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ProteinInfo.aspx.cs
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ProteinInfo.aspx.cs
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using System;
using System.Data;
using System.Configuration;
using System.Web;
using System.Web.Security;
using System.Web.UI;
using System.Web.UI.WebControls;
using System.Web.UI.WebControls.WebParts;
using System.Web.UI.HtmlControls;
using System.Data.SqlClient;
using ZJU.COPLib;
using System.Collections;
using ZJU.COPDB;
using Faust.Andrew.LiteWiki.DataAccess;
using Faust.Andrew.LiteWiki.TextFormatting;
using gov.nih.nlm.ncbi.eutils;
using System.Net;
public partial class ProteinInfo2 : System.Web.UI.Page
{
string M_T;
string M_V;
string NoInfo;
protected void Page_Load(object sender, EventArgs e)
{
string QueryType = Request.QueryString["QType"];
M_T = QueryType;
string QueryValue = Request.QueryString["QValue"];
M_V = QueryValue;
string queryShow = Request.QueryString["showInfo"];
NoInfo = queryShow;
//find correct intetactome
displayInteractome(M_V);
if (NoInfo == "T"){ // collapse
informationShow.Text = @"<div id='helpNote' class='collapse'>";
informationBtn.Text = @"<button type='button' class='close button collapsed' data-toggle='collapse' data-target='#helpNote'>×</button>";
}
else{
informationShow.Text = @"<div id='helpNote' class='collapse in'>";
informationBtn.Text = @"<button type='button' class='close button' data-toggle='collapse' data-target='#helpNote'>×</button>";
}
if ((!Page.IsPostBack) && QueryType != null && QueryValue != null)
{
Query(QueryType, QueryValue);
}
//lbEdit.Text = string.Format("<a href='DiseaseInfo.aspx?uniprot={0}' target='_blank'>More Information</a> ", lbProtein_ID.Text.Trim());
lbMoreInformation.Text = string.Format("<a href='WikiEdit.aspx?PageName={0}' target='_blank'>Edit</a> ", lbProtein_ID.Text);
AdditionalReport.Text = string.Format("<h5>iHOP <a href='http://www.ihop-net.org/UniPub/iHOP/?search={0}&field=UNIPROT__AC&ncbi_tax_id=0&organism_syn=' target='_blank'>{0}</a> </h5>", QueryValue);
}
private void displayInteractome(string M_V)
{
string webtext = "";
WebRequest request;
WebResponse response;
System.IO.StreamReader reader;
string[] files = new string[7] {"drosophila_mitochondria",
"human_mitochondria",
"human_proteosome",
"mouse_cytosol",
"mouse_mitochondria",
"mouse_nucleus",
"mouse_proteosome"};
for(int i = 0; i < 7; i++){
request = WebRequest.Create(string.Format("http://www.heartproteome.org/copa/js/copa_imex_interactome_{0}.js",files[i]));
response = request.GetResponse();
reader = new System.IO.StreamReader(response.GetResponseStream());
webtext = reader.ReadToEnd();
if (System.Text.RegularExpressions.Regex.IsMatch(webtext, M_V.ToUpper()))
{
if (i == 2)
interactomeDisplay.Text += string.Format("<a href='interactome_{0}.aspx?iid={1}'>View {0}</a><br />", "human_proteasome", M_V.ToUpper());
else if (i == 6)
interactomeDisplay.Text += string.Format("<a href='interactome_{0}.aspx?iid={1}'>View {0}</a><br />", "mouse_proteasome", M_V.ToUpper());
else
interactomeDisplay.Text += string.Format("<a href='interactome_{0}.aspx?iid={1}'>View {0}</a><br />", files[i], M_V.ToUpper());
}
