3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
4 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
21 <meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
22 <title>Jalopy User Manual</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="next" href="dedication.html" title="Dedication"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index">
23 <meta name="description" content="Jalopy Java Source Code Formatter Beautifier Pretty Printer">
24 <meta http-equiv="pics-label" content='(pics-1.1 "http://www.icra.org/ratingsv02.html" l gen true for "http://jalopy.sf.net" r (cz 1 lz 1 nz 1 oz 1 vz 1) "http://www.rsac.org/ratingsv01.html" l gen true for "http://jalopy.sf.net" r (n 0 s 0 v 0 l 0))'>
25 </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
26 <a href="./download.html" class="navlink">Download</a> •
27 <a href="./docs.html" class="navlink">Documentation</a> •
28 <a href="./plugins.html" class="navlink">Plug-ins</a> •
29 <a href="./links.html" class="navlink">Links</a> •
30 <a href="./contact.html" class="navlink">Contact</a></td></tr><tr><td height="1" bgcolor="#ffffff"></td></tr></tbody></table></td></tr><tr valign="top"><td valign="top" bgcolor="#ffffff"><table border="0" cellpadding="0" cellspacing="0" width="100%"><tbody><tr><td height="20" bgcolor="#faebd7" style="padding-left:15px"><a href="./features.html" class="navlink2">Features</a> |
31 <a href="./history.html" class="navlink2">History</a> |
32 <a href="./manual.html" class="navlink2">Manual</a> |
33 <a href="./faq.html" class="navlink2">FAQ</a> |
34 <a href="./api/index.html" class="navlink2">Javadoc</a></td></tr><tr><td height="20" bgcolor="#ffffff"></td></tr><tr><td bgcolor="#eeeecc" height="17" align="right" style="font-size:10px;padding-right:3px">
35 This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">Jalopy User Manual</th></tr><tr><td width="20%" align="left"> </td><th width="60%" align="center"> </th><td width="20%" align="right"> <a accesskey="n" href="dedication.html">Next</a></td></tr></table><hr></div><div class="book" lang="en"><div class="titlepage"><div><div><h1 class="title"><a name="d0e2"></a>Jalopy User Manual</h1></div><div><p class="copyright">Copyright © 2004 Marco Hunsicker</p></div><div><div class="legalnotice"><p class="legalnotice-title"><b>Legal Notice</b></p><p>
36 Permission is granted to copy, distribute and/or modify this document under
37 the terms of the GNU Free Documentation License, Version 1.1 or any later
38 version published by the Free Software Foundation; with no "Invariant Sections",
39 "Front-Cover Texts" or "Back-Cover Texts", each as defined in the license.
41 For a copy of the license terms refer to <a href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000">Appendix F, <i>GNU Free Documentation License Version 1.1, March 2000</i></a>.
42 </p></div></div></div><div></div><hr></div><div class="toc"><p><b>Table of Contents</b></p><ul><li><span class="preface"><a href="dedication.html">Dedication</a></span></li><li><span class="preface"><a href="acknowledge.html">Acknowledgements</a></span></li><li><span class="preface"><a href="introduction.html">Introduction</a></span></li><li><span class="part"><a href="part-core.html">I. Jalopy core</a></span><ul><li><span class="chapter"><a href="installation.html">1. Installation</a></span></li><li><span class="chapter"><a href="build.html">2. Building</a></span></li><li><span class="chapter"><a href="usage.html">3. Usage</a></span></li><li><span class="chapter"><a href="settings.html">4. Settings</a></span><ul><li><span class="sect1"><a href="settings.html#general">4.1. General</a></span><ul><li><span class="sect2"><a href="settings.html#general-convention">4.1.1. Convention</a></span></li><li><span class="sect2"><a href="settings.html#general-compliance">4.1.2. Compliance</a></span></li><li><span class="sect2"><a href="settings.html#import-export">4.1.3. Import/Export</a></span></li></ul></li><li><span class="sect1"><a href="project.html">4.2. Projects</a></span></li><li><span class="sect1"><a href="printer.html">4.3. Printer</a></span><ul><li><span class="sect2"><a href="printer.html#braces">4.3.1. Braces</a></span></li><li><span class="sect2"><a href="whitespace.html">4.3.2. White Space</a></span></li><li><span class="sect2"><a href="indentation.html">4.3.3. Indentation</a></span></li><li><span class="sect2"><a href="wrapping.html">4.3.4. Line Wrapping</a></span></li><li><span class="sect2"><a href="separation.html">4.3.5. Blank Lines</a></span></li><li><span class="sect2"><a href="comments.html">4.3.6. Comments</a></span></li><li><span class="sect2"><a href="imports.html">4.3.7. Imports</a></span></li><li><span class="sect2"><a href="environment.html">4.3.8. Environment</a></span></li><li><span class="sect2"><a href="javadoc.html">4.3.9. Javadoc</a></span></li><li><span class="sect2"><a href="header.html">4.3.10. Header</a></span></li><li><span class="sect2"><a href="footer.html">4.3.11. Footer</a></span></li><li><span class="sect2"><a href="sorting.html">4.3.12. Sorting</a></span></li><li><span class="sect2"><a href="misc.html">4.3.13. Misc</a></span></li></ul></li><li><span class="sect1"><a href="inspector.html">4.4. Code Inspector</a></span><ul><li><span class="sect2"><a href="inspector.html#d0e5095">4.4.1. General</a></span></li><li><span class="sect2"><a href="inspector-naming.html">4.4.2. Naming</a></span></li></ul></li><li><span