/// <summary>
/// Create a new Query Result from Selectome
/// </summary>
/// <param name="status"></param>
/// <param name="gene"></param>
public SelectomeQueryResult(QueryResult status, SelectomeGene gene = null)
{
this.Result = status;
this.pGene = gene;
}
/// <summary>
/// Create a new Query Result from Selectome
/// </summary>
/// <param name="status"></param>
/// <param name="gene"></param>
public SelectomeQueryResult(QueryResult status, SelectomeGene gene = null)
{
this.Result = status;
this.pGene = gene;
}
/// <summary>
/// This method expects a single XML document and returns one BlastResult.
/// </summary>
/// <returns>The BlastResult.</returns>
private static SelectomeQueryResult ParseXML(string webResponse)
{
webResponse = ReplaceHtmlText(webResponse);
//PARSE THE XML, example below:
//<?xml version="1.0" standalone="yes"?>
//<?xml-stylesheet type="text/xsl" href="features.xsl"?>
//<!DOCTYPE DASGFF SYSTEM "http://www.biodas.org/dtd/dasgff.dtd">
//<DASGFF>
// <GFF href="http://selectome.unil.ch/das/selectome/features">
//<SEGMENT id="ENSCPOT00000004318" start="1">
//<FEATURE id="ENSGT00550000074701_Euteleostomi_1_ENSCPOT00000004318" label="ENSCPOT00000004318">
//<TYPE id="Positive selection" />
//<METHOD id="codeml branch-site model" />
//<NOTE>Positions under positive selection found in ENSCPOT00000004318
//(sub-family ENSGT00550000074701.Euteleostomi.1)
//in<br/>Sarcopterygii/Clupeocephala (57 amino-acid positions, pval = 0.00089362)</NOTE>
//<LINK href="http://selectome.unil.ch/cgi-bin/subfamily.cgi?ac=ENSGT00550000074701&sub=1&tax=Euteleostomi" />
//</FEATURE>
//</SEGMENT>
// </GFF>
//</DASGFF>
//Because the selection results and links appear on different lines, going to merge them with dictionary, grr...
var results = new Dictionary <SelectomeTaxaGroup, SelectomeQuerySubResult>();
string geneName = String.Empty;
var settings = new XmlReaderSettings {
DtdProcessing = DtdProcessing.Ignore
};
using (var sr = new StringReader(webResponse))
{
using (XmlReader r = XmlReader.Create(sr, settings))
{
string curElement = string.Empty;
bool alreadyAdvanced = false;
while (alreadyAdvanced || r.Read())
{
alreadyAdvanced = false;
switch (r.NodeType)
{
case XmlNodeType.Element:
curElement = r.Name;
if (curElement == "FEATURE")
{
geneName = r.GetAttribute("label");
}
else if (curElement == "NOTE")
{
//Construct the data from the note
string innerText = r.ReadInnerXml();
alreadyAdvanced = true;
string[] groups = innerText.Split(NoteDivider, StringSplitOptions.RemoveEmptyEntries);
var tempResults = groups.Where(x => x.Contains("selection")).Select(ProcessSelectomeData).ToArray();
foreach (var selectionRes in tempResults)
{
results[selectionRes.Group] = selectionRes;
}
}
else if (curElement == "LINK")
{
//example a la =<LINK href="http://selectome.unil.ch/cgi-bin/subfamily.cgi?ac=ENSGT00390000009030&sub=1&tax=Euteleostomi" />
string linkText = r.GetAttribute("href");
var sp1 = linkText.Split('=');
var treename = sp1[1].Split('&')[0]; //ENSGT0039000000009446
var subTreeName = sp1[2].Split('&')[0]; //1
SelectomeTaxaGroup curGroup = (from kv in SelectomeConstantsAndEnums.GroupToNameList where sp1[3].Contains(kv.Value) select kv.Key).FirstOrDefault();
if (curGroup != SelectomeTaxaGroup.NotSet)
{
//Verify it isn't over-writing another gene
var sql = new SelectomeQueryLink(curGroup, treename, subTreeName);
if (results.ContainsKey(curGroup) && results[curGroup].RelatedLink != null)
{
var old = results[curGroup];
if ((old.RelatedLink.Group != sql.Group || old.RelatedLink.SubTree != sql.SubTree || old.RelatedLink.Tree != sql.Tree))
{
throw new ArgumentException("Over-writing past tree group, investigate this gene.\r\n" + webResponse);
}
}
else
{
results[curGroup].RelatedLink = sql;
}
}
}
break;
case XmlNodeType.XmlDeclaration:
break;
case XmlNodeType.ProcessingInstruction:
break;
case XmlNodeType.Comment:
break;
case XmlNodeType.EndElement:
break;
}
}
}
}
if (results != null && results.Count > 0)
{
if (!results.ContainsKey(SelectomeTaxaGroup.Euteleostomi))
{
return(new SelectomeQueryResult(QueryResult.NoVeterbrateTreeDataFound));
//throw new Exception("Could not parse the vertebrate group data from the XML received from selectome. XML is:\n" + webResponse);
}
SelectomeGene result = new SelectomeGene(results, geneName);
return(new SelectomeQueryResult(QueryResult.Success, result));
}
return(new SelectomeQueryResult(QueryResult.NoResultsFound));
}
/// <summary>
/// This method expects a single XML document and returns one BlastResult.
