/// <summary>
/// Generate the annotation of a proteoform sequence as a substring of a protein sequence.
/// </summary>
/// <param name="sequence">The proteoform sequence.</param>
/// <param name="proteinSequence">The protein sequence.</param>
/// <param name="modLocations">The locations of modifications in the proteoform sequence.</param>
private void GenerateAnnotation(Sequence sequence, Sequence proteinSequence, string modLocations)
{
var cleanSequenceStr = sequence.Aggregate(string.Empty, (current, aa) => current + aa.Residue);
var proteinSequenceStr = proteinSequence.Aggregate(string.Empty, (current, aa) => current + aa.Residue);
var prevResidueIndex = -1;
var nextResidueIndex = sequence.Count;
var index = proteinSequenceStr.IndexOf(cleanSequenceStr, StringComparison.Ordinal);
if (index >= 0)
{
if (index > 0)
{
prevResidueIndex = index - 1;
}
if (index < proteinSequenceStr.Length - 1)
{
nextResidueIndex = index + cleanSequenceStr.Length;
}
}
var labelBuilder = new StringBuilder();
if (prevResidueIndex >= 0)
{
labelBuilder.AppendFormat("{0}{1}.", proteinSequenceStr[prevResidueIndex], prevResidueIndex);
PreSequence = proteinSequenceStr.Substring(0, prevResidueIndex + 1);
}
labelBuilder.AppendFormat("({0})", modLocations.Length == 0 ? (cleanSequenceStr.Length < 30 ? cleanSequenceStr : "...") : modLocations);
if (nextResidueIndex < proteinSequenceStr.Length)
{
labelBuilder.AppendFormat(".{0}{1}", proteinSequenceStr[nextResidueIndex], nextResidueIndex);
PostSequence = proteinSequenceStr.Substring(nextResidueIndex);
}
Annotation = labelBuilder.ToString();
}
/// <summary>
/// Get precursor ion.
/// </summary>
/// <param name="sequence">Sequence for precursor ion.</param>
/// <param name="charge">Charge state of precursor ion.</param>
/// <returns>The precursor ion for the sequence and charge state..</returns>
public static Ion GetPrecursorIon(Sequence sequence, int charge)
{
var composition = sequence.Aggregate(Composition.H2O, (current, aa) => current + aa.Composition);
return(new Ion(composition, charge));
}
