public void TestAddDigestFeatures()
{
Sequence seq = new Sequence("Test", "AAANESAARBBBNPSBBKFFFNITFFRGGGNDTGGR");
Digest digest = new Digest();
digest.DigestProtease = ProteaseManager.CreateProtease("Trypsin_TestAddDigestFeatures", true, "RK", "P");
digest.ProteinSequence = seq;
digest.MaxMissedCleavages = 0;
digest.AddDigestFeatures();
List <DigestPeptideInfo> peptides = (List <DigestPeptideInfo>)seq.Annotation[Digest.PEPTIDE_FEATURE_TYPE];
Assert.AreEqual(4, peptides.Count);
digest.MaxMissedCleavages = 1;
digest.AddDigestFeatures();
List <DigestPeptideInfo> missedPeptides = (List <DigestPeptideInfo>)seq.Annotation[Digest.PEPTIDE_FEATURE_TYPE];
Assert.AreEqual(7, missedPeptides.Count);
IRangeLocationFilter nglycanFilter = new NGlycanFilter();
digest.MaxMissedCleavages = 0;
digest.Filter = nglycanFilter;
digest.AddDigestFeatures();
List <DigestPeptideInfo> nglycanPeptides = (List <DigestPeptideInfo>)seq.Annotation[Digest.PEPTIDE_FEATURE_TYPE];
Assert.AreEqual(2, nglycanPeptides.Count);
Assert.AreEqual("AAANESAAR", nglycanPeptides[0].PeptideSeq);
Assert.AreEqual("FFFNITFFR", nglycanPeptides[1].PeptideSeq);
}
public void TestLoadFromFile()
{
ProteaseManager.LoadFromFile(@TestContext.CurrentContext.TestDirectory + "/../../../data//proteases.xml");
Assert.IsTrue(ProteaseManager.Registered("Trypsin"));
Assert.IsTrue(ProteaseManager.Registered("Chymotrypsin"));
Assert.IsTrue(ProteaseManager.Registered("LysC/P+AspC"));
Assert.IsFalse(ProteaseManager.Registered("ProteaseNotExist"));
Protease trypsin = ProteaseManager.GetProteaseByName("Trypsin");
Assert.AreEqual("Trypsin", trypsin.Name);
Assert.AreEqual(true, trypsin.IsEndoProtease);
Assert.AreEqual("KR", trypsin.CleaveageResidues);
Assert.AreEqual("P", trypsin.NotCleaveResidues);
}
private void Read(string filename)
{
this.dtaProteaseMap = new Dictionary <string, Protease>();
using (var filein = new StreamReader(new FileStream(filename, FileMode.Open, FileAccess.Read)))
{
var enzymeMap = new Dictionary <string, Protease>();
string sline;
while ((sline = filein.ReadLine()) != null && sline.Length > 0)
{
Protease enzyme = ProteaseManager.ValueOf(sline);
string[] lines = Regex.Split(sline, "\t");
enzymeMap[lines[0]] = enzyme;
}
while ((sline = filein.ReadLine()) != null)
{
if (sline.StartsWith("DEFAULT_ENZYME"))
{
string[] lines = Regex.Split(sline, "\t");
this.defaultProtease = enzymeMap[lines[1]];
break;
}
}
while ((sline = filein.ReadLine()) != null)
{
if (sline.Length == 0)
{
continue;
}
string[] lines = Regex.Split(sline, "\t");
if (lines.Length < 2)
{
break;
}
this.dtaProteaseMap[lines[0]] = enzymeMap[lines[1]];
}
}
}
/// <summary>
/// Retrieves a reference to the named Protease.(Internally calls ProteaseManager.getProteaseByName())
/// </summary>
/// <param name="proteaseName">A protease name that is registered in the ProteaseManager (case sensitive)</param>
/// <returns> A Protease instance for the given protease name</returns>
public static Protease GetProteaseByName(string proteaseName)
{
return(ProteaseManager.GetProteaseByName(proteaseName));
}
/// <summary>
/// Get the list of Protease names defined in the ProteaseManager (Internally calls ProteaseManager).
/// </summary>
/// <returns>A string array of protease names</returns>
public static List <string> GetProteaseList()
{
return(ProteaseManager.GetNames());
}