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 btnChild_Click(object sender, EventArgs e)
{
SelectKitFrm open = new SelectKitFrm(SelectKitFrm.SELECT_KIT);
open.ShowDialog(this);
child_kit = open.getSelectedKit();
btnChild.Text = GGKUtilLib.getKitName(child_kit);
if ((father_kit != "Unknown" || mother_kit != "Unknown") && child_kit != "Unknown")
{
btnPhasing.Enabled = true;
}
}
public OneToOneCmpFrm(string kit1, string kit2)
{
InitializeComponent();
//
this.kit1 = kit1;
this.kit2 = kit2;
this.name1 = GGKUtilLib.getKitName(kit1);
this.name2 = GGKUtilLib.getKitName(kit2);
dgvMatching.Columns[3].HeaderText = name1;
dgvMatching.Columns[4].HeaderText = name2;
GGKUtilLib.setStatus("Comparing kits " + kit1 + " and " + kit2 + " ...");
bwCompare.RunWorkerAsync();
}
private void MitoMapFrm_Load(object sender, EventArgs e)
{
string csv = Genetic_Genealogy_Kit.Properties.Resources.mtdna_map;
StreamReader reader = new StreamReader(new MemoryStream(Encoding.ASCII.GetBytes(csv)));
string line = null;
string[] data = null;
Series series = series = mtdna_chart.Series[0];
//Map Locus Starting Ending bp Length Shorthand Description
dgvmtdna.Rows.Clear();
while ((line = reader.ReadLine()) != null)
{
data = line.Split(new char[] { ',' });
DataPoint dp = new DataPoint();
dp.IsVisibleInLegend = false;
dp.Label = data[0];
dp.YValues = new double[] { int.Parse(data[3]) };
dp.CustomProperties = "PieLineColor=Black, PieLabelStyle=Outside, Exploded=True";
series.Points.Add(dp);
//
dgvmtdna.Rows.Add(new object[] { data[0], data[1], data[2], data[3], data[4], data[5] });
}
reader.Close();
//
RSRS = GGKUtilLib.getRSRS();
for (int i = 0; i < RSRS.Length; i++)
{
nucleotides.Add(i + 1, new string[] { (i + 1).ToString(), RSRS[i].ToString(), RSRS[i].ToString() });
}
mutations = GGKUtilLib.queryValue("kit_mtdna", new string[] { "mutations" }, "where kit_no='" + kit + "'");
dgvNucleotides.Columns[2].HeaderText = GGKUtilLib.getKitName(kit) + " (" + kit + ")";
dgvmtdna.Columns[3].Visible = false;
loadKitMutations();
}
private void bwPhaseVisualizer_DoWork(object sender, DoWorkEventArgs e)
{
DataTable dt_existing = GGKUtilLib.QueryDB("select segment_image,segment_xml from cmp_phased where phased_kit='" + phased_kit + "' and match_kit='" + unphased_kit + "' and chromosome='" + chromosome + "' and start_position=" + start_position + " and end_position=" + end_position);
if (dt_existing.Rows.Count > 0)
{
object[] o = dt_existing.Rows[0].ItemArray;
string xml = o[1].ToString();
dt = new DataTable();
MemoryStream ms = new MemoryStream(Encoding.ASCII.GetBytes(xml));
dt.ReadXml(ms);
this.Invoke(new MethodInvoker(delegate
{
dgvSegment.DataSource = dt;
dgvSegment.Columns[0].HeaderText = "Position";
dgvSegment.Columns[1].HeaderText = GGKUtilLib.sqlSafe(GGKUtilLib.getKitName(unphased_kit));
dgvSegment.Columns[2].HeaderText = GGKUtilLib.sqlSafe(GGKUtilLib.getKitName(phased_kit)) + " (Paternal)";
dgvSegment.Columns[3].HeaderText = GGKUtilLib.sqlSafe(GGKUtilLib.getKitName(phased_kit)) + " (Maternal)";
dgvSegment.Columns[0].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgvSegment.Columns[1].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgvSegment.Columns[2].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgvSegment.Columns[3].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgvSegment.Columns[0].ReadOnly = true;
dgvSegment.Columns[1].ReadOnly = true;
dgvSegment.Columns[2].ReadOnly = true;
dgvSegment.Columns[3].ReadOnly = true;
}));
byte[] image_array = (byte[])o[0];
Image img = GGKUtilLib.byteArrayToImage(image_array);
