<mapID target="cursor" url="html/features/cursorMode.html"/>
<mapID target="search" url="html/features/search.html"/>
<mapID target="webservice" url="html/webServices/index.html"/>
+ <mapID target="jabaws" url="html/webServices/JABAWS.html"/>
+ <mapID target="wsparams" url="html/webServices/webServicesParams.html"/>
+ <mapID target="wsprefs" url="html/webServices/webServicesPrefs.html"/>
<mapID target="msaservice" url="html/webServices/msaclient.html"/>
<mapID target="clustal" url="html/webServices/clustalw.html"/>
<mapID target="muscle" url="html/webServices/muscle.html"/>
<tocitem text="DAS Feature Settings" target="das.settings"/>
</tocitem>
<tocitem text="Web Services" target="webservice" expand="false">
+ <tocitem text="JABAWS" target="jabaws"/>
+ <tocitem text="Web Service Preferences" target="wsprefs"/>
+ <tocitem text="Web Service Parameters" target="wsparams"/>
<tocitem text="Sequence Alignment" target="msaservice" expand="false">
<tocitem text="Clustal Alignment" target="clustal"/>
<tocitem text="Muscle Alignment" target="muscle"/>
--- /dev/null
+<!--
+ * 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>
+<body>
+<p><strong>The</strong> <strong><em>JA</em></strong>va <strong><em>B</em></strong>ioinformatics
+<strong><em>A</em></strong>nalysis <strong><em>W</em></strong>eb <strong><em>S</em></strong>ervices
+<strong>system</strong> (<strong>JABAWS</strong>)<br>
+Jalview includes a client for interacting with programmatic (SOAP) web
+services for the <a href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>
+service model, developed at the University of Dundee by Peter Troshin
+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
+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
+Panel</a>, and detailed information about a particular service is available
+from the help text and web pages accessible from its <a
+ href="webServicesParams.html">job parameters dialog box</a>.</p>
+<p><strong>Obtaining JABAWS</strong><br>
+One of the aims of JABAWS is to enable you to easily perform
+computationally intensive bioinformatics analysis tasks using your own
+computational facilities. It can be installed on a workstation to
+provide stand-alone execution of analysis programs, or as a job
+submission engine - enabling larger numbers of jobs to be handled. If
+you would like to download and install JABAWS for your own use, please
+go to <a href="http://www.compbio.dundee.ac.uk/jabaws">http://www.compbio.dundee.ac.uk/jabaws</a>
+for more information.</p>
+<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
+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
+submit jobs to the server via the alignment window's web services menu.
+Your JABAWS servers list is stored in your Jalview preferences, so you
+will only have to configure Jalview once for each new server.</p>
+<p><em>Support for accessing JABAWS servers was introduced in
+Jalview 2.6.</em></p>
+</body>
+</html>
<li>The <a href="dbreffetcher.html">Database Reference Fetcher</a>
transfers database references from records available from DAS or the
public sequence databases.</li>
- <li>Jalview SOAP Web Services for sequence and alignment analysis
- are provided by the University of Dundee, and are available from the
- Alignment window's <strong> Web Service</strong> menu.</li>
+ <li>The <strong>Web Services</strong> menu in each alignment
+ window also provides access to the following:
+ <ul>
+ <li>Jalview SOAP Web Services for sequence alignment and
+ secondary structure prediction based at the University of Dundee.</li>
+ <li>Services for submitting IDs and sequences to external
+ bioinformatics services such as <a href="#envision2">Envision2</a>.</li>
+ <li>Programs for multiple sequence alignment, made available <em>via</em>
+ <a href="JABAWS.html">Java Bioinformatic
+ Analysis Web Service (JABAWS)</a> servers.</li>
+ </ul>
+ The <a href="webServicesPrefs.html">Web Services Preference panel</a>
+ controls the display and appearance of the submission and analysis
+ services in the <strong>Web Services</strong> menu.</li>
+
</ul>
</p>
<p>Jalview's distributed computations are SOAP based services
of Life Sciences, University of Dundee, and are maintained by the Barton
