duckdb 1.1.3 → 1.1.4-dev9.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/.github/workflows/NodeJS.yml +5 -54
- package/binding.gyp +73 -52
- package/package.json +1 -1
- package/src/duckdb/{src → extension}/core_functions/aggregate/algebraic/avg.cpp +2 -2
- package/src/duckdb/{src → extension}/core_functions/aggregate/algebraic/corr.cpp +4 -4
- package/src/duckdb/{src → extension}/core_functions/aggregate/algebraic/covar.cpp +2 -2
- package/src/duckdb/{src → extension}/core_functions/aggregate/algebraic/stddev.cpp +2 -2
- package/src/duckdb/{src → extension}/core_functions/aggregate/distributive/approx_count.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/aggregate/distributive/arg_min_max.cpp +66 -18
- package/src/duckdb/{src → extension}/core_functions/aggregate/distributive/bitagg.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/aggregate/distributive/bitstring_agg.cpp +5 -7
- package/src/duckdb/{src → extension}/core_functions/aggregate/distributive/bool.cpp +3 -1
- package/src/duckdb/{src → extension}/core_functions/aggregate/distributive/kurtosis.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/aggregate/distributive/product.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/aggregate/distributive/skew.cpp +2 -2
- package/src/duckdb/{src → extension}/core_functions/aggregate/distributive/string_agg.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/aggregate/distributive/sum.cpp +13 -2
- package/src/duckdb/{src → extension}/core_functions/aggregate/holistic/approx_top_k.cpp +3 -3
- package/src/duckdb/{src → extension}/core_functions/aggregate/holistic/approximate_quantile.cpp +51 -15
- package/src/duckdb/{src → extension}/core_functions/aggregate/holistic/mad.cpp +25 -10
- package/src/duckdb/{src → extension}/core_functions/aggregate/holistic/mode.cpp +215 -71
- package/src/duckdb/{src → extension}/core_functions/aggregate/holistic/quantile.cpp +58 -31
- package/src/duckdb/{src → extension}/core_functions/aggregate/holistic/reservoir_quantile.cpp +2 -2
- package/src/duckdb/{src → extension}/core_functions/aggregate/nested/binned_histogram.cpp +9 -4
- package/src/duckdb/{src → extension}/core_functions/aggregate/nested/histogram.cpp +4 -2
- package/src/duckdb/{src → extension}/core_functions/aggregate/nested/list.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/aggregate/regression/regr_avg.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/aggregate/regression/regr_count.cpp +2 -2
- package/src/duckdb/{src → extension}/core_functions/aggregate/regression/regr_intercept.cpp +6 -2
- package/src/duckdb/{src → extension}/core_functions/aggregate/regression/regr_r2.cpp +2 -2
- package/src/duckdb/{src → extension}/core_functions/aggregate/regression/regr_slope.cpp +2 -2
- package/src/duckdb/{src → extension}/core_functions/aggregate/regression/regr_sxx_syy.cpp +2 -2
- package/src/duckdb/{src → extension}/core_functions/aggregate/regression/regr_sxy.cpp +3 -3
- package/src/duckdb/extension/core_functions/core_functions_extension.cpp +85 -0
- package/src/duckdb/{src → extension}/core_functions/function_list.cpp +30 -51
- package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/aggregate/algebraic/corr.hpp +3 -7
- package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/aggregate/algebraic_functions.hpp +1 -1
- package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/aggregate/distributive_functions.hpp +16 -21
- package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/aggregate/histogram_helpers.hpp +1 -1
- package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/aggregate/holistic_functions.hpp +1 -1
- package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/aggregate/nested_functions.hpp +1 -1
- package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/aggregate/quantile_helpers.hpp +2 -2
- package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/aggregate/quantile_sort_tree.hpp +140 -58
- package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/aggregate/quantile_state.hpp +50 -43
- package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/aggregate/regression/regr_count.hpp +2 -2
- package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/aggregate/regression/regr_slope.hpp +3 -7
- package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/aggregate/regression_functions.hpp +1 -1
- package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/scalar/array_functions.hpp +1 -1
- package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/scalar/bit_functions.hpp +1 -1
- package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/scalar/blob_functions.hpp +1 -10
- package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/scalar/date_functions.hpp +22 -55
- package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/scalar/debug_functions.hpp +1 -1
- package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/scalar/enum_functions.hpp +1 -1
- package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/scalar/generic_functions.hpp +1 -10
- package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/scalar/list_functions.hpp +4 -4
- package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/scalar/map_functions.hpp +1 -10
- package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/scalar/math_functions.hpp +1 -1
- package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/scalar/operators_functions.hpp +1 -1
- package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/scalar/random_functions.hpp +1 -1
- package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/scalar/string_functions.hpp +10 -103
- package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/scalar/struct_functions.hpp +1 -19
- package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/scalar/union_functions.hpp +1 -1
- package/src/duckdb/extension/core_functions/include/core_functions_extension.hpp +22 -0
- package/src/duckdb/{src → extension}/core_functions/lambda_functions.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/array/array_functions.cpp +11 -4
- package/src/duckdb/{src → extension}/core_functions/scalar/array/array_value.cpp +2 -2
- package/src/duckdb/{src → extension}/core_functions/scalar/bit/bitstring.cpp +12 -5
- package/src/duckdb/{src → extension}/core_functions/scalar/blob/base64.cpp +4 -2
- package/src/duckdb/{src → extension}/core_functions/scalar/blob/encode.cpp +4 -2
- package/src/duckdb/{src → extension}/core_functions/scalar/date/age.cpp +9 -3
- package/src/duckdb/extension/core_functions/scalar/date/current.cpp +29 -0
- package/src/duckdb/{src → extension}/core_functions/scalar/date/date_diff.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/date/date_part.cpp +42 -9
- package/src/duckdb/{src → extension}/core_functions/scalar/date/date_sub.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/date/date_trunc.cpp +4 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/date/epoch.cpp +19 -3
- package/src/duckdb/{src → extension}/core_functions/scalar/date/make_date.cpp +40 -5
- package/src/duckdb/{src → extension}/core_functions/scalar/date/time_bucket.cpp +4 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/date/to_interval.cpp +54 -28
- package/src/duckdb/{src → extension}/core_functions/scalar/debug/vector_type.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/enum/enum_functions.cpp +2 -7
- package/src/duckdb/{src → extension}/core_functions/scalar/generic/alias.cpp +2 -2
- package/src/duckdb/{src/function → extension/core_functions}/scalar/generic/binning.cpp +4 -3
- package/src/duckdb/{src → extension}/core_functions/scalar/generic/can_implicitly_cast.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/generic/current_setting.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/generic/hash.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/generic/least.cpp +30 -10
- package/src/duckdb/{src → extension}/core_functions/scalar/generic/stats.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/generic/system_functions.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/generic/typeof.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/list/array_slice.cpp +93 -88
- package/src/duckdb/{src → extension}/core_functions/scalar/list/flatten.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/list/list_aggregates.cpp +7 -3
- package/src/duckdb/{src → extension}/core_functions/scalar/list/list_distance.cpp +8 -2
- package/src/duckdb/{src → extension}/core_functions/scalar/list/list_filter.cpp +3 -3
- package/src/duckdb/{src → extension}/core_functions/scalar/list/list_has_any_or_all.cpp +3 -3
- package/src/duckdb/{src → extension}/core_functions/scalar/list/list_reduce.cpp +5 -5
- package/src/duckdb/{src → extension}/core_functions/scalar/list/list_sort.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/list/list_transform.cpp +3 -3
- package/src/duckdb/{src → extension}/core_functions/scalar/list/list_value.cpp +3 -3
- package/src/duckdb/{src → extension}/core_functions/scalar/list/range.cpp +7 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/map/cardinality.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/map/map.cpp +5 -4
- package/src/duckdb/{src → extension}/core_functions/scalar/map/map_concat.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/map/map_entries.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/map/map_extract.cpp +13 -25
- package/src/duckdb/{src → extension}/core_functions/scalar/map/map_from_entries.cpp +2 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/map/map_keys_values.cpp +11 -9
- package/src/duckdb/{src → extension}/core_functions/scalar/math/numeric.cpp +83 -37
- package/src/duckdb/{src → extension}/core_functions/scalar/operators/bitwise.cpp +19 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/random/random.cpp +4 -3
- package/src/duckdb/{src → extension}/core_functions/scalar/random/setseed.cpp +2 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/string/ascii.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/string/bar.cpp +6 -4
- package/src/duckdb/{src → extension}/core_functions/scalar/string/chr.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/string/damerau_levenshtein.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/string/format_bytes.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/string/hamming.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/string/hex.cpp +7 -3
- package/src/duckdb/{src → extension}/core_functions/scalar/string/instr.cpp +4 -4
- package/src/duckdb/{src → extension}/core_functions/scalar/string/jaccard.cpp +1 -1
- package/src/duckdb/extension/core_functions/scalar/string/jaro_winkler.cpp +112 -0
- package/src/duckdb/{src → extension}/core_functions/scalar/string/left_right.cpp +6 -6
- package/src/duckdb/{src → extension}/core_functions/scalar/string/levenshtein.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/string/pad.cpp +9 -5
- package/src/duckdb/{src → extension}/core_functions/scalar/string/parse_path.cpp +4 -4
- package/src/duckdb/{src → extension}/core_functions/scalar/string/printf.cpp +3 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/string/repeat.cpp +4 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/string/replace.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/string/reverse.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/string/starts_with.cpp +5 -3
- package/src/duckdb/{src → extension}/core_functions/scalar/string/to_base.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/string/translate.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/string/trim.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/string/unicode.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/string/url_encode.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/struct/struct_insert.cpp +25 -31
- package/src/duckdb/{src → extension}/core_functions/scalar/union/union_extract.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/union/union_tag.cpp +1 -1
- package/src/duckdb/{src → extension}/core_functions/scalar/union/union_value.cpp +3 -3
- package/src/duckdb/extension/icu/icu-dateadd.cpp +16 -11
- package/src/duckdb/extension/icu/icu-datefunc.cpp +2 -2
- package/src/duckdb/extension/icu/icu-datepart.cpp +8 -5
- package/src/duckdb/extension/icu/icu-datesub.cpp +2 -2
- package/src/duckdb/extension/icu/icu-datetrunc.cpp +8 -1
- package/src/duckdb/extension/icu/icu-list-range.cpp +2 -2
- package/src/duckdb/extension/icu/icu-makedate.cpp +18 -7
- package/src/duckdb/extension/icu/icu-strptime.cpp +9 -3
- package/src/duckdb/extension/icu/icu-table-range.cpp +2 -2
- package/src/duckdb/extension/icu/icu-timebucket.cpp +4 -1
- package/src/duckdb/extension/icu/icu-timezone.cpp +67 -1
- package/src/duckdb/extension/icu/icu_extension.cpp +60 -5
- package/src/duckdb/extension/icu/include/icu-datefunc.hpp +2 -1
- package/src/duckdb/extension/icu/third_party/icu/common/bytestriebuilder.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/common/dtintrv.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/common/filteredbrk.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/common/locid.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/common/lsr.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/common/lsr.h +2 -2
- package/src/duckdb/extension/icu/third_party/icu/common/messagepattern.cpp +2 -2
- package/src/duckdb/extension/icu/third_party/icu/common/normlzr.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/common/rbbinode.h +1 -1
- package/src/duckdb/extension/icu/third_party/icu/common/schriter.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/common/stringtriebuilder.cpp +8 -8
- package/src/duckdb/extension/icu/third_party/icu/common/ucharstriebuilder.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/common/uchriter.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/common/unicode/brkiter.h +2 -2
- package/src/duckdb/extension/icu/third_party/icu/common/unicode/bytestriebuilder.h +1 -1
- package/src/duckdb/extension/icu/third_party/icu/common/unicode/chariter.h +3 -3
- package/src/duckdb/extension/icu/third_party/icu/common/unicode/dtintrv.h +3 -3
- package/src/duckdb/extension/icu/third_party/icu/common/unicode/locid.h +3 -3
- package/src/duckdb/extension/icu/third_party/icu/common/unicode/messagepattern.h +4 -4
- package/src/duckdb/extension/icu/third_party/icu/common/unicode/normlzr.h +3 -3
- package/src/duckdb/extension/icu/third_party/icu/common/unicode/parsepos.h +4 -4
- package/src/duckdb/extension/icu/third_party/icu/common/unicode/rbbi.h +2 -2
- package/src/duckdb/extension/icu/third_party/icu/common/unicode/schriter.h +1 -1
- package/src/duckdb/extension/icu/third_party/icu/common/unicode/strenum.h +2 -2
- package/src/duckdb/extension/icu/third_party/icu/common/unicode/stringpiece.h +1 -1
- package/src/duckdb/extension/icu/third_party/icu/common/unicode/stringtriebuilder.h +9 -9
- package/src/duckdb/extension/icu/third_party/icu/common/unicode/ucharstriebuilder.h +1 -1
- package/src/duckdb/extension/icu/third_party/icu/common/unicode/uchriter.h +1 -1
- package/src/duckdb/extension/icu/third_party/icu/common/unicode/uniset.h +3 -3
- package/src/duckdb/extension/icu/third_party/icu/common/unicode/unistr.h +12 -12
- package/src/duckdb/extension/icu/third_party/icu/common/unicode/uobject.h +2 -2
- package/src/duckdb/extension/icu/third_party/icu/common/unifiedcache.h +4 -4
- package/src/duckdb/extension/icu/third_party/icu/common/uniset.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/common/ustr_titlecase_brkiter.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/common/ustrenum.cpp +2 -2
- package/src/duckdb/extension/icu/third_party/icu/common/uvector.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/common/uvector.h +3 -3
- package/src/duckdb/extension/icu/third_party/icu/common/uvectr32.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/common/uvectr32.h +3 -3
- package/src/duckdb/extension/icu/third_party/icu/common/uvectr64.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/common/uvectr64.h +3 -3
- package/src/duckdb/extension/icu/third_party/icu/i18n/alphaindex.cpp +2 -2
- package/src/duckdb/extension/icu/third_party/icu/i18n/calendar.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/i18n/choicfmt.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/i18n/coleitr.cpp +2 -2
- package/src/duckdb/extension/icu/third_party/icu/i18n/coll.cpp +2 -2
- package/src/duckdb/extension/icu/third_party/icu/i18n/collationiterator.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/i18n/collationiterator.h +2 -2
- package/src/duckdb/extension/icu/third_party/icu/i18n/collationsettings.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/i18n/collationsettings.h +2 -2
- package/src/duckdb/extension/icu/third_party/icu/i18n/currpinf.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/i18n/datefmt.cpp +2 -2
- package/src/duckdb/extension/icu/third_party/icu/i18n/dcfmtsym.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/i18n/decimfmt.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/i18n/dtfmtsym.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/i18n/dtitvfmt.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/i18n/dtitvinf.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/i18n/dtptngen.cpp +2 -2
- package/src/duckdb/extension/icu/third_party/icu/i18n/dtptngen_impl.h +4 -4
- package/src/duckdb/extension/icu/third_party/icu/i18n/dtrule.cpp +2 -2
- package/src/duckdb/extension/icu/third_party/icu/i18n/fmtable.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/i18n/format.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/i18n/fpositer.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/i18n/measfmt.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/i18n/measunit.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/i18n/measure.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/i18n/msgfmt.cpp +2 -2
- package/src/duckdb/extension/icu/third_party/icu/i18n/nfrs.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/i18n/nfrs.h +2 -2
- package/src/duckdb/extension/icu/third_party/icu/i18n/nfrule.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/i18n/nfrule.h +2 -2
