# This script is not intended to be executed directly.  It is sourced by test-runner.sh and most functions you see here are defined in test-tools.sh
# The variables EXENAME, EXEBASE, OKDIR, and EXEDIR are defined externally.

beginTestBlock  # Begin a group of tests.
runMake -r @EXE EnergyPlot # run `make` for the main exe and any other listed programs
EXT=.ct  # set extension for @OKFILE and @OUTFILE placeholders (defaults for runDiff)

SEQ_ALN1=testFiles/testFile_rnasep_alignment.fasta

# Test AlignmentFold_without_options.
runFullTest 'without_options'  $SEQ_ALN1 @OUT.ct

runFullTest 'minimum_free_energy_option'  $SEQ_ALN1 @OUT.ct -mfe

runFullTest 'base_pairing_cutoff_option' -b 0.5 $SEQ_ALN1 @OUT.ct

runFullTest 'max_internal_loop_size_option' -l 50 $SEQ_ALN1 @OUT.ct

runFullTest 'max_structures_option' $SEQ_ALN1 @OUT.ct -k -m 3

runFullTest 'window_option' $SEQ_ALN1 @OUT.ct -k -w 1

runFullTest 'percent_option' $SEQ_ALN1 @OUT.ct -p 40

endTestBlock # End a group of tests. Also cleans up orphaned files etc.
