80 lines
2.5 KiB
Factor
80 lines
2.5 KiB
Factor
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! Copyright (C) 2020 Bubbler.
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! See http://factorcode.org/license.txt for BSD license.
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USING: arrays help.markup help.syntax kernel sequences strings ;
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IN: rosalind.lcsm
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HELP: dna>enum
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{ $values
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{ "string" string }
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{ "array" array }
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}
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{ $description "Maps each character of ACGT in the DNA string to 1 2 3 4 respectively, and adds a 0 at the end. This is the internal format used for the suffix trie algorithm." } ;
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HELP: enum>dna
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{ $values
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{ "array" array }
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{ "string" string }
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}
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{ $description "Undoes the operation of " { $snippet "dna>enum" } ": removes any trailing zeroes and maps 1 2 3 4 to ACGT respectively." } ;
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HELP: intersect-dnas
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{ $values
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{ "dnas" "A sequence of DNA strings" }
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{ "intersections" "A sequence of DNA strings" }
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}
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{ $description "Finds all common substrings found on the given set of DNAs." } ;
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HELP: lcsm
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{ $values
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{ "dnas" "A sequence of DNA strings" }
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{ "dna" "A DNA string" }
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}
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{ $description "Solves the problem LCSM on Rosalind: find a longest common substring of the given DNA sequences." } ;
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HELP: lcsm-main
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{ $description "Solves the problem LCSM on Rosalind, using a real dataset." } ;
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HELP: suffix-trie
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{ $values
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{ "string" "An enum-encoded sequence" }
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{ "trie" "A trie" }
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}
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{ $description "Generates a suffix trie by adding all suffixes of the given string to an empty trie." } ;
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HELP: trie-add
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{ $values
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{ "trie" "A trie" } { "string" "An enum-encoded sequence" }
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}
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{ $description "Adds the string to the trie as a side effect." } ;
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HELP: trie-init
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{ $values
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{ "trie" "An empty trie" }
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}
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{ $description "Creates an empty trie." } ;
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HELP: trie-intersect-string
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{ $values
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{ "trie" "A trie" } { "string" "An enum-encoded sequence" }
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}
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{ $description "Computes all longest common prefixes between the trie and the suffixes of the given string, and adds them to a new empty trie. The result is an intersection in the sense that it represents the intersection of all common substrings between the two objects." } ;
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HELP: trie-longest-prefix
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{ $values
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{ "trie" "A trie" } { "string" "An enum-encoded sequence" }
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}
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{ $description "Computes the longest prefix of the string that can be found in the trie." } ;
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HELP: trie-strings
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{ $values
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{ "trie" "A trie" }
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{ "seq" "A sequence of enum-encoded sequences" }
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}
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{ $description "Extracts all sequences which start at the root and end at a leaf from a trie." } ;
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ARTICLE: "rosalind.lcsm" "rosalind.lcsm"
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{ $vocab-link "rosalind.lcsm" }
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;
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ABOUT: "rosalind.lcsm"
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