this.Invoke(new MethodInvoker(delegate
{
original = new Bitmap(img, 600, 150);
pbSegment.Image = original;
}));
}
else
{
dt = GGKUtilLib.QueryDB("select a.position,a.genotype,p.paternal_genotype,p.maternal_genotype from kit_autosomal a,kit_phased p where a.kit_no='" + unphased_kit + "' and a.position>" + start_position + " and a.position<" + end_position + " and a.chromosome='" + chromosome + "' and p.rsid=a.rsid and p.kit_no='" + phased_kit + "' order by a.position");
if (dt.Rows.Count > 0)
{
if (this.IsHandleCreated)
{
this.Invoke(new MethodInvoker(delegate
{
dgvSegment.DataSource = dt;
dgvSegment.Columns[0].HeaderText = "Position";
dgvSegment.Columns[1].HeaderText = GGKUtilLib.sqlSafe(GGKUtilLib.getKitName(unphased_kit));
dgvSegment.Columns[2].HeaderText = GGKUtilLib.sqlSafe(GGKUtilLib.getKitName(phased_kit)) + " (Paternal)";
dgvSegment.Columns[3].HeaderText = GGKUtilLib.sqlSafe(GGKUtilLib.getKitName(phased_kit)) + " (Maternal)";
dgvSegment.Columns[0].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgvSegment.Columns[1].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgvSegment.Columns[2].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgvSegment.Columns[3].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgvSegment.Columns[0].ReadOnly = true;
dgvSegment.Columns[1].ReadOnly = true;
dgvSegment.Columns[2].ReadOnly = true;
dgvSegment.Columns[3].ReadOnly = true;
}));
Image img = GGKUtilLib.getPhasedSegmentImage(dt, chromosome);
this.Invoke(new MethodInvoker(delegate
{
original = img;
pbSegment.Image = img;
}));
}
dt.TableName = "cmp_phased";
StringBuilder sb = new StringBuilder();
StringWriter w = new StringWriter(sb);
dt.WriteXml(w, XmlWriteMode.WriteSchema);
string segment_xml = sb.ToString();
SQLiteConnection conn = GGKUtilLib.getDBConnection();
SQLiteCommand cmd = new SQLiteCommand("INSERT INTO cmp_phased(phased_kit,match_kit,chromosome,start_position,end_position,segment_image,segment_xml) VALUES (@phased_kit,@match_kit,@chromosome,@start_position,@end_position,@segment_image,@segment_xml)", conn);
cmd.Parameters.AddWithValue("@phased_kit", phased_kit);
cmd.Parameters.AddWithValue("@match_kit", unphased_kit);
cmd.Parameters.AddWithValue("@chromosome", chromosome);
cmd.Parameters.AddWithValue("@start_position", start_position);
cmd.Parameters.AddWithValue("@end_position", end_position);
byte[] image_bytes = GGKUtilLib.imageToByteArray(original);
cmd.Parameters.Add("@segment_image", DbType.Binary, image_bytes.Length).Value = image_bytes;
cmd.Parameters.AddWithValue("@segment_xml", segment_xml);
cmd.ExecuteNonQuery();
conn.Close();
}
}
}
private void AdmixtureFrm_Load(object sender, EventArgs e)
{
kitLbl.Text = kit + " (" + GGKUtilLib.getKitName(kit) + ")";
DataTable dt = GGKUtilLib.QueryDB("select name,at_total,at_longest,x,y FROM (select b.name,a.at_total,a.at_longest,b.x,b.y from cmp_status a,kit_master b where a.kit1='" + kit + "' and a.kit2=b.kit_no and a.kit2 like 'HGDP%' and a.status_autosomal=1 and a.at_longest<3 and a.at_total!=0 UNION select b.name,a.at_total,a.at_longest,b.x,b.y from cmp_status a,kit_master b where a.kit2='" + kit + "' and a.kit1=b.kit_no and a.kit1 like 'HGDP%' and a.status_autosomal=1 and a.at_longest<3 and a.at_total!=0) ORDER BY at_total DESC");
double total = 0.0;
foreach (DataRow row in dt.Rows)
{
total += double.Parse(row.ItemArray[1].ToString());
}
DataTable adx_table = new DataTable();
adx_table.Columns.Add("Population");
adx_table.Columns.Add("Location");
adx_table.Columns.Add("Total Shared (cM)");
adx_table.Columns.Add("Longest (cM)");
adx_table.Columns.Add("Percentage");
