public static Protease FindOrCreateProtease(
string name,
bool endoProtease,
string cleaveRes,
string notCleaveRes)
{
string newName = name;
int count = 1;
while (Registered(newName))
{
Protease p = GetProteaseByName(newName);
if (p.IsEndoProtease == endoProtease && p.CleaveageResidues.Equals(cleaveRes) &&
p.NotCleaveResidues.Equals(notCleaveRes))
{
return(p);
}
newName = name + "_" + count;
count++;
}
var result = new Protease(newName, endoProtease, cleaveRes, notCleaveRes);
RegisterProtease(result);
return(result);
}
public void TestGetNumProteaseTermini()
{
Protease trypsin = new Protease("Trypsin", true, "KR", "P");
Assert.AreEqual(0, trypsin.GetNumProteaseTermini('M', "ABCDE", 'N', '-', 3));
Assert.AreEqual(1, trypsin.GetNumProteaseTermini('M', "ABCDE", 'N', '-', 2));
Assert.AreEqual(2, trypsin.GetNumProteaseTermini('M', "ABCDR", 'N', '-', 2));
}
/**
* Creates and registers a new Protease. In future the Protease can be recovered
* using the getProteaseByName() method.
* @param name the name of the Protease
* @param endoProtease is it an endo protease?
* @param cleaveRes the cleavege residues
* @param notCleaveRes the exceptions to the cleavage residues
* @return a reference to the new Protease
* @throws IllegalSymbolException if the cleaveRes or notCleaveRes are not
* from the PROTEIN alphabet
* @throws BioException if a Protease with the same name already exists.
*/
public static Protease CreateProtease(
string name,
bool endoProtease,
string cleaveRes,
string notCleaveRes)
{
var p = new Protease(name, endoProtease, cleaveRes, notCleaveRes);
RegisterProtease(p);
return(p);
}
public void TestIsCleavageSite()
{
Protease trypsin = new Protease("Trypsin", true, "KR", "P");
Assert.AreEqual(true, trypsin.IsCleavageSite('K', 'A', '-'));
Assert.AreEqual(true, trypsin.IsCleavageSite('R', 'A', '-'));
Assert.AreEqual(true, trypsin.IsCleavageSite('K', '-', '-'));
Assert.AreEqual(true, trypsin.IsCleavageSite('R', '-', '-'));
Assert.AreEqual(false, trypsin.IsCleavageSite('K', 'P', '-'));
Assert.AreEqual(false, trypsin.IsCleavageSite('R', 'P', '-'));
Assert.AreEqual(false, trypsin.IsCleavageSite('N', 'A', '-'));
}
/**
* Registers a protease and ensures its flyweight status
* @param prot the Protease to register
*/
public static void RegisterProtease(Protease protease)
{
var name = GetShortName(protease.Name);
if (Registered(protease.Name))
{
throw new ArgumentException(
"A Protease has already been registered with the name "
+ protease.Name, "protease");
}
name2Protease[name] = protease;
}
public void TestGetMissCleavageSiteCount()
{
Protease trypsin = new Protease("Trypsin", true, "KR", "P");
Assert.AreEqual(0, trypsin.GetMissCleavageSiteCount("EGEABDR"));
Assert.AreEqual(0, trypsin.GetMissCleavageSiteCount("EGEKPABDR"));
Assert.AreEqual(0, trypsin.GetMissCleavageSiteCount("EGERPABDR"));
Assert.AreEqual(1, trypsin.GetMissCleavageSiteCount("EGEKABDR"));
Assert.AreEqual(1, trypsin.GetMissCleavageSiteCount("EGERABDR"));
Assert.AreEqual(2, trypsin.GetMissCleavageSiteCount("EGEKARBDR"));
Protease noenzyme = new Protease("Noenzyme", true, "", "");
Assert.AreEqual(0, noenzyme.GetMissCleavageSiteCount("EGEABDR"));
}
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]];
}
}
}