- package/src/duckdb/extension/icu/third_party/icu/i18n/nfsubs.cpp +9 -9
- package/src/duckdb/extension/icu/third_party/icu/i18n/nfsubs.h +2 -2
- package/src/duckdb/extension/icu/third_party/icu/i18n/number_asformat.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/i18n/number_asformat.h +1 -1
- package/src/duckdb/extension/icu/third_party/icu/i18n/numfmt.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/i18n/olsontz.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/i18n/olsontz.h +1 -1
- package/src/duckdb/extension/icu/third_party/icu/i18n/plurfmt.cpp +2 -2
- package/src/duckdb/extension/icu/third_party/icu/i18n/plurrule.cpp +1 -1
- package/src/duckdb/extension/icu/third_party/icu/i18n/rbnf.cpp +4 -4
- package/src/duckdb/extension/icu/third_party/icu/i18n/rbtz.cpp +2 -2
- package/src/duckdb/extension/icu/third_party/icu/i18n/region.cpp +2 -2
- package/src/duckdb/extension/icu/third_party/icu/i18n/reldtfmt.cpp +1 -1
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- package/src/duckdb/ub_src_function_scalar_map.cpp +2 -0
- package/src/duckdb/ub_src_function_scalar_operator.cpp +8 -0
- package/src/duckdb/ub_src_function_scalar_string.cpp +10 -0
- package/src/duckdb/ub_src_function_scalar_struct.cpp +4 -0
- package/src/duckdb/ub_src_function_scalar_system.cpp +2 -0
- package/src/duckdb/ub_src_function_table_system.cpp +6 -0
- package/src/duckdb/ub_src_function_window.cpp +36 -0
- package/src/duckdb/ub_src_logging.cpp +8 -0
- package/src/duckdb/ub_src_main_settings.cpp +3 -1
- package/src/duckdb/ub_src_optimizer.cpp +8 -0
- package/src/duckdb/ub_src_optimizer_pushdown.cpp +2 -0
- package/src/duckdb/ub_src_optimizer_rule.cpp +2 -0
- package/src/duckdb/ub_src_parser.cpp +2 -0
- package/src/duckdb/ub_src_parser_parsed_data.cpp +2 -0
- package/src/duckdb/ub_src_planner.cpp +2 -0
- package/src/duckdb/ub_src_planner_filter.cpp +6 -0
- package/src/duckdb/ub_src_storage_compression.cpp +4 -0
- package/src/duckdb/ub_src_storage_compression_dictionary.cpp +8 -0
- package/src/duckdb/ub_src_storage_compression_roaring.cpp +10 -0
- package/src/duckdb/ub_src_transaction.cpp +2 -0
- package/vendor.py +1 -1
- package/src/duckdb/extension/json/yyjson/include/yyjson.hpp +0 -6003
- package/src/duckdb/extension/json/yyjson/yyjson.cpp +0 -8218
- package/src/duckdb/src/common/arrow/appender/list_data.cpp +0 -78
- package/src/duckdb/src/common/arrow/appender/map_data.cpp +0 -91
- package/src/duckdb/src/common/cycle_counter.cpp +0 -76
- package/src/duckdb/src/common/field_writer.cpp +0 -97
- package/src/duckdb/src/common/http_state.cpp +0 -95
- package/src/duckdb/src/common/preserved_error.cpp +0 -87
- package/src/duckdb/src/common/row_operations/row_match.cpp +0 -359
- package/src/duckdb/src/common/serializer/buffered_deserializer.cpp +0 -27
- package/src/duckdb/src/common/serializer/buffered_serializer.cpp +0 -36
- package/src/duckdb/src/common/serializer/format_serializer.cpp +0 -15
- package/src/duckdb/src/common/serializer.cpp +0 -24
- package/src/duckdb/src/common/types/chunk_collection.cpp +0 -190
- package/src/duckdb/src/core_functions/aggregate/distributive/entropy.cpp +0 -183
- package/src/duckdb/src/core_functions/scalar/date/current.cpp +0 -54
- package/src/duckdb/src/core_functions/scalar/list/list_cosine_similarity.cpp +0 -78
- package/src/duckdb/src/core_functions/scalar/list/list_inner_product.cpp +0 -70
- package/src/duckdb/src/core_functions/scalar/list/list_lambdas.cpp +0 -412
- package/src/duckdb/src/core_functions/scalar/secret/which_secret.cpp +0 -28
- package/src/duckdb/src/core_functions/scalar/string/jaro_winkler.cpp +0 -71
- package/src/duckdb/src/execution/index/art/fixed_size_allocator.cpp +0 -238
- package/src/duckdb/src/execution/index/art/node16.cpp +0 -196
- package/src/duckdb/src/execution/index/art/node4.cpp +0 -189
- package/src/duckdb/src/execution/index/unknown_index.cpp +0 -65
- package/src/duckdb/src/execution/operator/csv_scanner/base_csv_reader.cpp +0 -595
- package/src/duckdb/src/execution/operator/csv_scanner/buffered_csv_reader.cpp +0 -434
- package/src/duckdb/src/execution/operator/csv_scanner/csv_buffer.cpp +0 -89
- package/src/duckdb/src/execution/operator/csv_scanner/csv_buffer_manager.cpp +0 -90
- package/src/duckdb/src/execution/operator/csv_scanner/csv_file_handle.cpp +0 -95
- package/src/duckdb/src/execution/operator/csv_scanner/csv_reader_options.cpp +0 -494
- package/src/duckdb/src/execution/operator/csv_scanner/csv_state_machine.cpp +0 -35
- package/src/duckdb/src/execution/operator/csv_scanner/csv_state_machine_cache.cpp +0 -99
- package/src/duckdb/src/execution/operator/csv_scanner/parallel_csv_reader.cpp +0 -689
- package/src/duckdb/src/execution/operator/join/physical_index_join.cpp +0 -242
- package/src/duckdb/src/execution/operator/persistent/base_csv_reader.cpp +0 -695
- package/src/duckdb/src/execution/operator/persistent/buffered_csv_reader.cpp +0 -1487
- package/src/duckdb/src/execution/operator/persistent/csv_buffer.cpp +0 -72
- package/src/duckdb/src/execution/operator/persistent/csv_file_handle.cpp +0 -158
- package/src/duckdb/src/execution/operator/persistent/csv_reader_options.cpp +0 -280
- package/src/duckdb/src/execution/operator/persistent/parallel_csv_reader.cpp +0 -666
- package/src/duckdb/src/execution/operator/persistent/physical_fixed_batch_copy.cpp +0 -499
- package/src/duckdb/src/execution/operator/schema/physical_create_index.cpp +0 -207
- package/src/duckdb/src/execution/partitionable_hashtable.cpp +0 -207
- package/src/duckdb/src/execution/physical_plan/plan_limit_percent.cpp +0 -18
- package/src/duckdb/src/execution/physical_plan/plan_show_select.cpp +0 -47
- package/src/duckdb/src/execution/reservoir_sample.cpp +0 -324
- package/src/duckdb/src/execution/window_executor.cpp +0 -1830
- package/src/duckdb/src/execution/window_segment_tree.cpp +0 -2073
- package/src/duckdb/src/extension_forward_decl/icu.cpp +0 -59
- package/src/duckdb/src/function/aggregate/distributive_functions.cpp +0 -15
- package/src/duckdb/src/function/scalar/compressed_materialization_functions.cpp +0 -29
- package/src/duckdb/src/function/scalar/generic_functions.cpp +0 -11
- package/src/duckdb/src/function/scalar/list/list_concat.cpp +0 -143
- package/src/duckdb/src/function/scalar/operators.cpp +0 -14
- package/src/duckdb/src/function/scalar/sequence_functions.cpp +0 -10
- package/src/duckdb/src/function/scalar/string_functions.cpp +0 -22
- package/src/duckdb/src/function/table/pragma_detailed_profiling_output.cpp +0 -173
- package/src/duckdb/src/function/table/pragma_last_profiling_output.cpp +0 -101
- package/src/duckdb/src/include/duckdb/catalog/mapping_value.hpp +0 -92
- package/src/duckdb/src/include/duckdb/common/arrow/arrow_types_extension.hpp +0 -42
- package/src/duckdb/src/include/duckdb/common/cycle_counter.hpp +0 -68
- package/src/duckdb/src/include/duckdb/common/enums/index_type.hpp +0 -34
- package/src/duckdb/src/include/duckdb/common/http_state.hpp +0 -113
- package/src/duckdb/src/include/duckdb/common/platform.h +0 -58
- package/src/duckdb/src/include/duckdb/common/preserved_error.hpp +0 -59
- package/src/duckdb/src/include/duckdb/common/serializer/deserialization_data.hpp +0 -192
- package/src/duckdb/src/include/duckdb/common/types/chunk_collection.hpp +0 -137
- package/src/duckdb/src/include/duckdb/execution/index/art/node16.hpp +0 -65
- package/src/duckdb/src/include/duckdb/execution/index/art/node4.hpp +0 -63
- package/src/duckdb/src/include/duckdb/execution/index/unknown_index.hpp +0 -65
- package/src/duckdb/src/include/duckdb/execution/operator/csv_scanner/buffer_manager/csv_buffer.hpp +0 -103
- package/src/duckdb/src/include/duckdb/execution/operator/csv_scanner/buffer_manager/csv_buffer_manager.hpp +0 -74
- package/src/duckdb/src/include/duckdb/execution/operator/csv_scanner/buffer_manager/csv_file_handle.hpp +0 -60
- package/src/duckdb/src/include/duckdb/execution/operator/csv_scanner/csv_sniffer.hpp +0 -253
- package/src/duckdb/src/include/duckdb/execution/operator/csv_scanner/options/csv_option.hpp +0 -155
- package/src/duckdb/src/include/duckdb/execution/operator/csv_scanner/options/csv_reader_options.hpp +0 -163
- package/src/duckdb/src/include/duckdb/execution/operator/csv_scanner/options/state_machine_options.hpp +0 -35
- package/src/duckdb/src/include/duckdb/execution/operator/csv_scanner/scanner/base_scanner.hpp +0 -228
- package/src/duckdb/src/include/duckdb/execution/operator/csv_scanner/scanner/column_count_scanner.hpp +0 -70
- package/src/duckdb/src/include/duckdb/execution/operator/csv_scanner/scanner/scanner_boundary.hpp +0 -93
- package/src/duckdb/src/include/duckdb/execution/operator/csv_scanner/scanner/skip_scanner.hpp +0 -60
- package/src/duckdb/src/include/duckdb/execution/operator/csv_scanner/scanner/string_value_scanner.hpp +0 -197
- package/src/duckdb/src/include/duckdb/execution/operator/csv_scanner/sniffer/quote_rules.hpp +0 -21
- package/src/duckdb/src/include/duckdb/execution/operator/csv_scanner/state_machine/csv_state.hpp +0 -30
- package/src/duckdb/src/include/duckdb/execution/operator/csv_scanner/state_machine/csv_state_machine.hpp +0 -99
- package/src/duckdb/src/include/duckdb/execution/operator/csv_scanner/state_machine/csv_state_machine_cache.hpp +0 -87
- package/src/duckdb/src/include/duckdb/execution/operator/csv_scanner/table_function/csv_file_scanner.hpp +0 -70
- package/src/duckdb/src/include/duckdb/execution/operator/csv_scanner/table_function/global_csv_state.hpp +0 -80
- package/src/duckdb/src/include/duckdb/execution/operator/csv_scanner/util/csv_casting.hpp +0 -137
- package/src/duckdb/src/include/duckdb/execution/operator/csv_scanner/util/csv_error.hpp +0 -104
- package/src/duckdb/src/include/duckdb/execution/operator/join/physical_index_join.hpp +0 -79
- package/src/duckdb/src/include/duckdb/execution/operator/scan/csv/base_csv_reader.hpp +0 -119
- package/src/duckdb/src/include/duckdb/execution/operator/scan/csv/buffered_csv_reader.hpp +0 -72
- package/src/duckdb/src/include/duckdb/execution/operator/scan/csv/csv_buffer.hpp +0 -110
- package/src/duckdb/src/include/duckdb/execution/operator/scan/csv/csv_buffer_manager.hpp +0 -103
- package/src/duckdb/src/include/duckdb/execution/operator/scan/csv/csv_file_handle.hpp +0 -59
- package/src/duckdb/src/include/duckdb/execution/operator/scan/csv/csv_line_info.hpp +0 -46
- package/src/duckdb/src/include/duckdb/execution/operator/scan/csv/csv_reader_options.hpp +0 -210
- package/src/duckdb/src/include/duckdb/execution/operator/scan/csv/csv_sniffer.hpp +0 -131
- package/src/duckdb/src/include/duckdb/execution/operator/scan/csv/csv_state.hpp +0 -28
- package/src/duckdb/src/include/duckdb/execution/operator/scan/csv/csv_state_machine.hpp +0 -70
- package/src/duckdb/src/include/duckdb/execution/operator/scan/csv/csv_state_machine_cache.hpp +0 -65
- package/src/duckdb/src/include/duckdb/execution/operator/scan/csv/parallel_csv_reader.hpp +0 -167
- package/src/duckdb/src/include/duckdb/execution/operator/scan/csv/quote_rules.hpp +0 -21
- package/src/duckdb/src/include/duckdb/execution/window_executor.hpp +0 -343
- package/src/duckdb/src/include/duckdb/execution/window_segment_tree.hpp +0 -165
- package/src/duckdb/src/include/duckdb/optimizer/column_lifetime_optimizer.hpp +0 -45
- package/src/duckdb/src/include/duckdb/optimizer/join_order/estimated_properties.hpp +0 -57
- package/src/duckdb/src/include/duckdb/parser/parsed_data/comment_on_info.hpp +0 -45
- package/src/duckdb/src/include/duckdb/parser/statement/show_statement.hpp +0 -32
- package/src/duckdb/src/include/duckdb/planner/operator/logical_limit_percent.hpp +0 -49
- package/src/duckdb/src/include/duckdb/planner/operator/logical_show.hpp +0 -42
- package/src/duckdb/src/main/settings/settings.cpp +0 -2056
- package/src/duckdb/src/optimizer/join_order/estimated_properties.cpp +0 -36
- package/src/duckdb/src/parser/parsed_data/comment_on_info.cpp +0 -19
- package/src/duckdb/src/parser/statement/show_statement.cpp +0 -15
- package/src/duckdb/src/planner/binder/statement/bind_show.cpp +0 -30
- package/src/duckdb/src/planner/operator/logical_limit_percent.cpp +0 -14
- package/src/duckdb/src/storage/statistics/numeric_stats_union.cpp +0 -70
- package/src/duckdb/third_party/fsst/fsst_avx512.cpp +0 -140
- package/src/duckdb/third_party/fsst/fsst_avx512.inc +0 -57
- package/src/duckdb/third_party/fsst/fsst_avx512_unroll1.inc +0 -57
- package/src/duckdb/third_party/fsst/fsst_avx512_unroll2.inc +0 -114
- package/src/duckdb/third_party/fsst/fsst_avx512_unroll3.inc +0 -171
- package/src/duckdb/third_party/fsst/fsst_avx512_unroll4.inc +0 -228
- package/src/duckdb/third_party/parquet/parquet_constants.cpp +0 -17
- package/src/duckdb/third_party/parquet/parquet_constants.h +0 -24
- package/src/duckdb/third_party/re2/util/pod_array.h +0 -55
- package/src/duckdb/third_party/re2/util/sparse_array.h +0 -392
- package/src/duckdb/third_party/re2/util/sparse_set.h +0 -264
- package/src/duckdb/third_party/zstd/include/zstd/common/fse_static.h +0 -421
- package/src/duckdb/third_party/zstd/include/zstd/common/huf_static.h +0 -238
- package/src/duckdb/third_party/zstd/include/zstd_static.h +0 -1070
- package/src/duckdb/ub_src_core_functions.cpp +0 -6
- package/src/duckdb/ub_src_core_functions_aggregate_algebraic.cpp +0 -8
- package/src/duckdb/ub_src_core_functions_aggregate_distributive.cpp +0 -24
- package/src/duckdb/ub_src_core_functions_aggregate_holistic.cpp +0 -12
- package/src/duckdb/ub_src_core_functions_aggregate_nested.cpp +0 -6
- package/src/duckdb/ub_src_core_functions_aggregate_regression.cpp +0 -14
- package/src/duckdb/ub_src_core_functions_scalar_array.cpp +0 -4
- package/src/duckdb/ub_src_core_functions_scalar_bit.cpp +0 -2
- package/src/duckdb/ub_src_core_functions_scalar_blob.cpp +0 -6
- package/src/duckdb/ub_src_core_functions_scalar_date.cpp +0 -22
- package/src/duckdb/ub_src_core_functions_scalar_debug.cpp +0 -2
- package/src/duckdb/ub_src_core_functions_scalar_enum.cpp +0 -2
- package/src/duckdb/ub_src_core_functions_scalar_generic.cpp +0 -18
- package/src/duckdb/ub_src_core_functions_scalar_list.cpp +0 -22
- package/src/duckdb/ub_src_core_functions_scalar_map.cpp +0 -16
- package/src/duckdb/ub_src_core_functions_scalar_math.cpp +0 -2
- package/src/duckdb/ub_src_core_functions_scalar_operators.cpp +0 -2
- package/src/duckdb/ub_src_core_functions_scalar_random.cpp +0 -4
- package/src/duckdb/ub_src_core_functions_scalar_secret.cpp +0 -2
- package/src/duckdb/ub_src_core_functions_scalar_string.cpp +0 -58
- package/src/duckdb/ub_src_core_functions_scalar_struct.cpp +0 -4
- package/src/duckdb/ub_src_core_functions_scalar_union.cpp +0 -6
- package/src/duckdb/ub_src_execution_operator_csv_scanner.cpp +0 -18
- package/src/duckdb/ub_src_function_scalar_operators.cpp +0 -8
- /package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/aggregate/algebraic/covar.hpp +0 -0
- /package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/aggregate/algebraic/stddev.hpp +0 -0
- /package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/aggregate/sum_helpers.hpp +0 -0
- /package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/array_kernels.hpp +0 -0
- /package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/function_list.hpp +0 -0
- /package/src/duckdb/{src/include/duckdb → extension/core_functions/include}/core_functions/scalar/secret_functions.hpp +0 -0
- /package/src/duckdb/src/function/scalar/{operators → operator}/multiply.cpp +0 -0
- /package/src/duckdb/src/function/scalar/{operators → operator}/subtract.cpp +0 -0
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/*
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#ifndef MAX
|
100
|
+
# define MAX(_a, _b) (((_a) > (_b)) ? (_a) : (_b))
|
101
|
+
#endif /* MAX */
|
102
|
+
#define STACK_PUSH(_a, _b, _c, _d)\
|
103
|
+
do {\
|
104
|
+
assert(ssize < STACK_SIZE);\
|
105
|
+
stack[ssize].a = (_a), stack[ssize].b = (_b),\
|
106
|
+
stack[ssize].c = (_c), stack[ssize++].d = (_d);\
|
107
|
+
} while(0)
|
108
|
+
#define STACK_PUSH5(_a, _b, _c, _d, _e)\
|
109
|
+
do {\
|
110
|
+
assert(ssize < STACK_SIZE);\
|
111
|
+
stack[ssize].a = (_a), stack[ssize].b = (_b),\
|
112
|
+
stack[ssize].c = (_c), stack[ssize].d = (_d), stack[ssize++].e = (_e);\
|
113
|
+
} while(0)
|
114
|
+
#define STACK_POP(_a, _b, _c, _d)\
|
115
|
+
do {\
|
116
|
+
assert(0 <= ssize);\
|
117
|
+
if(ssize == 0) { return; }\
|
118
|
+
(_a) = stack[--ssize].a, (_b) = stack[ssize].b,\
|
119
|
+
(_c) = stack[ssize].c, (_d) = stack[ssize].d;\
|
120
|
+
} while(0)
|
121
|
+
#define STACK_POP5(_a, _b, _c, _d, _e)\
|
122
|
+
do {\
|
123
|
+
assert(0 <= ssize);\
|
124
|
+
if(ssize == 0) { return; }\
|
125
|
+
(_a) = stack[--ssize].a, (_b) = stack[ssize].b,\
|
126
|
+
(_c) = stack[ssize].c, (_d) = stack[ssize].d, (_e) = stack[ssize].e;\
|
127
|
+
} while(0)
|
128
|
+
#define BUCKET_A(_c0) bucket_A[(_c0)]
|
129
|
+
#if ALPHABET_SIZE == 256
|
130
|
+
#define BUCKET_B(_c0, _c1) (bucket_B[((_c1) << 8) | (_c0)])
|
131
|
+
#define BUCKET_BSTAR(_c0, _c1) (bucket_B[((_c0) << 8) | (_c1)])
|
132
|
+
#else
|
133
|
+
#define BUCKET_B(_c0, _c1) (bucket_B[(_c1) * ALPHABET_SIZE + (_c0)])
|
134
|
+
#define BUCKET_BSTAR(_c0, _c1) (bucket_B[(_c0) * ALPHABET_SIZE + (_c1)])
|
135
|
+
#endif
|
136
|
+
|
137
|
+
namespace duckdb_zstd {
|
138
|
+
|
139
|
+
/*- Private Functions -*/
|
140
|
+
|
141
|
+
static const int lg_table[256]= {
|
142
|
+
-1,0,1,1,2,2,2,2,3,3,3,3,3,3,3,3,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,
|
143
|
+
5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,
|
144
|
+
6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,
|
145
|
+
6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,
|
146
|
+
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
|
147
|
+
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
|
148
|
+
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
|
149
|
+
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7
|
150
|
+
};
|
151
|
+
|
152
|
+
#if (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE)
|
153
|
+
|
154
|
+
static INLINE
|
155
|
+
int
|
156
|
+
ss_ilg(int n) {
|
157
|
+
#if SS_BLOCKSIZE == 0
|
158
|
+
return (n & 0xffff0000) ?
