | ||
| 91 | 3 | public String getGroupName() |
| 92 | { | |
| 93 | 3 | return groupName; |
| 94 | } | |
| 95 | ||
| 96 | 3 | public void setGroupName(String groupName) |
| 97 | { | |
| 98 | 3 | this.groupName = groupName; |
| 99 | } | |
| 100 | ||
| 101 | 3 | public String getDescription() |
| 102 | { | |
| 103 | 3 | return description; |
| 104 | } | |
| 105 | ||
| 106 | 3 | public void setDescription(String description) |
| 107 | { | |
| 108 | 3 | this.description = description; |
| 109 | } | |
| 110 | ||
| 111 | 3 | public boolean isDisplayBoxes() |
| 112 | { | |
| 113 | 3 | return displayBoxes; |
| 114 | } | |
| 115 | ||
| 116 | 3 | public void setDisplayBoxes(boolean displayBoxes) |
| 117 | { | |
| 118 | 3 | this.displayBoxes = displayBoxes; |
| 119 | } | |
| 120 | ||
| 121 | 3 | public boolean isDisplayText() |
| 122 | { | |
| 123 | 3 | return displayText; |
| 124 | } | |
| 125 | ||
| 126 | 3 | public void setDisplayText(boolean displayText) |
| 127 | { | |
| 128 | 3 | this.displayText = displayText; |
| 129 | } | |
| 130 | ||
| 131 | 3 | public boolean isColourText() |
| 132 | { | |
| 133 | 3 | return colourText; |
| 134 | } | |
| 135 | ||
| 136 | 3 | public void setColourText(boolean colourText) |
| 137 | { | |
| 138 | 3 | this.colourText = colourText; |
| 139 | } | |
| 140 | ||
| 141 | 3 | public boolean isShowNonconserved() |
| 142 | { | |
| 143 | 3 | return showNonconserved; |
| 144 | } | |
| 145 | ||
| 146 | 3 | public void setShowNonconserved(boolean showNonconserved) |
| 147 | { | |
| 148 | 3 | this.showNonconserved = showNonconserved; |
| 149 | } | |
| 150 | ||
| 151 | 3 | public int getStartRes() |
| 152 | { | |
| 153 | 3 | return startRes; |
| 154 | } | |
| 155 | ||
| 156 | 3 | public void setStartRes(int startRes) |
| 157 | { | |
| 158 | 3 | this.startRes = startRes; |
| 159 | } | |
| 160 | ||
| 161 | 3 | public int getEndRes() |
| 162 | { | |
| 163 | 3 | return endRes; |
| 164 | } | |
| 165 | ||
| 166 | 3 | public void setEndRes(int endRes) |
| 167 | { | |
| 168 | 3 | this.endRes = endRes; |
| 169 | } | |
| 170 | ||
| 171 | 15 | public ArrayList<String> getSequenceRefs() |
| 172 | { | |
| 173 | 15 | return sequenceRefs; |
| 174 | } | |
| 175 | ||
| 176 | 0 | public void setSequenceRefs(ArrayList<String> sequenceRefs) |
| 177 | { | |
| 178 | 0 | this.sequenceRefs = sequenceRefs; |
| 179 | } | |
| 180 | ||
| 181 | } |