--- /dev/null
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+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * 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.
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+ * Jalview is distributed in the hope that it will be useful, but
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+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<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="571" height="461"><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. The list includes a
+ colour coded status: green indicates that all services are available
+ for a given server, amber signifies that one or more services on the
+ server are not fully functional, and red highlights servers that
+ could not be contacted or are not functional for some other reason.
+ </p>
+ <p>
+ 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, and server status indications added in Jalview 2.8.</em>
+ </p>
+ <p>
+ <strong><a name="wswarnings">Web Services Invalid URL
+ warnings</a></strong><br> Jalview may inform you of any problems
+ contacting the web services by showing a dialog box like the one
+ below:<br>
+ <center>
+ <img src="invalidurldialog.gif" align="center"
+ alt="Web Services Invalid URL Warning dialog box" width="389"
+ height="258"><br> Web Services Invalid URL Warning
+ dialog box
+ </center>
+ <br>
+ <strong><em>Note:</em></strong> this warning will be shown if you are
+ running the Jalview desktop without any network connection, or if you
+ have configured
+ <a href="JABAWS.html">JABA services</a> which cannot be accessed from
+ your location. Should you wish to disable these warnings, then uncheck
+ the
+ <em>Display warnings</em> check box in the web services preferences.
+ </p>
+ <p>
+ <em>The web services warnings dialog box was added in Jalview
+ 2.6.1</em>
+ </p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff