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 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();
}
}
}
}
