<mapID target="importvcf" url="html/features/importvcf.html" />
<mapID target="importvcf.attribs" url="html/features/importvcf.html#attribs" />
+ <mapID target="logging" url="html/logging.html" />
</map>
<tocitem text="Virtual Features in CDS/Protein Views" target="splitframe.virtualfeats"/>
<tocitem text="VCF Variant Attributes" target="importvcf.attribs"/>
<tocitem text="Feature Filters and Attribute Colourschemes" target="features.featureschemes" />
-
+ <tocitem text="The Java Console, Logging and Reporting Bugs" target="logging" />
</tocitem>
<tocitem text="Editing Alignments" target="edit" />
</tocitem>
</tocitem>
<tocitem text="Preferences" target="preferences" />
+ <tocitem text="The Java Console, Logging and Reporting Bugs" target="logging" />
<tocitem text="Scripting with Groovy" target="groovy">
<tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
</tocitem>
<ul>
<li>Standard installation on Linux/Unix:<pre>
- /PATH_TO_JALVIEW/Jalview -open http://www.jalview.org/examples/jpred_msa.fasta -annotations http://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre>
+ /PATH_TO_JALVIEW/Jalview -open https://www.jalview.org/examples/jpred_msa.fasta -annotations https://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre>
</li>
<li>Standard installation on Windows:<pre>
\PATH_TO_JALVIEW\Jalview.exe -open %HOMEPATH%\myalignment.fa</pre>
installation of Groovy. Just select <strong>Tools→Groovy
Console...</strong> from the Jalview Desktop's drop-down menu. After a
short pause, you should then see the <a
- href="http://groovy-lang.org/groovyconsole.html">Groovy
+ href="https://groovy-lang.org/groovyconsole.html">Groovy
Console</a> appear. This allows you to interactively execute Groovy
scripts whilst Jalview is running. We've also provided a <strong>Calculations→Execute
Groovy Script</strong> button so you can execute the currently loaded
InstallAnywhere version of Jalview, you can find additional groovy
scripts in the examples/groovy subfolder of the installation
directory. The examples are also available at <a
- href="http://www.jalview.org/examples/groovy">http://www.jalview.org/examples/groovy</a>.
+ href="https://www.jalview.org/examples/groovy">https://www.jalview.org/examples/groovy</a>.
</p>
<p>
<em>Using Groovy to add new Alignment Calculations</em><br />We've
<em>Creating custom colourschemes</em><br/>
You can create your own alignment colourschemes with a groovy script. We've provided two examples:<br/>
<ul>
- <li><a href="http://www.jalview.org/examples/groovy/colourConserved.groovy">colourConserved.groovy</a> creates an 'Conserved' colourscheme - similar to the classic <a href="http://www.nrbsc.org/old/gfx/genedoc/">GeneDOC</a> shading model.</li>
- <li><a href="http://www.jalview.org/examples/groovy/colourUnconserved.groovy">colourUnconserved.groovy</a> creates an 'Unconserved' colourscheme, where any unconserved residues are coloured pink.</li>
+ <li><a href="https://www.jalview.org/examples/groovy/colourConserved.groovy">colourConserved.groovy</a> creates an 'Conserved' colourscheme - similar to the classic <a href="http://www.nrbsc.org/old/gfx/genedoc/">GeneDOC</a> shading model.</li>
+ <li><a href="https://www.jalview.org/examples/groovy/colourUnconserved.groovy">colourUnconserved.groovy</a> creates an 'Unconserved' colourscheme, where any unconserved residues are coloured pink.</li>
</ul>
</p>
<pre>
# Jalview Launch File
# Please install the Jalview Desktop from
-# http://www.jalview.org/getdown/release
+# https://www.jalview.org/getdown/release
# and then try to open this file again
jalview.apparg=-open
-jalview.apparg=http://www.jalview.org/examples/jpred_msa.fasta
+jalview.apparg=https://www.jalview.org/examples/jpred_msa.fasta
jalview.apparg=-annotations
-jalview.apparg=http://www.jalview.org/examples/jpred_msa.seq.concise
+jalview.apparg=https://www.jalview.org/examples/jpred_msa.seq.concise
jalview.apparg=-colour
jalview.apparg=Clustal
</pre>
# Please install the Jalview Desktop from
# http://www.jalview.org/getdown/release
# and then try to open this file again
-appbase=http://www.jalview.org/getdown/archive/2_10_5/
+appbase=https://www.jalview.org/getdown/archive/2_10_5/
</pre>
For security, the Jalview application will only allow
<em>appbase</em> URLs from www.jalview.org.
