private void buttonGo_Click(object sender, EventArgs e)
{
//Check if we have fileNames in the sparse matrix and index text box
if (radioButtonFormatProtein.Checked && comboBoxProteinContent.SelectedIndex == -1)
{
MessageBox.Show("Please select a protein quantitation type");
return;
}
buttonGo.Text = "Processing!";
this.Update();
toolStripStatusLabel2.Text = "Working...";
this.Update();
DateTime beginTime = DateTime.Now;
if (radioButtonSEPro.Checked)
{
if (radioButtonFormatPeptide.Checked || radioButtonFormatUniquePeptide.Checked)
{
PeptideParser pp = new PeptideParser();
pp.MyParameters = GetParametersFromGUI();
theParser = pp;
}
else
{
ProteinParser pp = new ProteinParser();
pp.UseNSAF = checkBoxNSAF.Checked;
pp.UseMaxParsimony = checkBoxUseMaxParsimony.Checked;
pp.MyParameters = GetParametersFromGUI();
theParser = pp;
}
}
else if (radioButtonPepExplorer.Checked)
{
PepExplorerParser pp = new PepExplorerParser();
theParser = pp;
}
else
{
MessageBox.Show("Please select a software (SEPro / PepExplorer)");
return;
}
theParser.ParseDirs(multipleDirectorySelector1.MyDirectoryDescriptionDictionary);
theParser.ProcessParsedData();
buttonGo.Text = "Go!";
if (radioButtonFormatProtein.Checked)
{
GenerateBirdsEyeView();
buttonSaveBirdsEyeView.Enabled = true;
}
buttonSavePatternLabProject.Enabled = true;
toolStripStatusLabel2.Text = "Processing time: " + Math.Ceiling((DateTime.Now - beginTime).TotalMilliseconds).ToString() + " ms.";
}
private void GenerateBirdsEyeView()
{
if (radioButtonPepExplorer.Checked)
{
buttonSaveBirdsEyeView.Enabled = false;
return;
}
else
{
buttonSaveBirdsEyeView.Enabled = true;
}
ProteinParser pp = (ProteinParser)theParser;
double[,] results = new double[pp.MyResultPackages.Count * 5, pp.TheIndex.Count];
for (int x1 = 0; x1 < pp.MyResultPackages.Count; x1++)
{
ResultEntry re = pp.MyResultPackages[x1];
//Calculate NSAF Factor
double nsafDenominator = 0;
for (int y = 0; y < pp.TheIndex.Count; y++)
{
ProteinIndexStruct i = pp.TheIndex[y];
int index = re.MyResultPackage.MyProteins.MyProteinList.FindIndex(a => a.Locus.Equals(i.Locus));
if (index > -1)
{
nsafDenominator += (double)re.MyResultPackage.MyProteins.MyProteinList[index].Scans.Count / (double)re.MyResultPackage.MyProteins.MyProteinList[index].Sequence.Length;
}
}
for (int y = 0; y < pp.TheIndex.Count; y++)
{
ProteinIndexStruct i = pp.TheIndex[y];
int index = re.MyResultPackage.MyProteins.MyProteinList.FindIndex(a => a.Locus.Equals(i.Locus));
int xPos = x1 * 5;
if (index > -1)
{
double nsaf = ((double)re.MyResultPackage.MyProteins.MyProteinList[index].Scans.Count / (double)re.MyResultPackage.MyProteins.MyProteinList[index].Length) / nsafDenominator;
results[xPos, y] = re.MyResultPackage.MyProteins.MyProteinList[index].ContainsUniquePeptide;
results[xPos + 1, y] = re.MyResultPackage.MyProteins.MyProteinList[index].PeptideResults.Count();
results[xPos + 2, y] = re.MyResultPackage.MyProteins.MyProteinList[index].Scans.Count;
results[xPos + 3, y] = nsaf;
results[xPos + 4, y] = re.MyResultPackage.MyProteins.MyProteinList[index].Coverage;
}
else
{
results[xPos, y] = -1.0;
results[xPos + 1, y] = -1.0;
results[xPos + 2, y] = -1.0;
results[xPos + 3, y] = -1.0;
results[xPos + 4, y] = -1.0;
}
}
}
dataGridViewBirdsEyeView.Columns.Clear();
dataGridViewBirdsEyeView.Rows.Clear();
foreach (ResultEntry re in pp.MyResultPackages)
{
var col = new DataGridViewTextBoxColumn();
col.HeaderText = re.ClassLabel + "::" + re.MyFileInfo.Name + "::" + "UniquePeptideCount";
col.HeaderCell.Style.Alignment = DataGridViewContentAlignment.MiddleLeft;
col.HeaderCell.Style.BackColor = PatternTools.pTools.color[re.ClassLabel + 1];
col.AutoSizeMode = DataGridViewAutoSizeColumnMode.DisplayedCells;
dataGridViewBirdsEyeView.Columns.Add(col);
var col2 = new DataGridViewTextBoxColumn();
col2.HeaderText = re.ClassLabel + "::" + re.MyFileInfo.Name + "::" + "PeptideCount";
col2.HeaderCell.Style.Alignment = DataGridViewContentAlignment.MiddleLeft;
col2.HeaderCell.Style.BackColor = PatternTools.pTools.color[re.ClassLabel + 1];
col2.AutoSizeMode = DataGridViewAutoSizeColumnMode.DisplayedCells;
dataGridViewBirdsEyeView.Columns.Add(col2);
var col3 = new DataGridViewTextBoxColumn();
col3.HeaderText = re.ClassLabel + "::" + re.MyFileInfo.Name + "::" + "SpecCount";
col3.HeaderCell.Style.Alignment = DataGridViewContentAlignment.MiddleLeft;
col3.HeaderCell.Style.BackColor = PatternTools.pTools.color[re.ClassLabel + 1];
col3.AutoSizeMode = DataGridViewAutoSizeColumnMode.DisplayedCells;
dataGridViewBirdsEyeView.Columns.Add(col3);
var col4 = new DataGridViewTextBoxColumn();
col4.HeaderText = re.ClassLabel + "::" + re.MyFileInfo.Name + "::" + "NSAF";
col4.HeaderCell.Style.Alignment = DataGridViewContentAlignment.MiddleLeft;
col4.HeaderCell.Style.BackColor = PatternTools.pTools.color[re.ClassLabel + 1];
col4.AutoSizeMode = DataGridViewAutoSizeColumnMode.DisplayedCells;
dataGridViewBirdsEyeView.Columns.Add(col4);
var col5 = new DataGridViewTextBoxColumn();
col5.HeaderText = re.ClassLabel + "::" + re.MyFileInfo.Name + "::" + "Coverage";
col5.HeaderCell.Style.Alignment = DataGridViewContentAlignment.MiddleLeft;
col5.HeaderCell.Style.BackColor = PatternTools.pTools.color[re.ClassLabel + 1];
col5.AutoSizeMode = DataGridViewAutoSizeColumnMode.DisplayedCells;
dataGridViewBirdsEyeView.Columns.Add(col5);
}
for (int y = 0; y < results.GetLength(1); y++)
{
int rowI = dataGridViewBirdsEyeView.Rows.Add();
dataGridViewBirdsEyeView.Rows[rowI].HeaderCell.Value = pp.TheIndex[y].Locus + "\t" + pp.TheIndex[y].Description;
for (int x = 0; x < results.GetLength(0); x++)
{
dataGridViewBirdsEyeView.Rows[y].Cells[x].Value = results[x, y];
}
}
this.Update();
}
