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;
20 import java.awt.Color;
23 * Holds all annotation values for a position in an AlignmentAnnotation row
28 public class Annotation
30 /** Character label - also shown below histogram */
31 public String displayCharacter = "";
34 * Text label for position: shown in mouse over and displayed on secondary
37 public String description = "";
40 * Secondary structure symbol: Protein symbols are H, E and S(?), RNA are
41 * WUSS/Vienna plus extended pseudoknot symbols
43 public char secondaryStructure = ' ';
45 /** Score for the position - used in histograms, line graphs and for shading */
48 /** Colour for position */
52 * Creates a new Annotation object.
63 public Annotation(String displayChar, String desc, char ss, float val)
65 displayCharacter = displayChar;
67 secondaryStructure = ss;
72 * Creates a new Annotation object.
85 public Annotation(String displayChar, String desc, char ss, float val,
88 this(displayChar, desc, ss, val);
93 * Copy constructor New annotation takes on the same (or duplicated)
94 * attributes as the given template
99 public Annotation(Annotation that)
101 if (that == null || this == that)
105 if (that.displayCharacter != null)
106 displayCharacter = new String(that.displayCharacter);
107 if (that.description != null)
108 description = new String(that.description);
109 secondaryStructure = that.secondaryStructure;
111 colour = that.colour;
115 * Value only annotation.
118 * value at this annotation position
120 public Annotation(float val)
122 this(null, null, ' ', val);
126 * human readable representation of an annotation row element.
128 * Format is 'display Char','secondary Structure
129 * Char',"description",score,[colourstring]
131 * fields may be missing if they are null, whitespace, or equivalent to
135 public String toString()
137 StringBuffer sb = new StringBuffer();
138 if (displayCharacter != null)
141 sb.append(displayCharacter);
147 if (secondaryStructure != 0
148 && !("" + displayCharacter).equals("" + secondaryStructure))
151 sb.append(secondaryStructure);
157 if (description != null && description.length() > 0)
160 sb.append(description);
166 if (value != Float.NaN)
177 sb.append(colour.getRed());
179 sb.append(colour.getGreen());
181 sb.append(colour.getBlue());
184 return sb.toString();