/// </summary>
/// <returns>The BlastResult.</returns>
private static SelectomeQueryResult ParseXML(string webResponse)
{
webResponse = ReplaceHtmlText(webResponse);
//PARSE THE XML, example below:
//<?xml version="1.0" standalone="yes"?>
//<?xml-stylesheet type="text/xsl" href="features.xsl"?>
//<!DOCTYPE DASGFF SYSTEM "http://www.biodas.org/dtd/dasgff.dtd">
//<DASGFF>
// <GFF href="http://selectome.unil.ch/das/selectome/features">
//<SEGMENT id="ENSCPOT00000004318" start="1">
//<FEATURE id="ENSGT00550000074701_Euteleostomi_1_ENSCPOT00000004318" label="ENSCPOT00000004318">
//<TYPE id="Positive selection" />
//<METHOD id="codeml branch-site model" />
//<NOTE>Positions under positive selection found in ENSCPOT00000004318
//(sub-family ENSGT00550000074701.Euteleostomi.1)
//in<br/>Sarcopterygii/Clupeocephala (57 amino-acid positions, pval = 0.00089362)</NOTE>
//<LINK href="http://selectome.unil.ch/cgi-bin/subfamily.cgi?ac=ENSGT00550000074701&sub=1&tax=Euteleostomi" />
//</FEATURE>
//</SEGMENT>
// </GFF>
//</DASGFF>
//Because the selection results and links appear on different lines, going to merge them with dictionary, grr...
var results = new Dictionary<SelectomeTaxaGroup,SelectomeQuerySubResult>();
string geneName = String.Empty;
var settings = new XmlReaderSettings { DtdProcessing = DtdProcessing.Ignore };
using (var sr = new StringReader(webResponse))
{
using (XmlReader r = XmlReader.Create(sr, settings))
{
string curElement = string.Empty;
bool alreadyAdvanced = false;
while (alreadyAdvanced || r.Read())
{
alreadyAdvanced = false;
switch (r.NodeType)
{
case XmlNodeType.Element:
curElement = r.Name;
if (curElement == "FEATURE")
{
geneName = r.GetAttribute("label");
}
else if (curElement == "NOTE")
{
//Construct the data from the note
string innerText = r.ReadInnerXml();
alreadyAdvanced = true;
string[] groups = innerText.Split(NoteDivider, StringSplitOptions.RemoveEmptyEntries);
var tempResults = groups.Where(x => x.Contains("selection")).Select(ProcessSelectomeData).ToArray();
foreach (var selectionRes in tempResults)
{
results[selectionRes.Group] = selectionRes;
}
}
else if (curElement == "LINK")
{
//example a la =<LINK href="http://selectome.unil.ch/cgi-bin/subfamily.cgi?ac=ENSGT00390000009030&sub=1&tax=Euteleostomi" />
string linkText = r.GetAttribute("href");
var sp1 = linkText.Split('=');
var treename = sp1[1].Split('&')[0];//ENSGT0039000000009446
var subTreeName = sp1[2].Split('&')[0]; //1
SelectomeTaxaGroup curGroup = (from kv in SelectomeConstantsAndEnums.GroupToNameList where sp1[3].Contains(kv.Value) select kv.Key).FirstOrDefault();
if (curGroup != SelectomeTaxaGroup.NotSet)
{
//Verify it isn't over-writing another gene
var sql = new SelectomeQueryLink(curGroup, treename, subTreeName);
if (results.ContainsKey(curGroup) && results[curGroup].RelatedLink!=null)
{
var old = results[curGroup];
if ((old.RelatedLink.Group != sql.Group || old.RelatedLink.SubTree != sql.SubTree || old.RelatedLink.Tree != sql.Tree))
throw new ArgumentException("Over-writing past tree group, investigate this gene.\r\n" + webResponse);
}
else
{
results[curGroup].RelatedLink = sql;
}
}
}
break;
case XmlNodeType.XmlDeclaration:
break;
case XmlNodeType.ProcessingInstruction:
break;
case XmlNodeType.Comment:
break;
case XmlNodeType.EndElement:
break;
}
}
}
}
if (results != null && results.Count> 0)
{
if (!results.ContainsKey(SelectomeTaxaGroup.Euteleostomi))
{
return new SelectomeQueryResult(QueryResult.NoVeterbrateTreeDataFound);
//throw new Exception("Could not parse the vertebrate group data from the XML received from selectome. XML is:\n" + webResponse);
}
SelectomeGene result = new SelectomeGene(results,geneName);
return new SelectomeQueryResult(QueryResult.Success, result);
}
return new SelectomeQueryResult(QueryResult.NoResultsFound);
}