The "Load Naming Scheme" command is in the File menu. It will bring up a dialogue requesting the pathname of a naming scheme file. The browse button will automatically bring up the file browser in the pregap4 naming scheme directory, however naming schemes can be loaded from elsewhere if desired. The "Save to config file" query determines whether the component is also copied to the current pregap4 configuration file to make this component the default for subsequent pregap4 runs.
The use of naming schemes within pregap4 is specifically for extracting information from a reading name in order to supply paramaters to other pregap4 modules or to gap4. For example a naming scheme may be used to indicate where both the forward and reverse primers have been used to generate two sequences, which gap4 can then use for checking assembly and suggesting possible contig joins.
Currently only two naming schemes are supplied with pregap4, both of which are from the Sanger Centre. To create your own naming schemes please see section Writing Your Own Naming Schemes.