/// <summary>
/// All input strings are delimited with "|"
/// PTMs are annotated with []
/// </summary>
/// <param name="fullSequenceString">All possible sequences (with modifications) for this PrSM</param>
/// <param name="geneString">All possible genes for this PrSM</param>
/// <returns></returns>
public static string ClassifyPrSM(string fullSequenceString, string geneString)
{
//separate delimited input
string[] sequences = fullSequenceString.Split('|');
string[] genes = geneString.Split('|');
//determine sequence ambiguity
string firstBaseSequence = PeptideWithSetModifications.GetBaseSequenceFromFullSequence(sequences[0]).ToUpper(); //get first sequence with modifications removed
bool sequenceIdentified = !SequenceContainsUnknownAminoAcids(firstBaseSequence); //check if there are any ambiguous amino acids (i.e. B, J, X, Z)
//for every other sequence reported
if (sequenceIdentified) //if there weren't any unknown amino acids reported.
{
for (int i = 1; i < sequences.Length; i++)
{
//if the unmodified sequences don't match, then there's sequence ambiguity
if (!firstBaseSequence.Equals(PeptideWithSetModifications.GetBaseSequenceFromFullSequence(sequences[i]).ToUpper()))
{
sequenceIdentified = false;
break;
}
}
}
//determine PTM localization and identification
List <(int index, string ptm)> firstPTMsSortedByIndex = GetPTMs(sequences[0]); //get ptms from the first sequence reported
List <string> firstPTMsSortedByPTM = firstPTMsSortedByIndex.Select(x => x.ptm).OrderBy(x => x).ToList(); //sort ptms alphabetically
//check if there are unknown mass shifts
bool ptmsIdentified = !PtmsContainUnknownMassShifts(firstPTMsSortedByPTM);
bool ptmsLocalized = true; //assume these are localized unless we determine otherwise
//for every other sequence reported
for (int seqIndex = 1; seqIndex < sequences.Length; seqIndex++)
{
List <(int index, string ptm)> currentPTMsSortedByIndex = GetPTMs(sequences[seqIndex]); //get ptms from this sequence
List <string> currentPTMsSortedByPTM = currentPTMsSortedByIndex.Select(x => x.ptm).OrderBy(x => x).ToList(); //sort ptms alphabetically
//are number of PTMs the same?
if (firstPTMsSortedByIndex.Count == currentPTMsSortedByIndex.Count)
{
//check localization (are indexes conserved?)
for (int i = 0; i < firstPTMsSortedByIndex.Count; i++)
{
if (firstPTMsSortedByIndex[i].index != currentPTMsSortedByIndex[i].index)
{
ptmsLocalized = false;
break;
}
}
//check PTM identification
for (int i = 0; i < firstPTMsSortedByPTM.Count; i++)
{
if (!firstPTMsSortedByPTM[i].Equals(currentPTMsSortedByPTM[i]))
{
ptmsIdentified = false;
break;
}
}
}
else
{
ptmsIdentified = false;
ptmsLocalized = false;
}
}
//handle an edge case where two PTMs are identified and localized to two residues, but it's unclear which PTM is localized to which residue.
if (ptmsIdentified && ptmsLocalized)
{
for (int seqIndex = 1; seqIndex < sequences.Length; seqIndex++)
{
List <(int index, string ptm)> currentPTMsSortedByIndex = GetPTMs(sequences[seqIndex]); //get ptms from this sequence
//check that the mods are in the same position
for (int ptmIndex = 0; ptmIndex < currentPTMsSortedByIndex.Count; ptmIndex++)
{
if (!firstPTMsSortedByIndex[ptmIndex].ptm.Equals(currentPTMsSortedByIndex[ptmIndex]))
{
ptmsLocalized = false;
break;
}
}
}
}
//determine gene ambiguity
bool geneIdentified = genes.Length == 1;
return(GetProteoformClassification(ptmsLocalized, ptmsIdentified, sequenceIdentified, geneIdentified));
}
