<toc version="1.0">
<tocitem text="Jalview Documentation" target="home" expand="true" >
<tocitem text="What's new" target="new" expand="true">
- <tocitem text="Graduated Feature Colours" target="features.featureschemes"/>
- <tocitem text="Sort by Features" target="seqfeatures.settings"/>
- <tocitem text="Envision2 Service" target="webservice"/>
+ <tocitem text="Jaba Web Services" target="jabaws"/>
+ <tocitem text="Superpositions with Jmol 12" target="pdbjmol"/>
+ <tocitem text="Web Service Parameters" target="wsparams"/>
+ <tocitem text="Web Service Preferences" target="wsprefs"/>
<tocitem text="Release History" target="release"/>
</tocitem>
<tocitem text="Editing Alignments" target ="edit"/>
<body>
<h1>Jalview local Jnlp File</h1>
<pre>
-<jnlp spec="1.0+" codebase="http://www.jalview.org/webstart/" href="http://www.jalview.org/webstart/jalview.jnlp">
+<jnlp spec="1.0+" codebase="http://www.jalview.org/webstart/">
<information>
<title>Jalview</title>
<vendor>The Barton Group</vendor>
<jar href="jhall.jar"/>
<jar href="log4j-1.2.8.jar"/>
<jar href="mail.jar"/>
- &jt;jar href="min-jaba-client.jar"/>
+ <jar href="min-jaba-client.jar"/>
<jar href="regex.jar"/>
<jar href="saaj.jar"/>
<jar href="vamsas-client.jar"/>
-<!--
+<html>
<!--
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-->
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
--->
-<html>
<head>
<title>The JABAWS system</title>
</head>
and Geoff Barton. This is an open source system that provides a
framework for wrapping command line bioinformatics analysis programs
that enables them to be executed locally or on a cluster using data and
-analysis parameters provided by a program linked with JABAWS directly or
+analysis parameters provided by a program linked with the JABA engine directly or
accessing it remotely <em>via</em> its web services interface.</p>
<p>The list of JABAWS servers known to the Jalview desktop is shown
in the <a href="webServicesPrefs.html">Web Services Preferences
<p><strong>Configuring your own JABAWS services for use by
Jalview</strong><br>
Once you have downloaded and installed JABAWS, and verified it is
-working, all that is needed is to add your new JABAWS server's URL to
+working, all that is needed is to add the URL for your JABAWS server(s) to
the list in the <a href="webServicesPrefs.html">Web Services
Preferences Panel</a>. After adding your service and saving your preferences
or hitting the 'refresh web services' button, you should be able to
Submits the sequences with existing gaps to clustalW, which will preserve
existing gaps and re-align those regions which are not optimal. </li>
</ul>
+<em>As of Jalview 2.6, alignment services accessed via the 'Alignment' submenu should be considered legacy Jalview SOAP services.</em>
</body>
</html>
The JNet method uses several different neural networks and decides on
the most likely prediction via a jury network. <br>
<ul>
- <li>
- Cole C., Barber J.D. and Barton G.J. (2008) The Jpred 3 secondary structure prediction server
- <em>Nucleic Acids Research</em> <strong>36</strong> W197-W201</li>
- <li>
- Cuff J. A and Barton G.J (1999) Application of enhanced
+ <li>Cole C., Barber J.D. and Barton G.J. (2008) The Jpred 3
+ secondary structure prediction server <em>Nucleic Acids Research</em> <strong>36</strong>
+ W197-W201</li>
+ <li>Cuff J. A and Barton G.J (1999) Application of enhanced
multiple sequence alignment profiles to improve protein secondary
structure prediction <em>Proteins</em> <strong>40</strong> 502-511</li>
</ul>
invoked to rationalise significantly different primary predictions.</em></li>
</ul>
</p>
+<em>As of Jalview 2.6, the Jnet service accessed accessed via the
+'Secondary structure prediction' submenu should be considered a legacy
+Jalview SOAP service, and will be replaced in the near future by a
+JABAWS Jnet service.</em>
+
</body>
</html>
sequence. The Jalview web service runs MAFFT using the
'--auto' option which picks optimal parameters
for the set of sequences to be aligned.</p>
+<em>As of Jalview 2.6, alignment services accessed via the 'Alignment' submenu should be considered legacy Jalview SOAP services.</em>
</body>
</html>
</head>
<body>
<strong>Multiple Sequence Alignment Web Services</strong>
-<p>
-Multiple sequence alignment services are accessed from the <strong>Web
-Service→Alignment</strong> menu. When an entry from this menu is
-selected, either the currently selected residues, or the whole
-sequence set (if there is no selection or only one sequence is
-selected) will be submitted for multiple sequence alignment.
-</p>
+<p>Multiple sequence alignment services can be accessed from either
+the <strong>Alignment</strong> or the <strong>JABAWS Alignment</strong>
+submenu of the Alignment Window's <strong>Web Service</strong> menu.
+When an entry from one of these menus is selected, either the currently
+selected residues, or the whole sequence set (if there is no selection
+or only one sequence is selected) will be submitted for multiple
+sequence alignment.</p>
<p>There are two kinds of multiple sequence alignment operations
-available:<ul>
-<li><em>alignment</em> - where a new alignment is constructed from the input
-</li>
-<li><em>realignment</em> -
-where any aligned sequences will be used by the service
-to construct a profile based alignment of the remaining unaligned sequences.
-</li>
+available:
+<ul>
+ <li><em>alignment</em> - where a new alignment is constructed from
+ the input</li>
+ <li><em>realignment</em> - where any aligned sequences will be
+ used by the service to construct a profile based alignment of the
+ remaining unaligned sequences.</li>
</ul>
-</p>
+The <a href="JABAWS.html">JABAWS Alignment services</a> also offer a
+range of predefined alignment settings and the opportunity for you to
+define your own set of parameters for running the alingment program.</p>
+<p><strong>Multiple Alignments of Sequences with hidden
+columns</strong><br>
+Multiple alignment services are 'column separable' analysis operations.
+If the input contains <a href="../features/hiddenRegions.html">hidden
+columns</a> then each visible segment of the input sequence set will be
+submitted for alignment separately, and the results concatenated (with
+the hidden regions preserved) once all alignment functions have
+completed. Each sub-job's state is reported in its own tab:
<p>
-<strong>Multiple Alignments of Sequences with hidden columns</strong><br>
-Multiple alignment services are 'column separable' analysis
-operations. If the input contains <a
-href="../features/hiddenRegions.html">hidden columns</a> then each
-visible segment of the input sequence set will be submitted for
-alignment separately, and the results concatenated (with the hidden
-regions preserved) once all alignment functions have completed. Each
-sub-job's state is reported in its own tab:
-<p><center><strong>Multiple Multiple Sequence Alignment sub jobs running at
-once</strong><center></p>
+<center><strong>Multiple Multiple Sequence Alignment
+sub jobs running at once</strong>
+<center>
+</p>
<center><img src="multimafftjbs.gif" align="centre"></center>
</p>
</body>
<p> This alignment method is applied to the selected region, if any, or the whole
sequence set when the <strong>Web Service→Alignment→Muscle
Protein Sequence Alignment</strong> menu item is selected. </p>
+<em>As of Jalview 2.6, alignment services accessed via the 'Alignment' submenu should be considered legacy Jalview SOAP services.</em>
</body>
</html>
git://source.jalview.org / jalview.git / commitdiff