<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.
-->
+<head>
+<title>Building Jalview from Source</title>
+</head>
+<body>
+<h1>Building Jalview from Source</h1>
+<P>
+<p>
+You will need the following (hopefully):<br>
+<ul>
+<li>Java development kit (JDK1.6 is the recommended platform for developing with Jalview, although JDK1.7 seems to work too!).</li>
+<li>Ant (we think 1.5.4 is quite sufficient to use the simple build
+file supplied, and it seems to work with later versions e.g. 1.7).</li>
+</ul>
+With any luck, after setting your paths and JAVA_HOME correctly, you
+just need to change to the Jalview directory and run ant (this works
+from JBuilder and eclipse too, but NetBeans is a bit trickier).
+<pre>
+ ant
+</pre>
+
+</p>
+<p><strong>Building a webstart version of jalview</strong></p>
+Jalview depends on several libraries contained in the libs directory
+of the distribution. In order to access them, they must all be signed
+jars - using the same jarsigner key as jalview itself. There is a
+build target in ant to make the signed jar files in a directory called
+dist. But first you need to make your own key:
+<p><strong>Making your own key</strong></p>
+
+<p>The ant 'makefulldist' target assumes that a keystore exists in a
+directory 'keys'. To make a key accessible using the default settings
+in the build.xml file then make the keys directory and add the
+jarsigner key with the following :
+</p>
+<pre>
+mkdir keys
+keytool -genkey -keystore keys/.keystore -keypass alignmentisfun
+-storepass alignmentisfun -alias jalview
+ (you will have to answer some personal questions here)
+ant makedist
+ (should eventually generate a Jalview.jnlp file
+ in ./dist along with a set of signed jars using the jalview
+ key)
+</pre>
+
+ <p>
+ <strong>Building the JalviewLite applet<br>
+ </strong> The JalviewLite applet is compiled using a subset of the packages in
+ the src directory (specifically: MCView, and jalview.{datamodel,
+ analysis, appletgui, utils, schemes, api, structure}, and
+ com.stevesoft.*). Once compiled, these class files are obfuscated to
+ make the code run efficiently. To compile the applet Jar, use the
+ makeApplet task - optionally passing in a 'donotobfuscate' property to
+ the ant build (e.g. -Ddonotobfuscate=true) to disable obfuscation. </p><p>
+ The ant target 'pubapplet' can be used to compile install the
+ jalviewApplet.jar and any dependent jars (under appletlib) into a copy
+ of the examples directory created under the <em>outputDir</em> build
+ property (which defaults to the 'dist' directory).
+ </p>
+ <p>
+<h1>using IDEs to build Jalview</h1>
+ <p>The Jalview source distribution includes project definitions for
+ Eclipse, Netbeans and some rather ancient Borland JBuilder .jpx
+ project files. These files should be sufficient to set up basic source
+ folders and build paths, but you will need to ensure that all .jar
+ files in the lib and appletlib directories are added to the build path
+ for your IDE project, and that the 'buildindices' target in Jalview's
+ build.xml is executed with the 'outputDir' ant property set to the
+ directory where the IDE expects to place compiled classes ('classes'
+ directory for eclipse, 'build/classes' for netbeans).</p>
+ <p>Note: It is generally not recommended that you distribute build
+ artefacts that were generated automatically via an IDE's own packaging
+ mechanism (e.g. Netbeans' executable Jar and dependent lib directory).
+ The hand-crafted ant build.xml is (currently) the only officially
+ supported method of building distributable versions of Jalview.</p>
+<address>
+<a href="mailto:help@jalview.org">Jalview development team</a>
+</address>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff