X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=doc%2Findex.html;h=e22099c704db42499b5ffa9164351026c2fb5586;hb=738cb8eba9f66dd726fd69e02e6f7c76306de2e8;hp=228f3e3eaa98838b5b00ac3070fbd007e49954f0;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git diff --git a/doc/index.html b/doc/index.html index 228f3e3..e22099c 100644 --- a/doc/index.html +++ b/doc/index.html @@ -1,149 +1,153 @@ - - - - -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.

- - - - - + + + + +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 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

+ + +