|
159
|
+
((n & 0xff000000) ?
|
160
|
+
24 + lg_table[(n >> 24) & 0xff] :
|
161
|
+
16 + lg_table[(n >> 16) & 0xff]) :
|
162
|
+
((n & 0x0000ff00) ?
|
163
|
+
8 + lg_table[(n >> 8) & 0xff] :
|
164
|
+
0 + lg_table[(n >> 0) & 0xff]);
|
165
|
+
#elif SS_BLOCKSIZE < 256
|
166
|
+
return lg_table[n];
|
167
|
+
#else
|
168
|
+
return (n & 0xff00) ?
|
169
|
+
8 + lg_table[(n >> 8) & 0xff] :
|
170
|
+
0 + lg_table[(n >> 0) & 0xff];
|
171
|
+
#endif
|
172
|
+
}
|
173
|
+
|
174
|
+
#endif /* (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE) */
|
175
|
+
|
176
|
+
#if SS_BLOCKSIZE != 0
|
177
|
+
|
178
|
+
static const int sqq_table[256] = {
|
179
|
+
0, 16, 22, 27, 32, 35, 39, 42, 45, 48, 50, 53, 55, 57, 59, 61,
|
180
|
+
64, 65, 67, 69, 71, 73, 75, 76, 78, 80, 81, 83, 84, 86, 87, 89,
|
181
|
+
90, 91, 93, 94, 96, 97, 98, 99, 101, 102, 103, 104, 106, 107, 108, 109,
|
182
|
+
110, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126,
|
183
|
+
128, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142,
|
184
|
+
143, 144, 144, 145, 146, 147, 148, 149, 150, 150, 151, 152, 153, 154, 155, 155,
|
185
|
+
156, 157, 158, 159, 160, 160, 161, 162, 163, 163, 164, 165, 166, 167, 167, 168,
|
186
|
+
169, 170, 170, 171, 172, 173, 173, 174, 175, 176, 176, 177, 178, 178, 179, 180,
|
187
|
+
181, 181, 182, 183, 183, 184, 185, 185, 186, 187, 187, 188, 189, 189, 190, 191,
|
188
|
+
192, 192, 193, 193, 194, 195, 195, 196, 197, 197, 198, 199, 199, 200, 201, 201,
|
189
|
+
202, 203, 203, 204, 204, 205, 206, 206, 207, 208, 208, 209, 209, 210, 211, 211,
|
190
|
+
212, 212, 213, 214, 214, 215, 215, 216, 217, 217, 218, 218, 219, 219, 220, 221,
|
191
|
+
221, 222, 222, 223, 224, 224, 225, 225, 226, 226, 227, 227, 228, 229, 229, 230,
|
192
|
+
230, 231, 231, 232, 232, 233, 234, 234, 235, 235, 236, 236, 237, 237, 238, 238,
|
193
|
+
239, 240, 240, 241, 241, 242, 242, 243, 243, 244, 244, 245, 245, 246, 246, 247,
|
194
|
+
247, 248, 248, 249, 249, 250, 250, 251, 251, 252, 252, 253, 253, 254, 254, 255
|
195
|
+
};
|
196
|
+
|
197
|
+
static INLINE
|
198
|
+
int
|
199
|
+
ss_isqrt(int x) {
|
200
|
+
int y, e;
|
201
|
+
|
202
|
+
if(x >= (SS_BLOCKSIZE * SS_BLOCKSIZE)) { return SS_BLOCKSIZE; }
|
203
|
+
e = (x & 0xffff0000) ?
|
204
|
+
((x & 0xff000000) ?
|
205
|
+
24 + lg_table[(x >> 24) & 0xff] :
|
206
|
+
16 + lg_table[(x >> 16) & 0xff]) :
|
207
|
+
((x & 0x0000ff00) ?
|
208
|
+
8 + lg_table[(x >> 8) & 0xff] :
|
209
|
+
0 + lg_table[(x >> 0) & 0xff]);
|
210
|
+
|
211
|
+
if(e >= 16) {
|
212
|
+
y = sqq_table[x >> ((e - 6) - (e & 1))] << ((e >> 1) - 7);
|
213
|
+
if(e >= 24) { y = (y + 1 + x / y) >> 1; }
|
214
|
+
y = (y + 1 + x / y) >> 1;
|
215
|
+
} else if(e >= 8) {
|
216
|
+
y = (sqq_table[x >> ((e - 6) - (e & 1))] >> (7 - (e >> 1))) + 1;
|
217
|
+
} else {
|
218
|
+
return sqq_table[x] >> 4;
|
219
|
+
}
|
220
|
+
|
221
|
+
return (x < (y * y)) ? y - 1 : y;
|
222
|
+
}
|
223
|
+
|
224
|
+
#endif /* SS_BLOCKSIZE != 0 */
|
225
|
+
|
226
|
+
|
227
|
+
/*---------------------------------------------------------------------------*/
|
228
|
+
|
229
|
+
/* Compares two suffixes. */
|
230
|
+
static INLINE
|
231
|
+
int
|
232
|
+
ss_compare(const unsigned char *T,
|
233
|
+
const int *p1, const int *p2,
|
234
|
+
int depth) {
|
235
|
+
const unsigned char *U1, *U2, *U1n, *U2n;
|
236
|
+
|
237
|
+
for(U1 = T + depth + *p1,
|
238
|
+
U2 = T + depth + *p2,
|
239
|
+
U1n = T + *(p1 + 1) + 2,
|
240
|
+
U2n = T + *(p2 + 1) + 2;
|
241
|
+
(U1 < U1n) && (U2 < U2n) && (*U1 == *U2);
|
242
|
+
++U1, ++U2) {
|
243
|
+
}
|
244
|
+
|
245
|
+
return U1 < U1n ?
|
246
|
+
(U2 < U2n ? *U1 - *U2 : 1) :
|
247
|
+
(U2 < U2n ? -1 : 0);
|
248
|
+
}
|
249
|
+
|
250
|
+
|
251
|
+
/*---------------------------------------------------------------------------*/
|
252
|
+
|
253
|
+
#if (SS_BLOCKSIZE != 1) && (SS_INSERTIONSORT_THRESHOLD != 1)
|
254
|
+
|
255
|
+
/* Insertionsort for small size groups */
|
256
|
+
static
|
257
|
+
void
|
258
|
+
ss_insertionsort(const unsigned char *T, const int *PA,
|
259
|
+
int *first, int *last, int depth) {
|
260
|
+
int *i, *j;
|
261
|
+
int t;
|
262
|
+
int r;
|
263
|
+
|
264
|
+
for(i = last - 2; first <= i; --i) {
|
265
|
+
for(t = *i, j = i + 1; 0 < (r = ss_compare(T, PA + t, PA + *j, depth));) {
|
266
|
+
do { *(j - 1) = *j; } while((++j < last) && (*j < 0));
|
267
|
+
if(last <= j) { break; }
|
268
|
+
}
|
269
|
+
if(r == 0) { *j = ~*j; }
|
270
|
+
*(j - 1) = t;
|
271
|
+
}
|
272
|
+
}
|
273
|
+
|
274
|
+
#endif /* (SS_BLOCKSIZE != 1) && (SS_INSERTIONSORT_THRESHOLD != 1) */
|
275
|
+
|
276
|
+
|
277
|
+
/*---------------------------------------------------------------------------*/
|
278
|
+
|
279
|
+
#if (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE)
|
280
|
+
|
281
|
+
static INLINE
|
282
|
+
void
|
283
|
+
ss_fixdown(const unsigned char *Td, const int *PA,
|
284
|
+
int *SA, int i, int size) {
|
285
|
+
int j, k;
|
286
|
+
int v;
|
287
|
+
int c, d, e;
|
288
|
+
|
289
|
+
for(v = SA[i], c = Td[PA[v]]; (j = 2 * i + 1) < size; SA[i] = SA[k], i = k) {
|
290
|
+
d = Td[PA[SA[k = j++]]];
|
291
|
+
if(d < (e = Td[PA[SA[j]]])) { k = j; d = e; }
|
292
|
+
if(d <= c) { break; }
|
293
|
+
}
|
294
|
+
SA[i] = v;
|
295
|
+
}
|
296
|
+
|
297
|
+
/* Simple top-down heapsort. */
|
298
|
+
static
|
299
|
+
void
|
300
|
+
ss_heapsort(const unsigned char *Td, const int *PA, int *SA, int size) {
|
301
|
+
int i, m;
|
302
|
+
int t;
|
303
|
+
|
304
|
+
m = size;
|
305
|
+
if((size % 2) == 0) {
|
306
|
+
m--;
|
307
|
+
if(Td[PA[SA[m / 2]]] < Td[PA[SA[m]]]) { SWAP(SA[m], SA[m / 2]); }
|
308
|
+
}
|
309
|
+
|
310
|
+
for(i = m / 2 - 1; 0 <= i; --i) { ss_fixdown(Td, PA, SA, i, m); }
|
311
|
+
if((size % 2) == 0) { SWAP(SA[0], SA[m]); ss_fixdown(Td, PA, SA, 0, m); }
|
312
|
+
for(i = m - 1; 0 < i; --i) {
|
313
|
+
t = SA[0], SA[0] = SA[i];
|
314
|
+
ss_fixdown(Td, PA, SA, 0, i);
|
315
|
+
SA[i] = t;
|
316
|
+
}
|
317
|
+
}
|
318
|
+
|
319
|
+
|
320
|
+
/*---------------------------------------------------------------------------*/
|
321
|
+
|
322
|
+
/* Returns the median of three elements. */
|
323
|
+
static INLINE
|
324
|
+
int *
|
325
|
+
ss_median3(const unsigned char *Td, const int *PA,
|
326
|
+
int *v1, int *v2, int *v3) {
|
327
|
+
int *t;
|
328
|
+
if(Td[PA[*v1]] > Td[PA[*v2]]) { SWAP(v1, v2); }
|
329
|
+
if(Td[PA[*v2]] > Td[PA[*v3]]) {
|
330
|
+
if(Td[PA[*v1]] > Td[PA[*v3]]) { return v1; }
|
331
|
+
else { return v3; }
|
332
|
+
}
|
333
|
+
return v2;
|
334
|
+
}
|
335
|
+
|
336
|
+
/* Returns the median of five elements. */
|
337
|
+
static INLINE
|
338
|
+
int *
|
339
|
+
ss_median5(const unsigned char *Td, const int *PA,
|
340
|
+
int *v1, int *v2, int *v3, int *v4, int *v5) {
|
341
|
+
int *t;
|
342
|
+
if(Td[PA[*v2]] > Td[PA[*v3]]) { SWAP(v2, v3); }
|
343
|
+
if(Td[PA[*v4]] > Td[PA[*v5]]) { SWAP(v4, v5); }
|
344
|
+
if(Td[PA[*v2]] > Td[PA[*v4]]) { SWAP(v2, v4); SWAP(v3, v5); }
|
345
|
+
if(Td[PA[*v1]] > Td[PA[*v3]]) { SWAP(v1, v3); }
|
346
|
+
if(Td[PA[*v1]] > Td[PA[*v4]]) { SWAP(v1, v4); SWAP(v3, v5); }
|
347
|
+
if(Td[PA[*v3]] > Td[PA[*v4]]) { return v4; }
|
348
|
+
return v3;
|
349
|
+
}
|
350
|
+
|
351
|
+
/* Returns the pivot element. */
|
352
|
+
static INLINE
|
353
|
+
int *
|
354
|
+
ss_pivot(const unsigned char *Td, const int *PA, int *first, int *last) {
|
355
|
+
int *middle;
|
356
|
+
int t;
|
357
|
+
|
358
|
+
t = last - first;
|
359
|
+
middle = first + t / 2;
|
360
|
+
|
361
|
+
if(t <= 512) {
|
362
|
+
if(t <= 32) {
|
363
|
+
return ss_median3(Td, PA, first, middle, last - 1);
|
364
|
+
} else {
|
365
|
+
t >>= 2;
|
366
|
+
return ss_median5(Td, PA, first, first + t, middle, last - 1 - t, last - 1);
|
367
|
+
}
|
368
|
+
}
|
369
|
+
t >>= 3;
|
370
|
+
first = ss_median3(Td, PA, first, first + t, first + (t << 1));
|
371
|
+
middle = ss_median3(Td, PA, middle - t, middle, middle + t);
|
372
|
+
last = ss_median3(Td, PA, last - 1 - (t << 1), last - 1 - t, last - 1);
|
373
|
+
return ss_median3(Td, PA, first, middle, last);
|
374
|
+
}
|
375
|
+
|
376
|
+
|
377
|
+
/*---------------------------------------------------------------------------*/
|
378
|
+
|
379
|
+
/* Binary partition for substrings. */
|
380
|
+
static INLINE
|
381
|
+
int *
|
382
|
+
ss_partition(const int *PA,
|
383
|
+
int *first, int *last, int depth) {
|
384
|
+
int *a, *b;
|
385
|
+
int t;
|
386
|
+
for(a = first - 1, b = last;;) {
|
387
|
+
for(; (++a < b) && ((PA[*a] + depth) >= (PA[*a + 1] + 1));) { *a = ~*a; }
|
388
|
+
for(; (a < --b) && ((PA[*b] + depth) < (PA[*b + 1] + 1));) { }
|
389
|
+
if(b <= a) { break; }
|
390
|
+
t = ~*b;
|
