<mapID target="edit" url="html/editing/index.html"/>
<mapID target="jalarchive" url="html/features/jalarchive.html"/>
<mapID target="multipleviews" url="html/features/multipleViews.html"/>
+ <mapID target="splitframe" url="html/features/splitView.html"/>
<mapID target="trees" url="html/calculations/tree.html"/>
<mapID target="treeviewer" url="html/calculations/treeviewer.html"/>
<mapID target="sorting" url="html/calculations/sorting.html"/>
<tocitem text="Making Figures" target="export" />
<tocitem text="Hidden Regions" target="hiddenRegions" />
<tocitem text="Multiple Views" target="multipleviews" />
+ <tocitem text="Split Frame View" target="splitframe" />
<tocitem text="Viewing Trees" target="treeviewer" expand="false" />
<tocitem text="Fetching Sequences" target="seqfetch" />
<tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false">
sequence). Chimera is available from the Jalview desktop, provided Chimera has been separately installed.</p>
<p>You can set a default choice of Jmol or Chimera structure viewer in <a href="preferences.html#structure"> Preferences</a>.
You can also optionally specify the path to the Chimera program here (if it differs from the standard paths searched by Jalview).
+<p>If you save your Jalview session as a project file, the state of any open Chimera windows will also be saved, and can be reopened by loading the project file on any machine with Chimera installed. <em>Since Jalview 2.9.</em>
<!-- <p>The following menu entries are provided for viewing structure data<br>
<ul>
<li>The <strong>"Structure→View
residue number and chain code
([RES]Num:Chain). Moving the mouse over an
associated residue in an alignment window highlights the associated
-atoms in the displayed structures. For comprehensive details of Chimera's commands, refer to the tool's Help menu.
+atoms in the displayed structures. When residues are selected in the Chimera window, they are highlighted on the alignment. For comprehensive details of Chimera's commands, refer to the tool's Help menu.
<p>Basic screen operations (see <a href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html">Chimera help</a>
-(http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html) for full details).
+at http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html for full details).
<table border="1">
<tr>
<td><strong>Action</strong></td>
<td>alt + Click<br>
and drag</td>
</tr>
+ <tr>
+ <td>Select Residues</td>
+ <td>Ctrl + Click (and drag to select a region)</td>
+ <td>Ctrl + Click (and drag)</td>
+ <td>Ctrl + Click (and drag)</td>
+ </tr>
</table>
</p>
<p><strong>Jalview Controls</strong>
-<p>The Jalview Chimera View window has up to five menus:
+<p>The Jalview Chimera View window has up to five menus:</p>
<ul>
<li><Strong>File<br>
</strong>
</ul>
</li>
</ul>
-</p>
+<p><strong>Chimera and Windows Firewall</strong></p>
+Jalview and Chimera communicate using Chimera's <a href="http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/restserver/restserver.html">REST service</a> (http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/restserver/restserver.html).<br>
+Technically this requires both Chimera and Jalview to open ports on the local network, and this may be blocked by Windows Firewall with a warning message such as<br/>
+"Windows Firewall has blocked some features of this program" (where the program may be jp2launcher.exe for Jalview Webstart, or java.exe or javaw.exe for the InstallAnywhere version).<br/>
+To allow Jalview and Chimera to interact, you may need to add permission for the program to communicate over the network. This can be done from the warning dialogue, or in Control Panel, Firewall settings.
</body>
</html>
<p><strong>Running Jalview from the command line</strong></p>
<p>Jalview is most easily run from the command line if you have built
it from source, or via the 'Jalview' executable created from the
- InstallAnywhere jalview installation. Both of these mechanisms allow
- true command line execution of jalview - allowing you to provide
+ InstallAnywhere Jalview installation. Both of these mechanisms allow
+ true command line execution of Jalview - allowing you to provide
additional options.</p><p>
The Java Webstart version of
- jalview can be executed from the command line using something like
+ Jalview can be executed from the command line using something like
:
<pre>javaws http://www.jalview.org/webstart/jalview.jnlp -open
<em>yourFileName</em></pre>
But, this is not guaranteed to work on all versions of webstart on all
operating systems, and doesn't let you execute Jalview with any
additional parameters.
- <p><strong>Running jalview from the InstallAnywhere
+ <p><strong>Running Jalview from the InstallAnywhere
installation</strong></p>
<p>If you install with InstallAnywhere you can use several more commands.
