2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.json.binding.biojson.v1;
23 import java.util.ArrayList;
25 import com.github.reinert.jjschema.Attributes;
27 public class SequenceGrpPojo
31 description = "The <a href=\"#colourScheme\">Colour Scheme</a> applied to the Sequence Group")
32 private String colourScheme;
36 description = "The name assigned to the seqGroup")
37 private String groupName;
41 description = "Serial version identifier for the <b>seqGroup</b> object model")
42 private String description;
46 description = "Determines if the seqGroup border should be visible or not")
47 private boolean displayBoxes;
51 description = "Determines if the texts of the group is displayed or not")
52 private boolean displayText;
56 description = "Determines if the residues text for the group is coloured")
57 private boolean colourText;
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;
66 description = "The index of the group’s first residue in the alignment space")
71 description = "The index of the group’s last residue in the alignment space")
78 description = "An array of the unique id's for the sequences belonging to the group")
79 private ArrayList<String> sequenceRefs = new ArrayList<String>();
81 public String getColourScheme()
86 public void setColourScheme(String colourScheme)
88 this.colourScheme = colourScheme;
91 public String getGroupName()
96 public void setGroupName(String groupName)
98 this.groupName = groupName;
101 public String getDescription()
106 public void setDescription(String description)
108 this.description = description;
111 public boolean isDisplayBoxes()
116 public void setDisplayBoxes(boolean displayBoxes)
118 this.displayBoxes = displayBoxes;
121 public boolean isDisplayText()
126 public void setDisplayText(boolean displayText)
128 this.displayText = displayText;
131 public boolean isColourText()
136 public void setColourText(boolean colourText)
138 this.colourText = colourText;
141 public boolean isShowNonconserved()
143 return showNonconserved;
146 public void setShowNonconserved(boolean showNonconserved)
148 this.showNonconserved = showNonconserved;
151 public int getStartRes()
156 public void setStartRes(int startRes)
158 this.startRes = startRes;
161 public int getEndRes()
166 public void setEndRes(int endRes)
168 this.endRes = endRes;
171 public ArrayList<String> getSequenceRefs()
176 public void setSequenceRefs(ArrayList<String> sequenceRefs)
178 this.sequenceRefs = sequenceRefs;