391
|
+
*b = *a;
|
392
|
+
*a = t;
|
393
|
+
}
|
394
|
+
if(first < a) { *first = ~*first; }
|
395
|
+
return a;
|
396
|
+
}
|
397
|
+
|
398
|
+
/* Multikey introsort for medium size groups. */
|
399
|
+
static
|
400
|
+
void
|
401
|
+
ss_mintrosort(const unsigned char *T, const int *PA,
|
402
|
+
int *first, int *last,
|
403
|
+
int depth) {
|
404
|
+
#define STACK_SIZE SS_MISORT_STACKSIZE
|
405
|
+
struct { int *a, *b, c; int d; } stack[STACK_SIZE];
|
406
|
+
const unsigned char *Td;
|
407
|
+
int *a, *b, *c, *d, *e, *f;
|
408
|
+
int s, t;
|
409
|
+
int ssize;
|
410
|
+
int limit;
|
411
|
+
int v, x = 0;
|
412
|
+
|
413
|
+
for(ssize = 0, limit = ss_ilg(last - first);;) {
|
414
|
+
|
415
|
+
if((last - first) <= SS_INSERTIONSORT_THRESHOLD) {
|
416
|
+
#if 1 < SS_INSERTIONSORT_THRESHOLD
|
417
|
+
if(1 < (last - first)) { ss_insertionsort(T, PA, first, last, depth); }
|
418
|
+
#endif
|
419
|
+
STACK_POP(first, last, depth, limit);
|
420
|
+
continue;
|
421
|
+
}
|
422
|
+
|
423
|
+
Td = T + depth;
|
424
|
+
if(limit-- == 0) { ss_heapsort(Td, PA, first, last - first); }
|
425
|
+
if(limit < 0) {
|
426
|
+
for(a = first + 1, v = Td[PA[*first]]; a < last; ++a) {
|
427
|
+
if((x = Td[PA[*a]]) != v) {
|
428
|
+
if(1 < (a - first)) { break; }
|
429
|
+
v = x;
|
430
|
+
first = a;
|
431
|
+
}
|
432
|
+
}
|
433
|
+
if(Td[PA[*first] - 1] < v) {
|
434
|
+
first = ss_partition(PA, first, a, depth);
|
435
|
+
}
|
436
|
+
if((a - first) <= (last - a)) {
|
437
|
+
if(1 < (a - first)) {
|
438
|
+
STACK_PUSH(a, last, depth, -1);
|
439
|
+
last = a, depth += 1, limit = ss_ilg(a - first);
|
440
|
+
} else {
|
441
|
+
first = a, limit = -1;
|
442
|
+
}
|
443
|
+
} else {
|
444
|
+
if(1 < (last - a)) {
|
445
|
+
STACK_PUSH(first, a, depth + 1, ss_ilg(a - first));
|
446
|
+
first = a, limit = -1;
|
447
|
+
} else {
|
448
|
+
last = a, depth += 1, limit = ss_ilg(a - first);
|
449
|
+
}
|
450
|
+
}
|
451
|
+
continue;
|
452
|
+
}
|
453
|
+
|
454
|
+
/* choose pivot */
|
455
|
+
a = ss_pivot(Td, PA, first, last);
|
456
|
+
v = Td[PA[*a]];
|
457
|
+
SWAP(*first, *a);
|
458
|
+
|
459
|
+
/* partition */
|
460
|
+
for(b = first; (++b < last) && ((x = Td[PA[*b]]) == v);) { }
|
461
|
+
if(((a = b) < last) && (x < v)) {
|
462
|
+
for(; (++b < last) && ((x = Td[PA[*b]]) <= v);) {
|
463
|
+
if(x == v) { SWAP(*b, *a); ++a; }
|
464
|
+
}
|
465
|
+
}
|
466
|
+
for(c = last; (b < --c) && ((x = Td[PA[*c]]) == v);) { }
|
467
|
+
if((b < (d = c)) && (x > v)) {
|
468
|
+
for(; (b < --c) && ((x = Td[PA[*c]]) >= v);) {
|
469
|
+
if(x == v) { SWAP(*c, *d); --d; }
|
470
|
+
}
|
471
|
+
}
|
472
|
+
for(; b < c;) {
|
473
|
+
SWAP(*b, *c);
|
474
|
+
for(; (++b < c) && ((x = Td[PA[*b]]) <= v);) {
|
475
|
+
if(x == v) { SWAP(*b, *a); ++a; }
|
476
|
+
}
|
477
|
+
for(; (b < --c) && ((x = Td[PA[*c]]) >= v);) {
|
478
|
+
if(x == v) { SWAP(*c, *d); --d; }
|
479
|
+
}
|
480
|
+
}
|
481
|
+
|
482
|
+
if(a <= d) {
|
483
|
+
c = b - 1;
|
484
|
+
|
485
|
+
if((s = a - first) > (t = b - a)) { s = t; }
|
486
|
+
for(e = first, f = b - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); }
|
487
|
+
if((s = d - c) > (t = last - d - 1)) { s = t; }
|
488
|
+
for(e = b, f = last - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); }
|
489
|
+
|
490
|
+
a = first + (b - a), c = last - (d - c);
|
491
|
+
b = (v <= Td[PA[*a] - 1]) ? a : ss_partition(PA, a, c, depth);
|
492
|
+
|
493
|
+
if((a - first) <= (last - c)) {
|
494
|
+
if((last - c) <= (c - b)) {
|
495
|
+
STACK_PUSH(b, c, depth + 1, ss_ilg(c - b));
|
496
|
+
STACK_PUSH(c, last, depth, limit);
|
497
|
+
last = a;
|
498
|
+
} else if((a - first) <= (c - b)) {
|
499
|
+
STACK_PUSH(c, last, depth, limit);
|
500
|
+
STACK_PUSH(b, c, depth + 1, ss_ilg(c - b));
|
501
|
+
last = a;
|
502
|
+
} else {
|
503
|
+
STACK_PUSH(c, last, depth, limit);
|
504
|
+
STACK_PUSH(first, a, depth, limit);
|
505
|
+
first = b, last = c, depth += 1, limit = ss_ilg(c - b);
|
506
|
+
}
|
507
|
+
} else {
|
508
|
+
if((a - first) <= (c - b)) {
|
509
|
+
STACK_PUSH(b, c, depth + 1, ss_ilg(c - b));
|
510
|
+
STACK_PUSH(first, a, depth, limit);
|
511
|
+
first = c;
|
512
|
+
} else if((last - c) <= (c - b)) {
|
513
|
+
STACK_PUSH(first, a, depth, limit);
|
514
|
+
STACK_PUSH(b, c, depth + 1, ss_ilg(c - b));
|
515
|
+
first = c;
|
516
|
+
} else {
|
517
|
+
STACK_PUSH(first, a, depth, limit);
|
518
|
+
STACK_PUSH(c, last, depth, limit);
|
519
|
+
first = b, last = c, depth += 1, limit = ss_ilg(c - b);
|
520
|
+
}
|
521
|
+
}
|
522
|
+
} else {
|
523
|
+
limit += 1;
|
524
|
+
if(Td[PA[*first] - 1] < v) {
|
525
|
+
first = ss_partition(PA, first, last, depth);
|
526
|
+
limit = ss_ilg(last - first);
|
527
|
+
}
|
528
|
+
depth += 1;
|
529
|
+
}
|
530
|
+
}
|
531
|
+
#undef STACK_SIZE
|
532
|
+
}
|
533
|
+
|
534
|
+
#endif /* (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE) */
|
535
|
+
|
536
|
+
|
537
|
+
/*---------------------------------------------------------------------------*/
|
538
|
+
|
539
|
+
#if SS_BLOCKSIZE != 0
|
540
|
+
|
541
|
+
static INLINE
|
542
|
+
void
|
543
|
+
ss_blockswap(int *a, int *b, int n) {
|
544
|
+
int t;
|
545
|
+
for(; 0 < n; --n, ++a, ++b) {
|
546
|
+
t = *a, *a = *b, *b = t;
|
547
|
+
}
|
548
|
+
}
|
549
|
+
|
550
|
+
static INLINE
|
551
|
+
void
|
552
|
+
ss_rotate(int *first, int *middle, int *last) {
|
553
|
+
int *a, *b, t;
|
554
|
+
int l, r;
|
555
|
+
l = middle - first, r = last - middle;
|
556
|
+
for(; (0 < l) && (0 < r);) {
|
557
|
+
if(l == r) { ss_blockswap(first, middle, l); break; }
|
558
|
+
if(l < r) {
|
559
|
+
a = last - 1, b = middle - 1;
|
560
|
+
t = *a;
|
561
|
+
do {
|
562
|
+
*a-- = *b, *b-- = *a;
|
563
|
+
if(b < first) {
|
564
|
+
*a = t;
|
565
|
+
last = a;
|
566
|
+
if((r -= l + 1) <= l) { break; }
|
567
|
+
a -= 1, b = middle - 1;
|
568
|
+
t = *a;
|
569
|
+
}
|
570
|
+
} while(1);
|
571
|
+
} else {
|
572
|
+
a = first, b = middle;
|
573
|
+
t = *a;
|
574
|
+
do {
|
575
|
+
*a++ = *b, *b++ = *a;
|
576
|
+
if(last <= b) {
|
577
|
+
*a = t;
|
578
|
+
first = a + 1;
|
579
|
+
if((l -= r + 1) <= r) { break; }
|
580
|
+
a += 1, b = middle;
|
581
|
+
t = *a;
|
582
|
+
}
|
583
|
+
} while(1);
|
584
|
+
}
|
585
|
+
}
|
586
|
+
}
|
587
|
+
|
588
|
+
|
589
|
+
/*---------------------------------------------------------------------------*/
|
590
|
+
|
591
|
+
static
|
592
|
+
void
|
593
|
+
ss_inplacemerge(const unsigned char *T, const int *PA,
|
594
|
+
int *first, int *middle, int *last,
|
595
|
+
int depth) {
|
596
|
+
const int *p;
|
597
|
+
int *a, *b;
|
598
|
+
int len, half;
|
599
|
+
int q, r;
|
600
|
+
int x;
|
601
|
+
|
602
|
+
for(;;) {
|
603
|
+
if(*(last - 1) < 0) { x = 1; p = PA + ~*(last - 1); }
|
604
|
+
else { x = 0; p = PA + *(last - 1); }
|
605
|
+
for(a = first, len = middle - first, half = len >> 1, r = -1;
|
606
|
+
0 < len;
|
607
|
+
len = half, half >>= 1) {
|
608
|
+
b = a + half;
|
609
|
+
q = ss_compare(T, PA + ((0 <= *b) ? *b : ~*b), p, depth);
|
610
|
+
if(q < 0) {
|
611
|
+
a = b + 1;
|
612
|
+
half -= (len & 1) ^ 1;
|
613
|
+
} else {
|
614
|
+
r = q;
|
615
|
+
}
|
616
|
+
}
|
617
|
+
if(a < middle) {
|
618
|
+
if(r == 0) { *a = ~*a; }
|
619
|
+
ss_rotate(a, middle, last);
|
620
|
+
last -= middle - a;
|
621
|
+
middle = a;
|
622
|
+
if(first == middle) { break; }
|
623
|
+
}
|
624
|
+
--last;
|
625
|
+
if(x != 0) { while(*--last < 0) { } }
|
626
|
+
if(middle == last) { break; }
|
627
|
+
}
|
628
|
+
}
|
629
|
+
|
630
|
+
|
631
|
+
/*---------------------------------------------------------------------------*/
|
632
|
+
|
633
|
+
/* Merge-forward with internal buffer. */
|
634
|
+
static
|
635
|
+
void
|
636
|
+
ss_mergeforward(const unsigned char *T, const int *PA,
|
637
|
+
int *first, int *middle, int *last,
|
638
|
+
int *buf, int depth) {
|
639
|
+
int *a, *b, *c, *bufend;
|
640
|
+
int t;
|
641
|
+
int r;
|
642
|
+
|
643
|
+
bufend = buf + (middle - first) - 1;
|
644
|
+
ss_blockswap(buf, first, middle - first);
|
645
|
+
|
646
|
+
for(t = *(a = first), b = buf, c = middle;;) {
|
647
|
+
r = ss_compare(T, PA + *b, PA + *c, depth);
|
648
|
+
if(r < 0) {
|
649
|
+
do {
|
650
|
+
*a++ = *b;
|
651
|
+
if(bufend <= b) { *bufend = t; return; }
|
652
|
+
*b++ = *a;
|
653
|
+
} while(*b < 0);
|
654
|
+
} else if(r > 0) {
|
655
|
+
do {
|
656
|
+
*a++ = *c, *c++ = *a;
|
657
|
+
if(last <= c) {
|
658
|
+
while(b < bufend) { *a++ = *b, *b++ = *a; }
|
659
|
+
*a = *b, *b = t;
|
660
|
+
return;
|
661
|
+
}
|
662
|
+
} while(*c < 0);
|
663
|
+
} else {
|
664
|
+
*c = ~*c;
|
665
|
+
do {
|
666
|
+
*a++ = *b;
|
667
|
+
if(bufend <= b) { *bufend = t; return; }
