public void WriteProteins(string outputFilepath, bool addDecoys)
{
var pd = new ProteomeData();
var pl = new ProteinListSimple();
var queryRows = session.CreateQuery("SELECT DISTINCT pro.Accession, pro.IsDecoy, pro.Description, pro.Sequence " +
DataFilter.GetFilteredQueryString(DataFilter.FromProtein))
.List <object[]>();
foreach (var queryRow in queryRows)
{
if ((bool)queryRow[1] == false) // skip decoys from the query
{
pl.proteins.Add(new proteome.Protein((string)queryRow[0],
pl.proteins.Count,
(string)queryRow[2],
(string)queryRow[3]));
}
}
if (addDecoys)
{
foreach (var queryRow in queryRows)
{
if ((bool)queryRow[1] == false) // skip decoys from the query
{
pl.proteins.Add(new proteome.Protein("rev_" + (string)queryRow[0],
pl.proteins.Count,
String.Empty, // decoys have no description
new string(((string)queryRow[3]).Reverse().ToArray())));
}
}
}
pd.proteinList = pl;
ProteomeDataFile.write(pd, outputFilepath);
}
