<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
<title>Web Service Job Parameter Dialog Box</title>
</head>
<body>
-<p><strong>Web service Job Parameter Dialog box</strong></p>
+ <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
-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>
+ <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 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>
git://source.jalview.org / jalview.git / blobdiff