adx_table.Columns.Add("X");
adx_table.Columns.Add("Y");
string population = null;
string location = null;
double at_total = 0.0;
string at_longest = null;
double percentage = 0.0;
string[] data = null;
for (int i = 0; i < dt.Rows.Count; i++)
{
data = dt.Rows[i].ItemArray[0].ToString().Replace("_", " ").Split(new char[] { ',' });
population = data[0];
location = data[1];
at_total = double.Parse(dt.Rows[i].ItemArray[1].ToString());
at_longest = dt.Rows[i].ItemArray[2].ToString();
percentage = (at_total * 100 / total);
adx_table.Rows.Add(new object[] { population, location, at_total, at_longest, percentage.ToString("#0.00"), dt.Rows[i].ItemArray[3], dt.Rows[i].ItemArray[4] });
chart1.Series[0].Points.AddXY(population + ", " + location + " (" + percentage.ToString("#0.00") + "%)", new object[] { percentage });
}
foreach (DataPoint p in chart1.Series[0].Points)
{
p.IsVisibleInLegend = false;
}
dgv_Admixture.Columns.Clear();
dgv_Admixture.DataSource = adx_table;
dgv_Admixture.Columns[0].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgv_Admixture.Columns[1].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgv_Admixture.Columns[2].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgv_Admixture.Columns[3].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgv_Admixture.Columns[4].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgv_Admixture.Columns[5].Visible = false;
dgv_Admixture.Columns[6].Visible = false;
int percent = 0;
int x = 0;
int y = 0;
Image img = pbWorldMap.Image;
Graphics g = Graphics.FromImage(img);
plotted.Clear();
foreach (DataRow row in adx_table.Rows)
{
percent = (int)double.Parse(row.ItemArray[4].ToString());
x = int.Parse(row.ItemArray[5].ToString());
y = int.Parse(row.ItemArray[6].ToString());
if (!plotted.Contains(x + ":" + y))
{
if (percent > 50) // plotting 100% is too big and ugly.
{
percent = 50;
}
setHeatMap(g, percent, x, y);
plotted.Add(x + ":" + y);
}
}
g.Save();
pbWorldMap.Image = img;
}
private void bwPhaseVisualizer_DoWork(object sender, DoWorkEventArgs e)
{
DataTable dt2 = GGKUtilLib.QueryDB("select distinct kit_no from kit_phased");
string phased_kit = null;
string unphased_kit = null;
string chromosome = null;
string start_position = null;
string end_position = null;
int percent = 0;
foreach (DataRow row in dt2.Rows)
{
if (bwPhaseVisualizer.CancellationPending)
{
break;
}
phased_kit = row.ItemArray[0].ToString();
percent = dt2.Rows.IndexOf(row) * 100 / dt2.Rows.Count;
bwPhaseVisualizer.ReportProgress(percent, "Phased Segments for kit #" + phased_kit + " (" + GGKUtilLib.getKitName(phased_kit) + ") - Processing ...");
DataTable dt3 = GGKUtilLib.QueryDB("select unphased_kit,chromosome,start_position,end_position FROM (select kit1'unphased_kit',chromosome,start_position,end_position from cmp_autosomal where kit2='" + phased_kit + "' UNION select kit2'unphased_kit',chromosome,start_position,end_position from cmp_autosomal where kit1='" + phased_kit + "') order by cast(chromosome as integer),start_position");
foreach (DataRow row3 in dt3.Rows)
{
if (bwPhaseVisualizer.CancellationPending)
{
break;
}
unphased_kit = row3.ItemArray[0].ToString();
chromosome = row3.ItemArray[1].ToString();
start_position = row3.ItemArray[2].ToString();
end_position = row3.ItemArray[3].ToString();
DataTable exists = GGKUtilLib.QueryDB("select * from cmp_phased where phased_kit='" + phased_kit + "' and match_kit='" + unphased_kit + "' and chromosome='" + chromosome + "' and start_position=" + start_position + " and end_position=" + end_position);
if (exists.Rows.Count > 0)
{
//already exists...