|
668
|
+
*b++ = *a;
|
669
|
+
} while(*b < 0);
|
670
|
+
|
671
|
+
do {
|
672
|
+
*a++ = *c, *c++ = *a;
|
673
|
+
if(last <= c) {
|
674
|
+
while(b < bufend) { *a++ = *b, *b++ = *a; }
|
675
|
+
*a = *b, *b = t;
|
676
|
+
return;
|
677
|
+
}
|
678
|
+
} while(*c < 0);
|
679
|
+
}
|
680
|
+
}
|
681
|
+
}
|
682
|
+
|
683
|
+
/* Merge-backward with internal buffer. */
|
684
|
+
static
|
685
|
+
void
|
686
|
+
ss_mergebackward(const unsigned char *T, const int *PA,
|
687
|
+
int *first, int *middle, int *last,
|
688
|
+
int *buf, int depth) {
|
689
|
+
const int *p1, *p2;
|
690
|
+
int *a, *b, *c, *bufend;
|
691
|
+
int t;
|
692
|
+
int r;
|
693
|
+
int x;
|
694
|
+
|
695
|
+
bufend = buf + (last - middle) - 1;
|
696
|
+
ss_blockswap(buf, middle, last - middle);
|
697
|
+
|
698
|
+
x = 0;
|
699
|
+
if(*bufend < 0) { p1 = PA + ~*bufend; x |= 1; }
|
700
|
+
else { p1 = PA + *bufend; }
|
701
|
+
if(*(middle - 1) < 0) { p2 = PA + ~*(middle - 1); x |= 2; }
|
702
|
+
else { p2 = PA + *(middle - 1); }
|
703
|
+
for(t = *(a = last - 1), b = bufend, c = middle - 1;;) {
|
704
|
+
r = ss_compare(T, p1, p2, depth);
|
705
|
+
if(0 < r) {
|
706
|
+
if(x & 1) { do { *a-- = *b, *b-- = *a; } while(*b < 0); x ^= 1; }
|
707
|
+
*a-- = *b;
|
708
|
+
if(b <= buf) { *buf = t; break; }
|
709
|
+
*b-- = *a;
|
710
|
+
if(*b < 0) { p1 = PA + ~*b; x |= 1; }
|
711
|
+
else { p1 = PA + *b; }
|
712
|
+
} else if(r < 0) {
|
713
|
+
if(x & 2) { do { *a-- = *c, *c-- = *a; } while(*c < 0); x ^= 2; }
|
714
|
+
*a-- = *c, *c-- = *a;
|
715
|
+
if(c < first) {
|
716
|
+
while(buf < b) { *a-- = *b, *b-- = *a; }
|
717
|
+
*a = *b, *b = t;
|
718
|
+
break;
|
719
|
+
}
|
720
|
+
if(*c < 0) { p2 = PA + ~*c; x |= 2; }
|
721
|
+
else { p2 = PA + *c; }
|
722
|
+
} else {
|
723
|
+
if(x & 1) { do { *a-- = *b, *b-- = *a; } while(*b < 0); x ^= 1; }
|
724
|
+
*a-- = ~*b;
|
725
|
+
if(b <= buf) { *buf = t; break; }
|
726
|
+
*b-- = *a;
|
727
|
+
if(x & 2) { do { *a-- = *c, *c-- = *a; } while(*c < 0); x ^= 2; }
|
728
|
+
*a-- = *c, *c-- = *a;
|
729
|
+
if(c < first) {
|
730
|
+
while(buf < b) { *a-- = *b, *b-- = *a; }
|
731
|
+
*a = *b, *b = t;
|
732
|
+
break;
|
733
|
+
}
|
734
|
+
if(*b < 0) { p1 = PA + ~*b; x |= 1; }
|
735
|
+
else { p1 = PA + *b; }
|
736
|
+
if(*c < 0) { p2 = PA + ~*c; x |= 2; }
|
737
|
+
else { p2 = PA + *c; }
|
738
|
+
}
|
739
|
+
}
|
740
|
+
}
|
741
|
+
|
742
|
+
/* D&C based merge. */
|
743
|
+
static
|
744
|
+
void
|
745
|
+
ss_swapmerge(const unsigned char *T, const int *PA,
|
746
|
+
int *first, int *middle, int *last,
|
747
|
+
int *buf, int bufsize, int depth) {
|
748
|
+
#define STACK_SIZE SS_SMERGE_STACKSIZE
|
749
|
+
#define GETIDX(a) ((0 <= (a)) ? (a) : (~(a)))
|
750
|
+
#define MERGE_CHECK(a, b, c)\
|
751
|
+
do {\
|
752
|
+
if(((c) & 1) ||\
|
753
|
+
(((c) & 2) && (ss_compare(T, PA + GETIDX(*((a) - 1)), PA + *(a), depth) == 0))) {\
|
754
|
+
*(a) = ~*(a);\
|
755
|
+
}\
|
756
|
+
if(((c) & 4) && ((ss_compare(T, PA + GETIDX(*((b) - 1)), PA + *(b), depth) == 0))) {\
|
757
|
+
*(b) = ~*(b);\
|
758
|
+
}\
|
759
|
+
} while(0)
|
760
|
+
struct { int *a, *b, *c; int d; } stack[STACK_SIZE];
|
761
|
+
int *l, *r, *lm, *rm;
|
762
|
+
int m, len, half;
|
763
|
+
int ssize;
|
764
|
+
int check, next;
|
765
|
+
|
766
|
+
for(check = 0, ssize = 0;;) {
|
767
|
+
if((last - middle) <= bufsize) {
|
768
|
+
if((first < middle) && (middle < last)) {
|
769
|
+
ss_mergebackward(T, PA, first, middle, last, buf, depth);
|
770
|
+
}
|
771
|
+
MERGE_CHECK(first, last, check);
|
772
|
+
STACK_POP(first, middle, last, check);
|
773
|
+
continue;
|
774
|
+
}
|
775
|
+
|
776
|
+
if((middle - first) <= bufsize) {
|
777
|
+
if(first < middle) {
|
778
|
+
ss_mergeforward(T, PA, first, middle, last, buf, depth);
|
779
|
+
}
|
780
|
+
MERGE_CHECK(first, last, check);
|
781
|
+
STACK_POP(first, middle, last, check);
|
782
|
+
continue;
|
783
|
+
}
|
784
|
+
|
785
|
+
for(m = 0, len = MIN(middle - first, last - middle), half = len >> 1;
|
786
|
+
0 < len;
|
787
|
+
len = half, half >>= 1) {
|
788
|
+
if(ss_compare(T, PA + GETIDX(*(middle + m + half)),
|
789
|
+
PA + GETIDX(*(middle - m - half - 1)), depth) < 0) {
|
790
|
+
m += half + 1;
|
791
|
+
half -= (len & 1) ^ 1;
|
792
|
+
}
|
793
|
+
}
|
794
|
+
|
795
|
+
if(0 < m) {
|
796
|
+
lm = middle - m, rm = middle + m;
|
797
|
+
ss_blockswap(lm, middle, m);
|
798
|
+
l = r = middle, next = 0;
|
799
|
+
if(rm < last) {
|
800
|
+
if(*rm < 0) {
|
801
|
+
*rm = ~*rm;
|
802
|
+
if(first < lm) { for(; *--l < 0;) { } next |= 4; }
|
803
|
+
next |= 1;
|
804
|
+
} else if(first < lm) {
|
805
|
+
for(; *r < 0; ++r) { }
|
806
|
+
next |= 2;
|
807
|
+
}
|
808
|
+
}
|
809
|
+
|
810
|
+
if((l - first) <= (last - r)) {
|
811
|
+
STACK_PUSH(r, rm, last, (next & 3) | (check & 4));
|
812
|
+
middle = lm, last = l, check = (check & 3) | (next & 4);
|
813
|
+
} else {
|
814
|
+
if((next & 2) && (r == middle)) { next ^= 6; }
|
815
|
+
STACK_PUSH(first, lm, l, (check & 3) | (next & 4));
|
816
|
+
first = r, middle = rm, check = (next & 3) | (check & 4);
|
817
|
+
}
|
818
|
+
} else {
|
819
|
+
if(ss_compare(T, PA + GETIDX(*(middle - 1)), PA + *middle, depth) == 0) {
|
820
|
+
*middle = ~*middle;
|
821
|
+
}
|
822
|
+
MERGE_CHECK(first, last, check);
|
823
|
+
STACK_POP(first, middle, last, check);
|
824
|
+
}
|
825
|
+
}
|
826
|
+
#undef STACK_SIZE
|
827
|
+
}
|
828
|
+
|
829
|
+
#endif /* SS_BLOCKSIZE != 0 */
|
830
|
+
|
831
|
+
|
832
|
+
/*---------------------------------------------------------------------------*/
|
833
|
+
|
834
|
+
/* Substring sort */
|
835
|
+
static
|
836
|
+
void
|
837
|
+
sssort(const unsigned char *T, const int *PA,
|
838
|
+
int *first, int *last,
|
839
|
+
int *buf, int bufsize,
|
840
|
+
int depth, int n, int lastsuffix) {
|
841
|
+
int *a;
|
842
|
+
#if SS_BLOCKSIZE != 0
|
843
|
+
int *b, *middle, *curbuf;
|
844
|
+
int j, k, curbufsize, limit;
|
845
|
+
#endif
|
846
|
+
int i;
|
847
|
+
|
848
|
+
if(lastsuffix != 0) { ++first; }
|
849
|
+
|
850
|
+
#if SS_BLOCKSIZE == 0
|
851
|
+
ss_mintrosort(T, PA, first, last, depth);
|
852
|
+
#else
|
853
|
+
if((bufsize < SS_BLOCKSIZE) &&
|
854
|
+
(bufsize < (last - first)) &&
|
855
|
+
(bufsize < (limit = ss_isqrt(last - first)))) {
|
856
|
+
if(SS_BLOCKSIZE < limit) { limit = SS_BLOCKSIZE; }
|
857
|
+
buf = middle = last - limit, bufsize = limit;
|
858
|
+
} else {
|
859
|
+
middle = last, limit = 0;
|
860
|
+
}
|
861
|
+
for(a = first, i = 0; SS_BLOCKSIZE < (middle - a); a += SS_BLOCKSIZE, ++i) {
|
862
|
+
#if SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE
|
863
|
+
ss_mintrosort(T, PA, a, a + SS_BLOCKSIZE, depth);
|
864
|
+
#elif 1 < SS_BLOCKSIZE
|
865
|
+
ss_insertionsort(T, PA, a, a + SS_BLOCKSIZE, depth);
|
866
|
+
#endif
|
867
|
+
curbufsize = last - (a + SS_BLOCKSIZE);
|
868
|
+
curbuf = a + SS_BLOCKSIZE;
|
869
|
+
if(curbufsize <= bufsize) { curbufsize = bufsize, curbuf = buf; }
|
870
|
+
for(b = a, k = SS_BLOCKSIZE, j = i; j & 1; b -= k, k <<= 1, j >>= 1) {
|
871
|
+
ss_swapmerge(T, PA, b - k, b, b + k, curbuf, curbufsize, depth);
|
872
|
+
}
|
873
|
+
}
|
874
|
+
#if SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE
|
875
|
+
ss_mintrosort(T, PA, a, middle, depth);
|
876
|
+
#elif 1 < SS_BLOCKSIZE
|
877
|
+
ss_insertionsort(T, PA, a, middle, depth);
|
878
|
+
#endif
|
879
|
+
for(k = SS_BLOCKSIZE; i != 0; k <<= 1, i >>= 1) {
|
880
|
+
if(i & 1) {
|
881
|
+
ss_swapmerge(T, PA, a - k, a, middle, buf, bufsize, depth);
|
882
|
+
a -= k;
|
883
|
+
}
|
884
|
+
}
|
885
|
+
if(limit != 0) {
|
886
|
+
#if SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE
|
887
|
+
ss_mintrosort(T, PA, middle, last, depth);
|
888
|
+
#elif 1 < SS_BLOCKSIZE
|
889
|
+
ss_insertionsort(T, PA, middle, last, depth);
|
890
|
+
#endif
|
891
|
+
ss_inplacemerge(T, PA, first, middle, last, depth);
|
892
|
+
}
|
893
|
+
#endif
|
894
|
+
|
895
|
+
if(lastsuffix != 0) {
|
896
|
+
/* Insert last type B* suffix. */
|
897
|
+
int PAi[2]; PAi[0] = PA[*(first - 1)], PAi[1] = n - 2;
|
898
|
+
for(a = first, i = *(first - 1);
|
899
|
+
(a < last) && ((*a < 0) || (0 < ss_compare(T, &(PAi[0]), PA + *a, depth)));
|
900
|
+
++a) {
|
901
|
+
*(a - 1) = *a;
|
902
|
+
}
|
903
|
+
*(a - 1) = i;
|
904
|
+
}
|
905
|
+
}
|
906
|
+
|
907
|
+
|
908
|
+
/*---------------------------------------------------------------------------*/
|
909
|
+
|
910
|
+
static INLINE
|
911
|
+
int
|
912
|
+
tr_ilg(int n) {
|
913
|
+
return (n & 0xffff0000) ?
|
914
|
+
((n & 0xff000000) ?
|
915
|
+
24 + lg_table[(n >> 24) & 0xff] :
|
916
|
+
16 + lg_table[(n >> 16) & 0xff]) :
|
917
|
+
((n & 0x0000ff00) ?
