WTF KEK

The WTF KEK

package com.company;

import java.io.*;
import java.nio.CharBuffer;
import java.nio.file.Files;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.regex.Pattern;
import java.util.stream.IntStream;
import java.util.stream.Stream;

public class Main {

    public static void main(String[] args) {
        if (args.length < 2) {
            System.out.println(":(");
            return;
        }
        String inPath = args[0];
        String outPath = args[1];
        long start = System.currentTimeMillis();
        try (Stream<String> stream = Files.lines(Paths.get(inPath))) {
            final StringBuilder resultString = new StringBuilder();
            final StringBuilder header = new StringBuilder();
            final AtomicInteger counter = new AtomicInteger(0);
            final StringBuilder charsBuilder = new StringBuilder();

            try (BufferedWriter out = new BufferedWriter(new FileWriter(outPath, true))) {
                out.write("MolID;Target;Ligand;Run;Pose;Rank;dG;VS;Atom;X;Y;Z");
                out.newLine();
                stream.skip(1).forEach(string -> {
                    boolean containsSpace = string.contains(" ");
                    boolean containsComma = string.contains(",");
                    if (!containsSpace && !containsComma) {
                        header.setLength(0);
                        header.append(counter.getAndIncrement());
                    } else if (containsComma) {
                        String[] wtfIsThis = string.split(",");
                        String[] wtfIsThis2 = wtfIsThis[0].split("-");
                        header.append(";").append(wtfIsThis2[0])
                                .append(";")
                                .append(wtfIsThis2[1])
                                .append(";")
                                .append(wtfIsThis2[4])
                                .append(";")
                                .append(wtfIsThis2[6])
                                .append(";")
                                .append(wtfIsThis[1])
                                .append(";")
                                .append(wtfIsThis[2])
                                .append(";")
                                .append(wtfIsThis[3])
                                .append(";");
                    } else {
                        int cnt = 0;
                        char[] arr = string.toCharArray();
                        char[] output = new char[arr.length];
                        boolean wasSpace = false;
                        charsBuilder.setLength(0);
                        for (char c : arr) {
                            if (Character.isWhitespace(c)) {
                                wasSpace = true;
                            } else {
                                if (wasSpace) {
                                    wasSpace = false;
                                    output[cnt++] = ';';
                                }
                                output[cnt++] = c;
                            }
                        }
                        resultString.append(header).append(String.valueOf(output, 0, cnt));
                        try {
                            out.write(resultString.toString());
                            out.newLine();
                            resultString.setLength(0);
                        } catch (IOException e) {
                            e.printStackTrace();
                        }
                    }
                });
            } catch (IOException e) {
                e.printStackTrace();
            }
        } catch (IOException e) {
            e.printStackTrace();
        }
        System.out.println("Elapsed time: " + (System.currentTimeMillis() - start));
    }
}