private void btnCompare_Click(object sender, EventArgs e)
{
string kit1 = dataGridView1.SelectedRows[0].Cells[0].Value.ToString();
string kit2 = dataGridView2.SelectedRows[0].Cells[0].Value.ToString();
if (kit1 == kit2)
{
MessageBox.Show("Please select different kits to compare.", "One-to-One Compare", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
// open mdi child
switch (selected_operation)
{
case SELECT_ADMIXTURE:
GGKUtilLib.hideAllMdiChildren();
OneToOneCmpFrm cmp = new OneToOneCmpFrm(kit1, kit2);
cmp.MdiParent = Program.GGKitFrmMainInst;
cmp.Visible = true;
cmp.WindowState = FormWindowState.Maximized;
this.Close();
break;
default:
break;
}
//
}
private void ProcessKitsFrm_FormClosing(object sender, FormClosingEventArgs e)
{
if (bwCompare.IsBusy || bwROH.IsBusy || bwPhaseVisualizer.IsBusy)
{
GGKUtilLib.setStatus("Cancelling...");
GGKUtilLib.setProgress(-1);
btnStart.Text = "Cancelling";
btnStart.Enabled = false;
if (bwCompare.IsBusy)
{
bwCompare.CancelAsync();
}
if (bwROH.IsBusy)
{
bwROH.CancelAsync();
}
if (bwPhaseVisualizer.IsBusy)
{
bwPhaseVisualizer.CancelAsync();
}
e.Cancel = true;
timer1.Enabled = true;
}
else
{
GGKUtilLib.setStatus("Done.");
GGKUtilLib.setProgress(-1);
}
}
private void mtdna_chart_MouseClick(object sender, MouseEventArgs e)
{
// Call Hit Test Method
HitTestResult result = mtdna_chart.HitTest(e.X, e.Y);
if (result.ChartElementType == ChartElementType.DataPoint || result.ChartElementType == ChartElementType.DataPointLabel)
{
foreach (DataPoint dp2 in mtdna_chart.Series[0].Points)
{
dp2.LabelBackColor = Color.White;
dp2.LabelForeColor = Color.Black;
}
DataPoint dp = (DataPoint)result.Object;
dp.LabelBackColor = Color.LightBlue;
GGKUtilLib.setStatus("Selected " + dp.Label);
foreach (DataGridViewRow row in dgvmtdna.Rows)
{
if (row.Cells[0].Value.ToString() == dp.Label)
{
row.Selected = true;
break;
}
}
}
}
void bWorker_DoWork(object sender, DoWorkEventArgs e)
{
string[] o = (string[])e.Argument;
string cmp_id = o[0];
string kit2 = o[1];
string name2 = o[2];
segment_dt = GGKUtilLib.QueryDB("select chromosome'Chromosome',start_position'Start Position',end_position'End Position',segment_length_cm'Segment Length (cM)',snp_count'SNP Count',segment_id from cmp_autosomal where cmp_id='" + cmp_id + "'");
if (GGKUtilLib.isPhased(kit))
{
phased_kit = kit;
unphased_kit = kit2;
phased = true;
}
else if (GGKUtilLib.isPhased(kit2))
{
phased_kit = kit2;
unphased_kit = kit;
phased = true;
}
else
{
phased = false;
}
e.Result = new string[] { kit2, name2 };
}
private void bwDelete_DoWork(object sender, DoWorkEventArgs e)
{
DataGridView dgv = (DataGridView)e.Argument;
SQLiteConnection conn = GGKUtilLib.getDBConnection();
List <DataGridViewRow> rows = new List <DataGridViewRow>();
using (SQLiteTransaction trans = conn.BeginTransaction())
{
foreach (DataGridViewRow row in dgv.SelectedRows)
{
SQLiteCommand upCmd = new SQLiteCommand("DELETE FROM kit_master WHERE kit_no=@kit_no", conn);
upCmd.Parameters.AddWithValue("@kit_no", row.Cells[0].Value.ToString());
upCmd.ExecuteNonQuery();
rows.Add(row);
}
//
trans.Commit();
}
this.Invoke(new MethodInvoker(delegate
{
foreach (DataGridViewRow row in rows)
{
dgvEditKit.Rows.Remove(row);
}
}));
}
private void NewKitFrm_FormClosing(object sender, FormClosingEventArgs e)
{
if (bwDelete.IsBusy)
{
bwDelete.CancelAsync();
}
if (bwSave.IsBusy)
{
bwSave.CancelAsync();
}
