//libDir = j8libDir
libDir = j11libDir
libDistDir = j8libDir
+ digestonlyDir = j8digestonlyDir
compile_source_compatibility = 1.8
compile_target_compatibility = 1.8
// these are getdown.txt properties defined dependent on the JAVA_VERSION
JAVA_INTEGER_VERSION = string("11")
libDir = j11libDir
libDistDir = j11libDir
+ digestonlyDir = j11digestonlyDir
compile_source_compatibility = 11
compile_target_compatibility = 11
getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
}
}
+ fileTree(dir: digestonlyDir, include: ["*"]).getFiles().sort().each{f ->
+ def name = f.getName()
+ def line = "digestonly = ${getdownAppDistDir}/${name}\n"
+ getdownTextString += line
+ copy {
+ from f.getPath()
+ into getdownAppDir
+ }
+ }
+
// NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
/*
if (JAVA_VERSION.equals("11")) {
-1.8.3-1.2.6_FJVL
+1.8.3-1.2.7_FJVL
-1.8.3-1.2.6_JVL
+1.8.3-1.2.7_JVL
<parent>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
- <version>1.8.3-1.2.6_FJVL</version>
+ <version>1.8.3-1.2.7_FJVL</version>
</parent>
<artifactId>getdown-ant</artifactId>
<parent>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
- <version>1.8.3-1.2.6_FJVL</version>
+ <version>1.8.3-1.2.7_FJVL</version>
</parent>
<artifactId>getdown-core</artifactId>
return _resources;
}
+ public List<Resource> getDigestOnly ()
+ {
+ return _digestonly;
+ }
+
/**
* Returns the digest of the given {@code resource}.
*/
// clear our arrays as we may be reinitializing
_codes.clear();
_resources.clear();
+ _digestonly.clear();
_auxgroups.clear();
_jvmargs.clear();
_appargs.clear();
parseResources(config, "presource", Resource.PRELOAD, _resources);
parseResources(config, "nresource", Resource.NATIVE, _resources);
+ parseResources(config, "digestonly", Resource.NORMAL, _digestonly);
+
// parse our auxiliary resource groups
for (String auxgroup : config.getList("auxgroups")) {
ArrayList<Resource> codes = new ArrayList<>();
protected List<Resource> _codes = new ArrayList<>();
protected List<Resource> _resources = new ArrayList<>();
+ protected List<Resource> _digestonly = new ArrayList<>();
protected boolean _useCodeCache;
protected int _codeCacheRetentionDays;
rsrcs.add(app.getConfigResource());
rsrcs.addAll(app.getCodeResources());
rsrcs.addAll(app.getResources());
+ rsrcs.addAll(app.getDigestOnly());
for (Application.AuxGroup ag : app.getAuxGroups()) {
rsrcs.addAll(ag.codes);
rsrcs.addAll(ag.rsrcs);
<parent>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
- <version>1.8.3-1.2.6_FJVL</version>
+ <version>1.8.3-1.2.7_FJVL</version>
</parent>
<artifactId>getdown-launcher</artifactId>
if [ x$JVLVERSION != x ]; then
export VERSION=$JVLVERSION
else
- export VERSION=1.8.3-1.2.6_JVL
+ export VERSION=1.8.3-1.2.7_JVL
fi
if [ x${VERSION%_JVL} = x$VERSION ]; then
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
<packaging>pom</packaging>
- <version>1.8.3-1.2.6_FJVL</version>
+ <version>1.8.3-1.2.7_FJVL</version>
<name>getdown</name>
<description>An application installer and updater.</description>
jre_installs_dir = ~/buildtools/jre
j8libDir = j8lib
+j8digestonlyDir = j8digestonly
j11libDir = j11lib
j11modDir = j11mod
j11modules = com.sun.istack.runtime,com.sun.xml.bind,com.sun.xml.fastinfoset,com.sun.xml.streambuffer,com.sun.xml.txw2,com.sun.xml.ws.policy,java.activation,java.annotation,java.base,java.compiler,java.datatransfer,java.desktop,java.logging,java.management,java.management.rmi,java.naming,java.prefs,java.rmi,java.scripting,java.security.sasl,java.sql,java.xml,java.xml.bind,java.xml.soap,java.xml.ws,javax.jws,jdk.httpserver,jdk.jsobject,jdk.unsupported,jdk.xml.dom,org.jvnet.mimepull,org.jvnet.staxex,javax.servlet.api,java.ws.rs
+j11digestonlyDir = j11digestonly
+
install4j_home_dir = ~/buildtools/install4j8
install4j_copyright_message = ...
