internal SelectomeGene(Dictionary <SelectomeTaxaGroup, SelectomeQuerySubResult> initiatingResults, string label)
{
if (!initiatingResults.ContainsKey(SelectomeTaxaGroup.Euteleostomi))
{
throw new FormatException("Could not parse the vertebrate group data from the XML received from selectome.\n");
}
this.Label = label;
this.vetebrateQueryResult = initiatingResults[SelectomeTaxaGroup.Euteleostomi];
}
internal SelectomeGene(Dictionary<SelectomeTaxaGroup,SelectomeQuerySubResult> initiatingResults, string label)
{
if (!initiatingResults.ContainsKey(SelectomeTaxaGroup.Euteleostomi))
{
throw new FormatException("Could not parse the vertebrate group data from the XML received from selectome.\n");
}
this.Label = label;
this.vetebrateQueryResult = initiatingResults[SelectomeTaxaGroup.Euteleostomi];
}
/// <summary>
/// Parses one line from the note section of the XML into a SelectomeResultObject
/// </summary>
/// <param name="data"></param>
/// <returns></returns>
private static SelectomeQuerySubResult ProcessSelectomeData(string data)
{
//First assign taxa to a group
SelectomeTaxaGroup group = SelectomeTaxaGroup.NotSet;
foreach (var kv in SelectomeConstantsAndEnums.GroupToNameList)
{
if (data.Contains(kv.Value))
{
group = kv.Key;
break;
}
}
//Now determine if positive seleciton has occurred.
bool positiveSelectionSignature = false;
if (data.Contains("Positive selection found"))
{
positiveSelectionSignature = true;
}
else if (data.Contains("No positive selection found"))
{
positiveSelectionSignature = false;
}
else if (data.Contains("Branch(es) under positive selection BUT no site found"))
{
positiveSelectionSignature = true;
}
else
{
throw new FormatException("Could not determine whether gene was under positive selection.\n XML was:" + data);
}
var result = new SelectomeQuerySubResult(group, positiveSelectionSignature);
return(result);
}
/// <summary>
/// Parses one line from the note section of the XML into a SelectomeResultObject
/// </summary>
/// <param name="data"></param>
/// <returns></returns>
private static SelectomeQuerySubResult ProcessSelectomeData(string data)
{
//First assign taxa to a group
SelectomeTaxaGroup group=SelectomeTaxaGroup.NotSet;
foreach(var kv in SelectomeConstantsAndEnums.GroupToNameList)
{
if(data.Contains(kv.Value))
{
group=kv.Key;
break;
}
}
//Now determine if positive seleciton has occurred.
bool positiveSelectionSignature = false;
if (data.Contains("Positive selection found"))
{
positiveSelectionSignature = true;
}
else if (data.Contains("No positive selection found"))
{
positiveSelectionSignature = false;
}
else if (data.Contains("Branch(es) under positive selection BUT no site found"))
{
positiveSelectionSignature=true;
}
else
{
throw new FormatException("Could not determine whether gene was under positive selection.\n XML was:" + data);
}
var result = new SelectomeQuerySubResult(group,positiveSelectionSignature);
return result;
}
