public static Dictionary <string, Protease> LoadProteaseDictionary(string path)
{
Dictionary <string, Protease> dict = new Dictionary <string, Protease>();
string[] myLines = File.ReadAllLines(path);
myLines = myLines.Skip(1).ToArray();
foreach (string line in myLines)
{
if (line.Trim() != string.Empty) // skip empty lines
{
string[] fields = line.Split('\t');
List <DigestionMotif> motifList = DigestionMotif.ParseDigestionMotifsFromString(fields[1]);
string name = fields[0];
var cleavageSpecificity = ((CleavageSpecificity)Enum.Parse(typeof(CleavageSpecificity), fields[4], true));
string psiMsAccessionNumber = fields[5];
string psiMsName = fields[6];
var protease = new Protease(name, cleavageSpecificity, psiMsAccessionNumber, psiMsName, motifList);
dict.Add(protease.Name, protease);
}
}
return(dict);
}
public static Dictionary <string, Protease> LoadProteaseDictionary(string path, List <Modification> proteaseMods = null)
{
Dictionary <string, Protease> dict = new Dictionary <string, Protease>();
string[] myLines = File.ReadAllLines(path);
myLines = myLines.Skip(1).ToArray();
foreach (string line in myLines)
{
if (line.Trim() != string.Empty) // skip empty lines
{
string[] fields = line.Split('\t');
List <DigestionMotif> motifList = DigestionMotif.ParseDigestionMotifsFromString(fields[1]);
string name = fields[0];
var cleavageSpecificity = ((CleavageSpecificity)Enum.Parse(typeof(CleavageSpecificity), fields[4], true));
string psiMsAccessionNumber = fields[5];
string psiMsName = fields[6];
//name of the modification that is associated with proteolytic cleavage
string proteaseModDetails = fields[8];
//if this protease has an associated modification, look it up in the list of mods loaded fro the protease mods file
if (proteaseModDetails != "" && proteaseMods != null)
{
if (proteaseMods.Select(p => p.IdWithMotif).ToList().Contains(proteaseModDetails))
{
Modification proteaseModification = proteaseMods.Where(p => p.IdWithMotif == proteaseModDetails).First();
var protease = new Protease(name, cleavageSpecificity, psiMsAccessionNumber, psiMsName, motifList, proteaseModification);
if (!dict.ContainsKey(protease.Name))
{
dict.Add(protease.Name, protease);
}
else
{
throw new MzLibException("More than one protease named " + protease.Name + " exists");
}
}
else
{
var protease = new Protease(name, cleavageSpecificity, psiMsAccessionNumber, psiMsName, motifList);
if (!dict.ContainsKey(protease.Name))
{
dict.Add(protease.Name, protease);
}
else
{
throw new MzLibException("More than one protease named " + protease.Name + " exists");
}
throw new MzLibException(proteaseModDetails + " is not a valid modification");
}
}
else
{
var protease = new Protease(name, cleavageSpecificity, psiMsAccessionNumber, psiMsName, motifList);
if (!dict.ContainsKey(protease.Name))
{
dict.Add(protease.Name, protease);
}
else
{
throw new MzLibException("More than one protease named " + protease.Name + " exists");
}
}
}
}
return(dict);
}
