From: jprocter Date: Fri, 21 Dec 2007 15:08:45 +0000 (+0000) Subject: source directory tree documentation X-Git-Tag: Release_2_4~161 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e944b72a600a30c630e842d70b0a1e1916859315;p=jalview.git source directory tree documentation --- diff --git a/doc/index.html b/doc/index.html new file mode 100644 index 0000000..ab12d5e --- /dev/null +++ b/doc/index.html @@ -0,0 +1,132 @@ + + + +Jalview Source Documentation + + +

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 Jalvew + 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.
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.
+
dist - where the Jars and JNLP file for the java webstart distribution is generated.
installAnywhere - where the installAnywhere build is generated
keys - you might not have this - see building for info on how to create it.

+ + + + + \ No newline at end of file