</p>
<p>The search box is displayed by pressing Control and F or
selecting "Find..." from the "Search" menu.</p>
- <img src="search.png" width="398" height="124">
+ <img src="search.png" width="400" height="152">
<p>"Find next" will find the next occurrence of the
specified and adjust the alignment window view to show it, and
"Find all" highlights all matches for a pattern. The
of posix and perl style regex - see below for a summary)</li>
<li>Gaps are ignored when matching the query to the sequences
in the alignment.</li>
+ <li>Hidden columns can optionally be ignored (<em>since Jalview 2.11</em>)</li>
<li>The search is applied to both sequences and their IDs, and
optionally also to the description string (<em>since Jalview
2.10</em>)
</li>
<li>If a region is selected, then search will <strong>only</strong>
- be performed on that region.
+ be performed on that region.<br />
+ <em>Tip: to quickly clear the current selection, click the
+ alignment view you wish to search, then press 'Escape'.</em>
</li>
- <li>To quickly clear the current selection, press the
- "Escape" key.</li>
<li>Tick the "Match Case" box to perform a case
sensitive search.</li>
- <li>To access a <a ref="#queryhistory">previously used
+ <li>To access a <a href="#queryhistory">previously used
query</a> press the down arrow or click on the button on the right
of the text field.
</ul>
stored along with your Jalview user preferences. To open the search
history, click on the button to the right of the query field, or
press the down arrow key.</p>
- <img src="searchhist.png" width="404" height="185" align="left" />
- <p>The search history keeps up to 99 queries by default. To clear
+ <p><img src="searchhist.png" width="404" height="185" />
+ </p><p>The search history keeps up to 99 queries by default. To clear
the history, or modify the size of the history, right-click the text
box.</p>
- <img src="searchclearhist.png" width="402" height="127" align="left" />
- <p>
+ <p><img src="searchclearhist.png" width="402" height="127"/>
+ </p>
+<p width="100%">
<strong>Other dialogs that provide a query history</strong>
</p>
<p>
"OK" to initiate the retrieval.</li>
</ol>
- <p>If you use the WSDBFetch sequence fetcher services (EMBL,
- UniProt, PFAM, and RFAM) in work for publication, please cite:</p>
- <p>
- Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate
- J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez
- R. <br> SOAP-based services provided by the European
- Bioinformatics Institute.<br> Nucleic Acids Res. 33(1):W25-W28
- (2005) <br> <br>
- </p>
+ <p>If you use the Sequence Fetcher, please remember to cite the
+ corresponding services (linked to below):</p>
+ <ul>
+ <li>Ensembl - <a
+ href="https://github.com/Ensembl/ensembl-rest/wiki#citing">The
+ Ensembl REST API</a></li>
+ <li>EMBL/EMBLCDS - Provided by the <a
+ href="https://www.ebi.ac.uk/ena/browser/api/#/ENA_Browser_Data_API/getFlatFileUsingGET">European
+ Nucleotide Archive's ENA Data API</a><br />
+ <em>Note: Versions of Jalview prior to 2.11.1.1 employed the
+ XML endpoint of the ENA browser, which was retired in August
+ 2020.</em></li>
+ <li>Uniprot - Free Text Search and Retrieval via the <a
+ href="https://www.uniprot.org/help/api">Uniprot REST API</a></li>
+ <li>PDB - Free Text Search via the <a
+ href="https://www.ebi.ac.uk/pdbe/api/doc/search.html">PDBe
+ REST API</a> and retrieval via <a
+ href="https://www.ebi.ac.uk/Tools/dbfetch/">WSDbFetch</a><br />
+ Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate
+ J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez
+ R. <br> SOAP-based services provided by the European
+ Bioinformatics Institute.<br> Nucleic Acids Res.
