<strong>Jalview Project Archives</strong>
</p>
- <p>These are java archives of an XML file containing alignments,
- trees and Jalview display information. A data exchange standard is
- currently being developed, so there is no stable schema yet, but
- Jalview web services will soon make use of the same interchange
- format.</p>
+ <p>These are Zip archives of an XML file containing alignments,
+ trees, Principal Component Analyses (since 2.11.0), 3D structures,
+ and display information for Jalview, VARNA, Jmol and UCSF Chimera.
+ XML documents conform to a schema, and changes to the format are
+ made to ensure future versions of Jalview will be able to read old
+ Jalview project files.</p>
<p>
- For those who want to know...<br> Jalview uses java classes
- automatically created using <a href="http://www.castor.org">Castor</a>.
- Jalview 2.08 uses descriptor classes which significantly increase
- the speed of marshalling / unmarshalling java objects into XML.
- Files created prior to Jalview 2.08 can still be read in, but they
- will be saved in the new format.
+ <em>For those who want to know...</em><br> Jalview 2.11.0
+ onwards employ the JAX-B java to XML binding framework to read and
+ write Jalview project files. Earlier versions of Jalview employed <a
+ href="http://www.castor.org">Castor</a>. Jalview 2.08 used
+ descriptor classes which significantly increase the speed of
+ marshalling / unmarshalling java objects into XML. <br /> <br />
+ Files created prior to Jalview 2.08 can no longer be read by Jalview
+ 2.11.0. If you need to import old project files, then please import
+ them to Jalview 2.10.5 (available from the Jalview version archive)
+ and save the project again to convert it to the new format.
</p>
</body>
</html>
overview that are hidden in the alignment.
</p>
<p>
- <em>Gap Colour</em> - The default colour scheme for a new alignment
- window. If the chosen option is "User Defined" then the
- last User Defined Colour loaded or saved via the User Defined
- Colours panel will be loaded.
- </p>
- <p>
<a name="structure"><strong>"Structure"
Preferences tab</strong></a><em> added in Jalview 2.8.2</em>
</p>
here, by entering the full path to the Chimera executable program.
Double-click this field to open a file chooser dialog.
<p>
+ <p>
+ <em>PDB Fields shown in Search and Structure Summaries</em> - ticks
+ in this table indicate fields shown by default when browsing results
+ of a free text search via the PDB sequence fetcher, or 3D structures
+ offered by the 3D Structure Chooser.<p>
+ <p>
<a name="connections"><strong>"Connections"
Preferences tab</strong></a>
</p>
statement</a> for more information.
</p>
<p>
+ <a name="backups"><strong>The "Backups" Preferences Tab</strong></a>
+ </p>
+ <p>Since Jalview 2.11.0, overwriting an existing file when saving
+ or exporting data will by default trigger a backup file to be
+ created. Several options are provided to control how backup files
+ are named, and how many old versions will be kept.</p>
+ <p>
+ <em>Schemes</em> - select from three default schemes <em>Single Backup</em>, <em>Keep All Versions</em>, and <em>Rolled Backup Files</em>, or choose <em>Custom</em> to enable a previously defined custom scheme.
+ </p><p>
+ <em>Custom</em> - Check this box to adjust the parameters of the currently selected scheme. Once <em>OK</em> is selected these parameters will be saved as the <em>Custom</em> scheme in your user preferences. To revert changes hit <em>Cancel</em>.
+ </p>
+ <p><em>Scheme Examples</em> - shows how backup files will appear according to the currently selected scheme and parameters.
+ </p>
+ <p><em>Deleting Old Backup Files</em> - these settings control how many backups are kept.</p>
+ <p><em>Backup filename strategy</em> - specify the naming convention for numbered backups and how they are ordered.</p>
+ <p>
<a name="links"><strong>The "Links" Preferences
tab</strong></a>
</p>
loaded onto the alignment will automatically sort the alignment.
</p>
<p> </p>
+ <em>Web Services Preferences</em> - documentation for this tab is
+ given in the
+ <a href="../webServices/webServicesPrefs.html">Web Services
+ Preferences section</a>.
<p> </p>
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</center>
</h2>
<p>
- Jalview sometimes runs out of memory. This is because of the way
- that Java runs on a computer - what is actually run is a program
- called a virtual machine (the JVM) which executes the java
- instructions. The JVM has limits on the memory that can be allocated
- to the java program - and you might need to increase them if you are
- working with particularly large datasets.<br> If Jalview has
- not explicitly told you that it has run out of memory, then a common
- sign is that a function that normally works seems to have no effect
- when working with a larger set of sequences (this might include open
- dialog boxes for saving PNG files, or when interpreting the result
- of a web service calculation).
