2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.datamodel;
28 public class Annotation
31 public String displayCharacter = "";
34 public String description = ""; // currently used as mouse over
37 public char secondaryStructure = ' '; // recognises H, E and S(?)
44 // add visual cues here
50 * Creates a new Annotation object.
61 public Annotation(String displayChar, String desc, char ss, float val)
63 displayCharacter = displayChar;
65 secondaryStructure = ss;
71 * Creates a new Annotation object.
84 public Annotation(String displayChar, String desc, char ss, float val,
87 this(displayChar, desc, ss, val);
92 * Copy constructor New annotation takes on the same (or duplicated)
93 * attributes as the given template
98 public Annotation(Annotation that)
100 if (that == null || this == that)
104 if (that.displayCharacter != null)
105 displayCharacter = new String(that.displayCharacter);
106 if (that.description != null)
107 description = new String(that.description);
108 secondaryStructure = that.secondaryStructure;
110 colour = that.colour;
115 * Value only annotation.
118 * value at this annotation position
120 public Annotation(float val)
122 this(null, null, ' ', val,null);