public ModifiedAminoAcid(AminoAcid aa, Modification modification)
: base(aa.Residue, aa.Name + "+" + modification.Name, aa.Composition + modification.Composition)
{
var modAa = aa as ModifiedAminoAcid;
if (modAa == null)
{
_modification = modification; // aa is not modified
}
else // aa is already modified
{
_modification = Modification.RegisterAndGetModification(modAa.Modification.Name + "+" + modification.Name, Composition);
}
}
/// <summary>
/// Parse the provided modification line
/// </summary>
/// <param name="line"></param>
/// <returns></returns>
public static List <SearchModification> ParseModification(string line)
{
var token = line.Split(',');
if (token.Length != 5)
{
return(null);
}
// Composition
var compStr = token[0].Trim();
var composition = Composition.Composition.ParseFromPlainString(compStr) ??
Composition.Composition.Parse(compStr);
if (composition == null)
{
throw new Exception(string.Format("Illegal Composition: \"{0}\" in \"{1}\"", compStr, line));
}
// Residues
var residueStr = token[1].Trim();
var isResidueStrLegitimate = residueStr.Equals("*") ||
residueStr.Any() && residueStr.All(AminoAcid.IsStandardAminoAcidResidue);
if (!isResidueStrLegitimate)
{
throw new Exception(string.Format("Illegal residues: \"{0}\" in \"{1}\"", residueStr, line));
}
// isFixedModification
bool isFixedModification;
if (token[2].Trim().Equals("fix", StringComparison.InvariantCultureIgnoreCase))
{
isFixedModification = true;
}
else if (token[2].Trim().Equals("opt", StringComparison.InvariantCultureIgnoreCase))
{
isFixedModification = false;
}
else
{
throw new Exception(string.Format("Illegal modification type (fix or opt): \"{0}\" in \"{1}\"", token[2].Trim(), line));
}
// Location
SequenceLocation location;
var locStr = token[3].Trim().Split()[0];
if (locStr.Equals("any", StringComparison.InvariantCultureIgnoreCase))
{
location = SequenceLocation.Everywhere;
}
else if (locStr.Equals("N-Term", StringComparison.InvariantCultureIgnoreCase) ||
locStr.Equals("NTerm", StringComparison.InvariantCultureIgnoreCase))
{
location = SequenceLocation.PeptideNTerm;
}
else if (locStr.Equals("C-Term", StringComparison.InvariantCultureIgnoreCase) ||
locStr.Equals("CTerm", StringComparison.InvariantCultureIgnoreCase))
{
location = SequenceLocation.PeptideCTerm;
}
else if (locStr.Equals("Prot-N-Term", StringComparison.InvariantCultureIgnoreCase) ||
locStr.Equals("ProtNTerm", StringComparison.InvariantCultureIgnoreCase))
{
location = SequenceLocation.ProteinNTerm;
}
else if (locStr.Equals("Prot-C-Term", StringComparison.InvariantCultureIgnoreCase) ||
locStr.Equals("ProtCTerm", StringComparison.InvariantCultureIgnoreCase))
{
location = SequenceLocation.ProteinCTerm;
}
else
{
throw new Exception(string.Format("Illegal modification location (any|(Prot-?)?(N|C)-?Term): \"{0}\" in \"{1}\"", token[3].Trim(), line));
}
// Check if it's valid
if (residueStr.Equals("*") && location == SequenceLocation.Everywhere)
{
throw new Exception(string.Format("Invalid modification: * should not be applied to \"any\": \"{0}\"", line));
}
var name = token[4].Split()[0].Trim();
var mod = Modification.Get(name) ?? Modification.RegisterAndGetModification(name, composition);
return(residueStr.Select(residue => new SearchModification(mod, residue, location, isFixedModification)).ToList());
}
private static IEnumerable <SearchModification> Parse(string modFilePath, out int maxNumDynModsPerPeptide)
{
var searchModList = new List <SearchModification>();
var numMods = 0;
var lineNum = 0;
foreach (var line in File.ReadLines(modFilePath))
{
lineNum++;
var tokenArr = line.Split('#');
if (tokenArr.Length == 0)
{
continue;
}
var s = tokenArr[0].Trim();
if (s.Length == 0)
{
continue;
}
if (s.StartsWith("NumMods="))
{
try {
numMods = Convert.ToInt32(s.Split('=')[1].Trim());
} catch (FormatException)
{
Console.WriteLine("{0}: Illegal NumMods parameter at line {1} - {2}", modFilePath, lineNum, s);
maxNumDynModsPerPeptide = -1;
return(null);
}
}
else
{
var token = s.Split(',');
if (token.Length != 5)
{
continue;
}
// Composition
var compStr = token[0].Trim();
var composition = Composition.Composition.ParseFromPlainString(compStr) ??