|
918
|
+
8 + lg_table[(n >> 8) & 0xff] :
|
919
|
+
0 + lg_table[(n >> 0) & 0xff]);
|
920
|
+
}
|
921
|
+
|
922
|
+
|
923
|
+
/*---------------------------------------------------------------------------*/
|
924
|
+
|
925
|
+
/* Simple insertionsort for small size groups. */
|
926
|
+
static
|
927
|
+
void
|
928
|
+
tr_insertionsort(const int *ISAd, int *first, int *last) {
|
929
|
+
int *a, *b;
|
930
|
+
int t, r;
|
931
|
+
|
932
|
+
for(a = first + 1; a < last; ++a) {
|
933
|
+
for(t = *a, b = a - 1; 0 > (r = ISAd[t] - ISAd[*b]);) {
|
934
|
+
do { *(b + 1) = *b; } while((first <= --b) && (*b < 0));
|
935
|
+
if(b < first) { break; }
|
936
|
+
}
|
937
|
+
if(r == 0) { *b = ~*b; }
|
938
|
+
*(b + 1) = t;
|
939
|
+
}
|
940
|
+
}
|
941
|
+
|
942
|
+
|
943
|
+
/*---------------------------------------------------------------------------*/
|
944
|
+
|
945
|
+
static INLINE
|
946
|
+
void
|
947
|
+
tr_fixdown(const int *ISAd, int *SA, int i, int size) {
|
948
|
+
int j, k;
|
949
|
+
int v;
|
950
|
+
int c, d, e;
|
951
|
+
|
952
|
+
for(v = SA[i], c = ISAd[v]; (j = 2 * i + 1) < size; SA[i] = SA[k], i = k) {
|
953
|
+
d = ISAd[SA[k = j++]];
|
954
|
+
if(d < (e = ISAd[SA[j]])) { k = j; d = e; }
|
955
|
+
if(d <= c) { break; }
|
956
|
+
}
|
957
|
+
SA[i] = v;
|
958
|
+
}
|
959
|
+
|
960
|
+
/* Simple top-down heapsort. */
|
961
|
+
static
|
962
|
+
void
|
963
|
+
tr_heapsort(const int *ISAd, int *SA, int size) {
|
964
|
+
int i, m;
|
965
|
+
int t;
|
966
|
+
|
967
|
+
m = size;
|
968
|
+
if((size % 2) == 0) {
|
969
|
+
m--;
|
970
|
+
if(ISAd[SA[m / 2]] < ISAd[SA[m]]) { SWAP(SA[m], SA[m / 2]); }
|
971
|
+
}
|
972
|
+
|
973
|
+
for(i = m / 2 - 1; 0 <= i; --i) { tr_fixdown(ISAd, SA, i, m); }
|
974
|
+
if((size % 2) == 0) { SWAP(SA[0], SA[m]); tr_fixdown(ISAd, SA, 0, m); }
|
975
|
+
for(i = m - 1; 0 < i; --i) {
|
976
|
+
t = SA[0], SA[0] = SA[i];
|
977
|
+
tr_fixdown(ISAd, SA, 0, i);
|
978
|
+
SA[i] = t;
|
979
|
+
}
|
980
|
+
}
|
981
|
+
|
982
|
+
|
983
|
+
/*---------------------------------------------------------------------------*/
|
984
|
+
|
985
|
+
/* Returns the median of three elements. */
|
986
|
+
static INLINE
|
987
|
+
int *
|
988
|
+
tr_median3(const int *ISAd, int *v1, int *v2, int *v3) {
|
989
|
+
int *t;
|
990
|
+
if(ISAd[*v1] > ISAd[*v2]) { SWAP(v1, v2); }
|
991
|
+
if(ISAd[*v2] > ISAd[*v3]) {
|
992
|
+
if(ISAd[*v1] > ISAd[*v3]) { return v1; }
|
993
|
+
else { return v3; }
|
994
|
+
}
|
995
|
+
return v2;
|
996
|
+
}
|
997
|
+
|
998
|
+
/* Returns the median of five elements. */
|
999
|
+
static INLINE
|
1000
|
+
int *
|
1001
|
+
tr_median5(const int *ISAd,
|
1002
|
+
int *v1, int *v2, int *v3, int *v4, int *v5) {
|
1003
|
+
int *t;
|
1004
|
+
if(ISAd[*v2] > ISAd[*v3]) { SWAP(v2, v3); }
|
1005
|
+
if(ISAd[*v4] > ISAd[*v5]) { SWAP(v4, v5); }
|
1006
|
+
if(ISAd[*v2] > ISAd[*v4]) { SWAP(v2, v4); SWAP(v3, v5); }
|
1007
|
+
if(ISAd[*v1] > ISAd[*v3]) { SWAP(v1, v3); }
|
1008
|
+
if(ISAd[*v1] > ISAd[*v4]) { SWAP(v1, v4); SWAP(v3, v5); }
|
1009
|
+
if(ISAd[*v3] > ISAd[*v4]) { return v4; }
|
1010
|
+
return v3;
|
1011
|
+
}
|
1012
|
+
|
1013
|
+
/* Returns the pivot element. */
|
1014
|
+
static INLINE
|
1015
|
+
int *
|
1016
|
+
tr_pivot(const int *ISAd, int *first, int *last) {
|
1017
|
+
int *middle;
|
1018
|
+
int t;
|
1019
|
+
|
1020
|
+
t = last - first;
|
1021
|
+
middle = first + t / 2;
|
1022
|
+
|
1023
|
+
if(t <= 512) {
|
1024
|
+
if(t <= 32) {
|
1025
|
+
return tr_median3(ISAd, first, middle, last - 1);
|
1026
|
+
} else {
|
1027
|
+
t >>= 2;
|
1028
|
+
return tr_median5(ISAd, first, first + t, middle, last - 1 - t, last - 1);
|
1029
|
+
}
|
1030
|
+
}
|
1031
|
+
t >>= 3;
|
1032
|
+
first = tr_median3(ISAd, first, first + t, first + (t << 1));
|
1033
|
+
middle = tr_median3(ISAd, middle - t, middle, middle + t);
|
1034
|
+
last = tr_median3(ISAd, last - 1 - (t << 1), last - 1 - t, last - 1);
|
1035
|
+
return tr_median3(ISAd, first, middle, last);
|
1036
|
+
}
|
1037
|
+
|
1038
|
+
|
1039
|
+
/*---------------------------------------------------------------------------*/
|
1040
|
+
|
1041
|
+
typedef struct _trbudget_t trbudget_t;
|
1042
|
+
struct _trbudget_t {
|
1043
|
+
int chance;
|
1044
|
+
int remain;
|
1045
|
+
int incval;
|
1046
|
+
int count;
|
1047
|
+
};
|
1048
|
+
|
1049
|
+
static INLINE
|
1050
|
+
void
|
1051
|
+
trbudget_init(trbudget_t *budget, int chance, int incval) {
|
1052
|
+
budget->chance = chance;
|
1053
|
+
budget->remain = budget->incval = incval;
|
1054
|
+
}
|
1055
|
+
|
1056
|
+
static INLINE
|
1057
|
+
int
|
1058
|
+
trbudget_check(trbudget_t *budget, int size) {
|
1059
|
+
if(size <= budget->remain) { budget->remain -= size; return 1; }
|
1060
|
+
if(budget->chance == 0) { budget->count += size; return 0; }
|
1061
|
+
budget->remain += budget->incval - size;
|
1062
|
+
budget->chance -= 1;
|
1063
|
+
return 1;
|
1064
|
+
}
|
1065
|
+
|
1066
|
+
|
1067
|
+
/*---------------------------------------------------------------------------*/
|
1068
|
+
|
1069
|
+
static INLINE
|
1070
|
+
void
|
1071
|
+
tr_partition(const int *ISAd,
|
1072
|
+
int *first, int *middle, int *last,
|
1073
|
+
int **pa, int **pb, int v) {
|
1074
|
+
int *a, *b, *c, *d, *e, *f;
|
1075
|
+
int t, s;
|
1076
|
+
int x = 0;
|
1077
|
+
|
1078
|
+
for(b = middle - 1; (++b < last) && ((x = ISAd[*b]) == v);) { }
|
1079
|
+
if(((a = b) < last) && (x < v)) {
|
1080
|
+
for(; (++b < last) && ((x = ISAd[*b]) <= v);) {
|
1081
|
+
if(x == v) { SWAP(*b, *a); ++a; }
|
1082
|
+
}
|
1083
|
+
}
|
1084
|
+
for(c = last; (b < --c) && ((x = ISAd[*c]) == v);) { }
|
1085
|
+
if((b < (d = c)) && (x > v)) {
|
1086
|
+
for(; (b < --c) && ((x = ISAd[*c]) >= v);) {
|
1087
|
+
if(x == v) { SWAP(*c, *d); --d; }
|
1088
|
+
}
|
1089
|
+
}
|
1090
|
+
for(; b < c;) {
|
1091
|
+
SWAP(*b, *c);
|
1092
|
+
for(; (++b < c) && ((x = ISAd[*b]) <= v);) {
|
1093
|
+
if(x == v) { SWAP(*b, *a); ++a; }
|
1094
|
+
}
|
1095
|
+
for(; (b < --c) && ((x = ISAd[*c]) >= v);) {
|
1096
|
+
if(x == v) { SWAP(*c, *d); --d; }
|
1097
|
+
}
|
1098
|
+
}
|
1099
|
+
|
1100
|
+
if(a <= d) {
|
1101
|
+
c = b - 1;
|
1102
|
+
if((s = a - first) > (t = b - a)) { s = t; }
|
1103
|
+
for(e = first, f = b - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); }
|
1104
|
+
if((s = d - c) > (t = last - d - 1)) { s = t; }
|
1105
|
+
for(e = b, f = last - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); }
|
1106
|
+
first += (b - a), last -= (d - c);
|
1107
|
+
}
|
1108
|
+
*pa = first, *pb = last;
|
1109
|
+
}
|
1110
|
+
|
1111
|
+
static
|
1112
|
+
void
|
1113
|
+
tr_copy(int *ISA, const int *SA,
|
1114
|
+
int *first, int *a, int *b, int *last,
|
1115
|
+
int depth) {
|
1116
|
+
/* sort suffixes of middle partition
|
1117
|
+
by using sorted order of suffixes of left and right partition. */
|
1118
|
+
int *c, *d, *e;
|
1119
|
+
int s, v;
|
1120
|
+
|
1121
|
+
v = b - SA - 1;
|
1122
|
+
for(c = first, d = a - 1; c <= d; ++c) {
|
1123
|
+
if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
|
1124
|
+
*++d = s;
|
1125
|
+
ISA[s] = d - SA;
|
1126
|
+
}
|
1127
|
+
}
|
1128
|
+
for(c = last - 1, e = d + 1, d = b; e < d; --c) {
|
1129
|
+
if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
|
1130
|
+
*--d = s;
|
1131
|
+
ISA[s] = d - SA;
|
1132
|
+
}
|
1133
|
+
}
|
1134
|
+
}
|
1135
|
+
|
1136
|
+
static
|
1137
|
+
void
|
1138
|
+
tr_partialcopy(int *ISA, const int *SA,
|
1139
|
+
int *first, int *a, int *b, int *last,
|
1140
|
+
int depth) {
|
1141
|
+
int *c, *d, *e;
|
1142
|
+
int s, v;
|
1143
|
+
int rank, lastrank, newrank = -1;
|
1144
|
+
|
1145
|
+
v = b - SA - 1;
|
1146
|
+
lastrank = -1;
|
1147
|
+
for(c = first, d = a - 1; c <= d; ++c) {
|
1148
|
+
if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
|
1149
|
+
*++d = s;
|
1150
|
+
rank = ISA[s + depth];
|
1151
|
+
if(lastrank != rank) { lastrank = rank; newrank = d - SA; }
|
1152
|
+
ISA[s] = newrank;
|
1153
|
+
}
|
1154
|
+
}
|
1155
|
+
|
1156
|
+
lastrank = -1;
|
1157
|
+
for(e = d; first <= e; --e) {
|
1158
|
+
rank = ISA[*e];
|
1159
|
+
if(lastrank != rank) { lastrank = rank; newrank = e - SA; }
|
1160
|
+
if(newrank != rank) { ISA[*e] = newrank; }
|
1161
|
+
}
|
1162
|
+
|
1163
|
+
lastrank = -1;
|
1164
|
+
for(c = last - 1, e = d + 1, d = b; e < d; --c) {
|
1165
|
+
if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
|
1166
|
+
*--d = s;
|
1167
|
+
rank = ISA[s + depth];
|
1168
|
+
if(lastrank != rank) { lastrank = rank; newrank = d - SA; }
|
1169
|
+
ISA[s] = newrank;
|
1170
|
+
}
|
1171
|
+
}
|
1172
|
+
}
|
1173
|
+
|
1174
|
+
static
|
1175
|
+
void
|
1176
|
+
tr_introsort(int *ISA, const int *ISAd,
|
1177
|
+
int *SA, int *first, int *last,
|
1178
|
+
trbudget_t *budget) {
|
1179
|
+
#define STACK_SIZE TR_STACKSIZE
|
1180
|
+
struct { const int *a; int *b, *c; int d, e; }stack[STACK_SIZE];
|
1181
|
+
int *a, *b, *c;
|
1182
|
+
int t;
|
1183
|
+
int v, x = 0;
|
1184
|
+
int incr = ISAd - ISA;
|
1185
|
+
int limit, next;
|
1186
|
+
int ssize, trlink = -1;
|
1187
|
+
|
1188
|
+
for(ssize = 0, limit = tr_ilg(last - first);;) {
|
1189
|
+
|
1190
|
+
if(limit < 0) {
|
1191
|
+
if(limit == -1) {
|
1192
|
+
/* tandem repeat partition */
|
1193
|
+
tr_partition(ISAd - incr, first, first, last, &a, &b, last - SA - 1);
|
1194
|
+
|
1195
|
+
/* update ranks */
|
1196
|
+
if(a < last) {
|
1197
|
+
for(c = first, v = a - SA - 1; c < a; ++c) { ISA[*c] = v; }
|
1198
|
+
}
|
1199
|
+
if(b < last) {
|
1200
|
+
for(c = a, v = b - SA - 1; c < b; ++c) { ISA[*c] = v; }
|
1201
|
+
}
|
1202
|
+
|
1203
|
+
/* push */
|
1204
|
+
if(1 < (b - a)) {
|
1205
|
+
STACK_PUSH5(NULL, a, b, 0, 0);
|
1206
|
+
STACK_PUSH5(ISAd - incr, first, last, -2, trlink);
|
1207
|
+
trlink = ssize - 2;
|
1208
|
+
}
|
1209
|
+
if((a - first) <= (last - b)) {
|
1210
|
+
if(1 < (a - first)) {
|
1211
|
+
STACK_PUSH5(ISAd, b, last, tr_ilg(last - b), trlink);
|
1212
|
+
last = a, limit = tr_ilg(a - first);
|
1213
|
+
} else if(1 < (last - b)) {
|
1214
|
+
first = b, limit = tr_ilg(last - b);
|
1215
|
+
} else {
|
1216
|
+
STACK_POP5(ISAd, first, last, limit, trlink);
|
1217
|
+
}
|
1218
|
+
} else {
|
1219
|
+
if(1 < (last - b)) {
|
1220
|
+
STACK_PUSH5(ISAd, first, a, tr_ilg(a - first), trlink);
|
1221
|
+
first = b, limit = tr_ilg(last - b);
|
1222
|
+
} else if(1 < (a - first)) {
|
1223
|
+
last = a, limit = tr_ilg(a - first);
|
1224
|
+
} else {
|
1225
|
+
STACK_POP5(ISAd, first, last, limit, trlink);
|
1226
|
+
}
|
1227
|
+
}
|
1228
|
+
} else if(limit == -2) {
|
1229
|
+
/* tandem repeat copy */
|
1230
|
+
a = stack[--ssize].b, b = stack[ssize].c;
|
1231
|
+
if(stack[ssize].d == 0) {
|
1232
|
+
tr_copy(ISA, SA, first, a, b, last, ISAd - ISA);
|
1233
|
+
} else {
|
1234
|
+
if(0 <= trlink) { stack[trlink].d = -1; }
|
1235
|
+
tr_partialcopy(ISA, SA, first, a, b, last, ISAd - ISA);
|
1236
|
+
}
|
1237
|
+
STACK_POP5(ISAd, first, last, limit, trlink);
|
1238
|
+
} else {
|
1239
|
+
/* sorted partition */
|
1240
|
+
if(0 <= *first) {
|
1241
|
+
a = first;
|
1242
|
+
do { ISA[*a] = a - SA; } while((++a < last) && (0 <= *a));
|
1243
|
+
first = a;
|
1244
|
+
}
|
1245
|
+
if(first < last) {
|
1246
|
+
a = first; do { *a = ~*a; } while(*++a < 0);
|
1247
|
+
next = (ISA[*a] != ISAd[*a]) ? tr_ilg(a - first + 1) : -1;
|
1248
|
+
if(++a < last) { for(b = first, v = a - SA - 1; b < a; ++b) { ISA[*b] = v; } }
|
1249
|
+
|
1250
|
+
/* push */
|
1251
|
+
if(trbudget_check(budget, a - first)) {
|
1252
|
+
if((a - first) <= (last - a)) {
