public static void Insilico_filter_U2(proteins prot, List <double> peakList, double tol)
{
double l_score;
double r_score;
double score;
bool left;
bool right;
insilico_obj comp;
comp = new insilico_obj();
r_score = 0;
l_score = 0;
comp = prot.insilico_details;
//comp.insilico_mass_right = frags.ElementAt(j).mw_right_ion;
for (int k = 0; k < prot.insilico_details.insilico_mass_left.Count; k++)
{
left = false;
for (int i = 0; i < peakList.Count; i++)
{
if (Math.Abs(prot.insilico_details.insilico_mass_left[k] - peakList[i]) < tol)
{
l_score++;
comp.peaklist_mass_left.Add(peakList[i]);
left = true;
}
}
if (left == false)
{
comp.peaklist_mass_left.Add(0);
}
}
for (int k = 0; k < prot.insilico_details.insilico_mass_right.Count; k++)
{
right = false;
for (int i = 0; i < peakList.Count; i++)
{
if (Math.Abs(prot.insilico_details.insilico_mass_right[k] - peakList[i]) < tol)
{
comp.peaklist_mass_right.Add(peakList[i]);
r_score++;
right = true;
}
}
if (right == false)
{
comp.peaklist_mass_right.Add(0);
}
}
score = (l_score + r_score) / (peakList.Count);
Console.WriteLine("Insilico score:");
Console.WriteLine(score);
prot.insilico_score = score;
prot.insilico_details = comp;
}
/// /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
public static void insilico_fragmentation_2(proteins prot, string clevageType, string ions)
{
frag1_2(prot, clevageType, ions, 0);
//return result;
}
public static void frag1_2(proteins prot, string clevageType, string HandleIon, int index)
{
string strprotein = prot.sequence;
int prtlength = strprotein.Length; //Gives length of Protein
strprotein = strprotein.ToUpper(); //Convert all amino aFragment letters into uppercase letters
if (prot.ptm_particulars != null)
{
if (prot.ptm_particulars.Count != 0)
{
for (int j = 0; j < prot.ptm_particulars.Count; j++)
{
prot.insilico_details.insilico_mass_right[0] += prot.ptm_particulars[j].mod_weight;
if (prot.ptm_particulars[j].i == 0)
{
prot.insilico_details.insilico_mass_left[0] += prot.ptm_particulars[j].mod_weight;
}
}
}
}
for (int ifragmentationposition = 1; ifragmentationposition < prtlength; ifragmentationposition++)
{
if (prot.ptm_particulars != null)
{
if (prot.ptm_particulars.Count != 0)
{
for (int j = 0; j < prot.ptm_particulars.Count; j++)
{
if (prot.ptm_particulars[j].i == ifragmentationposition)
{
for (int k = ifragmentationposition; k < prtlength; k++)
{
prot.insilico_details.insilico_mass_left[ifragmentationposition] += prot.ptm_particulars[j].mod_weight;
}
for (int k = ifragmentationposition; k > 0; k--)
{
prot.insilico_details.insilico_mass_right[ifragmentationposition] -= prot.ptm_particulars[j].mod_weight;
}
}
}
}
else
{
break;
}
}
else
{
break;
}
}
if (clevageType == "CID" || clevageType == "cid" || clevageType == "bird" || clevageType == "BIRD" || clevageType == "imd" || clevageType == "IMD" || clevageType == "HCD" || clevageType == "hcd" || clevageType == "SID" || clevageType == "sid")
{
for (int i = 0; i < prtlength; i++)//for Fragment
{
if (HandleIon == "bo")
{
prot.insilico_details.insilico_mass_left.Add(prot.insilico_details.insilico_mass_left[i] - 18 - 1.00794);
}
else if (HandleIon == "bstar")
{