+ 33(1):W25-W28 (2005) <br> <br>
+ </li>
+ </ul>
</body>
</html>
</ol>
<strong>Please note: The 2.10.2 feature counting interface is not compatible with earlier versions.</strong><br/><br/>
<em><a
- href="http://www.jalview.org/examples/groovy/featuresCounter.groovy">http://www.jalview.org/examples/groovy/featuresCounter.groovy</a>
+ href="https://www.jalview.org/examples/groovy/featuresCounter.groovy">https://www.jalview.org/examples/groovy/featuresCounter.groovy</a>
- rendered with <a href="http://hilite.me">hilite.me</a></em>
<!-- HTML generated using hilite.me --><div style="background: #f8f8f8; overflow:auto;width:auto;border:solid gray;border-width:.1em .1em .1em .8em;padding:.2em .6em;"><pre style="margin: 0; line-height: 125%"><span style="color: #408080; font-style: italic">/*</span>
<span style="color: #408080; font-style: italic"> * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)</span>
<p>
For more information, you might also want to take a look at the
documentation section of the Jalview website (<a
- href="http://www.jalview.org/about/documentation">http://www.jalview.org/about/documentation</a>).
+ href="https://www.jalview.org/about/documentation">https://www.jalview.org/about/documentation</a>).
</p>
<p>
If you are using the Jalview Desktop application and are looking for
google the online version of these pages. If you don't find what you
are looking for, or want to report a bug or make a feature request,
then get in contact over at <a
- href="http://www.jalview.org/community">http://www.jalview.org/community</a>
+ href="https://www.jalview.org/community">https://www.jalview.org/community</a>
+ </p>
+ <p>
+ <strong>Logging, troubleshooting and reporting bugs</strong><br />If
+ something seems to be wrong with your Jalview installation, or you
+ think you've found a problem, take a look at <a href="logging.html">Jalview's
+ logging and bug reporting</a> documentation.
</p>
-
<p>
<strong>Citing Jalview</strong><br />If you use Jalview in your
work, please cite the Jalview 2 paper in Bioinformatics:
--- /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>The Java Console, Logging and Reporting Bugs</title>
+</head>
+<body>
+ <p>
+ <strong>The Java Console, Logging and Reporting Bugs<br /></strong>
+ </p>
+ <p>
+ Like most programs, Jalview contains bugs, despite our best efforts.
+ However, Jalview also produces a series of messages during its
+ operation, often referred to as 'logs'. These logs provide a record
+ of Jalview's operation. They can also be extremely useful when <a
+ href="#reportingbugs">reporting bugs</a>, since they help the
+ Jalview developers diagnose and find 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, when tracking down problems preventing Jalview from
+ starting up properly, you need to look at the startup logs - which
+ are not shown in the Jalview Console. The location of these depends
+ on how you launched Jalview:</p>
+ <p>
+ <strong>Jalview Desktop Installation Launch Logs</strong><br />If you are using
+ a standard desktop version of Jalview installed from one of our
+ install4j installers, then messages about Jalview's initial launch
+ 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>
+ <p><strong>Jalview Executable Jar Launch Logs</strong><br/>If you are using the Jalview executable jar file (also
+ used by bioconda and OSX homebrew installations) then the default run class (
+ <em>jalview.bin.Launcher</em> -- a minimised launcher that will set
+ memory and linux dpi settings before re-launching
+ <em>jalview.bin.Jalview</em>), will output logging information to
+ STDOUT and STDERR.
+ </p>
+
+ <p><strong>
+ <a name="java_console">Java Console and Log Level</a>
+ </strong></p>
+ <p>
+ The Java Console is opened by selecting <strong>Tools
+ → Show Java Console</strong>. The visibility of the console is stored
+ in your preferences, so if you quit Jalview with the console open,
+ it will be shown the next time you start Jalview. You can close the
+ console by selecting the same menu option again, or just closing the
+ console window.
+ </p>
+ <p>The Java Console's text display always shows information about
+ your system and Jalview installation details. The rest are the most
+ recent messages output during your Jalview session. Some messages
+ are only captured by the console when it is open, so to get a full
+ log for debugging a problem, enable the console and then restart
+ Jalview.</p>
+
+ <p>
+ You can temporarily control the detail of what appears as output by
+ selecting a <em>Log level</em> using the drop-down list at the
+ bottom left of the console. There are several levels to choose from:
+ The most verbose is TRACE, followed by DEBUG, INFO, WARN. When the
+ Console is opened, the default level will be chosen (INFO).