+ When launched as an Application, Jalview automatically tries to
+ maximise the amount of memory allocated to it, but sometimes it may
+ run out of memory. This is because of the way that Java runs on a
+ computer - what is actually run is a program called a virtual
+ machine (the JVM) which executes the java instructions. The JVM has
+ limits on the memory that can be allocated to the java program - and
+ you might need to increase them if you are working with particularly
+ large datasets.<br> If Jalview has not explicitly told you that
+ it has run out of memory, then a common sign is that a function that
+ normally works seems to have no effect when working with a larger
+ set of sequences (this might include open dialog boxes for saving
+ PNG files, or when interpreting the result of a web service
+ calculation).
</p>
<p>
<em>Jalview Memory Usage Monitor</em>: If you are concerned about
window's background.
</p>
<p>
- <em>Increasing the memory available to Jalview</em><br> The way
- you increase the memory settings for the JVM depends on which
- installation of Jalview you use:
- </p>
- <ul>
- <li><em><font size="3">Web Start Version</font></em>
- <p>
- JavaWS sets the JVM parameters through special tags in the JNLP
- file. You can obtain a JNLP file with modified memory settings
- from our service with the following link (replace 2G with
- desired memory in G or M):<br /> <a
- href="http://www.jalview.org/services/launchApp?jvm-max-heap=2G">http://www.jalview.org/services/launchApp?jvm-max-heap=2G</a>
- </p>
- <p>
- Alternatively, if you want to create your own JNLP file then
- please download the latest JNLP file from <a
- href="http://www.jalview.org/webstart/jalview.jnlp">http://www.jalview.org/webstart/jalview.jnlp</a>
- and modify the max-heap-size parameter for the j2se tag in the
- <resources> element. e.g.
- <pre>
-<j2se version="1.7+" initial-heap-size="500M" max-heap-size="1000M"/>
-</pre> In both cases, you should save your new jnlp file somewhere and then
- either point your web browser at the file's url, launch it from
- your file browser, or from a terminal window run javaws (located
- in your Java installation's bin directory) with the file location
- as its argument. The file's url is something like :<br> <pre>
-file://<full path to file>
-</pre> If Jalview doesn't start up, see <a href="#memsetting">below</a>.
- You'll have to edit the above settings in the JNLP file using a
- text editor, save it, and try starting Jalview with it once more.
- </p></li>
- <li><em><font size="3">Install Anywhere version</font></em>
- <p>You need to change the InstallAnywhere configuration
- settings for the application. These are found in different
- places depending upon which operating system you have :
- <ul>
- <li><em>Unix/Windows</em>
- <p>Take a look inside the Jalview program installation
- directory (this might be in C:\Program Files\Jalview on
- windows). You should find a file called 'Jalview.lax' in it
- - make a backup, and then add the following lines to the end
- of the original file :
- <pre>
-lax.nl.java.option.java.heap.size.max=1000m
-lax.nl.java.option.java.heap.size.initial=500m
-</pre> Case and (lack of) spaces are important here! Do not add any spaces
- after the m in each line, and do not put any spaces before
- 'lax'.<br> Also there MUST be a carriage return after the
- final line.
- <p></p></li>
- <li><em>Mac OSX</em>
- <p>
- The lines you need to change are in the <em>Info.plist</em>
- file inside the <em>Jalview.app/Contents</em> directory
- (which is where the installAnywhere installation was made) :
-
-
- <pre>
-<key&ht;VMOptions</key&ht;
-<array>
-! <string>-Xms2M</string>
-! <string>-Xmx64M</string>
-</array>
-</pre>Exchange the above two string tags for : <pre>
-<string>-Xms500M</string>
-<string>-Xmx1000M</string>
-</pre>
- <p></p></li>
- </ul>
- <li><font size="3"><em>In all cases</em></font><br> Save
- the file and try to start Jalview in the normal way. If it doesn't
- start, see below...</li>
- </ul>
- <p>
- <em>Please Note:</em> We do modify the default memory settings in
- Jalview from time to time, so you may find different numbers to
- those shown in the examples above.
