Table 1 Operation modes of SLALOM. Each input is parsed twice, so that each annotation is at one point the query and the subject, respectively
Mode | Description |
|---|---|
Count modes (mutually exclusive, collectively exhaustive) | |
 Symbol-resolved | While calculating symbol-wise statistics, classify symbols to either present or absent in the query annotation. Calculate site-wise statistics according to the overlap logic. This is the default mode. |
 Gross | While calculating symbol-wise statistics, count each symbol gross, i.e., as many times as it occurs in all sites from the query annotation. Calculate site-wise statistics according to the overlap logic. |
 Enrichment | While calculating symbol-wise statistics, classify symbols to either enriched or non-enriched (including completely absent) in the query annotation based on the user-provided threshold on the number of occurrences. Do not calculate site-wise statistics. |
Comparison modes (mutually exclusive, collectively exhaustive) | |
 Equal | Treat the two input annotations as equal. Calculate only symmetric (not influenced by swapping) performance measures. |
 Benchmarking | Treat the first input annotation as the benchmark; treat the second one as a prediction. Calculate both symmetric and non-symmetric performance measures. |