+ </p>
+ <p>
+ <strong>Note! If you change the log level in the Java
+ Console, this change will only persist for as long as the console
+ is open. Once you close the console the log level will revert back
+ to what it had been when you opened the console (usually INFO).</strong>
+ </p>
+ <p><strong>Permanently changing Jalview's default log level</strong><br/>
+ You can change the default log level by editing the Jalview
+ preferences file, <em>.jalview_properties</em>, found in your home
+ directory (on Windows: %HOMEPATH%, or the folder above 'My
+ Documents'; on macOS: ~ or /Users/<em>username</em>; on linux/unix:
+ ~ or /home/<em>username</em>), and setting the property <em>logs.Jalview.level</em>
+ to the log level you prefer, e.g.
+ <pre>
+ logs.Jalview.level=DEBUG
+ </pre>
+ You can also set the property
+ <pre>
+ logs.Axis.level=DEBUG
+ </pre>
+ <p>to get debug information for Jalview's JPred service. The Axis log
+ level cannot be set from within the Java Console.
+ </p>
+ <p>
+ You can also set the <em>logs.jalview.level</em> property to a log level
+ not usually presented in the Java Console (though restricted to log
+ levels used by Apache Log4j -- see <a
+ href="https://logging.apache.org/log4j/2.x/manual/customloglevels.html">Log4j
+ Custom Log Levels</a> for details of the standard log levels
+ available). Jalview does not currently define any custom log levels.
+ If you do set the property with a log level that is normally not
+ visible in the Java Console this should be respected and visibly
+ selected when you open the console.
+ </p>
+ <p>
+ The <em>Clear</em> button at the bottom of the console will clear
+ all logging messages except for the initial system information which
+ is rewritten to the console.
+ </p>
+ <p>
+ The <em>Copy to clipboard</em> button at the bottom right of the
+ console will copy all of the text in the console to your system
+ clipboard, ready to paste into another application (e.g. email
+ composer or issue tracker).
+ </p>
+
+ <p><strong><a name="reportingbugs">Reporting Bugs</a></strong></p>
+
+ <p>
+ If you come across a problem in Jalview where something is not
+ working as described, or how you think it should, you should first
+ check the <a href="https://www.jalview.org/faq">Jalview FAQ</a> to
+ see if this is a known problem and if there is a suggested
+ workaround.
+ </p>
+ <p>
+ If there is no FAQ answer covering your problem then you can submit
+ a bug report on the <a href="https://issues.jalview.org/">Jalview
+ Issue Tracker</a>. It is good practice to search the issue tracker
+ first to see if the issue has already been reported. If an issue
+ already exists please continue to add your own comments to the issue
+ which may well help narrow down the problem, if not then you can
+ create an account and submit a new bug report:
+ </p>
+ <p>
+ Make sure that you set Project to <em>Jalview (JAL)</em>, and Issue
+ Type to <em>Bug</em> or <em>New Feature</em> or <em>Improvement</em>
+ appropriately.<br /> Give a one line summary of the issue in the <em>Summary</em>.
+ <br /> In the <em>Environment</em> text box you can describe the
+ system you are using. This is usually most easily done by opening
+ the Java Console, clicking the <em>Clear</em> button, and then
+ immediately on the <em>Copy to clipboard</em> button, and then
+ pasting the clipboard into the text box.
+ </p>
+ <p>
+ You can then give more detailed information about how to recreate
+ the problem in the <em>Description</em> text box. If you want to
+ attach any screenshots or example alignment files that demonstrate
+ the problem then you can drag them to the Create Issue dialog in
+ your browser, or use the <em>Attachment</em> browse facility to
+ locate them on your computer.
+ </p>
+
+ <p>
+ To help the Jalview team with diagnosing a particular issue, it is
+ really helpful if you can also add more detailed logs output whilst
+ re-creating the problem. To do this, open the Java Console, click
+ the <em>Clear</em> button and select TRACE in the <em>Log level</em>
+ drop down list. <br /> Whilst leaving the console open, perform the
+ task in Jalview that re-creates the problem. <br /> Then you can
+ copy the debug information in the Java Console by clicking on the <em>Copy
+ to clipboard</em> button and then paste that into the Description, or a
+ Comment of your issue.
+ </p>
+
+ <p>
+ For other queries or comments about Jalview, remember you can
+ contact the Jalview team using email via the
+ <a href="https://www.jalview.org/mailman/listinfo/jalview-discuss">Jalview
+ discussion list</a>, on Twitter <a
+ href="https://twitter.com/Jalview/">@Jalview</a>, or for technical
+ discussions, via the Jalview developer's chatroom at
+ <a href="https://gitter.im/jalview/developers">https://gitter.im/jalview/developers</a>.