if (bwNewKitAutosomalJob.IsBusy)
{
bwNewKitAutosomalJob.CancelAsync();
}
if (bwNewKitYDNAJob.IsBusy)
{
bwNewKitYDNAJob.CancelAsync();
}
if (bwPopuate.IsBusy)
{
bwPopuate.CancelAsync();
}
GGKUtilLib.disableSave();
GGKUtilLib.disable_DisableKitToolbarBtn();
GGKUtilLib.disable_EnableKitToolbarBtn();
GGKUtilLib.disableDeleteKitToolbarBtn();
GGKUtilLib.setStatus("Done.");
}
private void MatchingKitsFrm_Load(object sender, EventArgs e)
{
lblKit.Text = kit;
lblName.Text = GGKUtilLib.queryDatabase("kit_master", new string[] { "name" }, "WHERE kit_no='" + kit + "'").Rows[0].ItemArray[0].ToString();
DataTable dt = GGKUtilLib.QueryDB("SELECT cmp_id,kit'Kit No',name'Name',at_longest'Autosomal Longest',at_total'Autosomal Total',x_longest'X Longest',x_total'X Total',mrca'MRCA' FROM (SELECT a.cmp_id,a.kit1'kit',b.name,a.at_longest,a.at_total,a.x_longest,a.x_total,a.mrca FROM cmp_status a,kit_master b WHERE a.at_total!=0 AND a.kit1!='" + kit + "' AND a.kit2='" + kit + "' AND a.status_autosomal=1 AND b.kit_no=a.kit1 AND b.disabled=0 UNION SELECT a.cmp_id,a.kit2'kit',b.name,a.at_longest,a.at_total,a.x_longest,a.x_total,a.mrca FROM cmp_status a,kit_master b WHERE a.at_total!=0 AND a.kit2!='" + kit + "' AND a.kit1='" + kit + "' AND a.status_autosomal=1 AND b.kit_no=a.kit2 AND b.disabled=0) ORDER BY at_longest DESC,at_total DESC");
dgvMatches.Columns.Clear();
dgvMatches.DataSource = dt;
dgvMatches.Columns[0].Visible = false;
dgvMatches.Columns[1].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgvMatches.Columns[2].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgvMatches.Columns[3].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgvMatches.Columns[4].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgvMatches.Columns[5].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgvMatches.Columns[6].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgvMatches.Columns[7].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
DataGridViewCellStyle style = new DataGridViewCellStyle();
style.Format = "N2";
dgvMatches.Columns[3].DefaultCellStyle = style;
dgvMatches.Columns[4].DefaultCellStyle = style;
dgvMatches.Columns[5].DefaultCellStyle = style;
dgvMatches.Columns[6].DefaultCellStyle = style;
}
private void factoryResetToolStripMenuItem_Click(object sender, EventArgs e)
{
if (MessageBox.Show("Are you sure to delete everything and reset to factory defaults?", "Factory Reset", MessageBoxButtons.YesNo, MessageBoxIcon.Warning) == DialogResult.Yes)
{
GGKUtilLib.FactoryReset();
}
}
private void timer1_Tick(object sender, EventArgs e)
{
timer1.Enabled = false;
SQLiteConnection cnn = GGKUtilLib.getDBConnection();
dataGridView1.Rows.Clear();
dataGridView2.Rows.Clear();
SQLiteCommand query = new SQLiteCommand(select_sql, cnn);
SQLiteDataReader reader = query.ExecuteReader();
DataTable dt1 = null;
DataTable dt2 = null;
dt1 = new DataTable();
dt2 = new DataTable();
dt1.Load(reader);
reader = query.ExecuteReader();
dt2.Load(reader);
query.Dispose();
cnn.Dispose();
dataGridView1.DataSource = dt1;
dataGridView2.DataSource = dt2;
dataGridView1.Columns[0].AutoSizeMode = DataGridViewAutoSizeColumnMode.AllCells;
dataGridView2.Columns[0].AutoSizeMode = DataGridViewAutoSizeColumnMode.AllCells;
dataGridView1.Columns[1].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dataGridView2.Columns[1].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
}
