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+<!DOCTYPE html SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">\r
+<html xmlns="http://www.w3.org/1999/xhtml">\r
+<head>\r
+Jalview Source Documentation\r
+</head>\r
+<body>\r
+<h1>Jalview Source Documentation</h1>\r
+<p>The file structure of the Jalview Source tree is as follows:\r
+<ul>\r
+ <li>README - basic info for getting started with the source tree.</li>\r
+ <li>LICENCE - the GPL Licence</li>\r
+ <li>RELEASE - contains the name of the tag for the latest\r
+ 'official' Jalview release associated with the source.</li>\r
+ <li>build.xml - ant build for jalview - the 'help' task gives\r
+ information about each task, and there's lots of comments too.</li>\r
+ <li></li>\r
+ <li>src - all jalview source packages, including any specially\r
+ adapted code from other GPL programs. See <a href="developing.html">Jalvew\r
+ Development</a> for more info.</li>\r
+ <li>lib - All the libraries that Jalview depends on. Every jar\r
+ file in this directory should be added to the classpath when building\r
+ or running the jalview application.</li>\r
+ <li>help - the jalview JavaHelp documents<br>\r
+ <ul>\r
+ <li>help.hs - the main index page. This is generated by the\r
+ jhindexer program run by the 'buildindices' task in build.xml</li>\r
+ <li>help.jhm - helpTOC map - an XML document listing simple names\r
+ for each html page that is linked to in the help contents structure.</li>\r
+ <li>helpTOC.xml - the table of contents presented to the user\r
+ when the help is opened.</li>\r
+ <li>icons - widgets needed for the help system GUI</li>\r
+ <li>html - the help documentation. It loosely follows the\r
+ following structure: <br>\r
+ <ul>\r
+ <li>calculations - pages concerning the calculations menu</li>\r
+ <li>webServices - pages describing web services</li>\r
+ <li>colourSchemes - the ways amino acids can be coloured and the\r
+ user interface for defining them</li>\r
+ <li>editing - mechanisms and interfaces for editing alignments</li>\r
+ <li>features - used to be the sequence features documentation,\r
+ but now contains all sorts of jalview 'features'.</li>\r
+ <li>io - getting data in and out of jalview</li>\r
+ <li>menus - all the menus in Jalview (and the applet)</li>\r
+ <li>misc - useful info</li>\r
+ <li>By convention, we try to maintain the whatsNew.html document\r
+ with each release and complete the releases.html matrix to detail\r
+ what has changed from one version to another.</li>\r
+ <li>keys.html contains all the keystrokes in Jalview - please\r
+ keep this up to date.</li>\r
+ </ul>\r
+ </li>\r
+ </ul>\r
+ </li>\r
+ <li>resources - files needed at run-time for jalview execution.<br>\r
+ <ul>\r
+ <li>images - icons used by jalview</li>\r
+ <li>log4j and commons-logging.properties - configure default\r
+ appenders and logging for Jalview, castor.</li>\r
+ <li>embl_mapping.xml - castor mapping file for the EMBL XML\r
+ Schema.</li>\r
+ .\r
+ <li>uniprot_mapping.xml - castor mapping file for the Uniprot XML\r
+ Schema.</li>\r
+ </ul>\r
+ </li>\r
+ <li>schemas - XML schema definitions used or understood by\r
+ Jalview.<br>\r
+ Jalview uses castor to bind java to XML - either using mapping files\r
+ hand-crafted from a schema in this directory, or from java objects\r
+ generated from the schema and an associated set of properties. <br>\r
+ See the castorbinding task in the ant build.xml file for more info.\r
+ <ul>\r
+ <li>Jalview Project Archive XML Version 1<br>\r
+ vamsasJvV1.xsd<br>\r
+ jalviewJvV1.xsd<br>\r
+ jalview.nodesc.properties - sourcegenerator properties file</li>\r
+ <li>jalview Project Archive XML Version 2<br>\r
+ Jalview works out which version a project is by first trying\r
+ to parse XML with these schema definitions, and then if there are\r
+ problems, falls back to the V1 schema classes.\r
+ <ul>\r
+ <li>vamsas.xsd<br>\r
+ jalview.xsd<br>\r
+ jalview.properties - sourcegenerator properties file</li>\r
+ </ul></li>\r
+ <li>JalviewUserColours.xsd is used by both V1 and V2 project XML\r
+ definitions. This schema is also used to store user colour schemes\r
+ externally from the project file.</li>\r
+ </ul>\r
+ </li>\r
+ <li>utils - various resources needed when building or deploying\r
+ jalview.\r
+ <ul>\r
+ <li>InstallAnywhere\r
+ <ul>\r
+ <li>Jalview.iap_xml is the InstallAnywhere XML project used to\r
+ create the Jalview InstallAnywhere distribution.</li>\r
+ <li>All the other files are bundled into this for installer\r
+ displays. The README_IA appears in the installation directory.</li>\r
+ </ul>\r
+ <li>jalopy<br>\r
+ This is a legacy directory - we intended to use jalopy for\r
+ standardising the jalview source formatting, but found it had a number\r
+ of bugs.</li>\r
+ <li>axis-ant.jar - tasks for constructing client skeletons from\r
+ WSDL documents.</li>\r
+ <li>roxes-ant-tasks-1.2-2004-01-30.jar - conditionals and other\r
+ useful ant tasks.</li>\r
+ <li>castor-*-codegen.jar and castor-*-anttask.jar - codegenerator\r
+ task and library for regenerating the Java classes from schemas. It is\r
+ important to update these and rebuild the source if the version of\r
+ castor that Jalview uses is updated.</li>\r
+ <li>gff2annot.pl - useful script to translate gff to jalview\r
+ features file format - although its not needed since Jalview can parse\r
+ GFF natively (normally at least).</li>\r
+ <li>jhall.jar, jhindexer.jar - the java help system and indexer\r
+ code to build the jalview help in the help directory.</li>\r
+ <li>proguard.jar - obfuscator used when creating\r
+ jalviewApplet.jar. See the build.xml file and the building jalview\r
+ documentation.</li>\r
+ </ul>\r
+ </li>\r
+ <li>dist - where the Jars and JNLP file for the java webstart distribution is generated.</li>\r
+ <li>installAnywhere - where the installAnywhere build is generated</li>\r
+ <li><em>keys</em> - you might not have this - see <a\r
+ href="building.html">building</a> for info on how to create it.</li>\r
+</ul>\r
+</li>\r
+</ul>\r
+\r
+</body>\r
+</html>
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git://source.jalview.org / jalview.git / commitdiff