class="sect1"><a href="messages.html">4.5. Messages</a></span></li></ul></li></ul></li><li><span class="part"><a href="part-plugins.html">II. Plug-ins</a></span><ul><li><span class="chapter"><a href="plugin-ant.html">5. Ant Plug-in task</a></span><ul><li><span class="sect1"><a href="plugin-ant.html#plugin-ant-installation">5.1. Installation</a></span><ul><li><span class="sect2"><a href="plugin-ant.html#plugin-ant-installation-requirements">5.1.1. System requirements</a></span></li><li><span class="sect2"><a href="plugin-ant.html#plugin-ant-installation-installation">5.1.2. Installation</a></span></li></ul></li><li><span class="sect1"><a href="plugin-ant-config.html">5.2. Configuration</a></span></li><li><span class="sect1"><a href="plugin-ant-usage.html">5.3. Usage</a></span></li><li><span class="sect1"><a href="plugin-ant-license.html">5.4. License</a></span></li></ul></li><li><span class="chapter"><a href="plugin-console.html">6. Console Application</a></span><ul><li><span class="sect1"><a href="plugin-console.html#plugin-console-installation">6.1. Installation</a></span></li><li><span class="sect1"><a href="plugin-console-usage.html">6.2. Usage</a></span></li><li><span class="sect1"><a href="plugin-console-license.html">6.3. License</a></span></li></ul></li><li><span class="chapter"><a href="plugin-eclipse.html">7. Eclipse Plug-in</a></span><ul><li><span class="sect1"><a href="plugin-eclipse.html#plugin-eclipse-installation">7.1. Installation</a></span></li><li><span class="sect1"><a href="plugin-eclipse-integration.html">7.2. Integration</a></span></li><li><span class="sect1"><a href="plugin-eclipse-license.html">7.3. License</a></span></li></ul></li><li><span class="chapter"><a href="plugin-jbuilder.html">8. JBuilder OpenTool</a></span><ul><li><span class="sect1"><a href="plugin-jbuilder.html#plugin-jbuilder-installation">8.1. Installation</a></span></li><li><span class="sect1"><a href="plugin-jbuilder-integration.html">8.2. Integration</a></span></li><li><span class="sect1"><a href="plugin-jbuilder-license.html">8.3. License</a></span></li></ul></li><li><span class="chapter"><a href="plugin-jdev.html">9. JDeveloper Extension</a></span><ul><li><span class="sect1"><a href="plugin-jdev.html#plugin-jdev-installation">9.1. Installation</a></span></li><li><span class="sect1"><a href="plugin-jdev-integration.html">9.2. Integration</a></span></li><li><span class="sect1"><a href="plugin-jdev-license.html">9.3. License</a></span></li></ul></li><li><span class="chapter"><a href="plugin-jedit.html">10. jEdit Plug-in</a></span><ul><li><span class="sect1"><a href="plugin-jedit.html#plugin-jedit-installation">10.1. Installation</a></span></li><li><span class="sect1"><a href="plugin-jedit-integration.html">10.2. Integration</a></span></li><li><span class="sect1"><a href="plugin-jedit-license.html">10.3. License</a></span></li></ul></li><li><span class="chapter"><a href="plugin-netbeans.html">11. NetBeans/Sun ONE Studio module</a></span><ul><li><span class="sect1"><a href="plugin-netbeans.html#plugin-netbeans-installation">11.1. Installation</a></span></li><li><span class="sect1"><a href="plugin-netbeans-integration.html">11.2. Integration</a></span></li><li><span class="sect1"><a href="plugin-netbeans-license.html">11.3. License</a></span></li></ul></li></ul></li><li><span class="appendix"><a href="dependencies.html">A. Library Dependencies</a></span></li><li><span class="appendix"><a href="license-bsd.html">B. The Jalopy BSD License</a></span></li><li><span class="appendix"><a href="license-antlr.html">C. ANTLR SOFTWARE RIGHTS</a></span></li><li><span class="appendix"><a href="license-apache.html">D. The Apache Software License, Version 1.1</a></span></li><li><span class="appendix"><a href="license-gnu.html">E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991</a></span></li><li><span class="appendix"><a href="license-gnu-doc.html">F. GNU Free Documentation License Version 1.1, March 2000</a></span></li><li><span class="appendix"><a href="license-common-public.html">G. Common Public License Version 1.0</a></span></li><li><span class="appendix"><a href="license-sun-public.html">H. SUN PUBLIC LICENSE Version 1.0</a></span></li><li><span class="bibliography"><a href="bi01.html">Bibliography</a></span></li><li><span class="index"><a href="ix01.html">Index</a></span></li></ul></div><div class="list-of-tables"><p><b>List of Tables</b></p><ul><li>2.1. <a href="build.html#tab-build-prerequisites">Software needed to build from the sources</a></li><li>4.1. <a href="environment.html#tab-environment-local">Local environment variables</a></li><li>4.2. <a href="javadoc.html#tab-character-entities">Character entities</a></li><li>5.1. <a href="plugin-ant-usage.html#tab-ant-params">Jalopy Ant task parameters</a></li><li>A.1. <a href="dependencies.html#tab-library-dependencies">Library dependencies</a></li></ul></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"> </td><td width="20%" align="center"> </td><td width="40%" align="right"> <a accesskey="n" href="dedication.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top"> </td><td width="20%" align="center"> </td><td width="40%" align="right" valign="top"> Dedication</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
43 Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
git://source.jalview.org / jalview.git / blob