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pkg-auto: Add the highest-score-common-subsequence algorithm library
It's a more general variant of the longest-common-subsequence algorithm.
This commit is contained in:
Krzesimir Nowak
parent
3233f6eafe
commit
3b11e2404a
375
pkg_auto/impl/lcs.sh
Normal file
375
pkg_auto/impl/lcs.sh
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@ -0,0 +1,375 @@
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#!/bin/bash
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# Implementation of longest common subsequence (LCS) algorithm, with
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# memoization and scoring. The algorithm is a base of utilities like
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# diff - it finds the common items in two sequences.
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#
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# The memoization part is about remembering the results of LCS
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# computation for shorter sequences, so they can be reused when doing
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# computation for longer sequences.
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#
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# The scoring part is about generalization of the comparison function,
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# which normally would return a boolean value describing whether two
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# items are equal or not. With scoring, two things change. First is
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# that the returned value from the comparison/scoring function is not
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# a boolean, but rather an integer describing the degree of equality
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# of the items. And second is that with booleans, the winning
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# subsequence was the longest one, but with scores is not necessarily
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# the longest one, but with the highest total score. This changes the
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# algorithm a bit. While the typical LCS algorithm goes like as
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# follows (s1 and s2 are sequences, i1 and i2 are indices in their
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# respective sequences):
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#
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#
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#
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# LCS(s1, s2, i1, i2) -> sequence:
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# if (i1 >= len(s1) || i2 >= len(s2)): return ()
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# if (s1[i1] == s2[i2]):
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# l = LCS(s1, s2, i1 + 1, i2 + 1)
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# return (s1[i1], l...)
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# else:
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# l1 = LCS(s1, s2, i1 + 1, i2)
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# l2 = LCS(s1, s2, i1, i2 + 1)
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# if (len(l1) > len(l2)): return l1
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# return l2
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#
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#
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#
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# The score LCS goes more or less like this:
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#
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#
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#
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# SLCS(s1, s2, i1, i2) -> tuple(score, sequence):
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# if (i1 >= len(s1) || i2 >= len(21)): return (score: 0, sequence: ())
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# score = score_func(s1[i1], s2[i2])
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# if (score == max_score):
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# # matches the "equal" case in LCS above
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# l = SLCS(s1, s2, i1 + 1, i2 + 1)
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# return (score: score + l.score, sequence: (s1[i1], l.sequence...)
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# else if (score == 0):
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# # matches the "not equal" case in LCS above
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# l1 = SLCS(s1, s2, i1 + 1, i2)
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# l2 = SLCS(s1, s2, i1, i2 + 1)
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# if (l1.score > l2.score): return l1
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# return l2
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# else:
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# # new "equal, but not quite" case
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# l = SLCS(s1, s2, i1 + 1, i2 + 1)
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# l.score = score + l.score
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# l.sequence = (s1[i1], l.sequence...)
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# l1 = SLCS(s1, s2, i1 + 1, i2)
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# l2 = SLCS(s1, s2, i1, i2 + 1)
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# return tuple_with_max_score(l, l1, l2)
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#
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#
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#
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# The difference in the implementation below is that instead of
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# starting at index 0 and go up for each sequence, we start at max
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# index and go down.
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if [[ -z ${__LCS_SH_INCLUDED__:-} ]]; then
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__LCS_SH_INCLUDED__=x
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source "$(dirname "${BASH_SOURCE[0]}")/util.sh"
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# Constants to use for accessing fields in common items.
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declare -gri LCS_X1_IDX=0 LCS_X2_IDX=1 LCS_IDX1_IDX=2 LCS_IDX2_IDX=3
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# Computes the longest common subsequence of two sequences and stores
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# it in the passed array. The common items stored in the array with
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# longest common subsequence are actually names of arrays, where each
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# array stores an item from the first sequence, an item from the
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# second sequence, an index of the first item in first sequence and an
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# index of the second item in the second sequence. To access those
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# fields, use the LCS_*_IDX constants.