However, if you call the application with the link provided by InstallAnywhere
any output from the application will be sent to output.txt, not standard
out.<br>
- The jalview application also requires a number of additional
+ The Jalview application also requires a number of additional
libraries on the class path. The command line below adds the Jalview
installation's 'lib' directory to the list of directories that are
searched for jars to be added to the classpath:</p>
<p><strong>Updating the list of sources</strong></p>
<p>When the DAS Settings panel is first opened, and when the <strong>'Refresh
source'</strong> buton is pressed, a list of DAS sources is retrieved from the
-DAS registry URL (set by default to the DAS registration server at
-http://www.dasregistry.org/das/).</p>
+DAS registry URL. Note that the registry hosted at http://www.dasregistry.org/das/ was retired at the start of 2015.
+An alternative service is currently hosted at http://www.ebi.ac.uk/das-srv/registry/das/. To connect to this service, ensure your .jalview_properties file includes the following line:<br>
+<b>DAS_REGISTRY_URL=http\://www.ebi.ac.uk/das-srv/registry/das/</b>
+</p>
<p><strong>Adding your own DAS Sources</strong></p>
<p>You can add your own DAS source to the list by clicking the
"Add Local Source" button. Enter the URL and nickname of your
hovers over the sequence ID panel, and any embedded links can be
accessed from the popup menu.<br/> <em>Scores</em><br>
Scores can be associated with sequence features, and used to sort
-sequences or shade the alignment (this was added in jalview 2.5).
+sequences or shade the alignment (this was added in Jalview 2.5).
The score field is optional, and malformed scores will be
ignored.</p>
The jars are obtained from the <em>embedded</em> directory within the
<a href="http://dist.codehaus.org/groovy/distributions">groovy
distribution</a>. The easiest way of adding them to the Jalview classpath
- is to download and build jalview from its source distribution, and
+ is to download and build Jalview from its source distribution, and
then add the groovy-all-*.jar to the lib directory whose path is given
in the java.ext.dirs property.
</p>
</p>
<p>
<strong>Executing groovy scripts on Jalview startup</strong><br>
- The -groovy <script> option on the <a href="commandline.html" />
+ The -groovy <script> option on the <a href="commandline.html">
Jalview command line</a> will execute the contents of <script>.
<script> may be a file, a URL, or alternatively if it is
"STDIN" then the standard input will be used.<br>
<em>Note: The groovy script will be executed <strong>after</strong>
any data is loaded, and <strong>before</strong> images or any output
- files are written. This allows you to perform customised jalview
+ files are written. This allows you to perform customised Jalview
analysis workflows with groovy.</em>
</p>
<p>
object defined in the groovy environent which corresponds to the
<pre>jalview.gui.Desktop</pre>
object which manages all the Jalview windows.
- </p>
Here's an example to get you started:
<br>
<ul>
<li>Getting the title, alignment and first sequence from the
current alignFrame<br> <pre>
-def alf = Jalview.getAlignframes();
+def alf = Jalview.getAlignFrames();
print alf[0].getTitle();
def alignment = alf[0].viewport.alignment;
def seq = alignment.getSequenceAt(0);
<li>When running a groovy script from the command line, the alignment that was just loaded can be referred to like so:<br><pre>
print currentAlFrame.getTitle();</pre>
</ul>
- </p>
-
- <p> </p>
+If you have downloaded the InstallAnywhere version of Jalview, you can find additional groovy scripts in the examples/groovy subfolder of the installation directory.
</body>
</html>
<p><strong><em>Hidden Sequence Representatives and
Multiple Views</em></strong><br>
<em>A word of warning: hidden representative sequence groups are
-(still) only partly implemented in the jalview 2.5 release, and we hope
+(still) only partly implemented in the Jalview 2.5 release, and we hope
to deal with the following issues in the future.</em><br>
Currently, represented hidden groups are only made correctly if there is
just one alignment view. When multiple views on an alignment exist, then
controls the behaviour of single and double mouse clicking on the
structure, and the 'Console' option opens the Jmol scripting console.</p>
<p>The state of each Jmol display is stored within <a
- href="jalarchive.html">jalview archives</a> as a Jmol state recovery
+ href="jalarchive.html">Jalview archives</a> as a Jmol state recovery
script file. This means that any Jmol visualization effects that you add
beyond those provided by Jalview will be able to be stored and recovered
along with the displayed alignments in Jalview.</p>
proxy server and do not enter the settings here.</p>
<p><em>Usage statistics, Questionnaire and Version checks</em><br>
Uncheck these options to prevent Jalview from submitting usage
-statistics to google analytics, checking for jalview questionnaires or
+statistics to google analytics, checking for Jalview questionnaires or
retrieving details of the latest release version (at www.jalview.org).
