2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Web Service Job Parameter Dialog Box</title>
26 <p><strong>Web service Job Parameter Dialog box</strong></p>
28 <p>Some Jalview services, including those provided by <a
29 href="JABAWS.html">JABAWS</a>, support a range of parameters and
30 options, enabling you to employ the most appropriate settings for the
31 input data. In addition to any preset combinations provided by
32 services themselves, the Web services parameters dialog box also allows
33 you to create and store your own parameter sets, so they can be accessed
34 quickly from the presets menu.</p>
35 <p><Strong>Accessing the parameter dialog box</Strong><br>
36 The parameters dialog box is opened by selecting the 'Edit and Run' menu
37 entries within the JABAWS analysis submenu of the alignment window's web
38 services menu. Once opened, it presents the parameters and options
39 available for the chosen analysis for you to modify, and and also
40 enables you to browse any available service presets and select, create
41 or modify your own user defined parameter sets. Once you are satisfied
42 with the analysis parameters, press the <strong>Start Job</strong>
43 button to initiate the analysis.</p>
44 <p><Strong>Getting help on the analysis parameters</Strong><br>
45 Each option or parameter shown in the dialog is accompanied by a brief
46 description, which is shown as a tooltip when the mouse is moved over
47 it. For some, a link symbol will also be shown (as in the example
48 below), indicating that further information is available online. In this
49 case, right-clicking (or command-click) will open a pop-up menu allowing
50 you to select a URL to open in your web browser.</p>
52 <center><img src="wsparams.gif" align="center" width="480"
53 height="499" alt="Analysis Parameters Dialog Box for JABAWS Services">
55 Parameter settings dialog box for JABAWS MAFFT Service</center>
57 <p>The menu and text box at the top of the dialog box displays the
58 name of the current parameter set. The name can be edited, should you
59 wish to change or create a new user defined set, or clicked to present a
60 menu enabling other sets to be browsed. The description shown below may
61 also be edited (and the box resized to facilitate this), allowing you to
62 provide notes to accompany the parameter set. The modification of these
63 or any of the option or parameter settings will enable one or more of
64 the following buttons, that allow you to:
66 <li><em>Revert</em> the changes you have made. This will undo any
67 changes you have made to the parameters and options with respect to the
68 currently selected parameter set, reverting each setting to its default
69 or last saved value.</li>
70 <li><em>Create</em> a new parameter set. Selecting this option
71 will create a new parameter set with the given name. New parameter sets
72 will be saved for the current session, but a file chooser will also
73 open which gives you the option to save the set for use in future
75 <li><em>Update</em> an existing user defined parameter set. This
76 button will save any modifications you have made to the current
78 <li><em>Rename</em> the current user defined parameter set. This
79 will update the name recorded for the current parameter set.</li>
80 <li><em>Delete</em> the current parameter set. Selecting this will
81 erase the current user defined parameter set from memory, and delete
82 its associated parameter file (if it exists).</li>
85 <p><em>Support for adjusting and saving web service parameter
86 sets was added in Jalview 2.6</em></p>