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#
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# The function optionally takes a name of the score function. If no
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# such function is passed, the simple string score function is used
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# (gives score 1 if strings are equal, otherwise gives score 0). The
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# function should take either one or three parameters. The first
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# parameter is always a name of a score integer variable. If only one
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# parameter is passed, the function should write the maximum score to
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# the score variable. When three parameters are passed, then the
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# second and third are items from the sequences passed to lcs_run and
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# they should be compared and rated. The function should rate the
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# items with zero if they are completely different, with max score if
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# they are the same, and with something in between zero and max score
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# if they are somewhat equal but not really.
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#
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# Params:
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#
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# 1 - a name of an array variable containing the first sequence
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# 2 - a name of an array variable containing the second sequence
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# 3 - a name of an array variable where the longest common subsequence
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# will be stored
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# 4 - optional, a name of a score function
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#
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# Example:
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#
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# a=( A B C D E F G )
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# b=( B C D G K )
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# c=()
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#
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# lcs_run a b c
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#
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# echo "a: ${a[*]}"
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# echo "b: ${b[*]}"
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#
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# cn=()
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# for i in "${c[@]}"; do
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# declare -n ref=${i}
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# n=${ref[LCS_X1_IDX]}
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# unset -n ref
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# cn+=( "${n}" )
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# done
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# echo "c: ${cn[*]}"
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# unset "${c[@]}"
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function lcs_run() {
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local seq1_name=${1}; shift
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local seq2_name=${1}; shift
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local common_name=${1}; shift
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local score_func=__lcs_str_score
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if [[ ${#} -gt 0 ]]; then
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score_func=${1}; shift
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fi
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if ! declare -pF "${score_func}" >/dev/null 2>/dev/null; then
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fail "${score_func@Q} is not a function"
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fi
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local -i lr_max_score
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"${score_func}" lr_max_score
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# lcs_memo_items_set is a set of common item names; the set owns
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# the common items
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#
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# lcs_memo_map is a mapping from a memo key (which encodes indices
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# from both sequences) to a pair, being a score and a name of an
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# longest common subsequence for the encoded indices, separated
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# with semicolon
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local -A lcs_memo_map=() lcs_memo_items_set=()
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local -a lr_lcs_state=( "${score_func}" lcs_memo_map lcs_memo_items_set "${seq1_name}" "${seq2_name}" "${lr_max_score}" )
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local -n seq1=${seq1_name} seq2=${seq2_name}
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local -i idx1=$(( ${#seq1[@]} - 1 )) idx2=$(( ${#seq2[@]} - 1 ))
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unset -n seq1 seq2
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__lcs_recurse lr_lcs_state "${idx1}" "${idx2}"
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local -n common_ref=${common_name}
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local lr_memo_key=''
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__lcs_make_memo_key "${idx1}" "${idx2}" lr_memo_key
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local pair=${lcs_memo_map["${lr_memo_key}"]}
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local -n memoized_items_ref=${pair#*:}
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common_ref=( "${memoized_items_ref[@]}" )
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# steal the items from the items set that are a part of desired
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# LCS, so they are not freed now, but later, when the LCS is freed
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local item
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for item in "${common_ref[@]}"; do
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unset "lcs_memo_items_set[${item}]"
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done
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# free the unneeded items