<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" />
"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>
then get in contact over at <a
href="http://www.jalview.org/community">http://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:
<td>Redo the last sequence edit undone.</td>
</tr>
<tr>
- <td><strong>Up Arrow</strong></td>
- <td>Both</td>
- <td>Moves selected sequence(s) up the alignment.<br />In
- Cursor mode press Alt key to move selection or sequence under
- cursor.
- </td>
- </tr>
- <tr>
- <td><strong>Down Arrow</strong></td>
- <td>Both</td>
- <td>Moves selected sequence(s) down the alignment.<br />In
- Cursor mode press Alt key to move selection or sequence under
- cursor.
- </td>
- </tr>
- <tr>
- <td><strong>Left Arrow</strong></td>
- <td>Normal</td>
- <td>Slides selected sequence(s) left. Press Alt key to slide
- in cursor mode</td>
- </tr>
- <tr>
- <td><strong>Right Arrow</strong></td>
- <td>Normal</td>
- <td>Slides selected sequence(s) right. Press Alt key to slide
- in cursor mode</td>
- </tr>
- <tr>
<td><strong>Cursor Keys<br> (Arrow Keys)
</strong></td>
<td>Cursor</td>
</td>
</tr>
<tr>
+ <td><strong>Cursor Keys<br> (Arrow Keys)
+ </strong></td>
+ <td>Normal<br />
+ <em>(+Alt in Cursor)</em></td>
+ <td>Moves selected sequence(s) up, down, left, or right
+ according to the direction pressed.<br>
+ <br>
+ <em>Alt+Arrow key to move selection or sequence under cursor
+ in cursor mode.</em>
+ </td>
+ </tr>
+ <tr>
<td><strong>Page Up</strong></td>
<td>Both</td>
<td>Scroll up the alignment view</td>
<title>The Java Console, Logging and Reporting Bugs</title>
</head>
<body>
- <h2>
- <center>
- <strong>The Java Console, 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.
+ <strong>The Java Console, Logging and Reporting Bugs<br /></strong>
</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.
+ 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 Java Console will show you information about what the Jalview application is doing (often in the background) whilst it is running.
+ 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>
- 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 standard desktop version of Jalview installed from one of our install4j installers, then Jalview's initial launch logging can be found in
+ <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:
+ 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>
+ <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 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>
-
- <h3><a name="java_console">Java Console and Log Level</a></h3>
- <p>
- The Java Console is opened by selecting <strong>Tools → Show Java Console</strong>. This option is saved across Jalview sessions so you can start Jalview with the Java Console already open by previously quitting Jalview with the Java Console already opened. Selecting <em>Show Java Console</em> in the <em>Tools</em> menu a second time will deselect the option and close the window. Closing the window in your system's usual way will also deselect the option in the <em>Tools</em> menu.
- </p>
- <p>
- The Java Console's text display always shows information about your system and Jalview installation setup, which is followed by messages output from some of the processes that your Jalview session has performed since opening the console.
- </p>
- <p>
- You can 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 of logging that you can choose from: in decreasing levels of verbosity they are: TRACE, DEBUG, INFO, WARN. By default the level initially chosen is 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><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 change the default log level by editing the Jalview preferenecs 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.
+ 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>
<pre>
logs.Axis.level=DEBUG
</pre>
- to get debug information for the SOAP services, and
- <pre>
- logs.Castor.level=DEBUG
- </pre>
- to get excessive information on XML serialisation and deserialisation! These last two properties cannot be set from within the Java Console.
+ <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 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.
+ 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.
+ 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).
+ 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>
- <h3>Reporting Bugs</h3>
+ <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.
+ 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:
+ 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.
+ 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.
+ 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.
+ 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> or on Twitter <a href="https://twitter.com/Jalview/">@Jalview</a>!
+ <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>
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>Developing Jalview</em>
<ul>
<li>
tooltips. (Also affects v2.11.1.0)
</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.
- Workaround is to try to save the file again, and if that
- fails, delete the original file and save in place.
- </li>
- <li>
<!-- JAL-3702 -->Drag and drop of alignment file onto
- alignment window not working correctly when in a HiDPI
- scaled mode in Linux
+ 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
</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 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>
git://source.jalview.org / jalview.git / commitdiff