/*
 * Copyright © 2025 Piyush Acharya. Some rights reserved.
 * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
 *
 * You are entirely responsible for the use of this application, including any and all activities that occur.
 * While DNAnalyzer strives to fix all major bugs that may be either reported by a user or discovered while debugging,
 * they will not be held liable for any loss that the user may incur as a result of using this application, under any circumstances.
 *
 * For further inquiries, please contact reach out to contact@dnanalyzer.live
 */

package DNAnalyzer.utils.protein;

import java.util.ArrayList;
import java.util.Collections;
import java.util.List;

import DNAnalyzer.data.codon.CodonDataConstants;
import DNAnalyzer.data.codon.CodonDataUtils;

/**
 * Find proteins in a DNA sequence (contains the main algorithm).
 *
 * @author Piyush Acharya (@VerisimilitudeX)
 * @version 1.2.1
 */
public class ProteinFinder {

  /** Utility classes should not have public constructors */
  private ProteinFinder() {}

  /**
   * Gets proteins from dna and amino acid
   *
   * @param dna dna
   * @param aminoAcid amino acid
   * @return list of proteins
   */
  public static List<String> getProtein(final String dna, final String aminoAcid) {

    final List<String> proteinList = new ArrayList<>();
    final List<String> aminoAcidList = new ArrayList<>(CodonDataUtils.getAminoAcid(aminoAcid));

    // Outer loop loops through the start codons for the amino acids that the user
    // entered.
    // store the start index
    for (final String startCodon : aminoAcidList) {
      addProtein(dna, proteinList, dna.indexOf(startCodon.toLowerCase()));
    }

    // if no proteins are found, return null
    if (proteinList.isEmpty()) {
      // Return null if no protein found in DNA sequence
      System.out.println("No proteins found");
      return Collections.emptyList();
    }

    // Return list of proteins found in the DNA sequence
    return proteinList;
  }

  /**
   * Add protein to protein list
   *
   * @param dna DNA sequence
   * @param proteinList List of proteins
   * @param startIndex Start index for checking for proteins
   */
  private static void addProtein(
      final String dna, final List<String> proteinList, final int startIndex) {

    // Inner loop loops through the stop that the user entered.
    // store the stopIndex
    // if index is not -1 then store the substring of dna with start and stop index
    // in the protein list
    final List<String> stopCodonList = CodonDataConstants.STOP;
    int stopIndex;
    for (final String stopCodon : stopCodonList) {

      stopIndex = dna.indexOf(stopCodon.toLowerCase(), startIndex + 3);

      if ((startIndex != -1) && (stopIndex != -1)) {
        proteinList.add(dna.substring(startIndex, stopIndex + 3).toUpperCase());
        break;
      }
    }
  }

  /*
   * Boyer-Moore algorithm
   * public static ArrayList<Integer> findProteins(String protein) {
   *
   * }
   */
}