See the <a href="../privacy.html">user privacy statement</a> for more
information.</p>
EPS files will be a mixture of text and lineart. This produces compact
files that can be edited easily in programs like Microsoft Word and
Adobe Illustrator, but can be problematic if the fonts available to
- jalview are not accessible by the program reading the EPS file.
+ Jalview are not accessible by the program reading the EPS file.
</ul>
<p><em>Automatically set ID width</em><br>
When enabled, the column containing sequence and annotation labels at the left hand side of an exported figure will be made large enough to display each sequence ID and annotation label in its own line. Enable this if you have particularly long sequence IDs and need to generate EPS or PNG figures or web pages.</p>
one or more accession ids (as a semi-colon separated list), or press the
"Example" button to paste the example accession for the currently selected database into the retrieval box.
Finally, press "OK" to initiate the retrieval.</p>
- <p>Since Jalview 2.9 if PDB is selected as the sequence database, a specialised interface - <a href="pdbsequencefetcher.html">PDB Sequence Fetcher</a> is used for discovering and retrieving the sequenec data. </p>
+ <p>Since Jalview 2.9 if PDB is selected as the sequence database, a specialised interface - <a href="pdbsequencefetcher.html">PDB Sequence Fetcher</a> is used for discovering and retrieving the sequence data. </p>
<p><strong>Specifying chains for PDB IDs</strong>
If you are retrieving sequences from the PDB, you can retrieve
specific chains by appending a colon and the chain id to the PDB
<p><strong><em>Add Sequences</em></strong></p>
<p>If you add (coding) DNA sequences to an open peptide alignment, or vice versa, <em>and</em> at least one DNA sequence translates to one of the
peptide sequences, then the option to open in a split window is offered. The DNA may include start and/or stop codons, but no non-coding (intron)
-sequence.</p>
+sequence.<br>
+If more than one cDNA variant is present in the alignment, Jalview will first try to match these to protein sequences based on any retrieved cross-references, and failing that, pairwise as they are ordered in the alignments.
<p>This option is available in Jalview Desktop (when adding sequences by any supported method), and Jalview applet (adding from textbox).
The additional options below apply to Jalview Desktop only.</p>
<p>Menu option <strong><a href="../menus/alwcalculate.html">"Calculate | Get Cross-References"</a></strong> is available for fetched sequences which have cross-references to other databases.
On selecting protein cross-references (for a cDNA alignment), or DNA xrefs (for peptide), a Split Frame view is opened showing cDNA and peptide.</p>
-<p><strong><em>Realign Split View</em></strong></p>
+<p><strong><em>Realign a Split View</em></strong></p>
<p>If you invoke a web service to realign either half of a Split Frame, then the resulting realignment is displayed in a new
Split Frame.</p>
<ul>
</ul>
-<p><em>Split Frame Views were introduced in Jalview 2.?.?</em></p>
+<p><em>Split Frame Views were introduced in Jalview 2.9</em></p>
</body>
</html>
sequence or alignment). In the pop-up menu all structures that
are associated with this sequence and all sequences that are
associated with the alignment are available.
+<p>Saving a Jalview session as a project file includes the state of any Varna viewers, which are reopened when the project is reloaded <em>(since Jalview 2.9)</em>.
<p><strong>Different structures</strong></p>
<ul>
<p><strong>More Information</strong></p>
<p>VARNA is a very powerful RNA viewer on its own. Only the
essentials have been described here - the interested reader is
-referred to <a href="http://varna.lri.fr/usermanual.html">VARNA's own
+referred to <a href="http://varna.lri.fr/index.php?page=manual&css=varna">VARNA's own
comprehensive online documentation</a>.</p>
</body>
</html>
have an ID like '1gaq'.