prot.insilico_details.insilico_mass_left.Add(prot.insilico_details.insilico_mass_left[i] - 17.026549 - 1.00794);
}
else if (HandleIon == "ystar")
{
prot.insilico_details.insilico_mass_right.Add(prot.insilico_details.insilico_mass_right[i] - 17.026549 + 1.00794);
}
else if (HandleIon == "yo")
{
prot.insilico_details.insilico_mass_right.Add(prot.insilico_details.insilico_mass_right[i] - 18 + 1.00794);
}
prot.insilico_details.insilico_mass_left[i] -= 1.00794;
prot.insilico_details.insilico_mass_right[i] += 1.00794;
}
}
else if (clevageType == "ECD" || clevageType == "ecd" || clevageType == "ETD" || clevageType == "etd")
{
for (int i = 0; i < prtlength; i++)//for Fragment
{
if (HandleIon == "zd")
{
prot.insilico_details.insilico_mass_right.Add(prot.insilico_details.insilico_mass_right[i] + 1 - 16.02258);
}
else if (HandleIon == "zdd")
{
prot.insilico_details.insilico_mass_right.Add(prot.insilico_details.insilico_mass_right[i] + 2 - 16.02258);
}
prot.insilico_details.insilico_mass_left[i] += 16.02258;
prot.insilico_details.insilico_mass_right[i] -= 16.02258;
}
}
else if (clevageType == "EDD" || clevageType == "edd" || clevageType == "NETD" || clevageType == "netd")
{
for (int i = 0; i < prtlength; i++)//for Fragment
{
if (HandleIon == "ao")
{
prot.insilico_details.insilico_mass_left.Add(prot.insilico_details.insilico_mass_left[i] - 18 - 29.01804);
}
else if (HandleIon == "astar")
{
prot.insilico_details.insilico_mass_left.Add(prot.insilico_details.insilico_mass_left[i] - 17.026549 - 29.01804);
}
prot.insilico_details.insilico_mass_left[i] -= 29.01804;
prot.insilico_details.insilico_mass_right[i] += 27.02534;
}
}
//return output;
}
//Returns Search History of specific query ie. search parameters and Results
public searchview retrieve_searchview_db(string qid)
{
searchview result = new searchview();
QuerryParameters qp = new QuerryParameters();
Results r = new Results();
string[] QIDArr = qid.Split('z');
qid = QIDArr[0];
int file_id = Convert.ToInt32(QIDArr[1]);
string query1 = "SELECT * FROM proteomics.query where QueryId='" + qid + "';";
string queryT = "SELECT * FROM proteomics.timings where querry_ID='" + qid + "';";
if (this.OpenConnection() == true)
{
try
{
using (MySqlTransaction trans = connection.BeginTransaction())
{
MySqlCommand cmd = new MySqlCommand(queryT, connection);
MySqlDataReader reader = cmd.ExecuteReader();
if (reader.Read())
{
r.times.insilico_time = reader.GetValue(1).ToString();
r.times.ptm_time = reader.GetValue(2).ToString();
r.times.tuner_time = reader.GetValue(3).ToString();
r.times.mw_filter_time = reader.GetValue(4).ToString();
r.times.pst_time = reader.GetValue(5).ToString();
r.times.total_time = reader.GetValue(6).ToString();
r.times.file = reader.GetValue(7).ToString();
}
reader.Close();
cmd = new MySqlCommand(query1, connection);
reader = cmd.ExecuteReader();
if (reader.Read())
{
qp.queryid = reader.GetValue(0).ToString();
qp.userID = reader.GetValue(1).ToString();
qp.title = reader.GetValue(2).ToString();
qp.protDB = reader.GetValue(3).ToString();
qp.outputFormat = Convert.ToInt32(reader.GetValue(4));
qp.insilico_frag_type = reader.GetValue(5).ToString();
