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InfiniteDiscoveryMachineSimulator.cs
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InfiniteDiscoveryMachineSimulator.cs
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using System;
using System.Collections.Generic;
using System.ComponentModel;
using System.Data;
using System.Drawing;
using System.Linq;
using System.Text;
using System.Threading.Tasks;
using System.Windows.Forms;
using System.IO;
using System.IO.Ports;
using System.Threading;
namespace Binomics_Labs_Software_Suite
{
public partial class InfiniteDiscoveryMachineSimulator : Form
{
public InfiniteDiscoveryMachineSimulator()
{
InitializeComponent();
string[] ports = SerialPort.GetPortNames();
foreach (string comport in ports)
{
cmbPortsList.Items.Add(comport);
}
if (cmbPortsList.Items.Count > 0)
{
cmbPortsList.SelectedIndex = 0;
}
}
//stats stuff
public int desiredRandomDNALength = 0;
public int countA = 0;
public int countT = 0;
public int countC = 0;
public int countG = 0;
public int avgRNG = 0;
public int sumRNG = 0;
public double percentA = 0.0;
public double percentT = 0.0;
public double percentC = 0.0;
public double percentG = 0.0;
public double percentRNG = 0.0;
//random generator stuff
public Random softwareRNG; //internal software RNG of low quality entropy pool, for demo purposes only until TrueRNG v3 class for handling 64bit numbers is made
public int[] rngRawNums;
public char[] rngNucleotides;
public string[] codons;
public string rngDNA;
public string rngRaw;
public bool generatorThreadComplete;
public bool hasHardwareRNG = false;
//shredder stuff
public int shredderCutPosition;
string choppedFragment;
string remainingFragment;
public List<string> fragments = new List<string>();
public List<int> fragLengths = new List<int>();
public int fragmentChoice;
public BackgroundWorker backgroundWorker = new BackgroundWorker();
public int shredderFragmentCount;
public int shredderFragmentLengthAverage;
public long shredderTotalBases;
//glue stuff
public List<string> ligatedFragments = new List<string>();
public List<int> ligatedFragLengths = new List<int>();
//filter stuff
public List<string> openReadingFramesPassList = new List<string>();
public List<string> openReadingFramesFailList = new List<string>();
public List<string> stopCodonPassList = new List<string>();
public List<string> stopCodonFailList = new List<string>();
public List<string> startCodonPassList = new List<string>();
public List<string> startCodonFailList = new List<string>();
public List<string> finalDNAList = new List<string>();
public List<string> finalProteinList = new List<string>();
//bitmap data vis stuff
public Bitmap bmpDNA;
public int entropyImageHeight;
public int colorPosition = 0;
public Color colorA;
public Color colorT;
public Color colorC;
public Color colorG;
public Color mouseColor;
//misc stuff
string desktopPath = Environment.GetFolderPath(System.Environment.SpecialFolder.DesktopDirectory);
private SerialPort rngPort = new SerialPort();
private int sensorBaud = 115200;
private void IDMsimulator_Load(object sender, EventArgs e)
{
pickNucleotideColor();
panel1.VerticalScroll.Visible = true;
}
private void IDMsimulator_FormClosing(object sender, FormClosingEventArgs e)
{
if (rngPort.IsOpen == true)