group.</p>
<p><strong><a name="envision2">Envision2 Services</a></strong></p>
-<p>Jalview 2.5 includes a client to enable the user to submit one or
-more sequences or sequence IDs to analysis workflows provided by the <a
+<p>Since version 2.5, Jalview has included a client to enable the
+user to submit one or more sequences or sequence IDs to analysis
+workflows provided by the <a
href="http://www.ebi.ac.uk/enfin-srv/envision2">EnVision2 web
application</a>. This allows Jalview users to easily access the EnCore
-network of databases and analysis services developed by members of <a
- href="http://www.enfin.org">ENFIN</a>.</p>
+network of databases and analysis services developed by ENFIN (<a
+ href="http://www.enfin.org">www.enfin.org</a>).</p>
<br />
<p><strong>Web Service Dialog Box</strong></p>
<img src="clwqueued.gif">
Multiple Alignment with Fast Fourier Transforms - a highly accurate
and high throughput dna and amino acid alignment method, performing at
least as well as ClustalW and Muscle.</li>
+ <li>Other alignment methods are also available via <a
+ href="JABAWS.html">JABAWS</a>. For more information about a
+ particular service, see the documentation available via the <a
+ href="webServicesParams.html">web services parameter dialog box</a>.</li>
</ul>
</li>
<li><strong>Secondary Structure Prediction</strong>
<ul>
<li><a href="jnet.html">JNet</a><br>
- This is a front end to the existing <a
+ This is a front end to the <a
href="http://www.compbio.dundee.ac.uk/www-jpred/">JNet www server</a>
allowing single sequence or profile based prediction.</li>
</ul>
</li>
</ul>
</p>
-<!-- <p>Watch this space! These are some of the services
- planned to be released soon:<ul>
- <li>More alignment services: PROBCONS, T-COFFEE</li>
- <li>Repeat analysis
- </li>
- <li>Remote Homology Detection<br>
- </li>
- </ul>
- In the future, Jalview will also be able to new discover services
- dynamically, and distribute expensive analysis functions like <a
- href="../calculations/pca.html">PCA</a> to the Dundee machines.</p>-->
+
</body>
</html>
<li><em>alignment</em> - where a new alignment is constructed from the input
</li>
<li><em>realignment</em> -
-where any existing alignments in the input are passed to the service
-for profile based alignment.
+where any aligned sequences will be used by the service
+to construct a profile based alignment of the remaining unaligned sequences.
</li>
</ul>
</p>
--- /dev/null
+
+<!--
+ * 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>Web Service Job Parameter Dialog Box</title>
+</head>
+<body>
+<p><strong>Web service Job Parameter Dialog box</strong></p>
+
+<p>Some Jalview services including those provided by <a
+ href="JABAWS.html">JABAWS</a>, support a range of parameters and
+options, enabling you to employ the most appropriate settings for the
+input data. In addition to any preset combinations provided by the
+services themselves, the Web services parameters dialog box also allows
+you to create and store your own parameter sets, so they can be accessed
+quickly from the presets menu.</p>
+<p><Strong>Accessing the parameter dialog box</Strong><br>
+The parameters dialog box is opened by selecting the 'Edit and Run' menu
+entries within the JABAWS analysis submenu of the alignment window's web
+services menu. Once opened, it presents the parameters and options
+available for the chosen analysis for you to modify, and and also
+enables you to browse any available service presets and select, create
+or modify your own user defined parameter sets. Once you are satisfied
+with the analysis parameters, press the <strong>Start Job</strong>
+button to initiate the analysis.</p>
+<p><Strong>Getting help on the analysis parameters</Strong><br>
+Each option or parameter shown in the dialog is accompanied by a brief
+description, which is shown as a tooltip when the mouse is moved over
+it. For some, a link symbol will also be shown (as in the example
+below), indicating that further information is available online. In this
+case, right-clicking (or command-click) will open a pop-up menu allowing
+you to select a URL to open in your web browser.</p>
+<p>
