public static List <string> GetAutoCompleteData(string prefixText, int count)
{
const int minPrefixLength = 3;
List <string> valuesList = new List <string>();
if (prefixText.Length >= minPrefixLength)
{
try
{
List <Protein_Information> proteins = EF_Data.GetProteinsInfoQuery(prefixText);
foreach (Protein_Information p in proteins)
{
valuesList.Add(p.Protein_Short_Name);
valuesList.Add(p.Protein_Full_Name);
valuesList.Add(p.NCBI_Gene_ID);
valuesList.Add(p.PDB_Protein_Name);
valuesList.Add(p.Protein_Alias);
valuesList.Add(p.UniProt_ID);
valuesList.Add(p.NCBI_RefSeq_NP_ID);
valuesList.Add(p.NCBI_Gene_Name);
valuesList.Add(p.PhosphoNET_Name);
}
}
catch (Exception)
{
throw;
}
}
return(DataUtilities.FilterDropdownList(valuesList, prefixText, true));
}
public static List <string> GetAutoCompleteData(string prefixText, int count)
{
const int minPrefixLength = 3;
List <string> valuesList = new List <string>();
if (prefixText.Length >= minPrefixLength)
{
try
{
List <Drug_Information> drugs = EF_Data.GetDrugsQuery(prefixText);
foreach (Drug_Information drug in drugs)
{
valuesList.Add(drug.Other_Drug_Name_Alias);
valuesList.Add(drug.Drug_Common_Name);
valuesList.Add(drug.Drug_Chemical_Name);
valuesList.Add(drug.Compound_CAS_ID);
valuesList.Add(drug.PubChem_CID);
valuesList.Add(drug.ChEMBL_ID);
}
}
catch (Exception)
{
throw;
}
}
return(DataUtilities.FilterDropdownList(valuesList, prefixText));
}
public static List <string> GetAutoCompleteData(string prefixText, int count)
{
List <string> valuesList = new List <string>();
const int minPrefixLength = 14;
if (prefixText.Length >= minPrefixLength)
{
try
{
List <SNV_Mutation> SNV_Mutation = EF_Data.GetMutationsBySNVIDKeyContains(prefixText);
foreach (SNV_Mutation mutation in SNV_Mutation)
{
valuesList.AddRange(new List <string> {
mutation.SNV_P1W_ID, mutation.SNV_P2W_ID, mutation.SNV_P3W_ID,
mutation.SNV_P1M1_ID, mutation.SNV_P1M2_ID, mutation.SNV_P1M3_ID,
mutation.SNV_P2M1_ID, mutation.SNV_P2M2_ID, mutation.SNV_P2M3_ID,
mutation.SNV_P3M1_ID, mutation.SNV_P3M2_ID, mutation.SNV_P3M3_ID,
}
);
}
}
catch (Exception)
{
throw;
}
}
return(DataUtilities.FilterDropdownList(valuesList, prefixText, true));
}
/// <summary>
/// Author: Andy Tang
/// </summary>
protected void Search_Textbox_Changed(object sender, EventArgs e)
{
search_drop_down.Items.Clear();
search_drop_down.Items.Add(DROP_DOWN_PROMPT_MESSAGE);
List <Protein_Information> proteinList = new List <Protein_Information>();
const int minPrefixLength = 3;
if (search_textBox.Text.Length < minPrefixLength)
{
return;
}
Drug_Information drug = EF_Data.GetDrugsQuery(search_textBox.Text).FirstOrDefault();
if (drug != null)
{
List <PDB_Information> pdbInfoList = EF_Data.GetPDBInfoUsingDrug(drug.Drug_PDB_ID);
foreach (PDB_Information pdb in pdbInfoList)
{
Protein_Information protein = EF_Data.GetProteinByUniprotID(pdb.UniProt_ID);
if (protein != null)
{
proteinList.Add(protein);
}
}
}
if (proteinList.Count > 0)
{
List <string> valuesList = new List <string>();
foreach (Protein_Information protein in proteinList)
{
valuesList.Add(protein.UniProt_ID);
valuesList.Add(protein.Protein_Short_Name);
valuesList.Add(protein.Protein_Full_Name);