qp.filterDB = Convert.ToInt32(reader.GetValue(6));
qp.ptm_tolerance = Convert.ToDouble(reader.GetValue(7));
qp.MWTolUnit = reader.GetValue(8).ToString();
qp.MW_tolerance = Convert.ToDouble(reader.GetValue(9));
qp.hopThreshhold = Convert.ToDouble(reader.GetValue(10));
qp.minimum_est_length = Convert.ToInt32(reader.GetValue(11));
qp.maximum_est_length = Convert.ToInt32(reader.GetValue(12));
// public double pst_tolerance;
qp.GUI_mass = Convert.ToDouble(reader.GetValue(13));
qp.HandleIons = reader.GetValue(14).ToString();
qp.autotune = Convert.ToInt32(reader.GetValue(15));
qp.peakListFile = reader.GetValue(16).ToString().Split('<');
qp.fileType = reader.GetValue(17).ToString();
// public double peptideTol;
//added
qp.hopTolUnit = reader.GetValue(18).ToString();
qp.MW_sweight = Convert.ToDouble(reader.GetValue(19));
qp.PST_sweight = Convert.ToDouble(reader.GetValue(20));
qp.Insilico_sweight = Convert.ToDouble(reader.GetValue(21));
qp.NumberOfOutputs = Convert.ToInt32(reader.GetValue(22));
/////
qp.denovo_allow = Convert.ToInt32(reader.GetValue(23));
qp.ptm_allow = Convert.ToInt32(reader.GetValue(24));
}
reader.Close();
query1 = "SELECT fixed_mod FROM fixed_modifications where QuerryId='" + qid + "';";
cmd = new MySqlCommand(query1, connection);
using (reader = cmd.ExecuteReader())
{
qp.ptm_code_fix = new List <int>();
while (reader.Read())
{
qp.ptm_code_fix.Add(Convert.ToInt32(reader["fixed_mod"]));
}
}
reader.Close();
query1 = "SELECT variable_mod FROM variable_modifications where QuerryId='" + qid + "';";
cmd = new MySqlCommand(query1, connection);
using (reader = cmd.ExecuteReader())
{
qp.ptm_code_var = new List <int>();
while (reader.Read())
{
qp.ptm_code_var.Add(Convert.ToInt32(reader["variable_mod"]));
}
}
reader.Close();
// SELECT * FROM proteomics.results Where Querry_ID = 'fe29e39e-97ee-4f5e-9cab-4d414b5e902a' ORDER BY score DESC LIMIT 3;
string query2 = "SELECT * FROM results where Querry_ID='" + qid + "' AND file_ID = " + file_id + " ORDER BY score DESC LIMIT " + qp.NumberOfOutputs + ";";
cmd = new MySqlCommand(query2, connection);
r.querryID = qid;
r.final_prot = new List <proteins>();
proteins temp_prot = new proteins();
List <string> resid = new List <string>();
using (reader = cmd.ExecuteReader())
{
while (reader.Read())
{
temp_prot = new proteins();
resid.Add(reader.GetValue(0).ToString());
temp_prot.header = reader.GetValue(2).ToString();
temp_prot.sequence = reader.GetValue(3).ToString();
temp_prot.est_score = Convert.ToDouble(reader.GetValue(4));
temp_prot.insilico_score = Convert.ToDouble(reader.GetValue(5));
temp_prot.ptm_score = Convert.ToDouble(reader.GetValue(6));
temp_prot.score = Convert.ToDouble(reader.GetValue(7));
temp_prot.MW_score = Convert.ToDouble(reader.GetValue(8));
temp_prot.MW = Convert.ToDouble(reader.GetValue(9));
r.final_prot.Add(temp_prot);
}
}
reader.Close();
Sites temp_site = new Sites();
string tempaa;
for (int i = 0; i < resid.Count; i++)
{
query2 = "SELECT * FROM ptm_sites where result_id='" + resid[i] + "';";
cmd = new MySqlCommand(query2, connection);
using (reader = cmd.ExecuteReader())
{
while (reader.Read())
{
temp_site = new Sites();
temp_site.i = Convert.ToInt32(reader.GetValue(1));