private void bwROH_DoWork(object sender, DoWorkEventArgs e)
{
DataTable dt = GGKUtilLib.QueryDB("select kit_no,roh_status from kit_master where reference=0 and disabled=0");
string kit = null;
string roh = null;
foreach (DataRow row in dt.Rows)
{
if (bwROH.CancellationPending)
{
break;
}
kit = row.ItemArray[0].ToString();
roh = row.ItemArray[1].ToString();
if (roh == "0")
{
bwROH.ReportProgress(dt.Rows.IndexOf(row) * 100 / dt.Rows.Count, "Runs of Homozygosity for kit #" + kit + " (" + GGKUtilLib.getKitName(kit) + ") - Processing ...");
GGKUtilLib.ROH(kit);
}
else if (roh == "1")
{
bwROH.ReportProgress(dt.Rows.IndexOf(row) * 100 / dt.Rows.Count, "Runs of Homozygosity for kit #" + kit + " (" + GGKUtilLib.getKitName(kit) + ") - Already Exists. Skipping..");
}
}
}
private void QuickEditKit_FormClosing(object sender, FormClosingEventArgs e)
{
GGKUtilLib.disableSave();
GGKUtilLib.disableDeleteKitToolbarBtn();
GGKUtilLib.disable_DisableKitToolbarBtn();
GGKUtilLib.disable_EnableKitToolbarBtn();
}
private void timer1_Tick(object sender, EventArgs e)
{
timer1.Enabled = false;
label2.Text = GGKUtilLib.getKitName(kit);
txtSNPs.Text = GGKUtilLib.queryValue("kit_ysnps", new string[] { "ysnps" }, "where kit_no='" + kit + "'");
GGKUtilLib.setStatus("Plotting on ISOGG Y-Tree ...");
//
XDocument doc = XDocument.Parse(Genetic_Genealogy_Kit.Properties.Resources.ytree);
TreeNode root = new TreeNode("Adam");
treeView1.Nodes.Add(root);
foreach (XElement el in doc.Root.Elements())
{
buildTree(root, el);
}
root.Expand();
//
snp_on_tree.AddRange(Genetic_Genealogy_Kit.Properties.Resources.snps_on_tree.Split(new char[] { ',' }));
my_snp = txtSNPs.Text;
snp_array = filterSNPsOnTree(my_snp);
timer2.Enabled = true;
}
private void MainFrm_Load(object sender, EventArgs e)
{
label2.Text = kit + " - " + GGKUtilLib.getKitName(kit);
this.Text = "Mitocondrial Phylogeny - (" + kit + ")" + GGKUtilLib.getKitName(kit);
xml_phylogeny = Genetic_Genealogy_Kit.Properties.Resources.mtDNAPhylogeny;
timer1.Enabled = true;
}
private void btnStart_Click(object sender, EventArgs e)
{
if (btnStart.Text == "Start")
{
redo_again = cbDontSkip.Checked;
redo_visual = cbRedoVisual.Checked;
no_admixture = cbNoAdmixture.Checked;
GGKUtilLib.setStatus("Processing Kits ...");
if (bwCompare.IsBusy)
{
MessageBox.Show("Process is busy!", "Please Wait!", MessageBoxButtons.OK, MessageBoxIcon.Stop);
}
else
{
bwCompare.RunWorkerAsync();
btnStart.Text = "Stop";
}
}
else if (btnStart.Text == "Stop")
{
if (MessageBox.Show("Are you sure you want to cancel the process?", "Cancel?", MessageBoxButtons.YesNo, MessageBoxIcon.Question) == DialogResult.Yes)
{
GGKUtilLib.setStatus("Done.");
GGKUtilLib.setProgress(-1);
bwCompare.CancelAsync();
bwROH.CancelAsync();
bwPhaseVisualizer.CancelAsync();
btnStart.Text = "Cancelling";
btnStart.Enabled = false;
}
}
}
public void Save()
{
if (saveFileDlg.ShowDialog(this) == DialogResult.OK)
{
StringBuilder sb = new StringBuilder();
sb.Append("RSID,CHROMOSOME,POSITION,RESULT\r\n");
object[] data = null;
foreach (DataTable dt in segments)
{
foreach (DataRow row in dt.Rows)
{
data = row.ItemArray;
if (data[5].ToString() == "--")
{
continue;
}
if (data[5].ToString().Length == 2)
{
sb.Append(("\"" + data[0] + "\",\"" + data[1] + "\",\"" + data[2] + "\",\"" + data[5] + "\"\r\n"));
}
else if (data[5].ToString().Length == 1)
{
sb.Append(("\"" + data[0] + "\",\"" + data[1] + "\",\"" + data[2] + "\",\"" + data[5] + data[5] + "\"\r\n"));