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unset "${!lcs_memo_items_set[@]}"
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# free all the LCSes, we already have a copy of the one we wanted
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local items_var_name memo_key
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for memo_key in "${!lcs_memo_map[@]}"; do
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pair=${lcs_memo_map["${memo_key}"]}
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items_var_name=${pair#*:}
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if [[ ${items_var_name} != EMPTY_ARRAY ]]; then
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unset "${items_var_name}"
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fi
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done
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}
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##
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## Details
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##
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declare -gri __LCS_SCORE_IDX=0 __LCS_MEMO_MAP_IDX=1 __LCS_MEMO_ITEMS_SET_IDX=2 __LCS_SEQ1_IDX=3 __LCS_SEQ2_IDX=4 __LCS_MAX_SCORE_IDX=5
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function __lcs_recurse() {
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local lcs_state_name=${1}; shift
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local -i i1=${1}; shift
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local -i i2=${1}; shift
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if [[ i1 -lt 0 || i2 -lt 0 ]]; then
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return 0
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fi
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local -n lcs_state=${lcs_state_name}
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local -n memo_map_ref=${lcs_state[__LCS_MEMO_MAP_IDX]}
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local memo_key=''
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__lcs_make_memo_key ${i1} ${i2} memo_key
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local pair=${memo_map_ref["${memo_key}"]:-}
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if [[ -n ${pair} ]]; then
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return 0
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fi
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unset pair memo_key
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unset -n memo_map_ref
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local -n seq1_ref=${lcs_state[__LCS_SEQ1_IDX]}
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local -n seq2_ref=${lcs_state[__LCS_SEQ2_IDX]}
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local x1=${seq1_ref[i1]}
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local x2=${seq2_ref[i2]}
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unset -n seq2_ref seq1_ref
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local -i lr_diff_score
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local score_func=${lcs_state[__LCS_SCORE_IDX]}
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"${score_func}" lr_diff_score "${x1}" "${x2}"
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unset score_func
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local -i max_score=${lcs_state[__LCS_MAX_SCORE_IDX]}
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if [[ lr_diff_score -gt max_score ]]; then
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lr_diff_score=max_score
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fi
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if [[ lr_diff_score -lt 0 ]]; then
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lr_diff_score=0
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fi
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if [[ lr_diff_score -eq max_score ]]; then
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unset max_score
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__lcs_recurse "${lcs_state_name}" $((i1 - 1)) $((i2 - 1))
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local n
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gen_varname __LCS_COMMON n
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declare -a -g "${n}=()"
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# retrieve memoized result for i1-1 and i2-1 (what we just
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# called above), make a copy of it, add the prepared item and
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# memoize that copy for i1 and i2; also add the prepared item
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# to the set of prepared items
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local -n memo_map_ref=${lcs_state[__LCS_MEMO_MAP_IDX]}
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local previous_memo_key
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__lcs_make_memo_key $((i1 - 1)) $((i2 - 1)) previous_memo_key
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local previous_pair=${memo_map_ref["${previous_memo_key}"]:-'0:EMPTY_ARRAY'}
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local previous_score=${previous_pair%%:*}
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local -n previous_memoized_prepared_items_ref=${previous_pair#*:}
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local -n c_ref=${n}
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local prepared_item_to_insert
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gen_varname __LCS_PREP prepared_item_to_insert
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declare -g -a "${prepared_item_to_insert}=( ${x1@Q} ${x2@Q} ${i1@Q} ${i2@Q} )"
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c_ref=( "${previous_memoized_prepared_items_ref[@]}" "${prepared_item_to_insert}" )
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local memo_key
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__lcs_make_memo_key ${i1} ${i2} memo_key
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memo_map_ref["${memo_key}"]="$((lr_diff_score + previous_score)):${n}"
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local -n memo_items_set=${lcs_state[__LCS_MEMO_ITEMS_SET_IDX]}
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memo_items_set["${prepared_item_to_insert}"]=x
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elif [[ lr_diff_score -eq 0 ]]; then
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unset max_score
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__lcs_recurse "${lcs_state_name}" ${i1} $((i2 - 1))
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__lcs_recurse "${lcs_state_name}" $((i1 - 1)) ${i2}
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# retrieve memoized results for i1 and i2-1 and for i1-1 and
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# i2 (what we just called above), and memoize the longer
