NeedlemanWunsch.sol

// SPDX-License-Identifier: MIT
// Created by ZENODE (zenodeapp - https://github.com/zenodeapp/)

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pragma solidity ^0.8.17;
import './_PairwiseAlignment.sol';

contract NeedlemanWunsch is PairwiseAlignment {

  constructor(SubstitutionMatrices _matricesAddress) PairwiseAlignment(_matricesAddress) {}

  function needlemanWunsch(string memory sequenceA, string memory sequenceB, int gap, uint limit, string memory matrix)
  public view returns(AlignmentOutput memory) {
    return _needlemanWunsch(sequenceA, sequenceB, AlignmentOptions(gap, limit, matrix));
  }

  function _needlemanWunsch(string memory sequenceA, string memory sequenceB, AlignmentOptions memory alignmentOptions)
  public view returns(AlignmentOutput memory alignmentOutput) {
    alignmentOptions = _before(sequenceA, sequenceB, alignmentOptions);
    
    // Initialize matrices
    (AlignmentData memory alignmentData, int[] memory scoreMatrix) = initializeMatrices(
      sequenceA,
      sequenceB,
      alignmentOptions.gap,
      [TracebackCommand.STOP, TracebackCommand.LEFT, TracebackCommand.UP]
    );

    // Score matrices
    ScoreOptions memory scoreOptions;
    scoreOptions.enableFloor = false;
    alignmentData = scoreMatrices(scoreMatrix, alignmentData, alignmentOptions, scoreOptions);

    // Get starting points (For Needleman-Wunsch there is only a single starting point)
    uint[] memory startingPoints = new uint[](1);
    startingPoints[0] = alignmentData.width * alignmentData.height - 1;

    // Traceback
    alignmentOutput.alignments = traceback(alignmentData, startingPoints, alignmentOptions.limit);
    
    // Remaining output
    alignmentOutput.sequenceA = sequenceA;
    alignmentOutput.sequenceB = sequenceB;
    alignmentOutput.score = scoreMatrix[startingPoints[0]];
    alignmentOutput.count = alignmentOutput.alignments.length;
  }
}