Composition.Composition.Parse(compStr);
if (composition == null)
{
Console.WriteLine("{0}: Illegal Composition at line {1} - {2}", modFilePath, lineNum, s);
maxNumDynModsPerPeptide = -1;
return(null);
}
// Residues
var residueStr = token[1].Trim();
var isResidueStrLegitimate = residueStr.Equals("*") ||
residueStr.Any() && residueStr.All(AminoAcid.IsStandardAminoAcidResidue);
if (!isResidueStrLegitimate)
{
Console.WriteLine("{0}: Illegal residues at line {1} - {2}", modFilePath, lineNum, s);
maxNumDynModsPerPeptide = -1;
return(null);
}
// isFixedModification
bool isFixedModification;
if (token[2].Trim().Equals("fix", StringComparison.InvariantCultureIgnoreCase))
{
isFixedModification = true;
}
else if (token[2].Trim().Equals("opt", StringComparison.InvariantCultureIgnoreCase))
{
isFixedModification = false;
}
else
{
Console.WriteLine("{0}: Illegal modification type (fix or opt) at line {1} - {2}", modFilePath, lineNum, s);
maxNumDynModsPerPeptide = -1;
return(null);
}
// Location
SequenceLocation location;
var locStr = token[3].Trim().Split()[0];
if (locStr.Equals("any", StringComparison.InvariantCultureIgnoreCase))
{
location = SequenceLocation.Everywhere;
}
else if (locStr.Equals("N-Term", StringComparison.InvariantCultureIgnoreCase) ||
locStr.Equals("NTerm", StringComparison.InvariantCultureIgnoreCase))
{
location = SequenceLocation.PeptideNTerm;
}
else if (locStr.Equals("C-Term", StringComparison.InvariantCultureIgnoreCase) ||
locStr.Equals("CTerm", StringComparison.InvariantCultureIgnoreCase))
{
location = SequenceLocation.PeptideCTerm;
}
else if (locStr.Equals("Prot-N-Term", StringComparison.InvariantCultureIgnoreCase) ||
locStr.Equals("ProtNTerm", StringComparison.InvariantCultureIgnoreCase))
{
location = SequenceLocation.ProteinNTerm;
}
else if (locStr.Equals("Prot-C-Term", StringComparison.InvariantCultureIgnoreCase) ||
locStr.Equals("ProtCTerm", StringComparison.InvariantCultureIgnoreCase))
{
location = SequenceLocation.ProteinCTerm;
}
else
{
Console.WriteLine("{0}: Illegal modification location (fix or opt) at line {1} - {2}", modFilePath, lineNum, s);
maxNumDynModsPerPeptide = -1;
return(null);
}
// Check if it's valid
if (residueStr.Equals("*") && location == SequenceLocation.Everywhere)
{
Console.WriteLine("{0}: Invalid modification: * should not be applied to \"any\"", modFilePath);
maxNumDynModsPerPeptide = -1;
return(null);
}
var name = token[4].Split()[0].Trim();
var mod = Modification.Get(name) ?? Modification.RegisterAndGetModification(name, composition);
searchModList.AddRange(residueStr.Select(
residue => new SearchModification(mod, residue, location, isFixedModification)
));
}
}
maxNumDynModsPerPeptide = numMods;
return(searchModList);
}