}
}
private void Query(string QueryType, string QueryValue)
{
switch (QueryType)
{
case "Protein ID":
QueryProteinID(QueryValue);
break;
}
}
private void QueryProteinID(string ProteinID)
{
ProteinID = ProteinID.ToUpper();
if (!ProteinID.StartsWith("IPI"))
{
int pno;
try
{
pno = int.Parse(ProteinID);
ProteinID = string.Format("IPI{0:D8}", pno);
}
catch (Exception ex) { }
}
string strSQL = string.Format("select Protein_COP_ID,Ref_Protein_ID,Protein_name,Organism_Source,Protein_Sequence,sequence_length,Chromosome,Molecular_Weight,Isoelectric_Point,GRAVY,Transmembrane_Domain ,Gene_Symbol,REF_KB_ID,ensemblegeneid from protein_tbl where Protein_COP_ID = '{0}'", DBInterface.SQLValidString(ProteinID));
DataSet result = DBInterface.QuerySQL2(strSQL);
if (result != null)
{
if (result.Tables[0].Rows.Count > 0)
{
ShowProteinInfo(result);
}
else
{
Response.Redirect(string.Format("ProteinList.aspx?Name={0}&T={1}&V={2}", ProteinID, M_T, M_V));
}
}
QueryPeptides(lbProtein_ID.Text);
ShowWiki(lbProtein_ID.Text.Trim());
}
private void ShowProteinInfo(DataSet result)
{
if (result == null)
return;
if (result.Tables[0].Rows.Count > 0)
{
// ID
lbProtein_ID.Text = result.Tables[0].Rows[0].ItemArray[0].ToString();
// Description
lbProtein_Name.Text = result.Tables[0].Rows[0].ItemArray[2].ToString();
// Gene Symbol
if (result.Tables[0].Rows[0].IsNull(11))
lbGeneSymbol.Text = "";
else
lbGeneSymbol.Text = result.Tables[0].Rows[0].ItemArray[11].ToString();
// Uniprot w/ url
lbUniprot.Text = lbProtein_ID.Text;
// Species
lbOrganism_Source.Text = result.Tables[0].Rows[0].ItemArray[3].ToString();
// Seq Length
lbSequence_Length.Text = result.Tables[0].Rows[0].ItemArray[5].ToString();
// Seq
lbSequence.Text = AlignSequence(result.Tables[0].Rows[0].ItemArray[4].ToString());
if (result.Tables[0].Rows[0].IsNull(7))
lbMolecuar_Weight.Text = "";
else
lbMolecuar_Weight.Text = result.Tables[0].Rows[0].ItemArray[7].ToString();
if (result.Tables[0].Rows[0].IsNull(12))
lbRefKB.Text = "";
else
lbRefKB.Text = GetKBURL(result.Tables[0].Rows[0].ItemArray[12].ToString());
string HumanAtlas = "";
if (result.Tables[0].Rows[0].IsNull(13))
{
string[] genes = lbGeneSymbol.Text.Split(new string[] { "," }, StringSplitOptions.RemoveEmptyEntries);
foreach (string gene in genes)
{
HumanAtlas += string.Format("<a href='http://www.proteinatlas.org/search/{0}' target='_blank'>{0}</a> ", gene);
}
HPAImg.Visible = false;
IHCImg.Visible = false;
}
else
{
string imageID = "";
string imageID2 = "";
string MainSubcelluar = "";
string AdditionalSubcelluar = "";
string IHC_summary = "";
string IHC_heart_expression = "";
string HPAENSGID = GetImageURL(result.Tables[0].Rows[0].ItemArray[13].ToString(), ref imageID, ref imageID2, ref MainSubcelluar, ref AdditionalSubcelluar, ref IHC_summary, ref IHC_heart_expression); //GetHPAENSGID(result.Tables[0].Rows[0].ItemArray[13].ToString(), ref imageID);
if (HPAENSGID == "")
{
HumanAtlas = string.Format("<a href='http://www.proteinatlas.org/{0}' target='_blank'>{0}</a> ", result.Tables[0].Rows[0].ItemArray[13].ToString());
HPAImg.Visible = false;
IHCImg.Visible = false;
}
else
{
HumanAtlas = string.Format("<a href='http://www.proteinatlas.org/{0}' target='_blank'>{0}</a> ", HPAENSGID);
