9.9. Documentation

9.9.1. Jemboss User Guide

  • Click on the Help menu on the Jemboss window and select the About Jemboss option.

This is the Jemboss user guide and opens with the About section. The window is divided into two sections: the left hand pane allows selection of a specific topic, the right hand pane displays the selected information. To hide and redisplay the left hand pane, use the arrows at the top of the pane divider.

  • Left click to highlight the Home option.

This is the Jemboss Web launch page from the EMBOSS homepages site ( http://emboss.open-bio.org/Jemboss/ ) with access to installation and launch information as well as documentation. Reading through the rest of the guide will complement any information in this chapter.

  • Close the user guide window.

9.9.2. Application Documentation

  • Type translate in the Keyword Search box at the bottom of the left hand Jemboss pane and hit Go. Click on the blue underscored program name of backtranseq to open the manual entry for this EMBOSS application. A short description of the backtranseq program is displayed on the right hand side of the table.

This documentation explains the functioning of individual EMBOSS programs, however the details pertain to the EMBOSS application and not the Jemboss interface and examples of a program run are only offered for the command line. All parameters labelled "qualifiers" in the documentation are the options seen on the Jemboss interface.

  • Type backtranseq into the GoTo box on the left hand Jemboss pane and hit return to retrieve the program input interface. Click on the blue information icon at the bottom of the input field (to the right of the GO button).

This retrieves the same manual information as retrieved above and thus contains the information for the EMBOSS program.

9.9.3. Version Number

  • Click on the Help menu in the Jemboss window and select the Version option.

This is the version number of the Jemboss interface used and should be quoted with any correspondence to the EMBOSS/Jemboss team.

9.9.4. Tooltips Mouseover Tips

  • Type emma into the GoTo field on the left hand Jemboss pane (overwriting other entries in this field as necessary). Place the mouse over the LOAD SEQUENCE ATTRIBUTES button in the central pane to retrieve a basic description of the function of this button.

Place the mouse over the first Select Matrix option to see information pertaining to this parameter.

Not all parameters have mouseover information, this is often to save duplicating information that is already in the EMBOSS application documentation.

Several of the function buttons (such as file manager open/close and documentation launch) have tooltip information. Static Tips

  • Go to the File menu and select the Saved Results option. Information on usage of this results manager is available in the right hand panel of the Saved Results list on Server window (Section 9.4.35, “Saving Jemboss Graphics”). On selection of a result this information disappears for the remainder of the session.

A similar static tip is also available on opening the Job manager (Section 9.6.3, “Job Manager).