temp_site.score = Convert.ToInt32(reader.GetValue(2));
temp_site.mod_weight = Convert.ToInt32(reader.GetValue(3));
temp_site.mod_name = reader.GetValue(4).ToString();
temp_site.site = Convert.ToChar(reader.GetValue(5));
tempaa = reader.GetValue(6).ToString();
for (int j = 0; j < tempaa.Length; j++)
{
temp_site.AA.Add(tempaa[j]);
}
r.final_prot[i].ptm_particulars.Add(temp_site);
}
}
}
reader.Close();
///////////
//temp_p.insilico_details.insilico_mass_left = dataPs[3].Split(',').Select(t => double.Parse(t)).ToList<double>();
string xx;
for (int i = 0; i < resid.Count; i++)
{
query2 = "SELECT matched_peak_left FROM insilico_matches_left where result_id='" + resid[i] + "';";
cmd = new MySqlCommand(query2, connection);
using (reader = cmd.ExecuteReader())
{
temp_site = new Sites();
if (reader.Read())
{
xx = reader.GetValue(0).ToString();
r.final_prot[i].insilico_details.peaklist_mass_left = xx.Split(',').Select(t => double.Parse(t)).ToList <double>();
}
}
query2 = "SELECT Ions FROM leftions where ProteinID='" + r.final_prot[i].header + "';";
cmd = new MySqlCommand(query2, connection);
using (reader = cmd.ExecuteReader())
{
temp_site = new Sites();
if (reader.Read())
{
xx = reader.GetValue(0).ToString();
xx = Decompress(xx);
r.final_prot[i].insilico_details.insilico_mass_left = xx.Split(',').Select(t => double.Parse(t)).ToList <double>();
}
}
}
reader.Close();
//////////////////////////////////////////////////////////////
for (int i = 0; i < resid.Count; i++)
{
query2 = "SELECT matchedpeak_right FROM insilico_matches_right where result_id='" + resid[i] + "';";
cmd = new MySqlCommand(query2, connection);
using (reader = cmd.ExecuteReader())
{
temp_site = new Sites();
if (reader.Read())
{
xx = reader.GetValue(0).ToString();
r.final_prot[i].insilico_details.peaklist_mass_right = xx.Split(',').Select(t => double.Parse(t)).ToList <double>();
}
}
query2 = "SELECT Ions FROM rightions where ProteinID='" + r.final_prot[i].header + "';";
cmd = new MySqlCommand(query2, connection);
using (reader = cmd.ExecuteReader())
{
temp_site = new Sites();
if (reader.Read())
{
xx = reader.GetValue(0).ToString();
xx = Decompress(xx);
r.final_prot[i].insilico_details.insilico_mass_right = xx.Split(',').Select(t => double.Parse(t)).ToList <double>();
}
}
}
reader.Close();
//////////////////////////////////////////////////////////////
//for (int i = 0; i < resid.Count; i++)
//{
// query2 = "SELECT * FROM insilico_mass_right where result_id='" + resid[i] + "';";
// cmd = new MySqlCommand(query2, connection);
// using (reader = cmd.ExecuteReader())
// {
// while (reader.Read())
// {
// temp_site = new Sites();
// r.final_prot[i].insilico_details.insilico_mass_right.Add(Convert.ToDouble(reader.GetValue(1)));
// r.final_prot[i].insilico_details.peaklist_mass_right.Add(Convert.ToDouble(reader.GetValue(2)));
// }
// }
//}
//reader.Close();
////////////
result.param = qp;
result.result = r;
trans.Commit();
connection.Close();
}
}
catch (Exception e)
{
System.Diagnostics.Debug.WriteLine(e.Message);
}
}
// result.result.final_prot = result.result.final_prot.OrderByDescending(o => o.score).ToList();
return(result);
}