}
}
}
File.WriteAllText(saveFileDlg.FileName, sb.ToString());
sb.Length = 0;
GGKUtilLib.setStatus("CA Profile saved.");
}
}
private void QuickEditKit_Load(object sender, EventArgs e)
{
GGKUtilLib.enableSave();
GGKUtilLib.enableDeleteKitToolbarBtn();
GGKUtilLib.enable_DisableKitToolbarBtn();
GGKUtilLib.enable_EnableKitToolbarBtn();
timer1.Enabled = true;
}
private void bwROH_DoWork(object sender, DoWorkEventArgs e)
{
string kit = e.Argument.ToString();
object[] roh_results = GGKUtilLib.ROH(kit);
segment_idx = (DataTable)roh_results[0];
segments = (List <DataTable>)roh_results[1];
}
private void bwDelete_RunWorkerCompleted(object sender, RunWorkerCompletedEventArgs e)
{
GGKUtilLib.setStatus("Deleted.");
this.Enabled = true;
GGKUtilLib.enableMenu();
GGKUtilLib.enableToolbar();
}
private void bwSave_ProgressChanged(object sender, ProgressChangedEventArgs e)
{
GGKUtilLib.setProgress(e.ProgressPercentage);
if (e.UserState != null)
{
GGKUtilLib.setStatus(e.UserState.ToString());
}
}
public void Save()
{
GGKUtilLib.setStatus("Saving ...");
SQLiteConnection conn = GGKUtilLib.getDBConnection();
string sex = "";
string location = "";
using (SQLiteTransaction trans = conn.BeginTransaction())
{
foreach (DataGridViewRow row in dgvEditKit.Rows)
{
SQLiteCommand upCmd = new SQLiteCommand("UPDATE kit_master set name=@name, sex=@sex, disabled=@disabled, x=@x, y=@y WHERE kit_no=@kit_no", conn);
upCmd.Parameters.AddWithValue("@name", row.Cells[1].Value.ToString());
sex = row.Cells[2].Value.ToString();
if (sex == "Unknown")
{
upCmd.Parameters.AddWithValue("@sex", "U");
}
else if (sex == "Male")
{
upCmd.Parameters.AddWithValue("@sex", "M");
}
else if (sex == "Female")
{
upCmd.Parameters.AddWithValue("@sex", "F");
}
if (((bool)row.Cells[3].Value))
{
upCmd.Parameters.AddWithValue("@disabled", "1");
}
else
{
upCmd.Parameters.AddWithValue("@disabled", "0");
}
location = row.Cells[4].Value.ToString();
if (location == "Unknown")
{
upCmd.Parameters.AddWithValue("@x", "0");
upCmd.Parameters.AddWithValue("@y", "0");
}
else
{
upCmd.Parameters.AddWithValue("@x", location.Split(new char[] { ':' })[0]);
upCmd.Parameters.AddWithValue("@y", location.Split(new char[] { ':' })[1]);
}
upCmd.Parameters.AddWithValue("@kit_no", row.Cells[0].Value.ToString());
upCmd.ExecuteNonQuery();
}
//
trans.Commit();
}
GGKUtilLib.setStatus("Saved.");
}
private void bwExport_DoWork(object sender, DoWorkEventArgs e)
{
string kit_no = ((string[])e.Argument)[0];
string filename = ((string[])e.Argument)[1];
int option = int.Parse(((string[])e.Argument)[2]);
//
GGKUtilLib.exportKit(kit_no, filename, option);
}
private void populateFields(string kit)
{
foreach (Control ctrl in editableCtrls)
{
ctrl.Enabled = false;
}
GGKUtilLib.setStatus("Please wait ...");
bwPopuate.RunWorkerAsync(kit);
}
private void backgroundWorker1_RunWorkerCompleted(object sender, RunWorkerCompletedEventArgs e)
{
treeView1.Nodes.Clear();
lblSb.Text = "";
lblyhg.Text = "";
mutations_map.Clear();
match_map.Clear();
GGKUtilLib.setStatus("Done.");
timer1.Enabled = true;
}
private void bwPopuate_RunWorkerCompleted(object sender, RunWorkerCompletedEventArgs e)
{
foreach (Control ctrl in editableCtrls)
{
ctrl.Enabled = true;
}
//
doControlActivities(kit_disabled);
GGKUtilLib.setStatus("Done.");
}
private void textBoxYDNA_DragDrop(object sender, DragEventArgs e)
{
// file dropped.
