2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
3 * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
19 package jalview.datamodel;
29 public class Annotation
32 public String displayCharacter = "";
35 public String description = ""; // currently used as mouse over
38 public char secondaryStructure = ' '; // recognises H and E
43 // add visual cues here
49 * Creates a new Annotation object.
60 public Annotation(String displayChar, String desc, char ss, float val)
62 displayCharacter = displayChar;
64 secondaryStructure = ss;
69 * Creates a new Annotation object.
82 public Annotation(String displayChar, String desc, char ss, float val,
85 this(displayChar, desc, ss, val);
90 * Copy constructor New annotation takes on the same (or duplicated)
91 * attributes as the given template
96 public Annotation(Annotation that)
98 if (that == null || this == that)
102 if (that.displayCharacter != null)
103 displayCharacter = new String(that.displayCharacter);
104 if (that.description != null)
105 description = new String(that.description);
106 secondaryStructure = that.secondaryStructure;
108 colour = that.colour;
112 * Value only annotation.
115 * value at this annotation position
117 public Annotation(float val)
119 this(null, null, ' ', val);