X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=utils%2Fjalopy%2Fdocs%2Fmanual.html;h=ab4e6946568f24f14347d05b676993452d83b51d;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=91bc975c6b8b90079adbeb32409cea308de69583;hpb=67a30bbaa5190c0bd0b12e521e9465cc46214d56;p=jalview.git

diff --git a/utils/jalopy/docs/manual.html b/utils/jalopy/docs/manual.html
index 91bc975..ab4e694 100755
--- a/utils/jalopy/docs/manual.html
+++ b/utils/jalopy/docs/manual.html
@@ -1,4 +1,21 @@
-
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * 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.
+-->
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@@ -23,4 +40,4 @@ version published by the Free Software Foundation; with no "Invariant Sections",
 </p><p>
 For a copy of the license terms refer to <a href="license-gnu-doc.html" title="Appendix&nbsp;F.&nbsp;GNU Free Documentation License Version 1.1, March 2000">Appendix&nbsp;F, <i>GNU Free Documentation License Version 1.1, March 2000</i></a>.
 </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">&nbsp;</td><td width="20%" align="center">&nbsp;</td><td width="40%" align="right">&nbsp;<a accesskey="n" href="dedication.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">&nbsp;</td><td width="20%" align="center">&nbsp;</td><td width="40%" align="right" valign="top">&nbsp;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">
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+            Copyright &copy; 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&amp;type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
