X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAnnotation.java;h=93b6ff69bfd57b10bd2d3b0d7926a9e9bf9396e4;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=e0c49c8ab5ab8df48a5745309f6f1fa61fc42ea6;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java index e0c49c8..93b6ff6 100755 --- a/src/jalview/datamodel/Annotation.java +++ b/src/jalview/datamodel/Annotation.java @@ -1,79 +1,187 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ -package jalview.datamodel; - -import java.awt.*; - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class Annotation -{ - /** DOCUMENT ME!! */ - public String displayCharacter = ""; - - /** DOCUMENT ME!! */ - public String description = ""; // currently used as mouse over - - /** DOCUMENT ME!! */ - public char secondaryStructure = ' '; // recognises H and E - - /** DOCUMENT ME!! */ - public float value; - - // add visual cues here - - /** DOCUMENT ME!! */ - public Color colour = Color.black; - - /** - * Creates a new Annotation object. - * - * @param displayChar DOCUMENT ME! - * @param desc DOCUMENT ME! - * @param ss DOCUMENT ME! - * @param val DOCUMENT ME! - */ - public Annotation(String displayChar, String desc, char ss, float val) - { - displayCharacter = displayChar; - description = desc; - secondaryStructure = ss; - value = val; - } - - /** - * Creates a new Annotation object. - * - * @param displayChar DOCUMENT ME! - * @param desc DOCUMENT ME! - * @param ss DOCUMENT ME! - * @param val DOCUMENT ME! - * @param colour DOCUMENT ME! - */ - public Annotation(String displayChar, String desc, char ss, float val, - Color colour) - { - this(displayChar, desc, ss, val); - this.colour = colour; - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1) + * Copyright (C) 2014 The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.datamodel; + +import java.awt.Color; + +/** + * Holds all annotation values for a position in an AlignmentAnnotation row + * + * @author $author$ + * @version $Revision$ + */ +public class Annotation +{ + /** Character label - also shown below histogram */ + public String displayCharacter = ""; + + /** + * Text label for position: shown in mouse over and displayed on secondary + * structure glyphs + */ + public String description = ""; + + /** + * Secondary structure symbol: Protein symbols are H, E and S(?), RNA are + * WUSS/Vienna plus extended pseudoknot symbols + */ + public char secondaryStructure = ' '; + + /** Score for the position - used in histograms, line graphs and for shading */ + public float value; + + /** Colour for position */ + public Color colour; + + /** + * Creates a new Annotation object. + * + * @param displayChar + * DOCUMENT ME! + * @param desc + * DOCUMENT ME! + * @param ss + * DOCUMENT ME! + * @param val + * DOCUMENT ME! + */ + public Annotation(String displayChar, String desc, char ss, float val) + { + displayCharacter = displayChar; + description = desc; + secondaryStructure = ss; + value = val; + } + + /** + * Creates a new Annotation object. + * + * @param displayChar + * DOCUMENT ME! + * @param desc + * DOCUMENT ME! + * @param ss + * DOCUMENT ME! + * @param val + * DOCUMENT ME! + * @param colour + * DOCUMENT ME! + */ + public Annotation(String displayChar, String desc, char ss, float val, + Color colour) + { + this(displayChar, desc, ss, val); + this.colour = colour; + } + + /** + * Copy constructor New annotation takes on the same (or duplicated) + * attributes as the given template + * + * @param that + * template annotation + */ + public Annotation(Annotation that) + { + if (that == null || this == that) + { + return; + } + if (that.displayCharacter != null) + displayCharacter = new String(that.displayCharacter); + if (that.description != null) + description = new String(that.description); + secondaryStructure = that.secondaryStructure; + value = that.value; + colour = that.colour; + } + + /** + * Value only annotation. + * + * @param val + * value at this annotation position + */ + public Annotation(float val) + { + this(null, null, ' ', val); + } + + /** + * human readable representation of an annotation row element. + * + * Format is 'display Char','secondary Structure + * Char',"description",score,[colourstring] + * + * fields may be missing if they are null, whitespace, or equivalent to + * Float.NaN + */ + @Override + public String toString() + { + StringBuffer sb = new StringBuffer(); + if (displayCharacter != null) + { + sb.append("\'"); + sb.append(displayCharacter); + sb.append("\'"); + } + { + sb.append(","); + } + if (secondaryStructure != 0 + && !("" + displayCharacter).equals("" + secondaryStructure)) + { + sb.append("\'"); + sb.append(secondaryStructure); + sb.append("\'"); + } + { + sb.append(","); + } + if (description != null && description.length() > 0) + { + sb.append("\""); + sb.append(description); + sb.append("\""); + } + { + sb.append(","); + } + if (value != Float.NaN) + { + sb.append(value); + } + if (colour != null) + { + if (sb.length() > 0) + { + sb.append(","); + } + sb.append("["); + sb.append(colour.getRed()); + sb.append(","); + sb.append(colour.getGreen()); + sb.append(","); + sb.append(colour.getBlue()); + sb.append("]"); + } + return sb.toString(); + } +}