public Protease(string name, IEnumerable<string> sequencesInducingCleavage, IEnumerable<string> sequencesPreventingCleavage, Terminus cleavageTerminus, CleavageSpecificity cleavageSpecificity)
{
Name = name;
SequencesInducingCleavage = sequencesInducingCleavage;
SequencesPreventingCleavage = sequencesPreventingCleavage;
CleavageTerminus = cleavageTerminus;
CleavageSpecificity = cleavageSpecificity;
}
public Protease(string name, IEnumerable<string> sequencesInducingCleavage, IEnumerable<string> sequencesPreventingCleavage, Terminus cleavageTerminus, CleavageSpecificity cleavageSpecificity, string psiMsAccessionNumber, string psiMsName, string siteRegexp)
{
Name = name;
SequencesInducingCleavage = sequencesInducingCleavage;
SequencesPreventingCleavage = sequencesPreventingCleavage;
CleavageTerminus = cleavageTerminus;
CleavageSpecificity = cleavageSpecificity;
PsiMsAccessionNumber = psiMsAccessionNumber;
PsiMsName = psiMsName;
SiteRegexp = siteRegexp;
}
public Protease(string name, Terminus terminus, string cut, string nocut = "", string cleavePattern = "")
{
Name = name;
Terminal = terminus;
Cut = cut;
NoCut = nocut;
if (string.IsNullOrEmpty(cleavePattern))
{
StringBuilder constructedRegex = new StringBuilder();
// Add grouping [ ] if more than one residue
string cutregex = (Cut.Length > 1) ? "[" + Cut + "]" : Cut;
string nocutregex = (NoCut.Length > 1) ? "[" + NoCut + "]" : NoCut;
if (terminus == Terminus.N)
{
// Apply negative look-a-head for N-terminal no cuts
if (!string.IsNullOrEmpty(nocut))
{
constructedRegex.Append("(?<!" + nocutregex + ")");
}
constructedRegex.Append("(?'cut')");
constructedRegex.Append(cutregex);
}
else
{
constructedRegex.Append(cutregex);
constructedRegex.Append("(?'cut')");
if (!string.IsNullOrEmpty(nocut))
{
constructedRegex.Append("(?!" + nocutregex + ")");
}
}
_cleavageRegex = new Regex(constructedRegex.ToString(), RegexOptions.Compiled);
}
else
{
_cleavageRegex = new Regex(cleavePattern, RegexOptions.Compiled);
}
}
public void AddVariableModification(IMass modificaiton, Terminus terminus)
{
}
public static Protease AddProtease(string name, Terminus terminus, string cut, string noCut = "")
{
Protease protease = new Protease(name, terminus, cut, noCut);
Proteases[name] = protease;
OnProteasesChanged();
return protease;
}
public static Protease AddProtease(string name, Terminus terminus, string cut, string noCut = "")
{
Protease protease = new Protease(name, terminus, cut, noCut);
Proteases.Add(protease.Name, protease);
return protease;
}