if (!redo_visual)
{
bwPhaseVisualizer.ReportProgress(percent, "Segment [" + GGKUtilLib.getKitName(phased_kit) + ":" + GGKUtilLib.getKitName(unphased_kit) + "] Chr " + chromosome + ": " + start_position + "-" + end_position + ", Already Processed. Skipping ...");
continue;
}
else
{
GGKUtilLib.UpdateDB("DELETE from cmp_phased where phased_kit='" + phased_kit + "'");
}
}
bwPhaseVisualizer.ReportProgress(percent, "Segment [" + GGKUtilLib.getKitName(phased_kit) + ":" + GGKUtilLib.getKitName(unphased_kit) + "] Chr " + chromosome + ": " + start_position + "-" + end_position + ", Processing ...");
DataTable dt = GGKUtilLib.QueryDB("select a.position,a.genotype,p.paternal_genotype,p.maternal_genotype from kit_autosomal a,kit_phased p where a.kit_no='" + unphased_kit + "' and a.position>" + start_position + " and a.position<" + end_position + " and a.chromosome='" + chromosome + "' and p.rsid=a.rsid and p.kit_no='" + phased_kit + "' order by a.position");
if (dt.Rows.Count > 0)
{
if (bwPhaseVisualizer.CancellationPending)
{
break;
}
Image img = GGKUtilLib.getPhasedSegmentImage(dt, chromosome);
dt.TableName = "cmp_phased";
StringBuilder sb = new StringBuilder();
StringWriter w = new StringWriter(sb);
dt.WriteXml(w, XmlWriteMode.WriteSchema);
string segment_xml = sb.ToString();
SQLiteConnection conn = GGKUtilLib.getDBConnection();
SQLiteCommand cmd = new SQLiteCommand("INSERT INTO cmp_phased(phased_kit,match_kit,chromosome,start_position,end_position,segment_image,segment_xml) VALUES (@phased_kit,@match_kit,@chromosome,@start_position,@end_position,@segment_image,@segment_xml)", conn);
cmd.Parameters.AddWithValue("@phased_kit", phased_kit);
cmd.Parameters.AddWithValue("@match_kit", unphased_kit);
cmd.Parameters.AddWithValue("@chromosome", chromosome);
cmd.Parameters.AddWithValue("@start_position", start_position);
cmd.Parameters.AddWithValue("@end_position", end_position);
byte[] image_bytes = GGKUtilLib.imageToByteArray(img);
cmd.Parameters.Add("@segment_image", DbType.Binary, image_bytes.Length).Value = image_bytes;
cmd.Parameters.AddWithValue("@segment_xml", segment_xml);
cmd.ExecuteNonQuery();
conn.Close();
}
}
}
}
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..");
}
}
}
public MitoMapFrm(string kit)
{
InitializeComponent();
this.kit = kit;
label1.Text = " " + kit + " (" + GGKUtilLib.getKitName(kit) + ")";
}
public void markOnTree()
{
match_map.Clear();
foreach (TreeNode node in mutations_map.Keys)
{
node.ForeColor = Color.Black;
}
treeView1.CollapseAll();
TreeNode name_maxpath = null;
string my_marker = txtSNPs.Text;
//dirty but ok for now
my_marker = my_marker.Replace(",", " ").Replace("\t", " ").Replace("\r", " ").Replace("\n", " ");
RegexOptions options = RegexOptions.None;
Regex regex = new Regex(@"[ ]{2,}", options);
my_marker = regex.Replace(my_marker, @" ");
my_marker = my_marker.Replace(" ", ",");
string[] marker_array = my_marker.Split(",".ToCharArray());
string marker_names = "";
string m_name = "";
