void listBox1_MouseDoubleClick(object sender, MouseEventArgs e)
{
string[] fg_list = { "black" };
string[] bg_list = { "orange" };
string[] intersection_gene_pathways = new string[1];
intersection_gene_pathways[0] = "hsa:" + LocusID;
string pathway_map_html = "";
KEGG ServKegg = new KEGG();
foreach (string item in ListP.listBoxPathways.SelectedItems)
{
pathway_map_html = ServKegg.get_html_of_colored_pathway_by_objects(item, intersection_gene_pathways, fg_list, bg_list);
}
string GenInfo = ServKegg.bget((string)ListP.listBoxPathways.SelectedItem);
string[] Genes = GenInfo.Split(new char[] { '\n' });
string Res = "";
foreach (string item in Genes)
{
string[] fre = item.Split(' ');
string[] STRsection = fre[0].Split('_');
if (STRsection[0] != "NAME") continue;
for (int i = 1; i < fre.Length; i++)
{
if (fre[i] == "") continue;
Res += fre[i] + " ";
}
}
FormForKegg KeggWin = new FormForKegg();
if (pathway_map_html.Length == 0) return;
KeggWin.Text = Res;
KeggWin.Show();
KeggWin.webBrowser.Navigate(pathway_map_html);
}
void DisplayPathways(object sender, EventArgs e)
{
if (LocusID == -1) return;
FormForKeggGene KeggWin = new FormForKeggGene();
KEGG ServKegg = new KEGG();
string[] intersection_gene_pathways = new string[1];
intersection_gene_pathways[0] = "hsa:" + LocusID;
string[] Pathways = ServKegg.get_pathways_by_genes(intersection_gene_pathways);
if ((Pathways == null) || (Pathways.Length == 0))
{
MessageBox.Show("No pathway founded !", "Warning", MessageBoxButtons.OK, MessageBoxIcon.Exclamation);
return;
}
string GenInfo = ServKegg.bget(intersection_gene_pathways[0]);
// FormForPathway PathwaysGenes = new FormForPathway();
KeggWin.richTextBox.Text = GenInfo;
KeggWin.Text = "Gene Infos";
//PathwaysGenes.Show();
ListP = new FormForPathway();
ListP.listBoxPathways.DataSource = Pathways;
ListP.Text = this.Name;
ListP.Show();
//foreach (string item in Pathways)
//{
// string PathwayInfo = ServKegg.bget(item);
// FormPathwaysGenes PathwaysGenes = new FormPathwaysGenes();
// PathwaysGenes.richTextBox1.Text = PathwayInfo;
// PathwaysGenes.Text = "Pathways Infos";
// PathwaysGenes.Show();
//}
string[] fg_list = { "black" };
string[] bg_list = { "orange" };
// string[] intersection_gene_pathways = new string[1];
// intersection_gene_pathways[0] = "hsa:" + LocusID;
string pathway_map_html = "";
// KEGG ServKegg = new KEGG();
pathway_map_html = ServKegg.get_html_of_colored_pathway_by_objects((string)(ListP.listBoxPathways.SelectedItem), 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 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 FormForPie PathWayAnalysis(int Class)
{
//int Idx = 0;
int NumberOfPlates = CompleteScreening.ListPlatesActive.Count;
KEGG ServKegg = new KEGG();
List<cPathWay> ListPathway = new List<cPathWay>();
// 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) || (TmpWell.GetClass() != Class) || (TmpWell.LocusID == -1)) continue;
string[] intersection_gene_pathways = new string[1];
intersection_gene_pathways[0] = "hsa:" + TmpWell.LocusID;
string[] Pathways = ServKegg.get_pathways_by_genes(intersection_gene_pathways);
if ((Pathways == null) || (Pathways.Length == 0)) continue;
for (int Idx = 0; Idx < Pathways.Length; Idx++)
{
// string PathName = Pathways[Idx].Remove(0, 8);
string GenInfo = ServKegg.bget(Pathways[Idx]);
string[] Genes = GenInfo.Split(new char[] { '\n' });
string PathName = "";
foreach (string item in Genes)
{
string[] fre = item.Split(' ');
string[] STRsection = fre[0].Split('_');
