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3.1 Run type selection

The first menu displayed is:

0 Regular run (default)
1 Save run
2 Continuation run

In a regular run, the program takes an RNA sequence as input, computes the energy matrices (the fill algorithm) and proceeds to the output section. Because the fill algorithm requires most of the computation time, the computation can be broken into two stages. A save run computes the energy matrices, writes the results to a large file on disk, and exits. The save file cannot be read by a user. A continuation run reads a previously computed save file, and proceeds directly to the output stage. When a regular or continuation run type is selected, execution continues with run mode selection (3.3). When a save run is selected, execution continues with output save file name selection (3.2).

Michael Zuker
Thu Nov 2 14:28:14 CST 1995