valuesList.Add(protein.Protein_Alias);
valuesList.Add(protein.NCBI_RefSeq_NP_ID);
valuesList.Add(protein.PhosphoNET_Name);
valuesList.Add(protein.PDB_Protein_Name);
}
valuesList = DataUtilities.FilterDropdownList(valuesList);
foreach (string value in valuesList)
{
search_drop_down.Items.Add(new ListItem(value, value, true));
}
}
else
{
search_drop_down.Items.Clear();
search_drop_down.Items.Add(DROP_DOWN_NO_MATCHES_MESSAGE);
}
}
/// <summary>
/// Author: Andy Tang
/// </summary>
protected void Search_Textbox_Changed(object sender, EventArgs e)
{
search_drop_down.Items.Clear();
search_drop_down.Items.Add(DROP_DOWN_PROMPT_MESSAGE);
List <Drug_Information> drugList = new List <Drug_Information>();
const int minPrefixLength = 3;
if (search_textBox.Text.Length < minPrefixLength)
{
return;
}
Protein_Information protein = EF_Data.GetProteinsInfoQuery(search_textBox.Text).FirstOrDefault();
if (protein != null)
{
List <PDB_Information> pdbInfoList = EF_Data.GetPDBInfoUsingProtein(protein.UniProt_ID);
foreach (PDB_Information pdb in pdbInfoList)
{
Drug_Information drug = EF_Data.GetDrugByDrugPDBID(pdb.Drug_PDB_ID);
if (drug != null)
{
drugList.Add(drug);
}
}
}
if (drugList.Count > 0)
{
List <string> valuesList = new List <string>();
foreach (Drug_Information drug in drugList)
{
valuesList.Add(drug.Other_Drug_Name_Alias);
valuesList.Add(drug.Drug_Common_Name);
valuesList.Add(drug.Drug_Chemical_Name);
valuesList.Add(drug.Compound_CAS_ID);
valuesList.Add(drug.PubChem_CID);
valuesList.Add(drug.ChEMBL_ID);
}
valuesList = DataUtilities.FilterDropdownList(valuesList);
foreach (string value in valuesList)
{
search_drop_down.Items.Add(new ListItem(value, value, true));
}
}
else
{
search_drop_down.Items.Clear();
search_drop_down.Items.Add(DROP_DOWN_NO_MATCHES_MESSAGE);
}
}
protected void Search_Textbox_Changed(object sender, EventArgs e)
{
drug_specification_drop_down.Items.Clear();
drug_specification_drop_down.Items.Add(DROP_DOWN_PROMPT_MESSAGE);
amino_acid_specification_drop_down.Items.Clear();
amino_acid_specification_drop_down.Items.Add(DROP_DOWN_PROMPT_MESSAGE);
const int minPrefixLength = 3;
if (search_textBox.Text.Length < minPrefixLength)
{
return;
}
Protein_Information protein = EF_Data.GetProteinsInfoQuery(search_textBox.Text).FirstOrDefault();
if (protein != null)
{
List <PDB_Information> pdbList = EF_Data.GetPDBInfoUsingProtein(protein.UniProt_ID);
List <Drug_Information> drugList = new List <Drug_Information>();
foreach (PDB_Information pdb in pdbList)
{
Drug_Information drug = EF_Data.GetDrugByDrugPDBID(pdb.Drug_PDB_ID);
if (drug != null)
{
drugList.Add(drug);
}
}
if (drugList.Count > 0)
{
List <string> dropdownValues = new List <string>();
foreach (Drug_Information drug in drugList)
{
dropdownValues.Add(drug.Drug_Name_for_Pull_Down_Menu);
}
dropdownValues = DataUtilities.FilterDropdownList(dropdownValues);
foreach (string dropdownValue in dropdownValues)
{
drug_specification_drop_down.Items.Add(dropdownValue);
}
}
else
{
drug_specification_drop_down.Items.Clear();
drug_specification_drop_down.Items.Add(DROP_DOWN_NO_MATCHES_MESSAGE);
}
}
}
/// <summary>
/// Author: Andy Tang
/// </summary>
