--- /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>
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