{
rngPort.DiscardInBuffer();
rngPort.DiscardOutBuffer();
rngPort.Dispose();
rngPort.Close();
}
}
public static IEnumerable<string> ChunksUpto(string str, int maxChunkSize)
{
for (int i = 0; i < str.Length; i += maxChunkSize)
{
yield return str.Substring(i, Math.Min(maxChunkSize, str.Length - i));
}
}
private void btnGenerate_Click(object sender, EventArgs e)
{
if (checkHardwareRNG.Checked)
{
try
{
UpdateStatusBar("Generating Truly Random DNA...");
desiredRandomDNALength = Convert.ToInt32(txtDNALength.Text);
rngPort = new SerialPort(cmbPortsList.Text, sensorBaud);
rngPort.DtrEnable = true;
rngPort.ReadBufferSize = desiredRandomDNALength;
rngPort.ReceivedBytesThreshold = desiredRandomDNALength;
if (rngPort.IsOpen == false)
{
rngPort.Open();
}
generateHardwareRandomDNA();
txtDNA.Text = rngDNA;
txtDNALength.Text = rngDNA.Length.ToString();
visualizeDNA(rngNucleotides);
computeStats();
}
catch
{
UpdateStatusBar("Can't seem to talk to the RNG. Check ports and restart app!");
}
}
else
{
UpdateStatusBar("Generating Pseudo-Random DNA...");
desiredRandomDNALength = Convert.ToInt32(txtDNALength.Text);
generateSoftwareRandomDNA();
txtDNA.Text = rngDNA;
txtDNALength.Text = rngDNA.Length.ToString();
visualizeDNA(rngNucleotides);
computeStats();
}
}
private void btnLoadFile_Click(object sender, EventArgs e)
{
Stream myStream = null;
OpenFileDialog openFileDialog1 = new OpenFileDialog();
rngDNA = "";
openFileDialog1.InitialDirectory = "c:\\";
openFileDialog1.Filter = "txt files (*.txt)|*.txt|All files (*.*)|*.*";
openFileDialog1.FilterIndex = 2;
openFileDialog1.RestoreDirectory = true;
if (openFileDialog1.ShowDialog() == DialogResult.OK)
{
try
{
if ((myStream = openFileDialog1.OpenFile()) != null)
{
using (myStream)
{
rngDNA = File.ReadAllText(openFileDialog1.FileName);
}
}
}
catch (Exception ex)
{
MessageBox.Show("Error: Could not read file from disk. Original error: " + ex.Message);
}
}
if (rngDNA.StartsWith("A") || rngDNA.StartsWith("T") || rngDNA.StartsWith("C") || rngDNA.StartsWith("G")) //check if input is DNA in all caps
{
txtDNA.Text = rngDNA;
txtDNALength.Text = rngDNA.Length.ToString();
desiredRandomDNALength = rngDNA.Length;
rngNucleotides = new char[desiredRandomDNALength];
rngNucleotides = rngDNA.ToCharArray();
visualizeDNA(rngNucleotides);
computeStats();
UpdateStatusBar("DNA Loaded!");
btnShred.Enabled = true;
btnSave.Enabled = true;
btnGlue.Enabled = true;
}
else
{
UpdateStatusBar("Check DNA input format. All caps, no craps!");
}
}
private void btnSave_Click(object sender, EventArgs e)
{
UpdateStatusBar("Saving Entropy Map to image file...");
bmpDNA.Save(desktopPath + "\\EntropyGraph " + DateTime.Now.ToString("MM-dd-yyyy HH.mm.ss") + ".png", System.Drawing.Imaging.ImageFormat.Png);
UpdateStatusBar("Entropy Map saved!");
}
private void btnShred_Click(object sender, EventArgs e)
{
shredderFragmentCount = 0;
shredderCutPosition = 0;
shredderFragmentLengthAverage = 0;
shredderTotalBases = 0;
fragments = new List<string>();
fragLengths = new List<int>();
fragments.Add(txtDNA.Text); //loads dna sequence into first slot of fragments list
fragLengths.Add(txtDNA.Text.Length);
Thread shredThread = new Thread(shredDNA);
shredThread.Start();
}
private void btnGlue_Click(object sender, EventArgs e)
{