protected new void Page_Load(object sender, EventArgs e)
{
base.Page_Load(sender, e);
string query = Request.QueryString["query_string"];
Protein_Information protein = EF_Data.GetProteinsInfoQuery(query).FirstOrDefault();
if (protein != null)
{
LoadData(protein);
}
else
{
Page.Master.FindControl("BodyContentPlaceHolder").Visible = false;
ExceptionUtilities.DisplayAlert(this, QUERY_PAGE);
}
}
protected void LoadAminoAcidDropDown(object sender, EventArgs e)
{
amino_acid_specification_drop_down.Items.Clear();
amino_acid_specification_drop_down.Items.Add(DROP_DOWN_PROMPT_MESSAGE);
try
{
if (drug_specification_drop_down.SelectedItem.Value != DROP_DOWN_PROMPT_MESSAGE)
{
Protein_Information protein = EF_Data.GetProtein(search_textBox.Text);
Drug_Information drug = EF_Data.GetDrugUsingDropDownName(drug_specification_drop_down.SelectedItem.Value);
PDB_Information PDB = EF_Data.GetPDBInfo(protein, drug);
List <SNV_Mutation> mutations = EF_Data.GetMutations(protein.UniProt_ID, drug.Drug_PDB_ID, PDB.PDB_File_ID);
if (mutations.Count > 0)
{
List <string> dropdownValues = new List <string>();
foreach (SNV_Mutation mutation in mutations)
{
dropdownValues.Add(mutation.SNV_Key);
}
dropdownValues = DataUtilities.FilterDropdownList(dropdownValues);
foreach (string dropdownValue in dropdownValues)
{
amino_acid_specification_drop_down.Items.Add(dropdownValue);
}
}
else
{
amino_acid_specification_drop_down.Items.Clear();
amino_acid_specification_drop_down.Items.Add(DROP_DOWN_NO_MATCHES_MESSAGE);
}
}
}
catch (Exception)
{
amino_acid_specification_drop_down.Items.Clear();
amino_acid_specification_drop_down.Items.Add(DROP_DOWN_PROMPT_MESSAGE);
}
}
/// <summary>
/// Author: Garth Nelson
/// </summary>
protected new void Page_Load(object sender, EventArgs e)
{
base.Page_Load(sender, e);
SNV_ID_Key = Request.QueryString["query_string"];
try
{
string stringAfterPDot = SNV_ID_Key.Substring(SNV_ID_Key.IndexOf("p.") + 2);
string specifiedAAType = new string(stringAfterPDot.TakeWhile(c => char.IsLetter(c)).ToArray());
string specifiedAANumber = new string(stringAfterPDot.Substring(specifiedAAType.Length).TakeWhile(c => char.IsNumber(c)).ToArray());
string specifiedAA = specifiedAAType + "-" + specifiedAANumber;
mutations = EF_Data.GetMutationsBySNVIDKey(SNV_ID_Key);
proteinMutation = EF_Data.GetMutationBySNVIDKey(SNV_ID_Key);
protein = EF_Data.GetProteinByUniprotID(proteinMutation.UniProt_ID);
foreach (SNV_Mutation mutation in mutations)
{
Drug_Information drug = EF_Data.GetDrugByDrugPDBID(mutation.Drug_PDB_ID);
drugs.Add(drug);
PDB_Interaction interaction = EF_Data.GetPDB_Interaction(mutation.UniProt_ID, mutation.Drug_PDB_ID, specifiedAA);
interactions.Add(interaction);
}
Session["drugs"] = drugs;
Session["interactions"] = interactions;
Session["mutations"] = mutations;
Session["SNV_ID_Key"] = SNV_ID_Key;
LoadSNVID(SNV_ID_Key);
LoadTargetGeneID(protein, mutations[0]);
CreateIDofPDILinkedSNVTable(drugs, interactions, mutations);
}
catch (Exception)
{
Page.Master.FindControl("BodyContentPlaceHolder").Visible = false;
ExceptionUtilities.DisplayAlert(this, QUERY_PAGE);
}
}
/// <summary>
/// Author: Andy Tang
/// </summary>
protected new void Page_Load(object sender, EventArgs e)
