using System;
using System.IO;

public class readsynth
{
    //Extract deprotection readings from 433A Applied Biosciences peptide synthesizer log files
    //V.V. 03/01/2011. vvostri@gmail.com
    public static void Main()
    {
        string filename;

        do
        {

            int Ncoupl = 1; //Since resin has Fmoc on
            bool error = false;

            Console.WriteLine("Enter synthesizer log file name (letter case is not important)");
            filename = Console.ReadLine();

            if (File.Exists(filename))
            {
                StreamReader streamvariable = File.OpenText(filename);
                string lineinfile;

                lineinfile = streamvariable.ReadLine();
                while (!lineinfile.Contains("Start"))
                {
                        lineinfile = streamvariable.ReadLine();

                        if (lineinfile == null)
                        {
                            Console.ForegroundColor = ConsoleColor.Red;
                            Console.WriteLine("Problem encountered. Append \"Start\" on the first line of the log");
                            Console.ForegroundColor = ConsoleColor.Gray;
                            error = true;
                            lineinfile = "Start";
                        }

                }

                while (lineinfile != null)
                {
                    if (lineinfile.Contains("Cartridge"))
                    {
                        if (lineinfile.Contains("Sending"))
                        { }
                        else
                        {
                            Ncoupl++;
                        }
                    }
                    lineinfile = streamvariable.ReadLine();
                }
                streamvariable.Close();

                int[,] readings = new int[2, Ncoupl * 10];
                string[] sequence = new string[Ncoupl * 10];
                string[] seq = new string[Ncoupl];

                for (int index = 0; index != Ncoupl * 10; index++)
                {
                    readings[0, index] = index;
                }

                Ncoupl = 0;
                int counter = 0;
                streamvariable = File.OpenText(filename);
                lineinfile = streamvariable.ReadLine();

                while (!lineinfile.Contains("Start"))
                {
                    lineinfile = streamvariable.ReadLine();

                    if (lineinfile == null)
                    {
                        lineinfile = "Start";
                    }

                }

                while (lineinfile != null)
                {
                    if (lineinfile.Contains("Cartridge"))
                    {
                        if (lineinfile.Contains("Sending"))
                        { }
                        else
                        {
                            Ncoupl++;
                            string[] split = lineinfile.Split(new string[] { "  " }, StringSplitOptions.None);
                            seq[Ncoupl] = split[1];
                            counter++;
                            while (counter % 10 != 0)
                            {
                                counter++;
                            }
                            split = lineinfile.Split(new string[] { "  " }, StringSplitOptions.None);

                            try
                            {
                                sequence[counter] = split[1];
                            }
                            catch
                            {
                                Console.ForegroundColor = ConsoleColor.Red;
                                Console.WriteLine("Problem encountered. Is number of deprotections 10+ for one of the residues?");
                                Console.ForegroundColor = ConsoleColor.Gray;
                                error = true;
                            }

                        }
                    }
                    sequence[0] = "resin";
                    seq[0] = "resin";
                    if (lineinfile.Contains("Peak"))
                    {
                        string[] split = lineinfile.Split(new string[] { "Peak " }, StringSplitOptions.None);

                        try
                        {
                            readings[1, counter] = Convert.ToInt16(split[1]);
                        }
                        catch
                        {
                            error = true;
                        }

                        counter++;

                    }
                    lineinfile = streamvariable.ReadLine();
                }
                streamvariable.Close();

                FileStream file = new FileStream(filename + ".csv", FileMode.Create, FileAccess.Write);
                StreamWriter sw = new StreamWriter(file);
                {
                    for (counter = 0; counter != (Ncoupl + 1) * 10; counter++)
                    {
                        sw.Write(readings[0, counter]);
                        sw.Write(",");
                        sw.Write(readings[1, counter]);
                        sw.Write(",");
                        sw.Write(sequence[counter]);
                        if (counter < Ncoupl +1)
                        {
                            sw.Write(",");
                            sw.Write(seq[counter]);
                        }
                        sw.Write("\r\n");
                    }

                }
                sw.Close();
                file.Close();

                if (error == true)
                {
                    Console.WriteLine("Problems were encountered with file {0}.\n", filename);
                }
                else
                {
                    Console.WriteLine("File {0} has been converted\n", filename);
                }

            }
            else
            {
                Console.ForegroundColor = ConsoleColor.Red;
                Console.WriteLine("File {0} not found\n", filename);
                Console.ForegroundColor = ConsoleColor.Gray;
            }
        } while (filename != "quit");
    }
}