lb_main_subcelluar.Text = MainSubcelluar;
lb_additional_subcellular.Text = AdditionalSubcelluar;
lb_IHC_summary.Text = IHC_summary;
HPAImg.Visible = true;
IHCImg.Visible = true;
if (imageID != "_image/not_available.jpg")
imageID = string.Format("http://{0}", imageID);
HPAImg.ImageUrl = imageID;
IHCImg.ImageUrl = imageID2;
lb_IHC_heart_expression.Text = string.Format("<a href='http://www.proteinatlas.org/{0}/normal/heart+muscle' target='_blank'>{1}</a>", HPAENSGID, IHC_heart_expression);
if (imageID != "_image/not_available.jpg")
{
HPAImg.Attributes.Add("src", imageID.Replace("if_selected_medium", "if_selected"));
HPAImg.Attributes.Add("class", "thumb");
HPAImg.Attributes.Add("width", "200px");
HPAImg.Attributes.Add("height", "200px");
linkHPAImgStart.Text = @"<a href='" + imageID.Replace("if_selected_medium", "if_selected") + "'>";
linkHPAImgClose.Text = @"</a>";
}
if (imageID2 != "_image/not_available.jpg")
{
IHCImg.Attributes.Add("src", imageID2);
IHCImg.Attributes.Add("class", "thumb1");
IHCImg.Attributes.Add("width", "200px");
IHCImg.Attributes.Add("height", "200px");
linkIHCImgStart.Text = @"<a href='" + imageID2 + "'>";
linkIHCImgClose.Text = @"</a>";
}
}
}
lbHumanProtAtlas.Text = HumanAtlas;
ShowBiology(lbGeneSymbol.Text);
}
}
private string GetImageURL(string ProteinID, ref string ImageID, ref string ImageID2, ref string mainsubcelluar, ref string additionsubcelluar, ref string IHCSummary, ref string IHCHeartExpression)
{
string strSQL = string.Format("select ensg_id,subcellular_image,main_subcellular,additional_subcellular, IHC_Summary,IHC_Heart_expression,IHC_IMAGE from hpa_crossref_tbl where ensg_id= '{0}'", DBInterface.SQLValidString(ProteinID));
DataSet result = DBInterface.QuerySQL2(strSQL);
if (result != null)
{
if (result.Tables[0].Rows.Count > 0)
{
if (result.Tables[0].Rows[0].IsNull(0) || result.Tables[0].Rows[0].ItemArray[0].ToString() == "#N/A")
return "";
else
{
if (!result.Tables[0].Rows[0].IsNull(1))
ImageID = result.Tables[0].Rows[0].ItemArray[1].ToString();
else
ImageID = "_image/not_available.jpg";
if (!result.Tables[0].Rows[0].IsNull(6))
ImageID2 = result.Tables[0].Rows[0].ItemArray[6].ToString();
else
ImageID2 = "_image/not_available.jpg";
if (!result.Tables[0].Rows[0].IsNull(2))
mainsubcelluar = result.Tables[0].Rows[0].ItemArray[2].ToString();
else
mainsubcelluar = "N/A";
if (!result.Tables[0].Rows[0].IsNull(3))
additionsubcelluar = result.Tables[0].Rows[0].ItemArray[3].ToString();
else
additionsubcelluar = "N/A";
IHCSummary = result.Tables[0].Rows[0].ItemArray[4].ToString();
IHCHeartExpression = result.Tables[0].Rows[0].ItemArray[5].ToString();
return result.Tables[0].Rows[0].ItemArray[0].ToString();
}
}
}
return "";
}
private void QueryPeptides(string ProteinID)
{
string PepIDURL = "<a href='PeptideInfo.aspx?QType=Peptide+ID&QValue={0}'>{1}</a>";
string strSQL = string.Format("select a.peptide_sequence, a.peptide_sequence,b.prevaa,b.nextaa,a.Molecular_weight,b.location,a.Enzyme_Specificity from peptide_tbl a, pp_relation_tbl b where a.peptide_sequence = b.peptide_sequence and b.location<> -1 and b.protein_id='{0}' order by b.location", DBInterface.SQLValidString(ProteinID));
