The preferred way of assigning reference traces to readings is by use of "naming conventions"; that is to have a simple set of rules which control the names given to the trace files. It can be seen in the figures showing the editor that forward and reverse readings from the same patient have names with a common root but which end either F or R. This both ties the two together (so the software knows which is the corresponding complementary trace when the user double clicks on a reading) and also enables the association of readings and their reference traces. Once a convention has been adopted the rules can be defined for pregap4 by loading them via the "Load Naming Scheme" option in its File menu (see section Pregap4 Naming Schemes). For any batch of readings the reference traces are defined within pregap4's "Reference Traces" module. Note that this mode of operation, by allowing the specification of only one forward and one reverse trace, limits each batch of traces processed to those which correspond to a given pair of reference traces. The size of the batch is unlimited.

The alternative way of specifying the reference traces is to right click on their names in the editor. This also allows positive trace controls to be specified (which is not possible in pregap4).