private void findGeneToolStripMenuItem_Click(object sender, EventArgs e)
{
if (CompleteScreening == null) return;
FormForNameRequest FormForRequest = new FormForNameRequest();
if (FormForRequest.ShowDialog() != System.Windows.Forms.DialogResult.OK) return;
int NumberOfPlates = CompleteScreening.ListPlatesActive.Count;
// loop on all the plate
for (int PlateIdx = 0; PlateIdx < NumberOfPlates; PlateIdx++)
{
cPlate CurrentPlateToProcess = CompleteScreening.ListPlatesActive.GetPlate(CompleteScreening.ListPlatesActive[PlateIdx].Name);
for (int IdxValue = 0; IdxValue < CompleteScreening.Columns; IdxValue++)
for (int IdxValue0 = 0; IdxValue0 < CompleteScreening.Rows; IdxValue0++)
{
cWell TmpWell = CurrentPlateToProcess.GetWell(IdxValue, IdxValue0, true);
if (TmpWell == null) continue;
if (TmpWell.Name == FormForRequest.textBoxForName.Text)
{
CurrentPlateToProcess.DisplayDistribution(CompleteScreening.ListDescriptors.CurrentSelectedDescriptor, false);
int Col = IdxValue + 1;
int row = IdxValue0 + 1;
MessageBox.Show("Column " + Col + " x Row " + row, TmpWell.Name, MessageBoxButtons.OK, MessageBoxIcon.Information);
return;
}
}
}
MessageBox.Show("Gene not found !", FormForRequest.textBoxForName.Text, MessageBoxButtons.OK, MessageBoxIcon.Warning);
}
private void findPathwayToolStripMenuItem_Click(object sender, EventArgs e)
{
if (CompleteScreening == null) return;
FormForNameRequest FormForRequest = new FormForNameRequest();
if (FormForRequest.ShowDialog() != System.Windows.Forms.DialogResult.OK) return;
int NumberOfPlates = CompleteScreening.ListPlatesActive.Count;
FormForKeggGene KeggWin = new FormForKeggGene();
KEGG ServKegg = new KEGG();
string[] intersection_gene_pathways = new string[1];
string[] Pathways = { FormForRequest.textBoxForName.Text };
intersection_gene_pathways = ServKegg.get_genes_by_pathway("path:" + Pathways[0]);
if ((Pathways == null) || (Pathways.Length == 0))
{
MessageBox.Show("No pathway founded !", "Warning", MessageBoxButtons.OK, MessageBoxIcon.Exclamation);
return;
}
string[] fg_list = { "black" };
string[] bg_list = { "orange" };
string pathway_map_html = "";
// KEGG ServKegg = new KEGG();
string[] ListGenesinPathway = ServKegg.get_genes_by_pathway("path:" + Pathways[0]);
if (ListGenesinPathway.Length == 0)
{
return;
}
double[] ListValues = new double[ListGenesinPathway.Length];
int IDxGeneOfInterest = 0;
foreach (cPlate CurrentPlate in CompleteScreening.ListPlatesActive)
{
foreach (cWell CurrentWell in CurrentPlate.ListActiveWells)
{
string CurrentLID = "hsa:" + (int)CurrentWell.LocusID;
for (int IdxGene = 0; IdxGene < ListGenesinPathway.Length; IdxGene++)
{
if (CurrentLID == intersection_gene_pathways[0])
IDxGeneOfInterest = IdxGene;
if (CurrentLID == ListGenesinPathway[IdxGene])
{
ListValues[IdxGene] = CurrentWell.ListDescriptors[CompleteScreening.ListDescriptors.CurrentSelectedDescriptor].GetValue();
break;
}
}
}
}
bg_list = new string[ListGenesinPathway.Length];
fg_list = new string[ListGenesinPathway.Length];
double MinValue = ListValues.Min();
double MaxValue = ListValues.Max();
for (int IdxCol = 0; IdxCol < bg_list.Length; IdxCol++)
{
int ConvertedValue = (int)((((CompleteScreening.GlobalInfo.LUTs.LUT_GREEN_TO_RED[0].Length - 1) * (ListValues[IdxCol] - MinValue)) / (MaxValue - MinValue)));
Color Coul = Color.FromArgb(CompleteScreening.GlobalInfo.LUTs.LUT_GREEN_TO_RED[0][ConvertedValue], CompleteScreening.GlobalInfo.LUTs.LUT_GREEN_TO_RED[1][ConvertedValue], CompleteScreening.GlobalInfo.LUTs.LUT_GREEN_TO_RED[2][ConvertedValue]);
if (IdxCol == IDxGeneOfInterest)