DataSet result = DBInterface.QuerySQL2(strSQL);
if (result != null)
{
for (int j = 0; j < result.Tables[0].Rows.Count; j++)
{
TableRow trCaption = new TableRow();
TableCell tcPepID = new TableCell();
string PeptideID = result.Tables[0].Rows[j].ItemArray[0].ToString();
tcPepID.Text = string.Format(PepIDURL, PeptideID, PeptideID);
tcPepID.HorizontalAlign = HorizontalAlign.Left;
trCaption.Cells.Add(tcPepID);
TableCell tcPreAA = new TableCell();
tcPreAA.Text = result.Tables[0].Rows[j].ItemArray[2].ToString();
tcPreAA.HorizontalAlign = HorizontalAlign.Center;
trCaption.Cells.Add(tcPreAA);
//TableCell tcSequence = new TableCell();
//tcSequence.Text = result.Tables[0].Rows[j].ItemArray[1].ToString();
//tcSequence.HorizontalAlign = HorizontalAlign.Left;
//trCaption.Cells.Add(tcSequence);
TableCell tcNextAA = new TableCell();
tcNextAA.Text = result.Tables[0].Rows[j].ItemArray[3].ToString();
tcNextAA.HorizontalAlign = HorizontalAlign.Center;
trCaption.Cells.Add(tcNextAA);
TableCell tcMW = new TableCell();
tcMW.Text = result.Tables[0].Rows[j].ItemArray[4].ToString();
tcMW.HorizontalAlign = HorizontalAlign.Right;
trCaption.Cells.Add(tcMW);
TableCell tcFully = new TableCell();
tcFully.Text = result.Tables[0].Rows[j].ItemArray[5].ToString();
tcFully.HorizontalAlign = HorizontalAlign.Right;
trCaption.Cells.Add(tcFully);
TableCell tcEnzyme = new TableCell();
tcEnzyme.Text = result.Tables[0].Rows[j].ItemArray[6].ToString();
tcEnzyme.HorizontalAlign = HorizontalAlign.Right;
trCaption.Cells.Add(tcEnzyme);
tbPeptides.Rows.Add(trCaption);
}
lbDistinct_Peptides.Text = result.Tables[0].Rows.Count.ToString();
imgPeptides.ImageUrl = String.Format("ProSeqImage.aspx?PID={0}&L={1}&NO={2:F0}", ProteinID, lbSequence_Length.Text, result.Tables[0].Rows.Count);
lbPeptideNumber.Text = string.Format("Totals: {0:F0}", result.Tables[0].Rows.Count);
try
{
PeptidesImageInfo PIF = new PeptidesImageInfo(ProteinID, int.Parse(lbSequence_Length.Text), result.Tables[0].Rows.Count);
int totalHeight = 0;
ArrayList RectArray = PIF.ComputeTheValues(ref totalHeight);
int j = 0;
for (j = 0; j < result.Tables[0].Rows.Count; j++)
{
PeptidesImageInfo.PepRectInfo rect = (PeptidesImageInfo.PepRectInfo)RectArray[j];
RectangleHotSpot recthot = new RectangleHotSpot();
recthot.Left = rect.left;
recthot.Right = rect.right;
recthot.Top = rect.top;
recthot.Bottom = rect.bottom;
recthot.NavigateUrl = string.Format("PeptideInfo.aspx?QType=Peptide+ID&QValue={0}", rect.PepID);
recthot.AlternateText = string.Format("{0}-{1}, {2}", rect.Location, rect.Location + rect.Length, rect.Sequence);
imgPeptides.HotSpots.Add(recthot);
}
}
catch (Exception ex)
{
}
}
}
//KBIDs will look like this: IPI:IPI00471246.2|SWISS-PROT:Q9JHI5|TREMBL:A3KGG9|ENSEMBL:ENSMUSP00000028807|REFSEQ:NP_062800|VEGA:OTTMUSP00000015718
private string GetKBURL(string KBIDs)
{
string[] tokens = KBIDs.Split(new string[] { "|" }, StringSplitOptions.RemoveEmptyEntries);
string URL = "";
string KBRef = "{0}";
string KBRecod = "<p>{0} {1}</p>";
foreach (string kbid in tokens)
{
string kb = kbid.Substring(0, kbid.IndexOf(";")).Trim().ToUpper();
string ids = kbid.Substring(kbid.IndexOf(";") + 1);
if (ids.EndsWith("."))