ligatedFragments = new List<string>();
ligatedFragLengths = new List<int>();
openReadingFramesPassList = new List<string>();
openReadingFramesFailList = new List<string>();
stopCodonPassList = new List<string>();
stopCodonFailList = new List<string>();
startCodonPassList = new List<string>();
startCodonFailList = new List<string>();
finalDNAList = new List<string>();
finalProteinList = new List<string>();
Thread shredThread = new Thread(glueDNA);
shredThread.Start();
}
public void generateHardwareRandomDNA()
{
try
{
UpdateStatusBar("Generating Random DNA...");
rngRawNums = new int[desiredRandomDNALength];
rngNucleotides = new char[desiredRandomDNALength];
for (int i = 0; i < desiredRandomDNALength; i++)
{
UpdateStatusBar("Generating Random DNA..." + ((i / desiredRandomDNALength) * 100).ToString());
rngRawNums[i] = rngPort.ReadByte();
if (rngRawNums[i] >= 0 && rngRawNums[i] <= 63)
{
rngNucleotides[i] = 'A';
}
else if (rngRawNums[i] >= 64 && rngRawNums[i] <= 127)
{
rngNucleotides[i] = 'T';
}
else if (rngRawNums[i] >= 128 && rngRawNums[i] <= 191)
{
rngNucleotides[i] = 'G';
}
else if (rngRawNums[i] >= 192 && rngRawNums[i] <= 255)
{
rngNucleotides[i] = 'C';
}
}
rngDNA = string.Join("", rngNucleotides);
rngRaw = string.Join(" ", rngRawNums);
rngPort.Close();
UpdateStatusBar("Generation Complete!");
txtDNA.Invoke((MethodInvoker)delegate
{
txtDNA.Text = rngDNA;
});
txtRawData.Invoke((MethodInvoker)delegate
{
txtRawData.Text = rngRaw;
});
btnShred.Invoke((MethodInvoker)delegate
{
btnShred.Enabled = true;
});
btnSave.Invoke((MethodInvoker)delegate
{
btnSave.Enabled = true;
});
btnGlue.Invoke((MethodInvoker)delegate
{
btnGlue.Enabled = true;
});
txtDNA.Invoke((MethodInvoker)delegate
{
txtDNA.Text = rngDNA;
});
txtDNALength.Invoke((MethodInvoker)delegate
{
txtDNALength.Text = rngDNA;
});
generatorThreadComplete = true;
}
catch (Exception e)
{
UpdateStatusBar("Generation Error. Check RNG connection...");
rngPort.Close();
MessageBox.Show(e.Message);
}
}
public void generateSoftwareRandomDNA()
{
try
{
UpdateStatusBar("Generating Pseudo-Random DNA...");
rngRawNums = new int[desiredRandomDNALength];
rngNucleotides = new char[desiredRandomDNALength];
softwareRNG = new Random();
for (int i = 0; i < desiredRandomDNALength; i++)
{
UpdateStatusBar("Generating Pseudo-Random DNA..." + ((i / desiredRandomDNALength) * 100).ToString());
rngRawNums[i] = softwareRNG.Next(0, 255); //use internal software RNG
if (rngRawNums[i] >= 0 && rngRawNums[i] <= 63)
{
rngNucleotides[i] = 'A';
}
else if (rngRawNums[i] >= 64 && rngRawNums[i] <= 127)
{
rngNucleotides[i] = 'T';
}
else if (rngRawNums[i] >= 128 && rngRawNums[i] <= 191)
{
rngNucleotides[i] = 'G';
}
else if (rngRawNums[i] >= 192 && rngRawNums[i] <= 255)
{
rngNucleotides[i] = 'C';
}
}
rngDNA = string.Join("", rngNucleotides);
rngRaw = string.Join(" ", rngRawNums);
UpdateStatusBar("Generation Complete!");
txtDNA.Invoke((MethodInvoker)delegate
{
txtDNA.Text = rngDNA;
});
txtRawData.Invoke((MethodInvoker)delegate
{
txtRawData.Text = rngRaw;
});
btnShred.Invoke((MethodInvoker)delegate
{
btnShred.Enabled = true;
});
btnSave.Invoke((MethodInvoker)delegate
{
btnSave.Enabled = true;
});
btnGlue.Invoke((MethodInvoker)delegate
{
btnGlue.Enabled = true;
});
txtDNA.Invoke((MethodInvoker)delegate
{