if (STRsection[0] == "NAME")
{
for (int i = 1; i < fre.Length; i++)
{
if (fre[i] == "") continue;
PathName += fre[i] + " ";
}
break;
}
}
if (ListPathway.Count == 0)
{
cPathWay CurrPath = new cPathWay();
CurrPath.Name = PathName;
CurrPath.Occurence = 1;
ListPathway.Add(CurrPath);
continue;
}
bool DidIt = false;
for (int i = 0; i < ListPathway.Count; i++)
{
if (PathName == ListPathway[i].Name)
{
ListPathway[i].Occurence++;
DidIt = true;
break;
}
}
if (DidIt == false)
{
cPathWay CurrPath1 = new cPathWay();
CurrPath1.Name = PathName;
CurrPath1.Occurence = 1;
ListPathway.Add(CurrPath1);
}
}
}
}
// now draw the pie
if (ListPathway.Count == 0)
{
MessageBox.Show("No pathway identified !", "Information", MessageBoxButtons.OK, MessageBoxIcon.Information);
return null;
}
FormForPie Pie = new FormForPie();
Series CurrentSeries = Pie.chartForPie.Series[0];
// loop on all the plate
int MaxOccurence = int.MinValue;
int MaxIdx = 0;
int TotalOcurrence = 0;
for (int Idx = 0; Idx < ListPathway.Count; Idx++)
{
if (ListPathway[Idx].Occurence > MaxOccurence)
{
MaxOccurence = ListPathway[Idx].Occurence;
MaxIdx = Idx;
}
TotalOcurrence += ListPathway[Idx].Occurence;
}
//CurrentSeries.CustomProperties = "PieLabelStyle=Outside";
for (int Idx = 0; Idx < ListPathway.Count; Idx++)
{
CurrentSeries.Points.Add(ListPathway[Idx].Occurence);
CurrentSeries.Points[Idx].Label = String.Format("{0:0.###}", ((100.0 * ListPathway[Idx].Occurence) / TotalOcurrence)) + " %";
CurrentSeries.Points[Idx].LegendText = ListPathway[Idx].Name;
CurrentSeries.Points[Idx].ToolTip = ListPathway[Idx].Name;
if (Idx == MaxIdx)
CurrentSeries.Points[Idx].SetCustomProperty("Exploded", "True");
}
return Pie;
}
void listBox1_MouseDoubleClick(object sender, MouseEventArgs e)
{
string[] fg_list = { "black" };
string[] bg_list = { "orange" };
string[] intersection_gene_pathways = new string[1];
intersection_gene_pathways[0] = "hsa:" + LocusID;
string pathway_map_html = "";
KEGG ServKegg = new KEGG();
string[] ListGenesinPathway = ServKegg.get_genes_by_pathway((string)ListP.listBoxPathways.SelectedItem);
double[] ListValues = new double[ListGenesinPathway.Length];
int IDxGeneOfInterest = 0;
foreach (cPlate CurrentPlate in Parent.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[Parent.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)((((Parent.GlobalInfo.LUTs.LUT_JET[0].Length - 1) * (ListValues[IdxCol] - MinValue)) / (MaxValue - MinValue)));
Color Coul = Color.FromArgb(Parent.GlobalInfo.LUTs.LUT_JET[0][ConvertedValue], Parent.GlobalInfo.LUTs.LUT_JET[1][ConvertedValue], Parent.GlobalInfo.LUTs.LUT_JET[2][ConvertedValue]);
if (IdxCol == IDxGeneOfInterest)
fg_list[IdxCol] = "white";
else
fg_list[IdxCol] = "#000000";
bg_list[IdxCol] = "#" + Coul.Name.Remove(0, 2);
}
pathway_map_html = ServKegg.get_html_of_colored_pathway_by_objects((string)ListP.listBoxPathways.SelectedItem, ListGenesinPathway, fg_list, bg_list);
string GenInfo = ServKegg.bget((string)ListP.listBoxPathways.SelectedItem);
string[] Genes = GenInfo.Split(new char[] { '\n' });
string Res = "";
foreach (string item in Genes)
{
string[] fre = item.Split(' ');
string[] STRsection = fre[0].Split('_');
if (STRsection[0] != "NAME") continue;
for (int i = 1; i < fre.Length; i++)
{
if (fre[i] == "") continue;
Res += fre[i] + " ";
}
}
FormForKegg KeggWin = new FormForKegg();
if (pathway_map_html.Length == 0) return;
KeggWin.Text = Res;
KeggWin.Show();
KeggWin.webBrowser.Navigate(pathway_map_html);
}