+<center><img src="wsparams.gif" align="center" width="480"
+ height="499" alt="Analysis Parameters Dialog Box for JABAWS Services">
+<br>
+Parameter settings dialog box for JABAWS MAFFT Service</center>
+</p>
+<p>The menu and text box at the top of the dialog box displays the
+name of the current parameter set. The name can be edited, should you
+wish to change or create a new user defined set, or clicked to present a
+menu enabling other sets to be browsed. The description shown below may
+also be edited (and the box resized to facilitate this), allowing you to
+provide notes to accompany the parameter set. The modification of these
+or any of the option or parameter settings will enable one or more of
+the following buttons, that allow you to:
+<ul>
+ <li><em>Revert</em> the changes you have made. This will undo any
+ changes you have made to the parameters and options with respect to the
+ currently selected parameter set, reverting each setting to its default
+ or last saved value.</li>
+ <li><em>Create</em> a new parameter set. Selecting this option
+ will create a new parameter set with the given name. New parameter sets
+ will be saved for the current session, but a file chooser will also
+ open which gives you the option to save the set for use in future
+ sessions.</li>
+ <li><em>Update</em> an existing user defined parameter set. This
+ button will save any modifications you have made to the current
+ parameter set.</li>
+ <li><em>Rename</em> the current user defined parameter set. This
+ will update the name recorded for the current parameter set.</li>
+ <li><em>Delete</em> the current parameter set. Selecting this will
+ erase the current user defined parameter set from memory, and delete
+ its associated parameter file (if it exists).</li>
+</ul>
+</p>
+<p><em>Support for adjusting and saving web service parameter
+sets was added in Jalview 2.6</em></p>
+</body>
+</html>
--- /dev/null
+
+<!--
+ * 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 Web Services Preferences Dialog Box</title>
+</head>
+<body>
+<p><strong>The Web Services Preferences Dialog Box</strong></p>
+
+<p>Jalview includes a range of web services clients for data
+retrieval and analysis. The <em>Web Services</em> menu found in each
+alignment window provides access to some of these services, and is
+configured <em>via</em> the web services preference dialog box,
+available from the <em>Preferences</em> panel from the <strong>Tools→Preferences...</strong>
+menu from the Jalview Desktop window's menu bar.</p>
+<p>
+<center><img src="wsprefs.gif" align="center"
+ alt="Web Services Preferences Panel" width="500" height="420"><br>
+Web Services Preference Panel</center>
+</p>
+<p><strong>Configuring the list of JABAWS servers</strong><br>
+The main area of the panel shows the list of <a href="JABAWS.html">JABAWS</a>
+servers that Jalview is currently aware of. A server's URL may be added,
+edited by double clicking on it, or deleted by selecting it and using
+the buttons below. After adding or editing a server's URL, you will be
+asked if you wish to test the server. If you wish to do so, then first
+ensure you can view the new server's test report, which will be output
+on Jalview's standard console output (you can open Jalview's built in
+console viewer via the <strong>Tools→Java Console</strong> menu
+option).</p>
+<p><strong>Controlling the layout of the Web Services Menu</strong><br>
+The range of services that Jalview is able to access depends upon your
+requirements, and local computational resources. However, when a large
+number of resources are available, then the entries and sub menus in the
+<strong>web services</strong> menu can quickly become unwieldly. The
+options in the lower part of the dialog box enable you to control the
+display of each type of analysis service client in the web services
+menu. In addition, indexing options are provided that enable you to
+define the layout of the menus provided for JABAWS services by sorting
+them into submenus according to analysis type and/or host server.</p>
+<p><em>The web services preferences panel was added in Jalview
+2.6</em></p>
+</body>
+</html>
git://source.jalview.org / jalview.git / commitdiff
