/// <summary>
/// Parses a string sequence of amino acids characters into a peptide object
/// </summary>
/// <param name="sequence"></param>
/// <returns></returns>
private void ParseSequence(string sequence)
{
bool inMod = false;
bool cterminalMod = false; // n or c terminal modification
int index = 0;
double monoMass = 0;
StringBuilder modSb = new StringBuilder(10);
foreach (char letter in sequence)
{
if (inMod)
{
if (letter == ']')
{
inMod = false; // end the modification phase
string modString = modSb.ToString();
modSb.Clear();
IHasMass modification;
try
{
modification = new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula(modString));
}
catch (MzLibException)
{
if (double.TryParse(modString, out double mass))
{
modification = new ModWithOnlyMass(mass);
}
else
{
throw new MzLibException("Unable to correctly parse the following modification: " + modString);
}
}
monoMass += modification.MonoisotopicMass;
if (_modifications == null)
{
_modifications = new IHasMass[Length + 2];
}
if (cterminalMod)
{
_modifications[index + 1] = modification;
}
else
{
_modifications[index] = modification;
}
cterminalMod = false;
}
else
{
modSb.Append(letter);
}
}
else
{
//char upperletter = char.ToUpper(letter); // moved to amino acid dictionary
if (Residue.TryGetResidue(letter, out Residue residue))
{
residues[index++] = residue;
monoMass += residue.MonoisotopicMass;
}
else
{
switch (letter)
{
case '[': // start of a modification
inMod = true;
break;
case '-': // End of an n-terminus mod or start of a c-terminus mod
cterminalMod = (index > 0);
break;
default:
throw new MzLibException(string.Format(CultureInfo.InvariantCulture, "Amino Acid Letter {0} does not exist in the Amino Acid Dictionary. {0} is also not a valid character", letter));
}
}
}
}
if (inMod)
{
throw new MzLibException("Couldn't find the closing ] for a modification in this sequence: " + sequence);
}
Length = index;
MonoisotopicMass += monoMass;
Array.Resize(ref residues, Length);
if (_modifications != null)
{
Array.Resize(ref _modifications, Length + 2);
}
}
public OldSchoolChemicalFormulaModification(OldSchoolChemicalFormulaModification other)
: this(ChemicalFormula.ParseFormula(other.ThisChemicalFormula.Formula), other.Name, other.Sites)
{
}