+ </p>
+
+</body>
+</html>
arguments, but you must put the <em>jvl</em> file first, e.g. <pre>
/PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl /path/to/alignments/myalignment.fa</pre> Alternatively, you can use the standard Jalview command line
arguments with or without the jvl file (first), e.g. <pre>
- /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl -open http://www.jalview.org/examples/jpred_msa.fasta -annotations http://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre> You can use command line arguments to control memory
+ /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl -open https://www.jalview.org/examples/jpred_msa.fasta -annotations https://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre> You can use command line arguments to control memory
settings in Windows and macOS too: <br /> In Windows you must
use, e.g. <pre>
\PATH_TO_JALVIEW\Jalview.exe %HOMEPATH%\mymemorysetting.jvl -open %HOMEPATH%\myalignment.fa</pre> In macOS you can use the macOS <em>open</em> command like this: <pre>
<tr>
<td width="60" align="center" nowrap><strong><a
id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
- <em>13/07/2020</em></strong></td>
+ <em>17/09/2020</em></strong></td>
<td align="left" valign="top">
<ul>
- <!-- -->
<li>
<!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
residue in cursor mode
ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
EMBL flat file
</li>
+ <li>
+ <!-- JAL-3667 -->Improved warning messages, debug logging
+ and fixed Retry action when Jalview encounters errors when
+ saving or making backup files.
+ </li>
+ <li>
+ <!-- JAL-3676 -->Enhanced Jalview Java Console:
+ <ul>
+ <li>Jalview's logging level can be configured</li>
+ <li>Copy to Clipboard Buttion</li>
+ </ul>
+ </li>
+ <li>
+ <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
+ when running on Linux (Requires Java 11+)
+ </li>
</ul> <em>Launching Jalview</em>
<ul>
<li>
<!-- JAL-3608 -->Configure Jalview Desktop's look and feel
through a system property
</li>
+ <li>
+ <!-- JAL-3477 -->Improved built-in documentation and command
+ line help for configuring Jalview's memory
+ </li>
</ul>
</td>
<td align="left" valign="top">
<ul>
<li>
+ <!-- JAL-3691 -->Conservation and Quality tracks are shown
+ but not calculated and no protein or DNA score models are
+ available for tree/PCA calculation when launched with
+ Turkish language locale
+ </li>
+ <li>
<!-- JAL-3493 -->Escape does not clear highlights on the
alignment (Since Jalview 2.10.3)
</li>
<li>
<!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
- doesn't slide selected sequences
+ doesn't slide selected sequences, just sequence under cursor
+ </li>
+ <li>
+ <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
+ sequence under the cursor
</li>
<li>
<!-- JAL-3613 -->Peptide-to-CDS tracking broken when
to the position under the cursor
</li>
<li>
+ <!-- JAL-3673 -->Sequence ID for reference sequence is
+ clipped when Right align Sequence IDs enabled
+ </li>
+ <li>
<!-- JAL-2983 -->Slider with negative range values not
rendered correctly in VAqua4 (Since 2.10.4)
</li>
- </ul>
- <em>New Known defects</em>
+ <li>
+ <!-- JAL-3685 -->Single quotes not displayed correctly in
+ internationalised text for some messages and log output
+ </li>
+ <li>
+ <!-- JAL-3490 -->Find doesn't report matches that span
+ hidden gapped columns
+ </li>
+ <li>
+ <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
+ panels, Alignment viewport and annotation renderer.
+ </li>
+ <li>
+ <!-- JAL-3561 -->Jalview ignores file format parameter
+ specifying output format when exporting an alignment via the
+ command line
+ </li>
+ <li>
+ <!-- JAL-3667 -->Windows 10: For a minority of users, if
+ backups are not enabled, Jalview sometimes fails to
+ overwrite an existing file and raises a warning dialog. (in
+ 2.11.0, and 2.11.1.0, the workaround is to try to save the
+ file again, and if that fails, delete the original file and
+ save in place.)
+ </li>
+ </ul> <em>Launching Jalview</em>
+ <ul>
+ <li>
+ <!-- JAL-3718 -->Jalview application fails when launched the
+ first time for a version that has different jars to the
+ previous launched version.
+ </li>
+ </ul> <em>Developing Jalview</em>
+ <ul>
+ <li>
+ <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
+ data, causing cloverReport gradle task to fail with an
+ OutOfMemory error.