|
1253
|
+
STACK_PUSH5(ISAd, a, last, -3, trlink);
|
1254
|
+
ISAd += incr, last = a, limit = next;
|
1255
|
+
} else {
|
1256
|
+
if(1 < (last - a)) {
|
1257
|
+
STACK_PUSH5(ISAd + incr, first, a, next, trlink);
|
1258
|
+
first = a, limit = -3;
|
1259
|
+
} else {
|
1260
|
+
ISAd += incr, last = a, limit = next;
|
1261
|
+
}
|
1262
|
+
}
|
1263
|
+
} else {
|
1264
|
+
if(0 <= trlink) { stack[trlink].d = -1; }
|
1265
|
+
if(1 < (last - a)) {
|
1266
|
+
first = a, limit = -3;
|
1267
|
+
} else {
|
1268
|
+
STACK_POP5(ISAd, first, last, limit, trlink);
|
1269
|
+
}
|
1270
|
+
}
|
1271
|
+
} else {
|
1272
|
+
STACK_POP5(ISAd, first, last, limit, trlink);
|
1273
|
+
}
|
1274
|
+
}
|
1275
|
+
continue;
|
1276
|
+
}
|
1277
|
+
|
1278
|
+
if((last - first) <= TR_INSERTIONSORT_THRESHOLD) {
|
1279
|
+
tr_insertionsort(ISAd, first, last);
|
1280
|
+
limit = -3;
|
1281
|
+
continue;
|
1282
|
+
}
|
1283
|
+
|
1284
|
+
if(limit-- == 0) {
|
1285
|
+
tr_heapsort(ISAd, first, last - first);
|
1286
|
+
for(a = last - 1; first < a; a = b) {
|
1287
|
+
for(x = ISAd[*a], b = a - 1; (first <= b) && (ISAd[*b] == x); --b) { *b = ~*b; }
|
1288
|
+
}
|
1289
|
+
limit = -3;
|
1290
|
+
continue;
|
1291
|
+
}
|
1292
|
+
|
1293
|
+
/* choose pivot */
|
1294
|
+
a = tr_pivot(ISAd, first, last);
|
1295
|
+
SWAP(*first, *a);
|
1296
|
+
v = ISAd[*first];
|
1297
|
+
|
1298
|
+
/* partition */
|
1299
|
+
tr_partition(ISAd, first, first + 1, last, &a, &b, v);
|
1300
|
+
if((last - first) != (b - a)) {
|
1301
|
+
next = (ISA[*a] != v) ? tr_ilg(b - a) : -1;
|
1302
|
+
|
1303
|
+
/* update ranks */
|
1304
|
+
for(c = first, v = a - SA - 1; c < a; ++c) { ISA[*c] = v; }
|
1305
|
+
if(b < last) { for(c = a, v = b - SA - 1; c < b; ++c) { ISA[*c] = v; } }
|
1306
|
+
|
1307
|
+
/* push */
|
1308
|
+
if((1 < (b - a)) && (trbudget_check(budget, b - a))) {
|
1309
|
+
if((a - first) <= (last - b)) {
|
1310
|
+
if((last - b) <= (b - a)) {
|
1311
|
+
if(1 < (a - first)) {
|
1312
|
+
STACK_PUSH5(ISAd + incr, a, b, next, trlink);
|
1313
|
+
STACK_PUSH5(ISAd, b, last, limit, trlink);
|
1314
|
+
last = a;
|
1315
|
+
} else if(1 < (last - b)) {
|
1316
|
+
STACK_PUSH5(ISAd + incr, a, b, next, trlink);
|
1317
|
+
first = b;
|
1318
|
+
} else {
|
1319
|
+
ISAd += incr, first = a, last = b, limit = next;
|
1320
|
+
}
|
1321
|
+
} else if((a - first) <= (b - a)) {
|
1322
|
+
if(1 < (a - first)) {
|
1323
|
+
STACK_PUSH5(ISAd, b, last, limit, trlink);
|
1324
|
+
STACK_PUSH5(ISAd + incr, a, b, next, trlink);
|
1325
|
+
last = a;
|
1326
|
+
} else {
|
1327
|
+
STACK_PUSH5(ISAd, b, last, limit, trlink);
|
1328
|
+
ISAd += incr, first = a, last = b, limit = next;
|
1329
|
+
}
|
1330
|
+
} else {
|
1331
|
+
STACK_PUSH5(ISAd, b, last, limit, trlink);
|
1332
|
+
STACK_PUSH5(ISAd, first, a, limit, trlink);
|
1333
|
+
ISAd += incr, first = a, last = b, limit = next;
|
1334
|
+
}
|
1335
|
+
} else {
|
1336
|
+
if((a - first) <= (b - a)) {
|
1337
|
+
if(1 < (last - b)) {
|
1338
|
+
STACK_PUSH5(ISAd + incr, a, b, next, trlink);
|
1339
|
+
STACK_PUSH5(ISAd, first, a, limit, trlink);
|
1340
|
+
first = b;
|
1341
|
+
} else if(1 < (a - first)) {
|
1342
|
+
STACK_PUSH5(ISAd + incr, a, b, next, trlink);
|
1343
|
+
last = a;
|
1344
|
+
} else {
|
1345
|
+
ISAd += incr, first = a, last = b, limit = next;
|
1346
|
+
}
|
1347
|
+
} else if((last - b) <= (b - a)) {
|
1348
|
+
if(1 < (last - b)) {
|
1349
|
+
STACK_PUSH5(ISAd, first, a, limit, trlink);
|
1350
|
+
STACK_PUSH5(ISAd + incr, a, b, next, trlink);
|
1351
|
+
first = b;
|
1352
|
+
} else {
|
1353
|
+
STACK_PUSH5(ISAd, first, a, limit, trlink);
|
1354
|
+
ISAd += incr, first = a, last = b, limit = next;
|
1355
|
+
}
|
1356
|
+
} else {
|
1357
|
+
STACK_PUSH5(ISAd, first, a, limit, trlink);
|
1358
|
+
STACK_PUSH5(ISAd, b, last, limit, trlink);
|
1359
|
+
ISAd += incr, first = a, last = b, limit = next;
|
1360
|
+
}
|
1361
|
+
}
|
1362
|
+
} else {
|
1363
|
+
if((1 < (b - a)) && (0 <= trlink)) { stack[trlink].d = -1; }
|
1364
|
+
if((a - first) <= (last - b)) {
|
1365
|
+
if(1 < (a - first)) {
|
1366
|
+
STACK_PUSH5(ISAd, b, last, limit, trlink);
|
1367
|
+
last = a;
|
1368
|
+
} else if(1 < (last - b)) {
|
1369
|
+
first = b;
|
1370
|
+
} else {
|
1371
|
+
STACK_POP5(ISAd, first, last, limit, trlink);
|
1372
|
+
}
|
1373
|
+
} else {
|
1374
|
+
if(1 < (last - b)) {
|
1375
|
+
STACK_PUSH5(ISAd, first, a, limit, trlink);
|
1376
|
+
first = b;
|
1377
|
+
} else if(1 < (a - first)) {
|
1378
|
+
last = a;
|
1379
|
+
} else {
|
1380
|
+
STACK_POP5(ISAd, first, last, limit, trlink);
|
1381
|
+
}
|
1382
|
+
}
|
1383
|
+
}
|
1384
|
+
} else {
|
1385
|
+
if(trbudget_check(budget, last - first)) {
|
1386
|
+
limit = tr_ilg(last - first), ISAd += incr;
|
1387
|
+
} else {
|
1388
|
+
if(0 <= trlink) { stack[trlink].d = -1; }
|
1389
|
+
STACK_POP5(ISAd, first, last, limit, trlink);
|
1390
|
+
}
|
1391
|
+
}
|
1392
|
+
}
|
1393
|
+
#undef STACK_SIZE
|
1394
|
+
}
|
1395
|
+
|
1396
|
+
|
1397
|
+
|
1398
|
+
/*---------------------------------------------------------------------------*/
|
1399
|
+
|
1400
|
+
/* Tandem repeat sort */
|
1401
|
+
static
|
1402
|
+
void
|
1403
|
+
trsort(int *ISA, int *SA, int n, int depth) {
|
1404
|
+
int *ISAd;
|
1405
|
+
int *first, *last;
|
1406
|
+
trbudget_t budget;
|
1407
|
+
int t, skip, unsorted;
|
1408
|
+
|
1409
|
+
trbudget_init(&budget, tr_ilg(n) * 2 / 3, n);
|
1410
|
+
/* trbudget_init(&budget, tr_ilg(n) * 3 / 4, n); */
|
1411
|
+
for(ISAd = ISA + depth; -n < *SA; ISAd += ISAd - ISA) {
|
1412
|
+
first = SA;
|
1413
|
+
skip = 0;
|
1414
|
+
unsorted = 0;
|
1415
|
+
do {
|
1416
|
+
if((t = *first) < 0) { first -= t; skip += t; }
|
1417
|
+
else {
|
1418
|
+
if(skip != 0) { *(first + skip) = skip; skip = 0; }
|
1419
|
+
last = SA + ISA[t] + 1;
|
1420
|
+
if(1 < (last - first)) {
|
1421
|
+
budget.count = 0;
|
1422
|
+
tr_introsort(ISA, ISAd, SA, first, last, &budget);
|
1423
|
+
if(budget.count != 0) { unsorted += budget.count; }
|
1424
|
+
else { skip = first - last; }
|
1425
|
+
} else if((last - first) == 1) {
|
1426
|
+
skip = -1;
|
1427
|
+
}
|
1428
|
+
first = last;
|
1429
|
+
}
|
1430
|
+
} while(first < (SA + n));
|
1431
|
+
if(skip != 0) { *(first + skip) = skip; }
|
1432
|
+
if(unsorted == 0) { break; }
|
1433
|
+
}
|
1434
|
+
}
|
1435
|
+
|
1436
|
+
|
1437
|
+
/*---------------------------------------------------------------------------*/
|
1438
|
+
|
1439
|
+
/* Sorts suffixes of type B*. */
|
1440
|
+
static
|
1441
|
+
int
|
1442
|
+
sort_typeBstar(const unsigned char *T, int *SA,
|
1443
|
+
int *bucket_A, int *bucket_B,
|
1444
|
+
int n, int openMP) {
|
1445
|
+
int *PAb, *ISAb, *buf;
|
1446
|
+
#ifdef LIBBSC_OPENMP
|
1447
|
+
int *curbuf;
|
1448
|
+
int l;
|
1449
|
+
#endif
|
1450
|
+
int i, j, k, t, m, bufsize;
|
1451
|
+
int c0, c1;
|
1452
|
+
#ifdef LIBBSC_OPENMP
|
1453
|
+
int d0, d1;
|
1454
|
+
#endif
|
1455
|
+
(void)openMP;
|
1456
|
+
|
1457
|
+
/* Initialize bucket arrays. */
|
1458
|
+
for(i = 0; i < BUCKET_A_SIZE; ++i) { bucket_A[i] = 0; }
|
1459
|
+
for(i = 0; i < BUCKET_B_SIZE; ++i) { bucket_B[i] = 0; }
|
1460
|
+
|
1461
|
+
/* Count the number of occurrences of the first one or two characters of each
|
1462
|
+
type A, B and B* suffix. Moreover, store the beginning position of all
|
1463
|
+
type B* suffixes into the array SA. */
|
1464
|
+
for(i = n - 1, m = n, c0 = T[n - 1]; 0 <= i;) {
|
1465
|
+
/* type A suffix. */
|
1466
|
+
do { ++BUCKET_A(c1 = c0); } while((0 <= --i) && ((c0 = T[i]) >= c1));
|
1467
|
+
if(0 <= i) {
|
1468
|
+
/* type B* suffix. */
|
1469
|
+
++BUCKET_BSTAR(c0, c1);
|
1470
|
+
SA[--m] = i;
|
1471
|
+
/* type B suffix. */
|
1472
|
+
for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) {
|
1473
|
+
++BUCKET_B(c0, c1);
|
1474
|
+
}
|
1475
|
+
}
|
1476
|
+
}
|
1477
|
+
m = n - m;
|
1478
|
+
/*
|
1479
|
+
note:
|
1480
|
+
A type B* suffix is lexicographically smaller than a type B suffix that
|
1481
|
+
begins with the same first two characters.
|
1482
|
+
*/
|
1483
|
+
|
1484
|
+
/* Calculate the index of start/end point of each bucket. */
|
1485
|
+
for(c0 = 0, i = 0, j = 0; c0 < ALPHABET_SIZE; ++c0) {
|
1486
|
+
t = i + BUCKET_A(c0);
|
1487
|
+
BUCKET_A(c0) = i + j; /* start point */
|
1488
|
+
i = t + BUCKET_B(c0, c0);
|
1489
|
+
for(c1 = c0 + 1; c1 < ALPHABET_SIZE; ++c1) {
|
1490
|
+
j += BUCKET_BSTAR(c0, c1);
|
1491
|
+
BUCKET_BSTAR(c0, c1) = j; /* end point */
|
1492
|
+
i += BUCKET_B(c0, c1);
|
1493
|
+
}
|
1494
|
+
}
|
1495
|
+
|
1496
|
+
if(0 < m) {
|
1497
|
+
/* Sort the type B* suffixes by their first two characters. */
|
1498
|
+
PAb = SA + n - m; ISAb = SA + m;
|
1499
|
+
for(i = m - 2; 0 <= i; --i) {
|
1500
|
+
t = PAb[i], c0 = T[t], c1 = T[t + 1];
|
1501
|
+
SA[--BUCKET_BSTAR(c0, c1)] = i;
|
1502
|
+
}
|
1503
|
+
t = PAb[m - 1], c0 = T[t], c1 = T[t + 1];
|
1504
|
+
SA[--BUCKET_BSTAR(c0, c1)] = m - 1;
|
1505
|
+
|
1506
|
+
/* Sort the type B* substrings using sssort. */
|
1507
|
+
#ifdef LIBBSC_OPENMP
|
1508
|
+
if (openMP)
|
1509
|
+
{
|
1510
|
+
buf = SA + m;
|
1511
|
+
c0 = ALPHABET_SIZE - 2, c1 = ALPHABET_SIZE - 1, j = m;
|
1512
|
+
#pragma omp parallel default(shared) private(bufsize, curbuf, k, l, d0, d1)
|
1513
|
+
{
|
1514
|
+
bufsize = (n - (2 * m)) / omp_get_num_threads();
|
1515
|
+
curbuf = buf + omp_get_thread_num() * bufsize;
|
1516
|
+
k = 0;
|
1517
|
+
for(;;) {
|
1518
|
+
#pragma omp critical(sssort_lock)
|
1519
|
+
{
|
1520
|
+
if(0 < (l = j)) {
|
1521
|
+
d0 = c0, d1 = c1;
|
1522
|
+
do {
|
1523
|
+
k = BUCKET_BSTAR(d0, d1);
|
1524
|
+
if(--d1 <= d0) {
|
1525
|
+
d1 = ALPHABET_SIZE - 1;
|
1526
|
+
if(--d0 < 0) { break; }
|
1527
|
+
}
|
1528
|
+
} while(((l - k) <= 1) && (0 < (l = k)));
|
1529
|
+
c0 = d0, c1 = d1, j = k;
|
1530
|
+
}
|
1531
|
+
}
|
1532
|
+
if(l == 0) { break; }
|
1533
|
+
sssort(T, PAb, SA + k, SA + l,
|
1534
|
+
curbuf, bufsize, 2, n, *(SA + k) == (m - 1));
|
1535
|
+
}
|
1536
|
+
}
|
1537
|
+
}
|
1538
|
+
else
|
1539
|
+
{
|
1540
|
+
buf = SA + m, bufsize = n - (2 * m);
|
1541
|
+
for(c0 = ALPHABET_SIZE - 2, j = m; 0 < j; --c0) {
|
1542
|
+
for(c1 = ALPHABET_SIZE - 1; c0 < c1; j = i, --c1) {
|
1543
|
+
i = BUCKET_BSTAR(c0, c1);
|
1544
|
+
if(1 < (j - i)) {
|
1545
|
+
sssort(T, PAb, SA + i, SA + j,
|
1546
|
+
buf, bufsize, 2, n, *(SA + i) == (m - 1));
|
1547
|
+
}
|
1548
|
+
}
|
1549
|
+
}
|
1550
|
+
}
|
1551
|
+
#else
|
1552
|
+
buf = SA + m, bufsize = n - (2 * m);
|
1553
|
+
for(c0 = ALPHABET_SIZE - 2, j = m; 0 < j; --c0) {
|
1554
|
+
for(c1 = ALPHABET_SIZE - 1; c0 < c1; j = i, --c1) {
|
1555
|
+
i = BUCKET_BSTAR(c0, c1);
|
1556
|
+
if(1 < (j - i)) {
|
1557
|
+
sssort(T, PAb, SA + i, SA + j,
|
1558
|
+
buf, bufsize, 2, n, *(SA + i) == (m - 1));
|
1559
|
+
}
|
1560
|
+
}
|
1561
|
+
}
|
1562
|
+
#endif
|
1563
|
+
|
1564
|
+
/* Compute ranks of type B* substrings. */
|
1565
|
+
for(i = m - 1; 0 <= i; --i) {
|
1566
|
+
if(0 <= SA[i]) {
|
1567
|
+
j = i;
|
1568
|
+
do { ISAb[SA[i]] = i; } while((0 <= --i) && (0 <= SA[i]));
|
1569
|
+
SA[i + 1] = i - j;
|
1570
|
+
if(i <= 0) { break; }
|
1571
|
+
}
|
1572
|
+
j = i;
|
1573
|
+
do { ISAb[SA[i] = ~SA[i]] = j; } while(SA[--i] < 0);
|
1574
|
+
ISAb[SA[i]] = j;
|
1575
|
+
}
|
1576
|
+
|
1577
|
+
/* Construct the inverse suffix array of type B* suffixes using trsort. */
|
1578
|
+
trsort(ISAb, SA, m, 1);
|
1579
|
+
|
1580
|
+
/* Set the sorted order of type B* suffixes. */
|
1581
|
+
for(i = n - 1, j = m, c0 = T[n - 1]; 0 <= i;) {
|
1582
|
+