ids = ids.Substring(0, ids.Length - 1);
string[] idtokens = ids.Split(new string[] { ";" }, StringSplitOptions.RemoveEmptyEntries);
string IDString = "";
switch (kb)
{
case "IPI":
//URL += "IPI:";
/*
foreach (string id in idtokens)
{
if (id.Trim ()!="-")
IDString += string.Format("<a href='http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+[IPI-AllText:{0}*]+-lv+30+-view+SeqSimpleView+-page+qResult' target='_blank'>{0}</a> ", id.Trim ());
}
URL += string.Format(KBRecod, kb, IDString);
*/
break;
case "SWISS-PROT":
//URL += "SWISS-PROT:";
foreach (string id in idtokens)
{
if (id.Trim() != "-")
IDString += string.Format("<a href='http://www.uniprot.org/uniprot/{0}' target='_blank'>{0}</a> ", id.Trim());
}
URL += string.Format(KBRecod, kb, IDString);
break;
case "TREMBL":
//URL += "TREMBL:";
foreach (string id in idtokens)
{
if (id.Trim() != "-")
IDString += string.Format("<a href='http://www.uniprot.org/uniprot/{0}' target='_blank'>{0}</a> ", id.Trim());
}
URL += string.Format(KBRecod, kb, IDString);
break;
case "ENSEMBL":
//URL += "ENSEMBL:";
/*
foreach (string id in idtokens)
{
if (id.Trim() != "-")
IDString += string.Format("<a href='http://www.ensembl.org/id/{0}' target='_blank'>{0}</a> ", id.Trim ());
}
URL += string.Format(KBRecod, kb, IDString);
* */
break;
case "REFSEQ":
//URL += "REFSEQ:";
foreach (string id in idtokens)
{
if (id.Trim() != "-")
IDString += string.Format("<a href='http://www.ncbi.nlm.nih.gov/protein/{0}' target='_blank'>{0}</a> ", id.Trim());
}
URL += string.Format(KBRecod, kb, IDString);
break;
case "VEGA":
//URL += "VEGA:";
foreach (string id in idtokens)
{
if (id.Trim() != "-")
IDString += string.Format("<a href='http://vega.sanger.ac.uk/Multi/Search/Results?species=all;idx=;q={0}' target='_blank'>{0}</a> ", id.Trim());
}
URL += string.Format(KBRecod, kb, IDString);
break;
case "PDB":
IDString += string.Format("<a href='http://www.rcsb.org/pdb/explore.do?structureId={0}' target='_blank'>{1}</a> ", idtokens[0].Trim(), ids);
URL += string.Format(KBRecod, kb, IDString);
break;
case "INTERPRO":
if (idtokens.Length == 2)
{
IDString += string.Format("<a href='http://www.ebi.ac.uk/interpro/ISearch?query={0}' target='_blank'>{1}</a> ", idtokens[0].Trim(), idtokens[1].Trim());
URL += string.Format(KBRecod, kb, IDString);
}
break;
}
}
return string.Format(KBRef, URL);
}
private string AlignSequence(string strSequence)
{
int iCount = 10;
string strAlignedSequence = "";
while (iCount < strSequence.Length)
{
strAlignedSequence += strSequence.Substring(iCount - 10, 10) + " ";
iCount += 10;
}
strAlignedSequence += strSequence.Substring(iCount - 10);
return strAlignedSequence;
}
protected void LinkButton3_Click(object sender, EventArgs e)
{
Response.Redirect(string.Format("DiseaseInfo.aspx?uniprot={0}", lbProtein_ID.Text));
}