string[] marker_names_on_hg = null;
ArrayList list = new ArrayList();
foreach (TreeNode key in mutations_map.Keys)
{
marker_names = (string)mutations_map[key];
marker_names_on_hg = marker_names.Split(",".ToCharArray());
foreach (string marker_name in marker_names_on_hg)
{
m_name = marker_name.Replace("(", "").Replace(")", "").Replace("!", "");
foreach (string marker in marker_array)
{
// if on ignore list, just ignore
//foreach (string ignore in ignore_list)
//{
// if (marker.IndexOf(ignore) != -1)
// continue;
//}
//if (m_name.Trim() == marker.Trim())
if (marker.Trim().IndexOf(m_name.Trim()) != -1 || m_name.Trim() == marker.Trim())
{
//if (key.GetNodeCount(true) == 0)
if (!list.Contains(key))
{
list.Add(key);
}
if (!match_map.ContainsKey(key))
{
match_map.Add(key, m_name);
}
key.ForeColor = Color.White;
key.BackColor = Color.DarkGreen;
key.EnsureVisible();
//break;
}
}
}
}
//
// go through all terminals with matches and count the number of matching parents. now, that's the score.
SortedList <int, ArrayList> best_score = new SortedList <int, ArrayList>();
int pm = 0;
ArrayList alist = new ArrayList();
foreach (TreeNode key in list)
{
pm = getParentMatches(key);
if (best_score.ContainsKey(pm))
{
alist = best_score[pm];
}
else
{
alist = new ArrayList();
}
alist.Add(key);
best_score.Remove(pm);
best_score.Add(pm, alist);
}
var desc = best_score.Reverse();
//
//int count = 1;
ArrayList mlist = null;
bool found_first = false;
bool found_second = false;
report.Clear();
//
report.Append("<html><head><title>mtDNA Report for " + GGKUtilLib.getKitName(kit) + " (" + kit + ")</title></head><body>");
report.Append("<h1>mtDNA Report for " + GGKUtilLib.getKitName(kit) + " (" + kit + ")</h2>");
report.Append("<b>User Entered Markers: </b>" + my_marker);
sorted_report_array.Clear();
sorted_hg_readjustment.Clear();
foreach (var item in desc)
{
KeyValuePair <int, ArrayList> kvp = item;
//
mlist = (ArrayList)kvp.Value;
string str = "";
if (!found_first)
{
foreach (TreeNode tn in mlist)
{
if (isMatchingAll(tn, marker_array))
{
name_maxpath = tn;
str = str + " " + tn.Text;
found_first = true;
}
}
lblyhg.Text = str.Trim().Replace(" ", ", ");
if (found_first)
{
continue;
}
}
else if (!found_second)
{
foreach (TreeNode tn in mlist)
{
if (isMatchingAll(tn, marker_array))
{
//name_maxpath = tn;
str = str + " " + tn.Text;
found_second = true;
}
}
lblSb.Text = str.Trim().Replace(" ", ", ");
if (found_second)
{
break;
}
}
//
//if (count == 1)
//{
// mlist = (ArrayList)kvp.Value;
// string str = "";
// foreach (TreeNode tn in mlist)
// {
// if (isMatchingAll(tn, marker_array))
// {
// name_maxpath = tn;
// str = str + " " + tn.Text;
// }
// }
// lblyhg.Text = str.Trim().Replace(" ", ", ");
//}
//else if (count == 2)
//{
// mlist = (ArrayList)kvp.Value;
// string str = "";
// foreach (TreeNode tn in mlist)
// {
// if (isMatchingAll(tn, marker_array))
// {
// str = str + " " + tn.Text;
// }
// }
// lblSb.Text = str.Trim().Replace(" ",", ");
//}
//else if(count>2)
