Web service Job Parameter Dialog box

Some Jalview services, including those provided by JABAWS, 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.

Accessing the parameter dialog box
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 Start Job button to initiate the analysis.

Getting help on the analysis parameters
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.

Parameter settings dialog box for JABAWS MAFFT Service

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:

• Revert 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.
• Create 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.
• Update an existing user defined parameter set. This button will save any modifications you have made to the current parameter set.
• Rename the current user defined parameter set. This will update the name recorded for the current parameter set.
• Delete 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).

Support for adjusting and saving web service parameter sets was added in Jalview 2.6