--- /dev/null
+<html>
+<!--
+ * 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.
+ -->
+<head>
+<title>Logging and Reporting Bugs</title>
+</head>
+<body>
+ <h2>
+ <center>
+ <strong>Logging and Reporting Bugs</strong>
+ </center>
+ </h2>
+
+ <h3>Logging</h3>
+ <p>
+ Jalview creates logs that can be extremely useful for diagnosing, or help to provide a workaround for, specific problems that you might encounter.
+ </p>
+ <p>
+ The primary place to look for logs is in the <a href="#java_console">Java Console</a> which you can open from within Jalview by going to the <em>Tools</em> menu and checking the box next to <em>Show Java Console</em>. This option is stored in your Jalview preferences file and so is remembered across Jalview sessions.
+ </p>
+ <p>
+ The Java Console will show you information about what the Jalview application is doing (often in the background) whilst it is running.
+ </p>
+ <p>
+ However, it is possible that some early logging information from when Jalview is initially launched, is not shown in the Java Console:
+ <br/>
+ If you are using a version of Jalview installed from one of our install4j installers, then Jalview's initial launch logging can be found in
+ <pre>JALVIEW_APP_DIR/launcher.log</pre>
+ where <em>JALVIEW_APP_DIR</em> is the directory that Jalview's application was installed into.
+ <br/>
+ For Jalview 2.11.0 onwards:
+ <ul>
+ <li>In Windows this is <em>%APPDATA%\Local\Jalview</em> by default</li>
+ <li>In macOS this is <em>/Applications/Jalview.app/Contents/Resources/app</em> by default</li>
+ <li>In Linux and other Unix OSes this is <em>~/opt/jalview</em> by default</li>
+ </ul>
+ <br/>
+ Whereas if you are using the Jalview executable jar file (also used by bioconda installations) then a minimised launcher will output logging information to STDOUT and STDERR.
+ </p>
+
+ <h3><a name="java_console">Java Console and Log Level</a></h3>
+
+
+ <h3>Reporting Bugs</h3>
+
+
+</body>
+</html>
git://source.jalview.org / jalview.git / commitdiff