for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) >= c1); --i, c1 = c0) { }
|
1583
|
+
if(0 <= i) {
|
1584
|
+
t = i;
|
1585
|
+
for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) { }
|
1586
|
+
SA[ISAb[--j]] = ((t == 0) || (1 < (t - i))) ? t : ~t;
|
1587
|
+
}
|
1588
|
+
}
|
1589
|
+
|
1590
|
+
/* Calculate the index of start/end point of each bucket. */
|
1591
|
+
BUCKET_B(ALPHABET_SIZE - 1, ALPHABET_SIZE - 1) = n; /* end point */
|
1592
|
+
for(c0 = ALPHABET_SIZE - 2, k = m - 1; 0 <= c0; --c0) {
|
1593
|
+
i = BUCKET_A(c0 + 1) - 1;
|
1594
|
+
for(c1 = ALPHABET_SIZE - 1; c0 < c1; --c1) {
|
1595
|
+
t = i - BUCKET_B(c0, c1);
|
1596
|
+
BUCKET_B(c0, c1) = i; /* end point */
|
1597
|
+
|
1598
|
+
/* Move all type B* suffixes to the correct position. */
|
1599
|
+
for(i = t, j = BUCKET_BSTAR(c0, c1);
|
1600
|
+
j <= k;
|
1601
|
+
--i, --k) { SA[i] = SA[k]; }
|
1602
|
+
}
|
1603
|
+
BUCKET_BSTAR(c0, c0 + 1) = i - BUCKET_B(c0, c0) + 1; /* start point */
|
1604
|
+
BUCKET_B(c0, c0) = i; /* end point */
|
1605
|
+
}
|
1606
|
+
}
|
1607
|
+
|
1608
|
+
return m;
|
1609
|
+
}
|
1610
|
+
|
1611
|
+
/* Constructs the suffix array by using the sorted order of type B* suffixes. */
|
1612
|
+
static
|
1613
|
+
void
|
1614
|
+
construct_SA(const unsigned char *T, int *SA,
|
1615
|
+
int *bucket_A, int *bucket_B,
|
1616
|
+
int n, int m) {
|
1617
|
+
int *i, *j, *k;
|
1618
|
+
int s;
|
1619
|
+
int c0, c1, c2;
|
1620
|
+
|
1621
|
+
if(0 < m) {
|
1622
|
+
/* Construct the sorted order of type B suffixes by using
|
1623
|
+
the sorted order of type B* suffixes. */
|
1624
|
+
for(c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) {
|
1625
|
+
/* Scan the suffix array from right to left. */
|
1626
|
+
for(i = SA + BUCKET_BSTAR(c1, c1 + 1),
|
1627
|
+
j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1;
|
1628
|
+
i <= j;
|
1629
|
+
--j) {
|
1630
|
+
if(0 < (s = *j)) {
|
1631
|
+
assert(T[s] == c1);
|
1632
|
+
assert(((s + 1) < n) && (T[s] <= T[s + 1]));
|
1633
|
+
assert(T[s - 1] <= T[s]);
|
1634
|
+
*j = ~s;
|
1635
|
+
c0 = T[--s];
|
1636
|
+
if((0 < s) && (T[s - 1] > c0)) { s = ~s; }
|
1637
|
+
if(c0 != c2) {
|
1638
|
+
if(0 <= c2) { BUCKET_B(c2, c1) = k - SA; }
|
1639
|
+
k = SA + BUCKET_B(c2 = c0, c1);
|
1640
|
+
}
|
1641
|
+
assert(k < j); assert(k != NULL);
|
1642
|
+
*k-- = s;
|
1643
|
+
} else {
|
1644
|
+
assert(((s == 0) && (T[s] == c1)) || (s < 0));
|
1645
|
+
*j = ~s;
|
1646
|
+
}
|
1647
|
+
}
|
1648
|
+
}
|
1649
|
+
}
|
1650
|
+
|
1651
|
+
/* Construct the suffix array by using
|
1652
|
+
the sorted order of type B suffixes. */
|
1653
|
+
k = SA + BUCKET_A(c2 = T[n - 1]);
|
1654
|
+
*k++ = (T[n - 2] < c2) ? ~(n - 1) : (n - 1);
|
1655
|
+
/* Scan the suffix array from left to right. */
|
1656
|
+
for(i = SA, j = SA + n; i < j; ++i) {
|
1657
|
+
if(0 < (s = *i)) {
|
1658
|
+
assert(T[s - 1] >= T[s]);
|
1659
|
+
c0 = T[--s];
|
1660
|
+
if((s == 0) || (T[s - 1] < c0)) { s = ~s; }
|
1661
|
+
if(c0 != c2) {
|
1662
|
+
BUCKET_A(c2) = k - SA;
|
1663
|
+
k = SA + BUCKET_A(c2 = c0);
|
1664
|
+
}
|
1665
|
+
assert(i < k);
|
1666
|
+
*k++ = s;
|
1667
|
+
} else {
|
1668
|
+
assert(s < 0);
|
1669
|
+
*i = ~s;
|
1670
|
+
}
|
1671
|
+
}
|
1672
|
+
}
|
1673
|
+
|
1674
|
+
/* Constructs the burrows-wheeler transformed string directly
|
1675
|
+
by using the sorted order of type B* suffixes. */
|
1676
|
+
static
|
1677
|
+
int
|
1678
|
+
construct_BWT(const unsigned char *T, int *SA,
|
1679
|
+
int *bucket_A, int *bucket_B,
|
1680
|
+
int n, int m) {
|
1681
|
+
int *i, *j, *k, *orig;
|
1682
|
+
int s;
|
1683
|
+
int c0, c1, c2;
|
1684
|
+
|
1685
|
+
if(0 < m) {
|
1686
|
+
/* Construct the sorted order of type B suffixes by using
|
1687
|
+
the sorted order of type B* suffixes. */
|
1688
|
+
for(c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) {
|
1689
|
+
/* Scan the suffix array from right to left. */
|
1690
|
+
for(i = SA + BUCKET_BSTAR(c1, c1 + 1),
|
1691
|
+
j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1;
|
1692
|
+
i <= j;
|
1693
|
+
--j) {
|
1694
|
+
if(0 < (s = *j)) {
|
1695
|
+
assert(T[s] == c1);
|
1696
|
+
assert(((s + 1) < n) && (T[s] <= T[s + 1]));
|
1697
|
+
assert(T[s - 1] <= T[s]);
|
1698
|
+
c0 = T[--s];
|
1699
|
+
*j = ~((int)c0);
|
1700
|
+
if((0 < s) && (T[s - 1] > c0)) { s = ~s; }
|
1701
|
+
if(c0 != c2) {
|
1702
|
+
if(0 <= c2) { BUCKET_B(c2, c1) = k - SA; }
|
1703
|
+
k = SA + BUCKET_B(c2 = c0, c1);
|
1704
|
+
}
|
1705
|
+
assert(k < j); assert(k != NULL);
|
1706
|
+
*k-- = s;
|
1707
|
+
} else if(s != 0) {
|
1708
|
+
*j = ~s;
|
1709
|
+
#ifndef NDEBUG
|
1710
|
+
} else {
|
1711
|
+
assert(T[s] == c1);
|
1712
|
+
#endif
|
1713
|
+
}
|
1714
|
+
}
|
1715
|
+
}
|
1716
|
+
}
|
1717
|
+
|
1718
|
+
/* Construct the BWTed string by using
|
1719
|
+
the sorted order of type B suffixes. */
|
1720
|
+
k = SA + BUCKET_A(c2 = T[n - 1]);
|
1721
|
+
*k++ = (T[n - 2] < c2) ? ~((int)T[n - 2]) : (n - 1);
|
1722
|
+
/* Scan the suffix array from left to right. */
|
1723
|
+
for(i = SA, j = SA + n, orig = SA; i < j; ++i) {
|
1724
|
+
if(0 < (s = *i)) {
|
1725
|
+
assert(T[s - 1] >= T[s]);
|
1726
|
+
c0 = T[--s];
|
1727
|
+
*i = c0;
|
1728
|
+
if((0 < s) && (T[s - 1] < c0)) { s = ~((int)T[s - 1]); }
|
1729
|
+
if(c0 != c2) {
|
1730
|
+
BUCKET_A(c2) = k - SA;
|
1731
|
+
k = SA + BUCKET_A(c2 = c0);
|
1732
|
+
}
|
1733
|
+
assert(i < k);
|
1734
|
+
*k++ = s;
|
1735
|
+
} else if(s != 0) {
|
1736
|
+
*i = ~s;
|
1737
|
+
} else {
|
1738
|
+
orig = i;
|
1739
|
+
}
|
1740
|
+
}
|
1741
|
+
|
1742
|
+
return orig - SA;
|
1743
|
+
}
|
1744
|
+
|
1745
|
+
/* Constructs the burrows-wheeler transformed string directly
|
1746
|
+
by using the sorted order of type B* suffixes. */
|
1747
|
+
static
|
1748
|
+
int
|
1749
|
+
construct_BWT_indexes(const unsigned char *T, int *SA,
|
1750
|
+
int *bucket_A, int *bucket_B,
|
1751
|
+
int n, int m,
|
1752
|
+
unsigned char * num_indexes, int * indexes) {
|
1753
|
+
int *i, *j, *k, *orig;
|
1754
|
+
int s;
|
1755
|
+
int c0, c1, c2;
|
1756
|
+
|
1757
|
+
int mod = n / 8;
|
1758
|
+
{
|
1759
|
+
mod |= mod >> 1; mod |= mod >> 2;
|
1760
|
+
mod |= mod >> 4; mod |= mod >> 8;
|
1761
|
+
mod |= mod >> 16; mod >>= 1;
|
1762
|
+
|
1763
|
+
*num_indexes = (unsigned char)((n - 1) / (mod + 1));
|
1764
|
+
}
|
1765
|
+
|
1766
|
+
if(0 < m) {
|
1767
|
+
/* Construct the sorted order of type B suffixes by using
|
1768
|
+
the sorted order of type B* suffixes. */
|
1769
|
+
for(c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) {
|
1770
|
+
/* Scan the suffix array from right to left. */
|
1771
|
+
for(i = SA + BUCKET_BSTAR(c1, c1 + 1),
|
1772
|
+
j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1;
|
1773
|
+
i <= j;
|
1774
|
+
--j) {
|
1775
|
+
if(0 < (s = *j)) {
|
1776
|
+
assert(T[s] == c1);
|
1777
|
+
assert(((s + 1) < n) && (T[s] <= T[s + 1]));
|
1778
|
+
assert(T[s - 1] <= T[s]);
|
1779
|
+
|
1780
|
+
if ((s & mod) == 0) indexes[s / (mod + 1) - 1] = j - SA;
|
1781
|
+
|
1782
|
+
c0 = T[--s];
|
1783
|
+
*j = ~((int)c0);
|
1784
|
+
if((0 < s) && (T[s - 1] > c0)) { s = ~s; }
|
1785
|
+
if(c0 != c2) {
|
1786
|
+
if(0 <= c2) { BUCKET_B(c2, c1) = k - SA; }
|
1787
|
+
k = SA + BUCKET_B(c2 = c0, c1);
|
1788
|
+
}
|
1789
|
+
assert(k < j); assert(k != NULL);
|
1790
|
+
*k-- = s;
|
1791
|
+
} else if(s != 0) {
|
1792
|
+
*j = ~s;
|
1793
|
+
#ifndef NDEBUG
|
1794
|
+
} else {
|
1795
|
+
assert(T[s] == c1);
|
1796
|
+
#endif
|
1797
|
+
}
|
1798
|
+
}
|
1799
|
+
}
|
1800
|
+
}
|
1801
|
+
|
1802
|
+
/* Construct the BWTed string by using
|
1803
|
+
the sorted order of type B suffixes. */
|
1804
|
+
k = SA + BUCKET_A(c2 = T[n - 1]);
|
1805
|
+
if (T[n - 2] < c2) {
|
1806
|
+
if (((n - 1) & mod) == 0) indexes[(n - 1) / (mod + 1) - 1] = k - SA;
|
1807
|
+
*k++ = ~((int)T[n - 2]);
|
1808
|
+
}
|
1809
|
+
else {
|
1810
|
+
*k++ = n - 1;
|
1811
|
+
}
|
1812
|
+
|
1813
|
+
/* Scan the suffix array from left to right. */
|
1814
|
+
for(i = SA, j = SA + n, orig = SA; i < j; ++i) {
|
1815
|
+
if(0 < (s = *i)) {
|
1816
|
+
assert(T[s - 1] >= T[s]);
|
1817
|
+
|
1818
|
+
if ((s & mod) == 0) indexes[s / (mod + 1) - 1] = i - SA;
|
1819
|
+
|
1820
|
+
c0 = T[--s];
|
1821
|
+
*i = c0;
|
1822
|
+
if(c0 != c2) {
|
1823
|
+
BUCKET_A(c2) = k - SA;
|
1824
|
+
k = SA + BUCKET_A(c2 = c0);
|
1825
|
+
}
|
1826
|
+
assert(i < k);
|
1827
|
+
if((0 < s) && (T[s - 1] < c0)) {
|
1828
|
+
if ((s & mod) == 0) indexes[s / (mod + 1) - 1] = k - SA;
|
1829
|
+
*k++ = ~((int)T[s - 1]);
|
1830
|
+
} else
|
1831
|
+
*k++ = s;
|
1832
|
+
} else if(s != 0) {
|
1833
|
+
*i = ~s;
|
1834
|
+
} else {
|
1835
|
+
orig = i;
|
1836
|
+
}
|
1837
|
+
}
|
1838
|
+
|
1839
|
+
return orig - SA;
|
1840
|
+
}
|
1841
|
+
|
1842
|
+
|
1843
|
+
/*---------------------------------------------------------------------------*/
|
1844
|
+
|
1845
|
+
/*- Function -*/
|
1846
|
+
|
1847
|
+
int
|
1848
|
+
divsufsort(const unsigned char *T, int *SA, int n, int openMP) {
|
1849
|
+
int *bucket_A, *bucket_B;
|
1850
|
+
int m;
|
1851
|
+
int err = 0;
|
1852
|
+
|
1853
|
+
/* Check arguments. */
|
1854
|
+
if((T == NULL) || (SA == NULL) || (n < 0)) { return -1; }
|
1855
|
+
else if(n == 0) { return 0; }
|
1856
|
+
else if(n == 1) { SA[0] = 0; return 0; }
|
1857
|
+
else if(n == 2) { m = (T[0] < T[1]); SA[m ^ 1] = 0, SA[m] = 1; return 0; }
|
1858
|
+
|
1859
|
+
bucket_A = (int *)malloc(BUCKET_A_SIZE * sizeof(int));
|
1860
|
+
bucket_B = (int *)malloc(BUCKET_B_SIZE * sizeof(int));
|
1861
|
+
|
1862
|
+
/* Suffixsort. */
|
1863
|
+
if((bucket_A != NULL) && (bucket_B != NULL)) {
|
1864
|
+
m = sort_typeBstar(T, SA, bucket_A, bucket_B, n, openMP);
|
1865
|
+
construct_SA(T, SA, bucket_A, bucket_B, n, m);
|
1866
|
+
} else {
|
1867
|
+
err = -2;
|
1868
|
+
}
|
1869
|
+
|
1870
|
+
free(bucket_B);
|
1871
|
+
free(bucket_A);
|
1872
|
+
|
1873
|
+
return err;
|
1874
|
+
}
|
1875
|
+
|
1876
|
+
int
|
1877
|
+
divbwt(const unsigned char *T, unsigned char *U, int *A, int n, unsigned char * num_indexes, int * indexes, int openMP) {
|
1878
|
+
int *B;
|
1879
|
+
int *bucket_A, *bucket_B;
|
1880
|
+
int m, pidx, i;
|
1881
|
+
|
1882
|
+
/* Check arguments. */
|
1883
|
+
if((T == NULL) || (U == NULL) || (n < 0)) { return -1; }
|
1884
|
+
else if(n <= 1) { if(n == 1) { U[0] = T[0]; } return n; }
|
1885
|
+
|
1886
|
+
if((B = A) == NULL) { B = (int *)malloc((size_t)(n + 1) * sizeof(int)); }
|
1887
|
+
bucket_A = (int *)malloc(BUCKET_A_SIZE * sizeof(int));
|
1888
|
+
bucket_B = (int *)malloc(BUCKET_B_SIZE * sizeof(int));
|
1889
|
+
|
1890
|
+
/* Burrows-Wheeler Transform. */
|
1891
|
+
if((B != NULL) && (bucket_A != NULL) && (bucket_B != NULL)) {
|
1892
|
+
m = sort_typeBstar(T, B, bucket_A, bucket_B, n, openMP);
|
1893
|
+
|
1894
|
+
if (num_indexes == NULL || indexes == NULL) {
|
1895
|
+
pidx = construct_BWT(T, B, bucket_A, bucket_B, n, m);
|
1896
|
+
} else {
|
1897
|
+
pidx = construct_BWT_indexes(T, B, bucket_A, bucket_B, n, m, num_indexes, indexes);
|
1898
|
+
}
|
1899
|
+
|
1900
|
+
/* Copy to output string. */
|
1901
|
+
U[0] = T[n - 1];
|
1902
|
+
for(i = 0; i < pidx; ++i) { U[i + 1] = (unsigned char)B[i]; }
|
1903
|
+
for(i += 1; i < n; ++i) { U[i] = (unsigned char)B[i]; }
|
1904
|
+
pidx += 1;
|
1905
|
+
} else {
|
1906
|
+
pidx = -2;
|
1907
|
+
}
|
1908
|
+
|
1909
|
+
free(bucket_B);
|
1910
|
+
free(bucket_A);
|
1911
|
+
if(A == NULL) { free(B); }
|
1912
|
+
|
1913
|
+
return pidx;
|
1914
|
+
}
|
1915
|
+
|
1916
|
+
} // namespace duckdb_zstd
|