public string GetModifiedSequence(string seq,
IsotopeLabelType labelType,
ExplicitMods mods,
SequenceModFormatType format = SequenceModFormatType.mass_diff,
bool useExplicitModsOnly = false)
{
return GetPrecursorCalc(labelType, mods).GetModifiedSequence(seq, format, useExplicitModsOnly);
}
public string GetModifiedSequence(string seq, ExplicitSequenceMods mods, SequenceModFormatType format, bool useExplicitModsOnly)
{
// If no modifications, do nothing
if (!IsModified(seq) && mods == null)
return seq;
// Otherwise, build a modified sequence string like AMC[+57.0]LP[-37.1]K
StringBuilder sb = new StringBuilder();
for (int i = 0, len = seq.Length; i < len; i++)
{
char c = seq[i];
var modMass = GetAAModMass(c, i, len, mods);
sb.Append(c);
if (modMass != 0)
{
StaticMod mod = mods != null ? mods.FindFirstMod(i) : null;
if (mod == null && useExplicitModsOnly)
continue;
sb.Append(GetModDiffDescription(modMass, mod, format));
}
}
return sb.ToString();
}
public static string GetModDiffDescription(double massDiff, StaticMod mod, SequenceModFormatType format)
{
switch (format)
{
case SequenceModFormatType.mass_diff:
// Non-narrow format is used for library look-up and must be consistent with LibKey format
return string.Format(CultureInfo.InvariantCulture, "[{0}{1:F01}]", (massDiff > 0 ? "+" : string.Empty), massDiff); // Not L10N
case SequenceModFormatType.mass_diff_narrow:
// Narrow format allows for removal of .0 when decimal is not present
// One of the more important cases is 15N labeling which produces a lot of
// [+1] and [+2] values. Also assumed to be for UI, so use local format.
return string.Format("[{0}{1}]", (massDiff > 0 ? "+" : string.Empty), Math.Round(massDiff, 1)); // Not L10N
case SequenceModFormatType.three_letter_code:
var shortName = mod.ShortName;
if (string.IsNullOrEmpty(shortName))
{
bool isStructural;
var foundMod = UniMod.GetModification(mod.Name, out isStructural);
if (foundMod != null)
shortName = foundMod.ShortName;
}
return shortName != null
? string.Format("[{0}]", shortName) // Not L10N
: GetModDiffDescription(massDiff, null, SequenceModFormatType.mass_diff_narrow);
default:
throw new ArgumentOutOfRangeException("format"); // Not L10N
}
}
public string GetModifiedSequence(string seq, SequenceModFormatType format, bool useExplicitModsOnly)
{
return GetModifiedSequence(seq, null, format, useExplicitModsOnly);
}
public string GetModifiedSequence(string seq, SequenceModFormatType format, bool useExplicitModsOnly)
{
return _massCalcBase.GetModifiedSequence(seq, _mods, format, useExplicitModsOnly);
}