// break;
//count++;
}
// -- final readjustment .. it's dirty
found_first = false;
found_second = false;
string mstr = "";
ArrayList m_list = null;
foreach (KeyValuePair <int, ArrayList> hg in sorted_hg_readjustment)
{
m_list = hg.Value;
foreach (TreeNode mhg in m_list)
{
mstr = mstr + " " + mhg.Text;
}
if (!found_first)
{
name_maxpath = (TreeNode)m_list[0];
lblyhg.Text = mstr.Trim().Replace(" ", ", ");
found_first = true;
mstr = "";
}
else if (!found_second)
{
lblSb.Text = mstr.Trim().Replace(" ", ", ");
break;
}
}
//
foreach (TreeNode node in mutations_map.Keys)
{
if (node.BackColor != Color.DarkGreen)
{
node.ForeColor = Color.LightGray;
}
}
if (name_maxpath != null)
{
//name_maxpath.NodeFont = new Font("Microsoft Sans Serif", 7.8f, FontStyle.Underline);
name_maxpath.EnsureVisible();
//lblyhg.Text = name_maxpath.Text;
//name_maxpath
treeView1.SelectedNode = name_maxpath;
}
//TreeNode parent=name_maxpath;
//mtchart.Series.Clear();
//while(parent.Text!="Eve")
//{
// Series series = mtchart.Series.Add(parent.Text);
// int count = mutations_map[parent].ToString().Split(new char[]{','}).Length;
// series.ChartType = SeriesChartType.StackedBar;
// series.LabelToolTip = parent.Text+" ("+count.ToString() + " mutations)";
// series.Points.AddY(count);
// parent = parent.Parent;
//}
}
private void ROHFrm_Load(object sender, EventArgs e)
{
GGKUtilLib.setStatus("Calculating ROH ...");
this.Text = "Runs of Homozygosity - " + kit + " (" + GGKUtilLib.getKitName(kit) + ")";
bwROH.RunWorkerAsync(kit);
}
private void bwSave_DoWork(object sender, DoWorkEventArgs e)
{
save_success = false;
Object[] args = (Object[])e.Argument;
string kit_no = args[0].ToString();
string name = args[1].ToString();
DataGridViewRowCollection rows = (DataGridViewRowCollection)args[2];
string ysnps_list = args[3].ToString();
string mutations = args[4].ToString();
DataGridViewRowCollection[] dgvy_rows = (DataGridViewRowCollection[])args[5];
string sex = args[6].ToString();
string fasta = args[7].ToString();
SQLiteConnection cnn = GGKUtilLib.getDBConnection();
try
{
SQLiteCommand upCmd = null;
//kit master
string kit_name = GGKUtilLib.getKitName(kit_no);
if (kit_name == "Unknown")
{
// new kit
upCmd = new SQLiteCommand(@"INSERT OR REPLACE INTO kit_master(kit_no, name, sex)values(@kit_no,@name,@sex)", cnn);
upCmd.Parameters.AddWithValue("@kit_no", kit_no);
upCmd.Parameters.AddWithValue("@name", name);
upCmd.Parameters.AddWithValue("@sex", sex[0].ToString());
upCmd.ExecuteNonQuery();
}
else
{
// kit exists
upCmd = new SQLiteCommand(@"UPDATE kit_master SET name=@name, sex=@sex WHERE kit_no=@kit_no", cnn);
upCmd.Parameters.AddWithValue("@name", name);
upCmd.Parameters.AddWithValue("@sex", sex[0].ToString());
upCmd.Parameters.AddWithValue("@kit_no", kit_no);
upCmd.ExecuteNonQuery();
}
upCmd.Dispose();
bwSave.ReportProgress(35, "Saving Autosomal data ...");
upCmd = new SQLiteCommand(@"DELETE from kit_autosomal where kit_no=@kit_no", cnn);
