X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2FwebServicesPrefs.html;h=ac25ed63da169a44bbc34d9def6edf23af1f93ad;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=9fc29db524781fd5d7ee83cec6d326916eeebc98;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git diff --git a/help/html/webServices/webServicesPrefs.html b/help/html/webServices/webServicesPrefs.html index 9fc29db..ac25ed6 100644 --- a/help/html/webServices/webServicesPrefs.html +++ b/help/html/webServices/webServicesPrefs.html @@ -1,79 +1,105 @@ - + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> The Web Services Preferences Dialog Box -

The Web Services Preferences Dialog Box

+

+ The Web Services Preferences Dialog Box +

-

Jalview includes a range of web services clients for data -retrieval and analysis. The Web Services menu found in each -alignment window provides access to some of these services, and is -configured via the web services preference dialog box, -available from the Preferences panel from the Tools→Preferences... -menu from the Jalview Desktop window's menu bar.

-

-

Web Services Preferences Panel
-Web Services Preference Panel
-

-

Configuring the list of JABAWS servers
-The main area of the panel shows the list of JABAWS -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 Tools→Java Console menu -option).

-

Controlling the layout of the Web Services Menu
-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 -web services 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.

-

The web services preferences panel was added in Jalview -2.6

-

Web Services Invalid -URL warnings
-Jalview may inform you of any problems contacting the web services by -showing a dialog box like the one below:
-

Web Services Invalid URL Warning dialog box
-Web Services Invalid URL Warning dialog box
-
-Note: this warning will be shown if you are running the Jalview desktop -without any network connection, or if you have configured -JABA services -which cannot be accessed from your location. Should you wish to disable -these warnings, then uncheck the -Display warnings -check box in the web services preferences. -

-

The web services warnings dialog box was added in -Jalview 2.6.1

+

+ Jalview includes a range of web services clients for data retrieval + and analysis. The Web Services menu found in each alignment + window provides access to some of these services, and is configured + via the web services preference dialog box, available from + the Preferences panel from the Tools→Preferences... + menu from the Jalview Desktop window's menu bar. +

+

+

+ Web Services Preferences Panel
Web Services Preference Panel +
+

+

+ Configuring the list of JABAWS servers
The + main area of the panel shows the list of JABAWS + 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. +

+

+ 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 Tools→Java Console menu option). +

+

+ Controlling the layout of the Web Services Menu
+ 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 web services 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. +

+

+ The web services preferences panel was added in Jalview + 2.6, and server status indications added in Jalview 2.8. +

+

+ Web Services Invalid URL + warnings
Jalview may inform you of any problems + contacting the web services by showing a dialog box like the one + below:
+

+ Web Services Invalid URL Warning dialog box
Web Services Invalid URL Warning dialog box +
+
+ Note: this warning will be shown if you are + running the Jalview desktop without any network connection, or if you + have configured + JABA services which cannot be accessed from + your location. Should you wish to disable these warnings, then uncheck + the + Display warnings check box in the web services preferences. +

+

+ The web services warnings dialog box was added in Jalview + 2.6.1 +