{
base.Page_Load(sender, e);
string query = Request.QueryString["query_string"];
try
{
drug = EF_Data.GetDrugUsingDropDownName(query);
if (drug != null)
{
LoadData(drug);
}
}
catch (Exception)
{
throw;
}
}
/// <summary>
/// Author: Garth Nelson
/// </summary>
protected new void Page_Load(object sender, EventArgs e)
{
base.Page_Load(sender, e);
try
{
string protein_specification = Request.QueryString["query_string"];
string drug_specification = Request.QueryString["drug_specification"];
string SNV_Key = Request.QueryString["snv_id_key"];
Session["SNV_Key"] = SNV_Key;
Protein_Information protein = EF_Data.GetProtein(protein_specification);
Drug_Information drug = EF_Data.GetDrugUsingDropDownName(drug_specification);
PDB_Information PDB = EF_Data.GetPDBInfo(protein, drug);
string[] SNV_KEYsplit = SNV_Key.Split('-');
// Retrieve second and third elements
string amino_acid_specification = SNV_KEYsplit[1] + "-" + SNV_KEYsplit[2];
PDB_Interaction interaction = EF_Data.GetPDB_Interaction(protein.Uniprot_ID, drug.Drug_PDB_ID, amino_acid_specification);
mutation = EF_Data.GetMutationBySNVKey(SNV_Key);
Session["mutation"] = mutation;
LoadProtein(protein, interaction, mutation);
LoadDrug(drug, mutation);
LoadPDB_Info(PDB);
CreateSNVIdentificationTable(mutation);
}
catch (Exception)
{
Page.Master.FindControl("BodyContentPlaceHolder").Visible = false;
ExceptionUtilities.DisplayAlert(this, QUERY_PAGE);
}
}
public static List <string> GetAutoCompleteData(string prefixText, int count)
{
const int minPrefixLength = 3;
List <string> valuesList = new List <string>();
if (prefixText.Length >= minPrefixLength)
{
try
{
List <Drug_Information> drugs = EF_Data.GetDrugsInfoQuery(prefixText);
foreach (Drug_Information drug in drugs)
{
valuesList.Add(drug.Drug_Name_for_Pull_Down_Menu);
}
}
catch (Exception)
{
throw;
}
}
return(DataUtilities.FilterDropdownList(valuesList));
}
/// <summary>
/// Author: Andy Tang, Ryan Liang
/// </summary>
protected new void Page_Load(object sender, EventArgs e)
{
base.Page_Load(sender, e);
if (!IsPostBack)
{
string fromPage = null;
string query_string = null;
try
{
query_string = Request.QueryString["query_string"];
drug_specification = Request.QueryString["drug_specification"];
protein_specification = Request.QueryString["protein_specification"];
if (!string.IsNullOrEmpty(drug_specification))
{
protein_specification = query_string;
fromPage = "protein";
}
else if (!string.IsNullOrEmpty(protein_specification))
{
drug_specification = query_string;
fromPage = "drug";
}
drug = EF_Data.GetDrugsQuery(drug_specification).FirstOrDefault();
protein = EF_Data.GetProteinsInfoQuery(protein_specification).FirstOrDefault();
PDB = EF_Data.GetPDBInfo(protein, drug);
Session["PDB_File_ID"] = PDB.PDB_File_ID;
interaction_distance = double.Parse(Request.QueryString["interaction_distance"]);
protein_chain = bool.Parse(Request.QueryString["protein_chain"]);
protein_atoms = bool.Parse(Request.QueryString["protein_atoms"]);
protein_residues = bool.Parse(Request.QueryString["protein_residues"]);
protein_residue_numbers = bool.Parse(Request.QueryString["protein_residue_numbers"]);
drug_atoms = bool.Parse(Request.QueryString["drug_atoms"]);