if (e.Data.GetDataPresent(DataFormats.FileDrop))
{
string[] filePaths = (string[])(e.Data.GetData(DataFormats.FileDrop));
GGKUtilLib.setStatus("Parsing Y-DNA file(s) ...");
bwNewKitYDNAJob.RunWorkerAsync(filePaths[0]);
}
}
private void timer1_Tick(object sender, EventArgs e)
{
timer1.Enabled = false;
DataGridViewCellStyle gray = new DataGridViewCellStyle();
gray.ForeColor = Color.LightGray;
SQLiteConnection cnn = GGKUtilLib.getDBConnection();
dgvEditKit.Rows.Clear();
SQLiteCommand query = new SQLiteCommand(@"SELECT kit_no,name,sex,disabled,coalesce(x,0),coalesce(y,0),last_modified FROM kit_master WHERE reference=0 order by last_modified DESC", cnn);
SQLiteDataReader reader = query.ExecuteReader();
string sex = "U";
string xy = null;
while (reader.Read())
{
int new_idx = dgvEditKit.Rows.Add();
DataGridViewRow row = dgvEditKit.Rows[new_idx];
row.Cells[0].Value = reader.GetString(0);
row.Cells[1].Value = reader.GetString(1);
sex = reader.GetString(2);
if (sex == "U")
{
row.Cells[2].Value = "Unknown";
}
else if (sex == "M")
{
row.Cells[2].Value = "Male";
}
else if (sex == "F")
{
row.Cells[2].Value = "Female";
}
if (reader.GetInt16(3) == 1)
{
row.Cells[3].Value = true;
}
else
{
row.Cells[3].Value = false;
}
xy = reader.GetInt16(4).ToString() + ":" + reader.GetInt16(5).ToString();
if (xy == "0:0")
{
xy = "Unknown";
}
row.Cells[4].Value = xy;
}
query.Dispose();
cnn.Dispose();
}
public void Delete()
{
if (MessageBox.Show("You had selected " + dgvEditKit.SelectedRows.Count.ToString() + " kits to be deleted. Are you sure?", "Confirm", MessageBoxButtons.YesNo, MessageBoxIcon.Question) == DialogResult.Yes)
{
GGKUtilLib.setStatus("Deleting " + dgvEditKit.SelectedRows.Count.ToString() + " kit(s) and all it's associated data ...");
this.Enabled = false;
GGKUtilLib.disableMenu();
GGKUtilLib.disableToolbar();
bwDelete.RunWorkerAsync(dgvEditKit);
}
}
private void bwSave_RunWorkerCompleted(object sender, RunWorkerCompletedEventArgs e)
{
GGKUtilLib.setProgress(-1);
this.Enabled = true;
GGKUtilLib.enableMenu();
GGKUtilLib.enableToolbar();
if (save_success)
{
this.Close();
}
}
public static void _addParameter(string key, string value, string desc, string read_only)
{
SQLiteConnection cnn = GGKUtilLib.getDBConnection();
SQLiteCommand upCmd = new SQLiteCommand(@"INSERT into ggk_settings(key,value,description,readonly) VALUES (@key,@value,@desc,@readonly)", cnn);
upCmd.Parameters.AddWithValue("@key", key);
upCmd.Parameters.AddWithValue("@value", value);
upCmd.Parameters.AddWithValue("@desc", desc);
upCmd.Parameters.AddWithValue("@readonly", read_only);
upCmd.ExecuteNonQuery();
upCmd.Dispose();
}
private void bwPhaseVisualizer_ProgressChanged(object sender, ProgressChangedEventArgs e)
{
lblComparing.Text = e.UserState.ToString();
GGKUtilLib.setProgress(e.ProgressPercentage);
GGKUtilLib.setStatus(e.UserState.ToString());
progressBar.Value = e.ProgressPercentage;
lblComparing.Text = e.UserState.ToString();
tbStatus.Text += e.UserState.ToString() + "\r\n";
tbStatus.Select(tbStatus.Text.Length - 1, 0);
tbStatus.ScrollToCaret();
}
