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3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
4 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 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 along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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21 Jalview Source Documentation
24 <h1>Jalview Source Documentation</h1>
25 <p>The file structure of the Jalview Source tree is as follows:
27 <li>README - basic info for getting started with the source tree.</li>
28 <li>LICENCE - the GPL Licence</li>
29 <li>RELEASE - contains the name of the tag for the latest
30 'official' Jalview release associated with the source.</li>
31 <li>build.xml - ant build for jalview - the 'help' task gives
32 information about each task, and there's lots of comments too.</li>
34 <li>src - all jalview source packages, including any specially
35 adapted code from other GPL programs. See <a href="developing.html">Jalview
36 Development</a> for more info.</li>
37 <li>lib - All the libraries that Jalview depends on. Every jar
38 file in this directory should be added to the classpath when building
39 or running the jalview application.</li>
40 <li>appletlib - Any libraries that are specifically required for compiling and/or running the jalviewLite applet (e.g. an applet build of Jmol).
41 <li>help - the jalview JavaHelp documents<br>
43 <li>help.hs - the main index page. This is generated by the
44 jhindexer program run by the 'buildindices' task in build.xml</li>
45 <li>help.jhm - helpTOC map - an XML document listing simple names
46 for each html page that is linked to in the help contents structure.</li>
47 <li>helpTOC.xml - the table of contents presented to the user
48 when the help is opened.</li>
49 <li>icons - widgets needed for the help system GUI</li>
50 <li>html - the help documentation. It loosely follows the
51 following structure: <br>
53 <li>calculations - pages concerning the calculations menu</li>
54 <li>webServices - pages describing web services</li>
55 <li>colourSchemes - the ways amino acids can be coloured and the
56 user interface for defining them</li>
57 <li>editing - mechanisms and interfaces for editing alignments</li>
58 <li>features - used to be the sequence features documentation,
59 but now contains all sorts of jalview 'features'.</li>
60 <li>io - getting data in and out of jalview</li>
61 <li>menus - all the menus in Jalview (and the applet)</li>
62 <li>misc - useful info</li>
63 <li>By convention, we try to maintain the whatsNew.html document
64 with each release and complete the releases.html matrix to detail
65 what has changed from one version to another.</li>
66 <li>keys.html contains all the keystrokes in Jalview - please
67 keep this up to date.</li>
72 <li>resources - files needed at run-time for jalview execution.<br>
74 <li>images - icons used by jalview</li>
75 <li>log4j and commons-logging.properties - configure default
76 appenders and logging for Jalview, castor.</li>
77 <li>embl_mapping.xml - castor mapping file for the EMBL XML
80 <li>uniprot_mapping.xml - castor mapping file for the Uniprot XML
84 <li>schemas - XML schema definitions used or understood by
86 Jalview uses castor to bind java to XML - either using mapping files
87 hand-crafted from a schema in this directory, or from java objects
88 generated from the schema and an associated set of properties. <br>
89 See the castorbinding task in the ant build.xml file for more info.
91 <li>Jalview Project Archive XML Version 1<br>
94 jalview.nodesc.properties - sourcegenerator properties file</li>
95 <li>jalview Project Archive XML Version 2<br>
96 Jalview works out which version a project is by first trying
97 to parse XML with these schema definitions, and then if there are
98 problems, falls back to the V1 schema classes.
102 jalview.properties - sourcegenerator properties file</li>
104 <li>JalviewUserColours.xsd is used by both V1 and V2 project XML
105 definitions. This schema is also used to store user colour schemes
106 externally from the project file.</li>
109 <li>utils - various resources needed when building or deploying
114 <li>Jalview.iap_xml is the InstallAnywhere XML project used to
115 create the Jalview InstallAnywhere distribution.</li>
116 <li>All the other files are bundled into this for installer
117 displays. The README_IA appears in the installation directory.</li>
120 This is a legacy directory - we intended to use jalopy for
121 standardising the jalview source formatting, but found it had a number
123 <li>axis-ant.jar - tasks for constructing client skeletons from
125 <li>roxes-ant-tasks-1.2-2004-01-30.jar - conditionals and other
126 useful ant tasks.</li>
127 <li>castor-*-codegen.jar and castor-*-anttask.jar - codegenerator
128 task and library for regenerating the Java classes from schemas. It is
129 important to update these and rebuild the source if the version of
130 castor that Jalview uses is updated.</li>
131 <li>gff2annot.pl - useful script to translate gff to jalview
132 features file format - although its not needed since Jalview can parse
133 GFF natively (normally at least).</li>
134 <li>jhall.jar, jhindexer.jar - the java help system and indexer
135 code to build the jalview help in the help directory.</li>
136 <li>proguard.jar - obfuscator used when creating
137 jalviewApplet.jar. See the build.xml file and the building jalview
141 <li>installAnywhere - where the installAnywhere build is generated</li>
142 <li><em>keys</em> - you might not have this - see <a
143 href="building.html">building</a> for info on how to create it.</li>
144 <li>dist - where the Jars and JNLP file for the java webstart distribution is generated, and where a copy of the examples directory is created complete with jalviewApplet.jar and the contents of appletlib/*.jar.</li>
145 <li>examples - a set of example jalview projects and web pages demonstrating the jalviewLite applet. This is essentially mirrors the <a href="http://www.jalview.org/examples/">www.jalview.org/examples</a> directory on Jalview's website.</li>
146 <li>nbbuild.xml - custom config used by the vanilla netbeans project in nbproject</li>
147 <li>nbproject - vanilla netbeans project</li>
148 <li>JalviewApplet.jpx, JalviewX.jpx - old JBuilder project files</li>
149 <li>.project - eclipse .project definition</li>