<br/><em>Note: This feature was added in Jalview 2.7</em>
</p>
-<p><em>Note for jalview applet users:<br>
+<p><em>Note for Jalview applet users:<br>
Due to the applet security constraints, PDB Files can currently only be
imported by cut and paste of the PDB file text into the text box opened
by the 'From File' entry of the structure menu.</em></p>
</li></ul>
<p><em>Tips for working with EPS Files</em></p>
-<li>The EPS file generated by jalview contains vector graphics which are directly
+<li>The EPS file generated by Jalview contains vector graphics which are directly
editable in graphics applications such as Adobe Illustrator.</li>
<li>EPS files can be produced as "Text" or "Lineart". Use
"Text" if you want the final document to be MUCH smaller in diskspace
<p><strong>Alignment File Formats</strong>
<p>Jalview understands a wide range of sequence alignment formats. In
order to determine which format has been used for an alignment,
-jalview tries to detect some text or formatting unique to one of the formats:
+Jalview tries to detect some text or formatting unique to one of the formats:
</p>
<table width="100%" border="1">
<tr><td width="17%">Format</td>
<td width="23%">.json</td>
</tr>
</table>
-<p>The file extensions are used to associate jalview alignment icons
+<p>The file extensions are used to associate Jalview alignment icons
with alignment files: <img src="file.png" width=12 height=12 >
</p>
</body>
then you will be given an error message. If you think Jalview really
should be able to read your file, then send an email containing the
problem file to help@jalview.org.</p>
-<p>Jalview can also read jalview specific files for <a
+<p>Jalview can also read Jalview specific files for <a
href="../features/featuresFormat.html">sequence features</a> and <a
href="../features/annotationsFormat.html">alignment annotation</a>.</p>
<p><strong>Output</strong></p>
clicking on an annotation row under the alignment.</p>
<p>You can also save the current set of alignments and their
colours, annotations and trees in a Jalview archive file using <strong>Desktop→Save
-project</strong>.</p>
+project</strong>.<br>The project data includes the state of any open structure viewers (Jmol, and <em>since Jalview 2.9</em> also Chimera and Varna).</p>
<p> </p>
</body>
</html>
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>.
+</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>
selected groups of the alignment will be subdivided according to
the contents of the currently selected region. <br />Use this to
subdivide an alignment based on the different combinations of
- residues observed at specific positions. (new in jalview 2.5)</em>
+ residues observed at specific positions. (new in Jalview 2.5)</em>
</li>
<li><strong>Undefine Groups (Control U)<br> </strong><em>The
alignment will be reset with no defined groups.<br> <strong>WARNING</strong>:
<li><strong>Show Memory Usage<br></strong>
<em>When ticked, the currently available memory will be displayed in the
bottom right of the desktop background area.<br>
- See the <a href="../memory.html">help on jalview memory settings</a> for more information.</em></li>
+ See the <a href="../memory.html">help on Jalview memory settings</a> for more information.</em></li>
<li><strong>Collect Garbage<br></strong>
<em>Selecting this will initiate the Java Virtual Machine garbage collector, which might help free up some memory... perhaps.
</em></li>
properties file.</i></li>
<li><i>The Jalview web services stack is contacted to
retrieve the currently available web services. All interactions with
- the public jalview web services are logged, but we delete all job data
+ the public Jalview web services are logged, but we delete all job data
(input data and results) after about two weeks.</i></li>
</ul><br>
</li>
<li>Hide sequence doesn't hide associated annotation</li>
<li>User defined colours dialog box too big to fit on screen
and buttons not visible</li>
- <li>author list isn't updated if already written to jalview
+ <li>author list isn't updated if already written to Jalview
properties</li>
<li>Popup menu won't open after retrieving sequence from
database</li>
</li>
<li>
<!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
- out of memory errors are not raised when saving jalview project
+ out of memory errors are not raised when saving Jalview project
from alignment window file menu
</li>
<li>
<li>Newly created RNA secondary structure line doesn't have
'display all symbols' flag set</li>
<li>T-COFFEE alignment score shading scheme and other
- annotation shading not saved in jalview project</li>
+ annotation shading not saved in Jalview project</li>
<li>Local file cannot be loaded in freshly downloaded Jalview</li>
<li>Jalview icon not shown on dock in Mountain Lion/Webstart</li>
<li>Load file from desktop file browser fails</li>
</li>
<li>Not all working JABAWS services are shown in Jalview's
menu</li>
- <li>JAVAWS version of jalview fails to launch with 'invalid
+ <li>JAVAWS version of Jalview fails to launch with 'invalid
literal/length code'</li>
<li>Annotation/RNA Helix colourschemes cannot be applied to
alignment with groups (actually fixed in 2.8.0b1)</li>
<li>Allow disorder predictions to be made on the current
selection (or visible selection) in the same way that JPred
works</li>
- <li>Groovy scripting for headless jalview operation</li>
+ <li>Groovy scripting for headless Jalview operation</li>
</ul> <em>Other improvements</em>
<ul>
<li>Upgrade desktop installer to InstallAnywhere 2013</li>
server = new Server(tp);
// 2 selector threads to handle incoming connections
ServerConnector connector = new ServerConnector(server, 0, 2);
+ // restrict to localhost
+ connector.setHost("localhost");
server.addConnector(connector);
/*
git://source.jalview.org / jalview.git / commitdiff