upCmd.Parameters.AddWithValue("@kit_no", kit_no);
upCmd.ExecuteNonQuery();
//kit autosomal
upCmd = new SQLiteCommand(@"INSERT OR REPLACE INTO kit_autosomal(kit_no, rsid,chromosome,position,genotype)values(@kit_no,@rsid,@chromosome,@position,@genotype)", cnn);
using (var transaction = cnn.BeginTransaction())
{
bool incomplete = false;
foreach (DataGridViewRow row in rows)
{
if (row.IsNewRow)
{
continue;
}
incomplete = false;
for (int c = 0; c < row.Cells.Count; c++)
{
if (row.Cells[c].Value == null)
{
incomplete = true;
break;
}
else if (row.Cells[c].Value.ToString().Trim() == "")
{
incomplete = true;
break;
}
}
if (incomplete)
{
continue;
}
upCmd.Parameters.AddWithValue("@kit_no", kit_no);
upCmd.Parameters.AddWithValue("@rsid", row.Cells[0].Value.ToString());
upCmd.Parameters.AddWithValue("@chromosome", row.Cells[1].Value.ToString());
upCmd.Parameters.AddWithValue("@position", row.Cells[2].Value.ToString());
upCmd.Parameters.AddWithValue("@genotype", row.Cells[3].Value.ToString());
upCmd.ExecuteNonQuery();
}
transaction.Commit();
}
upCmd.Dispose();
bwSave.ReportProgress(75, "Saving Y-SNPs ...");
if (ysnps_list.Trim() != "")
{
//kit ysnps
upCmd = new SQLiteCommand(@"INSERT OR REPLACE INTO kit_ysnps(kit_no, ysnps) values (@kit_no,@ysnps)", cnn);
upCmd.Parameters.AddWithValue("@kit_no", kit_no);
upCmd.Parameters.AddWithValue("@ysnps", ysnps_list);
upCmd.ExecuteNonQuery();
upCmd.Dispose();
}
//kit ystr
bwSave.ReportProgress(80, "Saving Y-STR Values ...");
upCmd = new SQLiteCommand(@"DELETE from kit_ystr where kit_no=@kit_no", cnn);
upCmd.Parameters.AddWithValue("@kit_no", kit_no);
upCmd.ExecuteNonQuery();
upCmd = new SQLiteCommand(@"INSERT OR REPLACE INTO kit_ystr(kit_no, marker, value)values(@kit_no,@marker,@value)", cnn);
using (var transaction = cnn.BeginTransaction())
{
foreach (DataGridViewRowCollection row_collection in dgvy_rows)
{
foreach (DataGridViewRow row in row_collection)
{
if (row.IsNewRow)
{
continue;
}
if (row.Cells[1].Value.ToString().Trim() == "")
{
continue;
}
upCmd.Parameters.AddWithValue("@kit_no", kit_no);
upCmd.Parameters.AddWithValue("@marker", row.Cells[0].Value.ToString());
upCmd.Parameters.AddWithValue("@value", row.Cells[1].Value.ToString());
upCmd.ExecuteNonQuery();
}
}
transaction.Commit();
}
upCmd.Dispose();
//kit mtdna
if (mutations.Trim() != "" || fasta.Trim() != "")
{
bwSave.ReportProgress(90, "Saving mtDNA mutations ...");
upCmd = new SQLiteCommand(@"INSERT OR REPLACE INTO kit_mtdna(kit_no, mutations,fasta)values(@kit_no,@mutations,@fasta)", cnn);
upCmd.Parameters.AddWithValue("@kit_no", kit_no);
upCmd.Parameters.AddWithValue("@mutations", mutations);
upCmd.Parameters.AddWithValue("@fasta", fasta);
upCmd.ExecuteNonQuery();
}
bwSave.ReportProgress(100, "Saved");
save_success = true;
}
catch (Exception err)
{
bwSave.ReportProgress(-1, "Not Saved. Tech Details: " + err.Message);
MessageBox.Show("Not Saved. Techical Details: " + err.Message, "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
cnn.Dispose();
}