* PURPOSE. See the GNU General Public License for more details.\r
* \r
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
---!>\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>\r
+-->\r