README
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gosaca
Description
Pure Go implementation of An Optimal Suffix Array Construction Algorithm, a paper by Ge Nong.
Benchmarks
More extensive tests and benchmarks run on large copora are available as gosaca-bigtests so as not to balloon the size of this repo.
The following table compares sa-is with gosaca running on a 2012 Macbook Pro. The comparision is not really fair in many senses (SA-IS is an earlier, slightly less efficient algorithm, but it's implemented in optimized C code); here it is nonetheless. Times are in seconds.
| File | Size | sa-is | gosaca |
|---|---|---|---|
| chr22dna | 34553758 | 5.893 | 10.807 |
| etext99 | 105277340 | 21.507 | 41.862 |
| gcc30tar | 86630400 | 10.252 | 23.149 |
| howto | 39422105 | 6.050 | 12.123 |
| jdk13c | 69728899 | 6.567 | 19.807 |
| linux245tar | 116254720 | 14.635 | 32.696 |
| rctail96 | 114711151 | 15.143 | 40.225 |
| rfc | 116421901 | 16.191 | 36.505 |
| sprot34dat | 109617186 | 17.485 | 39.164 |
| w3c2 | 104201579 | 10.395 | 30.164 |
| abac | 200000 | 0.005 | 0.016 |
| abba | 10500600 | 0.646 | 2.326 |
| book1x20 | 15375420 | 1.620 | 5.126 |
| fib_s14930352 | 14930352 | 0.981 | 4.579 |
| fss10 | 12078908 | 0.739 | 3.539 |
| fss9 | 2851443 | 0.145 | 0.518 |
| houston | 3840000 | 0.102 | 0.288 |
| paper5x80 | 981924 | 0.041 | 0.099 |
| test1 | 2097152 | 0.096 | 0.236 |
| test2 | 2097152 | 0.103 | 0.251 |
| test3 | 2097152 | 0.094 | 0.206 |
Copyright
Copyright © John Gallagher. MIT License; see LICENSE for further details.
Documentation
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Index ¶
Constants ¶
This section is empty.
Variables ¶
This section is empty.
Functions ¶
This section is empty.
Types ¶
type WorkSpace ¶
type WorkSpace struct {
// contains filtered or unexported fields
}
WorkSpace contains the O(1) scratch space used in constructing a suffix array with an alphabet of sisze 256 (any byte value).
func (*WorkSpace) ComputeSuffixArray ¶
Compute the suffix array of S, storing it into SA. len(S) and len(SA) must be equal.
Source Files