o DfZ @sgdZddlmZmZddlmZmZmZdZdZ dZ dZ ee Be Be BZ de d e d efd d Zde d ed ee fddZde d ed eee eeffddZde d ed ee fddZde d ed eee eeffddZde d ed eee eeffddZdS))AlignerPrefixComparerSuffixComparerhamming_spherehamming_environmentedit_environment edit_distance)IteratorTuple)rrrstreturnc Cst|}t|}tt|d}td|dD]B}|d}|dd7<td|dD],}t||d||dk}t|d|||d||dd} ||}| ||<q,q|dS)z Return the edit distance between the strings s and t. The edit distance is the sum of the numbers of insertions, deletions, and mismatches that is minimally necessary to transform one string into the other. r r)lenlistrangeintmin) rrmncostsjprevimatchcr W/var/www/html/software/conda/envs/catlas/lib/python3.10/site-packages/cutadapt/align.pyr!s"    rkc cs|dksJ|dkr|VdSt|}t||dD]9}|d|}||}||dd}dD]"}||kr9q2t||dD]}|||} t| |ksPJ| Vq@q2qdS)z Yield all strings t for which the hamming distance between s and t is exactly k, assuming the alphabet is A, C, G, T. rNr ACGTrrr) rr"rrprefixrsuffixchryr r r!r;s(   rccs@t|}t|dD]}t||D] }||||fVqq dS)a  Find all strings t for which the hamming distance between s and t is at most k, assuming the alphabet is A, C, G, T. Yield tuples (t, e, m), where e is the hamming distance between s and t and m is the number of matches (equal to len(t) - e). r Nr$)rr"rerr r r!rTsrccs|V|dkr dSt||dD]I}t|}dD]*}t|D]}|d||}|||dV|||ddVq||Vqt|D]}|d|||ddVqHqdS)zr Apply all possible edits up to edit distance k to string s. A string may be returned more than once. rNr r#)naive_edit_environmentrr)rr"rr'rr%r r r!r*bs     r*c cs~|r |t|nd}t||dt|d}t}t||D]}||vr$q||||}|dd\}}|||fVqdS) Find all strings t for which the edit distance between s and t is at most k, assuming the alphabet is A, C, G, T. Yield tuples (t, e, m), where e is the edit distance between s and t and m is the number of matches in the optimal alignment. r)Zmax_error_rateflagsZ min_overlapN)rrsetr*addZlocate) rr"ZrateZalignerseenrresultmatcheserrorsr r r!rws  rccst|}d}dtt|ddg|dfg}|r|\}}}t|}|d|kr5||d|dfV|||krs  $$(