fg_list[IdxCol] = "white";
else
fg_list[IdxCol] = "#000000";
bg_list[IdxCol] = "#" + Coul.Name.Remove(0, 2);
}
// foreach (string item in ListP.listBoxPathways.SelectedItems)
{
pathway_map_html = ServKegg.get_html_of_colored_pathway_by_objects(Pathways[0], ListGenesinPathway, fg_list, bg_list);
}
pathway_map_html = ServKegg.get_html_of_colored_pathway_by_objects((string)(Pathways[0]), intersection_gene_pathways, fg_list, bg_list);
// FormForKegg KeggWin = new FormForKegg();
if (pathway_map_html.Length == 0) return;
//
//KeggWin.Show();
//ListP.listBoxPathways.MouseDoubleClick += new MouseEventHandler(listBox1_MouseDoubleClick);
KeggWin.webBrowser.Navigate(pathway_map_html);
KeggWin.Show();
}
private void SingleCellOperationPhenotypToDesc(object sender, EventArgs e)
{
string description = "This descriptor has been generated by converting single cell phenotypic class into feature\n";
FormForNameRequest FFNR = new FormForNameRequest();
FFNR.Text = "Descriptor Name";
FFNR.textBoxForName.Text = "Phenotype Class";
if (FFNR.ShowDialog() != System.Windows.Forms.DialogResult.OK) return;
if (FFNR.textBoxForName.Text == "") return;
cDescriptorType NewDescType = new cDescriptorType(FFNR.textBoxForName.Text, true, cGlobalInfo.ListCellularPhenotypes.Count, true);
cGlobalInfo.CurrentScreening.ListDescriptors.AddNew(NewDescType);
FormForProgress ProgressWindow = new FormForProgress();
ProgressWindow.Show();
int IdxProgress = 0;
int MaxProgress = 0;
foreach (cPlate CurrentPlateToProcess in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
MaxProgress += (int)CurrentPlateToProcess.ListActiveWells.Count;
ProgressWindow.progressBar.Maximum = MaxProgress;
foreach (cPlate CurrentPlate in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
{
CurrentPlate.DBConnection.OpenConnection();
CurrentPlate.DBConnection.CreateNewColumnFromExisting(NewDescType, "Phenotype_Class", GlobalInfo, ref CurrentPlate.ListActiveWells);
CurrentPlate.DBConnection.CloseConnection();
ProgressWindow.progressBar.Value = IdxProgress++;
ProgressWindow.progressBar.Refresh();
}
ProgressWindow.Close();
int IdxNull = 0;
foreach (cPlate TmpPlate in cGlobalInfo.CurrentScreening.ListPlatesActive)
{
foreach (cWell TmpWell in TmpPlate.ListActiveWells)
if (TmpWell.ListSignatures.Count != cGlobalInfo.CurrentScreening.ListDescriptors.Count)
IdxNull++;
}
if (IdxNull > 0)
System.Windows.Forms.MessageBox.Show("List signature count is different from list descriptor count", "Critical Error !", MessageBoxButtons.OK, MessageBoxIcon.Error);
cGlobalInfo.CurrentScreening.ListDescriptors.UpDateDisplay();
// CompleteScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < cGlobalInfo.CurrentScreening.ListPlatesAvailable.Count; idxP++)
cGlobalInfo.CurrentScreening.ListPlatesActive[idxP].UpDataMinMax();
StartingUpDateUI();
this.toolStripcomboBoxPlateList.Items.Clear();
for (int IdxPlate = 0; IdxPlate < cGlobalInfo.CurrentScreening.ListPlatesActive.Count; IdxPlate++)
{
string Name = cGlobalInfo.CurrentScreening.ListPlatesActive.GetPlate(IdxPlate).GetName();
this.toolStripcomboBoxPlateList.Items.Add(Name);
PlateListWindow.listBoxPlateNameToProcess.Items.Add(Name);
PlateListWindow.listBoxAvaliableListPlates.Items.Add(Name);
}
cGlobalInfo.CurrentScreening.CurrentDisplayPlateIdx = 0;
cGlobalInfo.CurrentScreening.SetSelectionType(comboBoxClass.SelectedIndex - 1);
UpdateUIAfterLoading();
cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().DisplayDistribution(cGlobalInfo.CurrentScreening.ListDescriptors.GetActiveDescriptor(), false);
}