protected void LinkButton1_Click(object sender, EventArgs e)
{
Response.Redirect("WikiEdit.aspx?PageName=" + lbProtein_ID.Text.Trim());
}
private void ShowWiki(string copaPID)
{
WikiPage wikiPage = WikiOperations.GetWikiPage(copaPID.Trim());
if (wikiPage == null)
{
wikiPage = new WikiPage();
wikiPage.PageName = copaPID.Trim();
wikiPage.PageContent = "There is no Wiki page on record for this protein, please feel free to create one.";
wikiPage.ModifiedBy = User.Identity.IsAuthenticated ? User.Identity.Name : "Anonymous";
wikiPage.LastModified = DateTime.Now;
wikiPage.Created = DateTime.Now;
wikiPage.IsPrivate = User.Identity.IsAuthenticated ? true : false;
wikiPage.AllowAnonEdit = User.Identity.IsAuthenticated ? false : true;
}
SetPageContent(wikiPage);
}
private void SetPageContent(WikiPage wikiPage)
{
WikiTextFormatter wf = new WikiTextFormatter();
litContent.Text = wf.FormatPageForDisplay(wikiPage.PageContent);
if (DateTime.Now != wikiPage.Created)
lastMod.Text = wf.FormatPageForDisplay("<div class=\"rowfluid\"><div class=\"span12\">This wiki was last modified by " + wikiPage.ModifiedBy + " on " + wikiPage.LastModified + "</div></div>");
}
private void ShowBiology(string gene_symbol)
{
string strPubmed = "<table width='100%'><tr><td><a class='pubtitle' href='http://www.ncbi.nlm.nih.gov/pubmed/{0}' target='_blank'>{1}</a></td></tr><tr><td>{2}</td></tr></table>";
string strSQL = string.Format("select heartdisease, perturbation,description,pubmed_id,pubmed_title,pubmed_author from disease_tbl t where gene_symbol='{0}'", gene_symbol);
DataSet result = DBInterface.QuerySQL2(strSQL);
if (result != null)
{
if (result.Tables[0].Rows.Count == 0)
{
TableRow trNoResult = new TableRow();
TableCell tcNoResult = new TableCell();
tcNoResult.Text = "";
trNoResult.Cells.Add(tcNoResult);
tbDisease.Rows.Clear();
//tbDisease.Rows.Add(trNoResult);
tbDisease.Visible = false;
}
else
{
for (int j = 0; j < result.Tables[0].Rows.Count; j++)
{
TableRow trDisease = new TableRow();
TableCell tcPerturbation = new TableCell();
tcPerturbation.Text = result.Tables[0].Rows[j].ItemArray[1].ToString();
trDisease.Cells.Add(tcPerturbation);
TableCell tcDescription = new TableCell();
tcDescription.Text = result.Tables[0].Rows[j].ItemArray[2].ToString();
trDisease.Cells.Add(tcDescription);
TableCell tcHeartDiseasae = new TableCell();
tcHeartDiseasae.Text = result.Tables[0].Rows[j].ItemArray[0].ToString();
trDisease.Cells.Add(tcHeartDiseasae);
tbDisease.Rows.Add(trDisease);
TableRow trPubmed = new TableRow();
TableCell tcPubmed = new TableCell();
tcPubmed.Text = string.Format(strPubmed, result.Tables[0].Rows[j].ItemArray[3].ToString(), result.Tables[0].Rows[j].ItemArray[4].ToString(), result.Tables[0].Rows[j].ItemArray[5].ToString());
tcPubmed.ColumnSpan = 3;
trPubmed.Cells.Add(tcPubmed);
tbDisease.Rows.Add(trPubmed);
}
}
}
}
}