<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * 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>
<p>
You will need the following (hopefully):<br>
<ul>
-<li>Java development kit (we used JDK1.4SE but JDK1.5 will work too,
-and maybe even jikes).
+<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).
+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).
+from JBuilder and eclipse too, but NetBeans is a bit trickier).
<pre>
ant
</pre>
dist. But first you need to make your own key:
<p><strong>Making your own key</strong></p>
-<p>The ant 'makejars' target assumes that a keystore exists in a
+<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 :
keytool -genkey -keystore keys/.keystore -keypass alignmentisfun
-storepass alignmentisfun -alias jalview
(you will have to answer some personal questions here)
-ant makejars
- (should eventually generate a Jalview.jnlp file
+ant makedist
+ (should eventually generate a Jalview.jnlp file
in ./dist along with a set of signed jars using the jalview
key)
</pre>
-<p>
-
-<p>
+ <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:jalview-dev@jalview.org">Jim Procter (GJB)</a>
+<a href="mailto:help@jalview.org">Jalview development team</a>
</address>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff