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