3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
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11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
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19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>The Java Console, Logging and Reporting Bugs</title>
27 <strong>The Java Console, Logging and Reporting Bugs<br /></strong>
30 Like most programs, Jalview contains bugs, despite our best efforts.
31 However, Jalview also produces a series of messages during its
32 operation, often referred to as 'logs'. These logs provide a record
33 of Jalview's operation. They can also be extremely useful when <a
34 href="#reportingbugs">reporting bugs</a>, since they help the
35 Jalview developers diagnose and find a workaround for specific
36 problems that you might encounter.
39 The primary place to look for logs is in the <a href="#java_console">Java
40 Console</a> which you can open from within Jalview by going to the <em>Tools</em>
41 menu and checking the box next to <em>Show Java Console</em>. This
42 option is stored in your Jalview preferences file and so is
43 remembered across Jalview sessions.
45 <p>The Java Console will show you information about what the
46 Jalview application is doing (often in the background) whilst it is
48 <p>However, when tracking down problems preventing Jalview from
49 starting up properly, you need to look at the startup logs - which
50 are not shown in the Jalview Console. The location of these depends
51 on how you launched Jalview:</p>
53 <strong>Jalview Desktop Installation Launch Logs</strong><br />If you are using
54 a standard desktop version of Jalview installed from one of our
55 install4j installers, then messages about Jalview's initial launch
57 <pre>JALVIEW_APP_DIR/launcher.log</pre>
59 <em>JALVIEW_APP_DIR</em> is the directory that Jalview's application
61 <br /> For Jalview 2.11.0 onwards:
63 <li>In Windows this is <em>%APPDATA%\Local\Jalview</em> by
66 <li>In macOS this is <em>/Applications/Jalview.app/Contents/Resources/app</em>
69 <li>In Linux and other Unix OSes this is <em>~/opt/jalview</em>
73 <p><strong>Jalview Executable Jar Launch Logs</strong><br/>If you are using the Jalview executable jar file (also
74 used by bioconda and OSX homebrew installations) then the default run class (
75 <em>jalview.bin.Launcher</em> -- a minimised launcher that will set
76 memory and linux dpi settings before re-launching
77 <em>jalview.bin.Jalview</em>), will output logging information to
82 <a name="java_console">Java Console and Log Level</a>
85 The Java Console is opened by selecting <strong>Tools
86 → Show Java Console</strong>. The visibility of the console is stored
87 in your preferences, so if you quit Jalview with the console open,
88 it will be shown the next time you start Jalview. You can close the
89 console by selecting the same menu option again, or just closing the
92 <p>The Java Console's text display always shows information about
93 your system and Jalview installation details. The rest are the most
94 recent messages output during your Jalview session. Some messages
95 are only captured by the console when it is open, so to get a full
96 log for debugging a problem, enable the console and then restart
100 You can temporarily control the detail of what appears as output by
101 selecting a <em>Log level</em> using the drop-down list at the
102 bottom left of the console. There are several levels to choose from:
103 The most verbose is TRACE, followed by DEBUG, INFO, WARN. When the
104 Console is opened, the default level will be chosen (INFO).
107 <strong>Note! If you change the log level in the Java
108 Console, this change will only persist for as long as the console
109 is open. Once you close the console the log level will revert back
110 to what it had been when you opened the console (usually INFO).</strong>
112 <p><strong>Permanently changing Jalview's default log level</strong><br/>
113 You can change the default log level by editing the Jalview
114 preferences file, <em>.jalview_properties</em>, found in your home
115 directory (on Windows: %HOMEPATH%, or the folder above 'My
116 Documents'; on macOS: ~ or /Users/<em>username</em>; on linux/unix:
117 ~ or /home/<em>username</em>), and setting the property <em>logs.Jalview.level</em>
118 to the log level you prefer, e.g.
120 logs.Jalview.level=DEBUG
122 You can also set the property
124 logs.Axis.level=DEBUG
126 <p>to get debug information for Jalview's JPred service. The Axis log
127 level cannot be set from within the Java Console.
130 You can also set the <em>logs.jalview.level</em> property to a log level
131 not usually presented in the Java Console (though restricted to log
132 levels used by Apache Log4j -- see <a
133 href="https://logging.apache.org/log4j/2.x/manual/customloglevels.html">Log4j
134 Custom Log Levels</a> for details of the standard log levels
135 available). Jalview does not currently define any custom log levels.
136 If you do set the property with a log level that is normally not
137 visible in the Java Console this should be respected and visibly
138 selected when you open the console.
141 The <em>Clear</em> button at the bottom of the console will clear
142 all logging messages except for the initial system information which
143 is rewritten to the console.
146 The <em>Copy to clipboard</em> button at the bottom right of the
147 console will copy all of the text in the console to your system
148 clipboard, ready to paste into another application (e.g. email
149 composer or issue tracker).
152 <p><strong><a name="reportingbugs">Reporting Bugs</a></strong></p>
155 If you come across a problem in Jalview where something is not
156 working as described, or how you think it should, you should first
157 check the <a href="https://www.jalview.org/faq">Jalview FAQ</a> to
158 see if this is a known problem and if there is a suggested
162 If there is no FAQ answer covering your problem then you can submit
163 a bug report on the <a href="https://issues.jalview.org/">Jalview
164 Issue Tracker</a>. It is good practice to search the issue tracker
165 first to see if the issue has already been reported. If an issue
166 already exists please continue to add your own comments to the issue
167 which may well help narrow down the problem, if not then you can
168 create an account and submit a new bug report:
171 Make sure that you set Project to <em>Jalview (JAL)</em>, and Issue
172 Type to <em>Bug</em> or <em>New Feature</em> or <em>Improvement</em>
173 appropriately.<br /> Give a one line summary of the issue in the <em>Summary</em>.
174 <br /> In the <em>Environment</em> text box you can describe the
175 system you are using. This is usually most easily done by opening
176 the Java Console, clicking the <em>Clear</em> button, and then
177 immediately on the <em>Copy to clipboard</em> button, and then
178 pasting the clipboard into the text box.
181 You can then give more detailed information about how to recreate
182 the problem in the <em>Description</em> text box. If you want to
183 attach any screenshots or example alignment files that demonstrate
184 the problem then you can drag them to the Create Issue dialog in
185 your browser, or use the <em>Attachment</em> browse facility to
186 locate them on your computer.
190 To help the Jalview team with diagnosing a particular issue, it is
191 really helpful if you can also add more detailed logs output whilst
192 re-creating the problem. To do this, open the Java Console, click
193 the <em>Clear</em> button and select TRACE in the <em>Log level</em>
194 drop down list. <br /> Whilst leaving the console open, perform the
195 task in Jalview that re-creates the problem. <br /> Then you can
196 copy the debug information in the Java Console by clicking on the <em>Copy
197 to clipboard</em> button and then paste that into the Description, or a
198 Comment of your issue.
202 For other queries or comments about Jalview, remember you can
203 contact the Jalview team using email via the
204 <a href="https://www.jalview.org/mailman/listinfo/jalview-discuss">Jalview
205 discussion list</a>, on Twitter <a
206 href="https://twitter.com/Jalview/">@Jalview</a>, or for technical
207 discussions, via the Jalview developer's chatroom at
208 <a href="https://gitter.im/jalview/developers">https://gitter.im/jalview/developers</a>.