-<!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>
\ No newline at end of file
+<!--
+ *Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ *Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ *This file is part of Jalview.
+ *
+ *Jalview is free software: you can redistribute it and/or
+ *modify it under the terms of the GNU General Public License
+ *as published by the Free Software Foundation, either version 3
+ *of the License, or (at your option) any later version.
+ *
+ *Jalview is distributed in the hope that it will be useful, but
+ *WITHOUT ANY WARRANTY; without even the implied warranty
+ *of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ *PURPOSE. See the GNU General Public License for more details.
+ *
+ *You should have received a copy of the GNU General Public License
+ *along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ *The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
+<!DOCTYPE html SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+Jalview Source Documentation
+</head>
+<body>
+<h1>Jalview Source Documentation</h1>
+<p>The file structure of the Jalview Source tree is as follows:
+<ul>
+ <li>README - basic info for getting started with the source tree.</li>
+ <li>LICENCE - the GPL Licence</li>
+ <li>RELEASE - contains the name of the tag for the latest
+ 'official' Jalview release associated with the source.</li>
+ <li>build.xml - ant build for jalview - the 'help' task gives
+ information about each task, and there's lots of comments too.</li>
+ <li></li>
+ <li>src - all jalview source packages, including any specially
+ adapted code from other GPL programs. See <a href="developing.html">Jalview
+ Development</a> for more info.</li>
+ <li>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.</li>
+ <li>appletlib - Any libraries that are specifically required for compiling and/or running the jalviewLite applet (e.g. an applet build of Jmol).
+ <li>help - the jalview JavaHelp documents<br>
+ <ul>
+ <li>help.hs - the main index page. This is generated by the
+ jhindexer program run by the 'buildindices' task in build.xml</li>
+ <li>help.jhm - helpTOC map - an XML document listing simple names
+ for each html page that is linked to in the help contents structure.</li>
+ <li>helpTOC.xml - the table of contents presented to the user
+ when the help is opened.</li>
+ <li>icons - widgets needed for the help system GUI</li>
+ <li>html - the help documentation. It loosely follows the
+ following structure: <br>
+ <ul>
+ <li>calculations - pages concerning the calculations menu</li>
+ <li>webServices - pages describing web services</li>
+ <li>colourSchemes - the ways amino acids can be coloured and the
+ user interface for defining them</li>
+ <li>editing - mechanisms and interfaces for editing alignments</li>
+ <li>features - used to be the sequence features documentation,
+ but now contains all sorts of jalview 'features'.</li>
+ <li>io - getting data in and out of jalview</li>
+ <li>menus - all the menus in Jalview (and the applet)</li>
+ <li>misc - useful info</li>
+ <li>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.</li>
+ <li>keys.html contains all the keystrokes in Jalview - please
+ keep this up to date.</li>
+ </ul>
+ </li>
+ </ul>
+ </li>
+ <li>resources - files needed at run-time for jalview execution.<br>
+ <ul>
+ <li>images - icons used by jalview</li>
+ <li>log4j and commons-logging.properties - configure default
+ appenders and logging for Jalview, castor.</li>
+ <li>embl_mapping.xml - castor mapping file for the EMBL XML
+ Schema.</li>
+ .
+ <li>uniprot_mapping.xml - castor mapping file for the Uniprot XML
+ Schema.</li>
+ </ul>
+ </li>
+ <li>schemas - XML schema definitions used or understood by
+ Jalview.<br>
+ 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. <br>
+ See the castorbinding task in the ant build.xml file for more info.
+ <ul>
+ <li>Jalview Project Archive XML Version 1<br>
+ vamsasJvV1.xsd<br>
+ jalviewJvV1.xsd<br>
+ jalview.nodesc.properties - sourcegenerator properties file</li>
+ <li>jalview Project Archive XML Version 2<br>
+ 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.
+ <ul>
+ <li>vamsas.xsd<br>
+ jalview.xsd<br>
+ jalview.properties - sourcegenerator properties file</li>
+ </ul></li>
+ <li>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.</li>
+ </ul>
+ </li>
+ <li>utils - various resources needed when building or deploying
+ jalview.
+ <ul>
+ <li>InstallAnywhere
+ <ul>
+ <li>Jalview.iap_xml is the InstallAnywhere XML project used to
+ create the Jalview InstallAnywhere distribution.</li>
+ <li>All the other files are bundled into this for installer
+ displays. The README_IA appears in the installation directory.</li>
+ </ul>
+ <li>jalopy<br>
+ This is a legacy directory - we intended to use jalopy for
+ standardising the jalview source formatting, but found it had a number
+ of bugs.</li>
+ <li>axis-ant.jar - tasks for constructing client skeletons from
+ WSDL documents.</li>
+ <li>roxes-ant-tasks-1.2-2004-01-30.jar - conditionals and other
+ useful ant tasks.</li>
+ <li>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.</li>
+ <li>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).</li>
+ <li>jhall.jar, jhindexer.jar - the java help system and indexer
+ code to build the jalview help in the help directory.</li>
+ <li>proguard.jar - obfuscator used when creating
+ jalviewApplet.jar. See the build.xml file and the building jalview
+ documentation.</li>
+ </ul>
+ </li>
+ <li>installAnywhere - where the installAnywhere build is generated</li>
+ <li><em>keys</em> - you might not have this - see <a
+ href="building.html">building</a> for info on how to create it.</li>
+<li>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.</li>
+<li>examples - a set of example jalview projects and web pages demonstrating the jalviewLite applet. This is essentially mirrors the <a href="http://www.jalview.org/examples/">www.jalview.org/examples</a> directory on Jalview's website.</li>
+<li>nbbuild.xml - custom config used by the vanilla netbeans project in nbproject</li>
+<li>nbproject - vanilla netbeans project</li>
+<li>JalviewApplet.jpx, JalviewX.jpx - old JBuilder project files</li>
+<li>.project - eclipse .project definition</li>
+</ul>
+
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff