Chapter 8: How to Handle a Single Sequence

[ Previous chapter ][ This chapter ][ Next chapter ] The following description assumes that the set up for the GCG package has already been completed. These sequences used for input must be in GCG format . Use reformat or genmanual sequence_exchange for details on how to convert sequences into GCG format.

Many programs ask for an output file. This is mostly letter-by-letter output. You can review this text with the (command line) command more . WPI users may use the display function in the "output manager window".

To display graphics, you need to tell the GCG software that you want to use either display (=screen) or printer (=hardcopy). Command line users must be sure that everything is fine, to achieve this, initialise the display with the command setplot and select the option which seems best suitable to you. If you select X-Windows , you should

• be connected to the Ethernet or similar fast local area network ,

• run an X-Windows capable system (such as a workstation or PC/Mac with suitable X-Server program)

NOTE: A window should come upon your screen after the selection.

WPI users may use the display and print function in the "output manager window".

Check that display or printer work properly when you use them the first time and produce a test graphics with plottest .

NOTE: This is the last time that these details are described. The following chapters of the BioCompanion assume that all these setup operations have been successfully completed.

NOTE: Graphics files may become rather large. If display functionality stops working, make sure that the disk resources are sufficient. Also, if you use WPI, have the option 'delete' checked in the "output manager window" so that files get deleted on exit. If you work on the command line, make sure that intermediate .pnt and other files get erased frequently.