txtDNA.Text = rngDNA;
});
txtDNALength.Invoke((MethodInvoker)delegate
{
txtDNALength.Text = rngDNA;
});
generatorThreadComplete = true;
}
catch (Exception e)
{
UpdateStatusBar("Internal Software RNG error...");
MessageBox.Show(e.Message);
}
}
public void computeStats()
{
countA = 0;
countT = 0;
countC = 0;
countG = 0;
avgRNG = 0;
sumRNG = 0;
foreach (char nucleotide in rngNucleotides)
{
if (nucleotide == 'A')
{
countA++;
}
else if (nucleotide == 'T')
{
countT++;
}
else if (nucleotide == 'C')
{
countC++;
}
else if (nucleotide == 'G')
{
countG++;
}
}
try
{
}
catch
{
foreach (int num in rngRawNums)
{
sumRNG = sumRNG + num;
}
avgRNG = sumRNG / rngRawNums.Length;
}
percentA = Math.Truncate((countA / Convert.ToDouble(rngNucleotides.Length)) * 100);
percentT = Math.Truncate((countT / Convert.ToDouble(rngNucleotides.Length)) * 100);
percentC = Math.Truncate((countC / Convert.ToDouble(rngNucleotides.Length)) * 100);
percentG = Math.Truncate((countG / Convert.ToDouble(rngNucleotides.Length)) * 100);
}
public Image visualizeDNA(char[] input)
{
pickNucleotideColor();
if (desiredRandomDNALength / picEntropy.Width < 1)
{
entropyImageHeight = 1;
}
else
{
entropyImageHeight = desiredRandomDNALength / picEntropy.Width;
}
bmpDNA = new Bitmap(picEntropy.Width, entropyImageHeight);
if (desiredRandomDNALength > picEntropy.Width)
{
for (int y = 0; y < entropyImageHeight; y++)
{
for (int x = 0; x < picEntropy.Width; x++)
{
if (input[colorPosition] == 'A')
{
bmpDNA.SetPixel(x, y, colorA);
colorPosition++;
}
else if (input[colorPosition] == 'T')
{
bmpDNA.SetPixel(x, y, colorT);
colorPosition++;
}
else if (input[colorPosition] == 'G')
{
bmpDNA.SetPixel(x, y, colorG);
colorPosition++;
}
else if (input[colorPosition] == 'C')
{
bmpDNA.SetPixel(x, y, colorC);
colorPosition++;
}
}
}
}
else
{
for (int i = 0; i < desiredRandomDNALength; i++)
{
if (input[colorPosition] == 'A')
{
bmpDNA.SetPixel(i, 0, colorA);
colorPosition++;
}
else if (input[colorPosition] == 'T')
{
bmpDNA.SetPixel(i, 0, colorT);
colorPosition++;
}
else if (input[colorPosition] == 'G')
{
bmpDNA.SetPixel(i, 0, colorG);
colorPosition++;
}
else if (input[colorPosition] == 'C')
{
bmpDNA.SetPixel(i, 0, colorC);
colorPosition++;
}
}
}
picEntropy.SizeMode = PictureBoxSizeMode.AutoSize;
picEntropy.Image = bmpDNA;
colorPosition = 0;
return bmpDNA;
}
public void pickNucleotideColor()
{
try
{
colorA = Color.FromArgb(0, 230, 255); //cyan
colorT = Color.FromArgb(255, 255, 0); //yellow
colorC = Color.FromArgb(220, 0, 0); //red
colorG = Color.FromArgb(0, 0, 0); //black
/*
colorA = Color.FromArgb(Convert.ToInt16(txtColorAred.Text),
Convert.ToInt16(txtColorAgreen.Text),
Convert.ToInt16(txtColorAblue.Text));
colorT = Color.FromArgb(Convert.ToInt16(txtColorTred.Text),
Convert.ToInt16(txtColorTgreen.Text),
Convert.ToInt16(txtColorTblue.Text));
colorC = Color.FromArgb(Convert.ToInt16(txtColorCred.Text),
Convert.ToInt16(txtColorCgreen.Text),
Convert.ToInt16(txtColorCblue.Text));
colorG = Color.FromArgb(Convert.ToInt16(txtColorGred.Text),
Convert.ToInt16(txtColorGgreen.Text),
Convert.ToInt16(txtColorGblue.Text));
panColorPickerA.BackColor = colorA;
panColorPickerT.BackColor = colorT;
panColorPickerG.BackColor = colorG;
panColorPickerC.BackColor = colorC;
*/
}
catch (Exception e)
{