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# result for i1 and i2
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local -n memo_map_ref=${lcs_state[__LCS_MEMO_MAP_IDX]}
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local lr_memo_key=''
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__lcs_make_memo_key ${i1} $((i2 - 1)) lr_memo_key
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local previous_pair1=${memo_map_ref["${lr_memo_key}"]:-'0:EMPTY_ARRAY'}
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local -i previous_score1=${previous_pair1%%:*}
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__lcs_make_memo_key $((i1 - 1)) ${i2} lr_memo_key
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local previous_pair2=${memo_map_ref["${lr_memo_key}"]:-'0:EMPTY_ARRAY'}
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local -i previous_score2=${previous_pair2%%:*}
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__lcs_make_memo_key ${i1} ${i2} lr_memo_key
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if [[ previous_score1 -gt previous_score2 ]]; then
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memo_map_ref["${lr_memo_key}"]=${previous_pair1}
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else
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memo_map_ref["${lr_memo_key}"]=${previous_pair2}
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fi
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else
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unset max_score
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# 1
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__lcs_recurse "${lcs_state_name}" $((i1 - 1)) $((i2 - 1))
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# 2
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__lcs_recurse "${lcs_state_name}" ${i1} $((i2 - 1))
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# 3
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__lcs_recurse "${lcs_state_name}" $((i1 - 1)) ${i2}
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local lr_mk1 lr_mk2 lr_mk3
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__lcs_make_memo_key $((i1 - 1)) $((i2 - 1)) lr_mk1
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__lcs_make_memo_key ${i1} $((i2 - 1)) lr_mk2
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__lcs_make_memo_key $((i1 - 1)) ${i2} lr_mk3
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local -n memo_map_ref=${lcs_state[__LCS_MEMO_MAP_IDX]}
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local pair1=${memo_map_ref["${lr_mk1}"]:-'0:EMPTY_ARRAY'}
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local pair2=${memo_map_ref["${lr_mk2}"]:-'0:EMPTY_ARRAY'}
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local pair3=${memo_map_ref["${lr_mk3}"]:-'0:EMPTY_ARRAY'}
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local -i score1=${pair1%%:*}
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local -i score2=${pair2%%:*}
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local -i score3=${pair3%%:*}
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local -i pick # either 1, 2 or 3
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score1=$((score1 + lr_diff_score))
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if [[ score1 -gt score2 ]]; then
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if [[ score1 -gt score3 ]]; then
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pick=1
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else
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pick=3
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fi
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elif [[ score2 -gt score3 ]]; then
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pick=2
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else
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pick=3
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fi
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if [[ pick -eq 1 ]]; then
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local lr_new_lcs
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gen_varname __LCS_COMMON lr_new_lcs
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declare -a -g "${lr_new_lcs}=()"
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local -n previous_memoized_prepared_items_ref=${pair1#*:}
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local -n c_ref=${lr_new_lcs}
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local prepared_item_to_insert
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gen_varname __LCS_PREP prepared_item_to_insert
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declare -g -a "${prepared_item_to_insert}=( ${x1@Q} ${x2@Q} ${i1@Q} ${i2@Q} )"
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c_ref=( "${previous_memoized_prepared_items_ref[@]}" "${prepared_item_to_insert}" )
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local lr_memo_key
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__lcs_make_memo_key ${i1} ${i2} lr_memo_key
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memo_map_ref["${lr_memo_key}"]="${score1}:${lr_new_lcs}"
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local -n memo_items_set=${lcs_state[__LCS_MEMO_ITEMS_SET_IDX]}
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memo_items_set["${prepared_item_to_insert}"]=x
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else
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local -n picked_pair="pair${pick}"
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local lr_memo_key=''
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__lcs_make_memo_key ${i1} ${i2} lr_memo_key
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memo_map_ref["${lr_memo_key}"]=${picked_pair}
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fi
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fi
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}
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function __lcs_make_memo_key() {
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local i1=${1}; shift
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local i2=${1}; shift
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local -n ref=${1}; shift
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local key="x${i1}x${i2}x"
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key=${key//-/_}
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ref=${key}
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}
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function __lcs_str_score() {
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local -n score_ref=${1}; shift
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score_ref=1
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[[ ${#} -eq 0 || ${1} = "${2}" ]] || score_ref=0
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}
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fi
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