- </p>
- <font size="3"><em>Jalview doesn't start... What do the
- memory settings mean ?<a name="memsetting"></a>
- </em></font>
- <p>The 1000m value corresponds to the maximum number of megabytes
- of space that java objects can occupy. The 500m is the initial heap
- size that java will run in - increasing this can speed up memory
- allocation if you know you will need 500 meg of memory to begin with
- (ie it should speed up loading large alignments).</p>
- <p>If, after setting the initial and maximum heap size to some
- large value, you cannot actually start Jalview, then the max and
- initial sizes are too big for your machine (there seems to be a
- physical limit related to physical RAM - email the usual address to
- enlighten us if you know better!). Our experiments found 1000m to be
- the biggest setting that could be used on a 1GB machine. Just try
- reducing the sizes until Jalview starts up properly!</p>
- <p>
- We increased the default memory in Jalview 2.10.5 to 1G. To launch
- Jalview with the pre 2.10.5 default memory allocation, use the <a
- href="http://www.jalview.org/webstart/jalview_256MB.jnlp">Jalview
- 256MB JNLP</a>.
- </p>
- <p> </p>
+ <em>Increasing the memory available to Jalview</em><br>
+ Since Jalview 2.11, the program automatically configures the JVM memory settings to set the maximum memory available to Jalview to be 90% of physical memory.
+ <p> </p>
</body>
</html>
via the browser when downloading the application, or when the
Jalview Desktop user interface is launched.<br> <br>
<ul>
- <li><i>The JNLP file at
- www.jalview.org/webstart/jalview.jnlp is retrieved to
- determine if you are running the latest version of Jalview.</i></li>
+ <li><i>The Jalview Getdown Launcher</i> (Since 2.11.0) examines release
+ channels every time Jalview launches to determine if a new
+ release is available.</li>
<li><i>The questionnaire web service at
www.jalview.org/cgi-bin/questionnaire.pl is checked and a
unique cookie for the current questionnaire is stored in the
<ul>
<li><em>VCF Support</em>. Proteins and genomic contigs with
chromosomal location annotation (such as protein coding genes
- retrieved from Ensembl) can be annotated with variants imported
- from a local VCF file.</li>
+ retrieved from Ensembl) can be annotated with variants <a
+ href="features/importvcf.html">imported from a local VCF file</a>.</li>
<li><em>The Jalview Launcher and Update System</em><br />
Jalview's new installation model means you'll only need to
download and install Jalview once. After installation, Jalview
will automatically keep itself up to date. The launcher also sets
Jalview's memory automatically, so you'll never again have to
- manually configure Java's memory settings.<br />We are grateful to
- Install4J who provided us with a free license for their
+ manually configure Java's memory settings.<br />We are grateful
+ to Install4J who provided us with a free license for their
installation system, and Jalview's over the air update system is
- via Getdown.</li>
+ based on Three Rings' Getdown system.</li>
+ <li><em>Backup files</em><br />Jalview will automatically
+ create backups when overwriting existing files, and - unlike with
+ earlier versions, should Jalview crash during a save, the original
+ file will be unaffected.</li>
+ <li><em>PCA plots stored in Jalview Projects</em><br />The PCA
+ viewer has also been enhanced and the user interface revised.</li>
+ <li>
+ </li>
</ul>
<p>
The full list of bugs fixed in this release can be found in the <a
<p>
<strong>Jalview and Java 11, 13, and onwards</strong>
</p>
- <p>Java 11 provides improved performance and better OS
- integration, so we now recommend users select our Java 11 Jalview
- distribution rather than the legacy Java 8 build.</p>
- <em>Known Issues - update for 211 </em>
- <ul>
- <li>OSX: The 'Open File' dialog for Jalview's Groovy Console
- appears with the title 'Save As', and attempting to select a file
- to load yields a FileNotFound exception.</br>The workaround is to first
- clear the 'Untitled' filename before selecting the file you wish
- to load.
- </li>
- <li>OSX: Links don't open when clicked on or via the Sequence
- or Alignment window popup menu.</li>
- <li>OSX (Webstart): Jalview only displays old news feed items</li>
- </ul>
+ <p>The Jalview application comes bundled with its own independent
+ Java installation which will be updated automatically from
+ www.jalview.org. Version 2.11.0 includes an AdoptOpenJDK Java 1.8
+ runtime, but installations will be migrated to the latest Java
+ release once remaining issues have been addressed.</p>
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GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
new Insets(0, 2, 5, 5), 70, 1));
+ versioncheck.setVisible(false);
+
// Add padding so the panel doesn't look ridiculous
JPanel spacePanel = new JPanel();
connectTab.add(spacePanel,
git://source.jalview.org / jalview.git / commitdiff