MessageBox.Show(e.Message);
}
}
public void shredDNA()
{
UpdateStatusBar("Shredding DNA...");
string currentFragment;
softwareRNG = new Random();
while (fragLengths.Average() > 4)
{
UpdateStatusBar("Shredding DNA..." + Math.Ceiling(((4.00/(fragLengths.Average()))*100)).ToString()+"%");
fragmentChoice = softwareRNG.Next(0, fragments.Count);
if (fragments[fragmentChoice].Length > 4)
{
shredderCutPosition = softwareRNG.Next(1, fragments[fragmentChoice].Length - 1);
currentFragment = fragments[fragmentChoice];
choppedFragment = currentFragment.Substring(0, shredderCutPosition);
remainingFragment = currentFragment.Substring(shredderCutPosition);
if (choppedFragment.Length > 0 && remainingFragment.Length > 0)
{
fragments.Add(choppedFragment);
fragLengths.Add(choppedFragment.Length);
fragments.Add(remainingFragment);
fragLengths.Add(remainingFragment.Length);
fragments.Remove(currentFragment);
fragLengths.Remove(currentFragment.Length);
shredderFragmentCount = fragLengths.Count();
shredderFragmentLengthAverage = Convert.ToInt32(Math.Ceiling(fragLengths.Average()));
shredderTotalBases = fragLengths.Sum();
}
}
}
UpdateStatusBar("Writing Shreds to file...");
using (var countFile = File.CreateText(desktopPath + "\\Fragmentation Length Data" + DateTime.Now.ToBinary().ToString() + ".csv"))
{
foreach (int fragLength in fragLengths)
{
countFile.WriteLine(string.Join(",", fragLength.ToString()));
}
}
using (var fragFile = File.CreateText(desktopPath + "\\Fragmentation Pool" + DateTime.Now.ToBinary().ToString() + ".csv"))
{
foreach (string fragment in fragments)
{
fragFile.WriteLine(string.Join(",", fragment));
}
}
UpdateStatusBar("Shredding Complete!");
}
public void glueDNA()
{
UpdateStatusBar("Ligating DNA..." + Math.Ceiling((((fragLengths.Average())/500) * 100)).ToString() + "%");
ligatedFragments = fragments;
ligatedFragLengths = fragLengths;
while (shredderFragmentLengthAverage < 2000)
{
UpdateStatusBar("Ligating DNA..." + Math.Ceiling((((fragLengths.Average()) / 500) * 100)).ToString() + "%");
int firstFragmentChoice = softwareRNG.Next(0, fragments.Count);
string firstFragment = fragments[firstFragmentChoice];
int secondFragmentChoice = softwareRNG.Next(0, fragments.Count);
string secondFragment = fragments[secondFragmentChoice];
if (firstFragmentChoice != secondFragmentChoice)
{
string gluedFragment = string.Concat(ligatedFragments[firstFragmentChoice], ligatedFragments[secondFragmentChoice]);
ligatedFragments.Add(gluedFragment);
ligatedFragLengths.Add(gluedFragment.Length);
ligatedFragments.Remove(firstFragment);
ligatedFragments.Remove(secondFragment);
ligatedFragLengths.Remove(firstFragment.Length);
ligatedFragLengths.Remove(secondFragment.Length);
shredderFragmentCount = ligatedFragLengths.Count();
shredderFragmentLengthAverage = Convert.ToInt32((Math.Ceiling(ligatedFragLengths.Average())));
shredderTotalBases = (long)ligatedFragLengths.Sum();
}
}
UpdateStatusBar("Writing ligations to file...");
using (var ligLengthFile = File.CreateText(desktopPath + "\\Ligation Length Data" + DateTime.Now.ToBinary().ToString() + ".csv"))
{
foreach (int fragLength in fragLengths)
{
ligLengthFile.WriteLine(string.Join(",", fragLength.ToString()));
}
}
using (var ligPoolFile = File.CreateText(desktopPath + "\\Ligated DNA Pool" + DateTime.Now.ToBinary().ToString() + ".csv"))