+ </li>
+ <li>
+ <!-- JAL-3280 -->Migrated the Jalview Version Checker to
+ monitor the release channel
+ </li>
+ </ul> <em>New Known defects</em>
<ul>
- <li><!-- JAL-3701 -->Stale build data in jalview standalone jar builds (only affects 2.11.1.1 branch)
+ <li>
+ <!-- JAL-3748 -->CDS shown in result of submitting proteins
+ in a CDS/Protein alignment to a web service is wrong when
+ proteins share a common transcript sequence (e.g.
+ genome of RNA viruses)
+ </li>
+ <li>
+ <!-- JAL-3576 -->Co-located features exported and re-imported
+ are ordered differently when shown on alignment and in
+ tooltips. (Also affects v2.11.1.0)
+ </li>
+ <li>
+ <!-- JAL-3702 -->Drag and drop of alignment file onto
+ alignment window when in a HiDPI scaled mode in Linux only
+ works for the top left quadrant of the alignment window
+ </li>
+ <li>
+ <!-- JAL-3701 -->Stale build data in jalview standalone jar
+ builds (only affects 2.11.1.1 branch)
+ </li>
+ <li>
+ <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
+ when alignment view restored from project (since Jalview 2.11.0)
</li>
</ul>
</td>
<p>
<strong>The Jalview Desktop RSS News Reader</strong><br /> The
Jalview Desktop includes a built in news reader for the <a
- href="http://www.jalview.org/feeds/desktop/rss">Jalview
+ href="https://www.jalview.org/feeds/desktop/rss">Jalview
Desktop News Channel</a>.
</p>
<br />
<p>
The <em>Jalview news reader</em> was introduced in <a
- href="http://www.jalview.org/releaseHistory.html#Jalview2.7">Jalview
+ href="https://www.jalview.org/releaseHistory.html#Jalview2.7">Jalview
version 2.7</a>. Its implementation is based on <a
- href="http://jswingreader.sourceforge.net/">JSwingReader</a>.
+ href="https://jswingreader.sourceforge.net/">JSwingReader</a>.
</p>
<br />
<em>If you need to prevent the news-reader opening, then add the
</head>
<body>
<p>
- <strong>Jalview 2.11.1.0</strong>
- </p>
- <p>
- Jalview 2.11.1.0 is the first minor release for the 2.11 series.
- Along with a number of critical bug fixes and improvements it brings
- new functionality for mapping sequence features between CDS and
- Protein alignments. It is also the first release made under a new <em>four</em>
- number versioning scheme, which will allow us to keep track of
- patches and bug fixes.
+ <strong>Jalview 2.11.1.1</strong>
</p>
+ <p>Jalview 2.11.1.1 is the first patch release for Jalview version
+ 2.11.1. In addition to fixes for some critical bugs, it also
+ contains a handful of new features suggested by the Jalview
+ community.</p>
+ <ul>
+ <li>Shift+arrow keys navigate to next gap or residue in cursor
+ mode (enable with F2)</li>
+ <li>Support import of VCF 4.3 by updating HTSJDK from 2.12 to
+ 2.23</li>
+ <li>Improved recognition of GZipped files from local disk or
+ retrieved via the web</li>
+ <li>EMBL and EMBL CDS database records retrieved from the
+ European Nucleotide Archive's Data API as 'EMBL Flatfile' records</li>
+ <li>Improved <a href="logging.html">Java Console and
+ logging</a> to help track down problems
+ </li>
+ <li>Improved support for Hi-DPI (4K) screens when running on
+ Linux (Requires Java 11+)</li>
+ </ul>
+ <p>Critical bug fixes include</p>
<ul>
- <li><strong>Virtual Features</strong><br />In previous
- versions of Jalview, specific nucleotide sequence features such as
- genomic variants and exons were transferred to protein products on
- import. Jalview 2.11.1 instead provides 'virtual features' that
- can be enabled and overlaid on linked CDS/Protein views via their
- <a href="features/splitView.html#virtualfeats">Sequence
- Features dialog</a>. This allows more analyses of nucleotide and
- peptide sequence features on alignments in a more flexible and
- memory efficient way than in earlier versions.<br />
- <em>Note: Virtual features work best when variants are
- annotated with CSQ fields. Please <a
- href="features/importvcf.html#computepepvariants">see this
- Groovy script workaround</a> if you are working with VCF files
- without CSQ fields.