Session["interaction_distance"] = interaction_distance;
}
catch (Exception)
{
throw;
}
if (drug == null || protein == null || PDB == null)
{
Page.Master.FindControl("BodyContentPlaceHolder").Visible = false;
if (fromPage != null)
{
ExceptionUtilities.DisplayAlert(this, fromPage.Equals("drug") ? DRUG_QUERY_PAGE : PROTEIN_QUERY_PAGE);
}
else
{
ExceptionUtilities.DisplayAlert(this, DEFAULT_REDIRECT_PAGE);
}
}
else
{
Session["interaction_distance"] = interaction_distance;
Session["protein_chain"] = protein_chain;
Session["protein_atoms"] = protein_atoms;
Session["protein_residues"] = protein_residues;
Session["protein_residue_numbers"] = protein_residue_numbers;
Session["drug_atoms"] = drug_atoms;
LoadProtein(protein);
LoadDrug(drug, PDB);
LoadPDB_Info(PDB);
GetDrugAtomNumberingImage(drug);
CreateInteractionList(PDB, interaction_distance, protein_chain, protein_atoms, protein_residues, protein_residue_numbers, drug_atoms);
CreateInteractionSummary();
ScriptManager.RegisterStartupScript(Page, GetType(), "D_3DViewer", "javascript:loadDrugLigand('" + drug.Drug_PDB_ID + "');", true);
ScriptManager.RegisterStartupScript(Page, GetType(), "PDB_3DViewer", "javascript:loadStage('" + drug.PDB_File_ID + "', '" + drug.Drug_PDB_ID + "');", true);
}
}
}
/// <summary>
/// Author: Ryan Liang
/// </summary>
private void CreateInteractionList(PDB_Information PDB, double interaction_distance, bool protein_chain, bool protein_atoms, bool protein_residues, bool protein_residue_numbers, bool drug_atoms)
{
TableHeaderRow tableHeaderRow = new TableHeaderRow {
TableSection = TableRowSection.TableHeader
};
tableHeaderRow.Cells.Add(new TableHeaderCell {
Text = "Distance (Å)"
});
if (protein_chain)
{
tableHeaderRow.Cells.Add(new TableHeaderCell {
Text = "Protein Chain"
});
}
if (protein_residue_numbers)
{
tableHeaderRow.Cells.Add(new TableHeaderCell {
Text = "Protein Residue Number"
});
}
if (protein_residues)
{
tableHeaderRow.Cells.Add(new TableHeaderCell {
Text = "Amino Acid Residue Type"
});
}
if (protein_atoms)
{
tableHeaderRow.Cells.Add(new TableHeaderCell {
Text = "Amino Acid Residue Atom"
});
}
if (drug_atoms)
{
tableHeaderRow.Cells.Add(new TableHeaderCell {
Text = "Drug Atom"
});
}
interaction_list.Rows.Add(tableHeaderRow);
var DistanceAndUniprotResidueNumbers = EF_Data.GetDistanceAndUniprotResidueNumbers(PDB.PDB_File_ID, interaction_distance);
Session["DistanceAndUniprotResidueNumbers"] = DistanceAndUniprotResidueNumbers;
foreach (KeyValuePair <PDB_Distance, string> kvp in DistanceAndUniprotResidueNumbers)
{
TableRow tableRow = new TableRow();
tableRow.Cells.Add(new TableCell {
Text = kvp.Key.Distance.ToString("0.00")
});
if (protein_chain)
{
tableRow.Cells.Add(new TableCell {
Text = kvp.Key.Protein_Chain
});
}
if (protein_residue_numbers)
{
tableRow.Cells.Add(new TableCell {
Text = kvp.Value
});
}
if (protein_residues)
{
tableRow.Cells.Add(new TableCell {
Text = kvp.Key.Protein_Residue
});
}
if (protein_atoms)
{
tableRow.Cells.Add(new TableCell {
Text = kvp.Key.Protein_Atom
});
}
if (drug_atoms)
{
tableRow.Cells.Add(new TableCell {
Text = kvp.Key.Compound_Atom
});
}
interaction_list.Rows.Add(tableRow);
}
}