{
foreach (string fragment in fragments)
{
ligPoolFile.WriteLine(string.Join(",", fragment));
}
}
UpdateStatusBar("Ligations Complete!");
filterDNA();
}
public void filterDNA()
{
UpdateStatusBar("Filtering DNA...");
foreach (string fragment in fragments)
{
if (fragment.Length % 3 == 0)
{
openReadingFramesPassList.Add(fragment);
}
else
{
openReadingFramesFailList.Add(fragment);
}
}
if (openReadingFramesPassList.Count > 0) //check for stop codons inside ORF
{
foreach (string ORF in openReadingFramesPassList)
{
codons = ChunksUpto(ORF, 3).ToArray<string>();
bool stopDetected = codons.Contains("TAA") || codons.Contains("TAG") || codons.Contains("TGA");
if (stopDetected)
{
stopCodonFailList.Add(ORF);
}
else
{
stopCodonPassList.Add(ORF);
}
}
}
if (stopCodonPassList.Count > 0) //change to startCodonPassList if you want to screen for METs as well
{
UpdateStatusBar("Adding IDM motiffs...");
foreach (string ORF in stopCodonPassList)
{
string polishedFragment = "ATG" + ORF + "CATCACCATCACCATCACTTATAATAA";
finalDNAList.Add(polishedFragment);
}
using (var finalDNAFile = File.CreateText(desktopPath + "\\IDM Final DNA Data" + DateTime.Now.ToBinary().ToString() + ".csv"))
{
foreach (string cds in finalDNAList)
{
finalDNAFile.WriteLine(string.Join(",", cds));
}
}
}
if (finalDNAList.Count > 0)
{
UpdateStatusBar("Writing proteins to file...");
foreach (string CDS in finalDNAList)
{
finalProteinList.Add(ConvertToProtein(CDS));
}
using (var finalProteinFile = File.CreateText(desktopPath + "\\IDM Final Protein Data" + DateTime.Now.ToBinary().ToString() + ".csv"))
{
foreach (string cds in finalProteinList)
{
finalProteinFile.WriteLine(string.Join(",", cds));
}
}
}
UpdateStatusBar("Filtration Complete!");
}
public string ConvertToProtein(string inputDNA)
{
string cds = "";
codons = ChunksUpto(inputDNA, 3).ToArray<string>();
for (int i = 0; i < codons.Length; i++)
{
switch (codons[i])
{
case "TGG":
cds += "W";
break;
case "TAC":
cds += "Y";
break;
case "TAT":
cds += "Y";
break;
case "TGC":
cds += "C";
break;
case "TGT":
cds += "C";
break;
case "GAA":
cds += "E";
break;
case "GAG":
cds += "E";
break;
case "AAA":
cds += "K";
break;
case "AAG":
cds += "K";
break;
case "CAA":
cds += "Q";
break;
case "CAG":
cds += "Q";
break;
case "AGC":
cds += "S";
break;
case "AGT":
cds += "S";
break;
case "TCA":
cds += "S";
break;
case "TCC":
cds += "S";
break;
case "TCG":
cds += "S";
break;
case "TCT":
cds += "S";
break;
case "TTA":
cds += "L";
break;
case "TTG":
cds += "L";
break;
case "CTA":
cds += "L";
break;
case "CTC":
cds += "L";
break;
case "CTG":
cds += "L";
break;
case "CTT":
cds += "L";
break;
case "AGA":
cds += "R";
break;
case "AGG":
cds += "R";
break;
case "CGA":
cds += "R";
break;
case "CGC":
cds += "R";
break;
case "CGG":
cds += "R";
break;
case "CGT":
cds += "R";
break;
case "GGA":
cds += "G";
break;
case "GGC":
cds += "G";
break;
case "GGG":
cds += "G";
break;
case "GGT":
cds += "G";
break;
case "TTC":
cds += "F";
break;
case "TTT":
cds += "F";
break;
case "GAC":
cds += "D";
break;
case "GAT":
cds += "D";
break;
case "CAC":
cds += "H";
break;
case "CAT":
cds += "H";
break;
case "AAC":
cds += "N";
break;
case "AAT":
cds += "N";
break;
case "ATG":
cds += "M";
break;
case "GCA":
cds += "A";