- </em></li>
- <li><strong>Improved VCF data import</strong><br /> <a
- href="features/importvcf.html#attribs">Standard attributes for
- filtering variants</a> (e.g. position, QUAL field etc) are now
- extracted from VCF files. This new feature was suggested by a user
- at the Jalview booth during ISMB 2019.</li>
- <li><strong>Extended feature attributes are exported
- in GFF3</strong><br />Complex attributes from VCF files can be exported
- and imported via GFF3</li>
- <li><strong>Updated Jalview Installer and Launcher</strong><br />Jalview's
- installation packages are now built with Install4j 8, which brings
- better support for Linux and improved control of file
- associations. New <a href="memory.html#jvm">parameters on the
- Jalview launcher</a> allow an upper memory limit to be specified <em>via</em>
- a Jalview launch file, to prevent it from hogging your system.</li>
+ <li>Jalview runs correctly when launched with Turkish language
+ settings</li>
+ <li>Peptide-to-CDS tracking broken when multiple EMBL gene
+ products shown for a single contig (such as viral genomes)</li>
+ <li>Errors encountered when processing variants from VCF files
+ yield "Error processing VCF: Format specifier '%s'" on the console</li>
+ <li>Count of features not shown can be wrong when there are
+ both DNA and Protein features mapped to the position under
+ the cursor</li>
+ <li>Sequence ID for reference sequence is clipped when Right
+ align Sequence IDs enabled</li>
+ <li>Find doesn't report matches that span hidden gapped columns</li>
+ <li>Jalview ignores file format parameter specifying output
+ format when exporting an alignment via the command line</li>
</ul>
<p>
- See the <a href="releases.html#Jalview.2.11.1.0">2.11.1.0
- release notes</a> for full details of bugs fixed and new known issues.
+ For the full release notes, see <a href="releases.html#Jalview.2.11.1.1">the
+ Jalview 2.11.1.1 release notes</a>.
</p>
<p>
- <em>JalviewJS News</em><br />With the release of Jalview 2.11.1.0,
- the team are now focused on bringing JalviewJS to full production.
- To follow our progress take a look at <em>http://www.jalview.org/jalview-js/</em>
- and follow updates on our new <a
- href="https://github.com/jalview/jalview-js/">JalviewJS
- Releases github repository</a>.
+ <strong>Known Issues</strong>
</p>
+ <ul>
+ <li>We've had reports from a small number of windows 10 users
+ who see a warning dialog pop up when Jalview tries to save a new
+ version of an existing file. If you are affected by this bug and
+ this latest version of Jalview doesn't fix it, please let us know!</li>
+ <li>Co-located features exported and re-imported are ordered
+ differently when shown on alignment and in tooltips. (Also affects
+ v2.11.1.0)</li>
+ <li>Drag and drop of alignment file onto alignment window when
+ in a HiDPI scaled mode in Linux only works for the top left
+ quadrant of the alignment window</li>
+ </ul>
</body>
</html>
* when shading by annotation</li>
* <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
* when shading by annotation</li>
- * <li>www.jalview.org (http://www.jalview.org) a property enabling all HTTP
- * requests to be redirected to a mirror of http://www.jalview.org</li>
+ * <li>www.jalview.org (https://www.jalview.org) a property enabling all HTTP
+ * requests to be redirected to a mirror of https://www.jalview.org</li>
* <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
* alignment figure to accommodate even the longest sequence ID or annotation
* label.</li>
DEFAULT_CACHE_THRESHOLD_IN_DAYS));
IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
- "http://www.jalview.org/services/identifiers"));
+ "https://www.jalview.org/services/identifiers"));
IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
// String defurl =
// "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
// //
- String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
+ String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
Cache.log.debug(
"Starting questionnaire with default url: " + defurl);
desktop.checkForQuestionnaire(defurl);
* @j2sIgnore
*/
{
- file = Cache.getDefault("STARTUP_FILE",
- Cache.getDefault("www.jalview.org", "http://www.jalview.org")
- + "/examples/exampleFile_2_7.jar");
+ file = jalview.bin.Cache.getDefault("STARTUP_FILE",
+ jalview.bin.Cache.getDefault("www.jalview.org",
+ "https://www.jalview.org")
