public bool addModification(Modification modification)
{
if (modification == null){
return false;
}
SplitList<Modification> modList = Modifications;
if (modList == null){
modList = new SplitList<Modification>(MZTabConstants.COMMA);
Modifications = modList;
}
modList.Add(modification);
return true;
}
private static Modification ParseModification(Section section, string target)
{
target = ParseString(target);
// no modification
if (target.Equals("0")){
return Modification.CreateNoModification(section);
}
target = translateMinusToUnicode(target);
if (target == null){
return null;
}
target = translateTabToComma(target);
string[] items = target.Split("\\-".ToCharArray());
string modLabel;
string positionLabel;
if (items.Length > 2){
// error
return null;
}
if (items.Length == 2){
positionLabel = items[0];
modLabel = items[1];
}
else{
positionLabel = null;
modLabel = items[0];
}
Modification modification = null;
modLabel = translateUnicodeToMinus(modLabel);
Regex regex = new Regex("(MOD|UNIMOD|CHEMMOD|SUBST):([^\\|]+)(\\|\\[([^,]+)?,([^,]+)?,([^,]+),([^,]*)\\])?");
if (regex.IsMatch(modLabel)){
Modification.ModificationType type = Modification.FindType(regex.Match(target).Groups[1].Value);
string accession = regex.Match(target).Groups[2].Value;
modification = new Modification(section, type, accession);
if (positionLabel != null){
parsePosition(positionLabel, modification);
}
CVParam neutralLoss = string.IsNullOrEmpty(regex.Match(target).Groups[6].Value)
? null
: new CVParam(regex.Match(target).Groups[4].Value,
regex.Match(target).Groups[5].Value,
regex.Match(target).Groups[6].Value,
regex.Match(target).Groups[7].Value);
modification.NeutralLoss = neutralLoss;
}
return modification;
}
private static void parsePosition(string target, Modification modification)
{
target = translateTabToComma(target);
SplitList<string> list = ParseStringList(MZTabConstants.BAR, target);
Regex regex = new Regex("(\\d+)(\\[([^,]+)?,([^,]+)?,([^,]+),([^,]*)\\])?");
foreach (string item in list){
if (regex.IsMatch(item.Trim())){
int id = int.Parse(regex.Match(item.Trim()).Groups[1].Value);
CVParam param = string.IsNullOrEmpty(regex.Match(item.Trim()).Groups[5].Value)
? null
: new CVParam(regex.Match(item.Trim()).Groups[3].Value,
regex.Match(item.Trim()).Groups[4].Value,
regex.Match(item.Trim()).Groups[5].Value,
regex.Match(item.Trim()).Groups[6].Value);
modification.AddPosition(id, param);
}
}
}
public bool AddModification(Modification modification)
{
if (modification == null){
return false;
}
if (Modifications == null){
Modifications = new SplitList<Modification>(MZTabConstants.COMMA);
}
if (Modifications.All(x => x.Accession != modification.Accession)){
Modifications.Add(modification);
}
else{
var m = Modifications.First(x => x.Accession == modification.Accession);
foreach (int key in modification.PositionMap.Keys){
if (m.PositionMap.ContainsKey(key)){
continue;
}
m.AddPosition(key, modification.PositionMap[key]);
}
}
return true;
}