+ + "/examples/exampleFile_2_7.jvp");
if (file.equals(
- "http://www.jalview.org/examples/exampleFile_2_3.jar"))
+ "http://www.jalview.org/examples/exampleFile_2_3.jar") || file.equals(
+ "http://www.jalview.org/examples/exampleFile_2_7.jar"))
{
+ file.replace("http:", "https:");
// hardwire upgrade of the startup file
- file.replace("_2_3.jar", "_2_7.jar");
+ file.replace("_2_3", "_2_7");
+ file.replace("2_7.jar", "2_7.jvp");
// and remove the stale setting
Cache.removeProperty("STARTUP_FILE");
}
+ "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
+ "-jvmmempc=PERCENT\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to PERCENT% of total physical memory detected. This defaults to 90 if total physical memory can be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
+ "-jvmmemmax=MAXMEMORY\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m), gigabytes(g) or if you're lucky enough, terabytes(t). This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
- + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
+ + "\n~Read documentation in Application or visit https://www.jalview.org for description of Features and Annotations file~\n\n");
}
private static void startUsageStats(final Desktop desktop)
chan.setURL(
jalview.bin.Cache.getDefault("JALVIEW_NEWS_RSS",
jalview.bin.Cache.getDefault("www.jalview.org",
- "http://www.jalview.org")
+ "https://www.jalview.org")
+ "/feeds/desktop/rss"));
loadLastM();
_channelModel.addChannel(chan);
} catch (java.beans.PropertyVetoException ve) {
} catch (java.lang.ClassCastException cex) {
Cache.log.warn(
+<<<<<<< HEAD
"Squashed a possible GUI implementation error. If you can recreate this, please look at https://issues.jalview.org/browse/JAL-869",
cex);
+=======
+ "Squashed a possible GUI implementation error. If you can recreate this, please look at https://issues.jalview.org/browse/JAL-869",
+ cex);
+>>>>>>> 48040645e (JAL-3741 http to https (and jar to jvp for exampleFile defaults!))
}
}
JPanel panel = new JPanel(new GridLayout(2, 1));
panel.add(label);
+<<<<<<< HEAD
+=======
+ panel.add(history);
+ history.setPreferredSize(new Dimension(400, 20));
+ history.setEditable(true);
+ history.addItem("https://www.");
+
+ String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
+>>>>>>> 48040645e (JAL-3741 http to https (and jar to jvp for exampleFile defaults!))
/*
* the URL to fetch is input in Java: an editable combobox with history JS:
message.append("<div style=\"color: #FF0000;font-style: bold;\">");
}
+<<<<<<< HEAD
message.append("<br>!! Version ").append(Cache.getDefault("LATEST_VERSION", "..Checking.."))
.append(" is available for download from ")
.append(Cache.getDefault("www.jalview.org", "https://www.jalview.org")).append(" !!");
message.append("</div>");
return message.toString();
+=======
+ message.append("<br>!! Version "
+ + jalview.bin.Cache.getDefault("LATEST_VERSION",
+ "..Checking..")
+ + " is available for download from "
+ + jalview.bin.Cache.getDefault("www.jalview.org",
+ "https://www.jalview.org")
+ + " !!");
+ if (red)
+ {
+ message.append("</div>");
+ }
+ }
+ message.append("<br>Authors: " + jalview.bin.Cache.getDefault(
+ "AUTHORFNAMES",
+ "The Jalview Authors (See AUTHORS file for current list)")
+ + "<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
+ + "<br><br>For help, see the FAQ at <a href=\"https://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
+ + "<br><br>If you use Jalview, please cite:"
+ + "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
+ + "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+ + "<br>Bioinformatics doi: 10.1093/bioinformatics/btp033"
+ + "</html>");
+ return message;
+>>>>>>> 48040645e (JAL-3741 http to https (and jar to jvp for exampleFile defaults!))
}
/**
startupCheckbox
.setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
- Cache.getDefault("www.jalview.org", "http://www.jalview.org")
- + "/examples/exampleFile_2_3.jar"));
+ Cache.getDefault("www.jalview.org", "https://www.jalview.org")
+ + "/examples/exampleFile_2_7.jvp"));
/*
* Set Colours tab defaults
{
private static String version = new BuildDetails().getVersion();
- private String webstartUrl = "http://www.jalview.org/services/launchApp";
+ private String webstartUrl = "https://www.jalview.org/services/launchApp";
private String application = "Jalview";
git://source.jalview.org / jalview.git / commitdiff
