public static SrmPairedResult ToPairedResult(this List <SrmTransition> transList)
{
SrmPairedResult result = new SrmPairedResult();
//所有母离子有相同名称、相同质荷比认为是来自相同precursor，合并为一个peptide。
var pepgroup = transList.GroupBy(m => m.PrecursorFormula + MyConvert.Format("{0:0.0000}", m.PrecursorMZ));
var peptides = new List <SrmPeptideItem>();
foreach (var g in pepgroup)
{
var pep = new SrmPeptideItem();
pep.PrecursorMZ = g.First().PrecursorMZ;
pep.ProductIons = new List <SrmTransition>(g);
peptides.Add(pep);
}
//具有相同母离子名称和电荷的transition认为是轻重标。
var lhgroup = peptides.GroupBy(m => m.ProductIons[0].PrecursorFormula + "_" + m.ProductIons[0].PrecursorCharge.ToString()).ToList();
// var lhgroup = peptides.GroupBy(m => m.ProductIons[0].PrecursorFormula + "_" + m.ProductIons[0].PrecursorCharge.ToString()).ToList();
foreach (var g in lhgroup)
{
if (g.Count() > 2)
{
throw new Exception(string.Format("There are {0} transition with same precursor formula and precursor charge: {1}, {2}", g.Count(), g.First().ProductIons[0].PrecursorFormula, g.First().ProductIons[0].PrecursorCharge));
}
else if (g.Count() > 1)
{
var items = g.ToList();
items.Sort((m1, m2) => m1.PrecursorMZ.CompareTo(m2.PrecursorMZ));
SrmPairedPeptideItem light = new SrmPairedPeptideItem(items[0]);
SrmPairedPeptideItem heavy = new SrmPairedPeptideItem(items[1]);
if (!string.IsNullOrEmpty(light.ProductIonPairs[0].Light.Ion))
{
light.SetHeavyPeptideItemByIon(heavy);
}
else
{
light.SetHeavyPeptideItem(heavy);
}
result.Add(light);
}
else
{
SrmPairedPeptideItem light = new SrmPairedPeptideItem(g.First());
result.Add(light);
}
}
return(result);
}
private SrmPairedResult BuildResultBasedOnRealData(List <SrmTransition> mrms)
{
SrmPairedResult mrmPairs;
//将Transaction转换为MRMPeptideItem
var peptides = new List <SrmPeptideItem>();
foreach (var mrm in mrms)
{
bool bFound = false;
foreach (var pep in peptides)
{
if (mrm.IsBrother(pep.ProductIons[0], this.options.RetentionTimeToleranceInSecond, 0.0001))
{
pep.ProductIons.Add(mrm);
bFound = true;
break;
}
}
if (!bFound)
{
SrmPeptideItem item = new SrmPeptideItem();
item.PrecursorMZ = mrm.PrecursorMZ;
item.ProductIons.Add(mrm);
peptides.Add(item);
}
}
//按照precursormz排序
foreach (var pep in peptides)
{
pep.ProductIons.Sort((m1, m2) => m1.ProductIon.CompareTo(m2.ProductIon));
}
mrmPairs = new SrmPairedResult();
mrmPairs.AddRange(from p in peptides
orderby p.PrecursorMZ
select new SrmPairedPeptideItem(p));
//合并ProductIon完全一样或者差距相同的Item
for (int i = 0; i < mrmPairs.Count; i++)
{
var iLight = mrmPairs[i];
for (int j = i + 1; j < mrmPairs.Count; j++)
{
var jLight = mrmPairs[j];
if (Math.Abs(iLight.LightPrecursorMZ - jLight.LightPrecursorMZ) > this.options.MaxPrecursorDistance)
{
continue;
}
if (iLight.AddPerfectPairedPeptideItem(jLight, this.options.AllowedGaps, this.options.MzTolerance, this.options.RetentionTimeToleranceInSecond))
{
mrmPairs.RemoveAt(j);
break;
}
}
}
//容错情况下，合并ProductIon完全一样或者差距相同的Item
for (int i = 0; i < mrmPairs.Count; i++)
{
var iLight = mrmPairs[i];
if (iLight.IsPaired)
{
continue;
}
for (int j = i + 1; j < mrmPairs.Count; j++)
{
var jLight = mrmPairs[j];
if (jLight.IsPaired)
{
continue;
}
if (Math.Abs(iLight.LightPrecursorMZ - jLight.LightPrecursorMZ) > this.options.MaxPrecursorDistance)
{
continue;
}
if (iLight.AddErrorPairedPeptideItem(jLight, this.options.AllowedGaps, this.options.MzTolerance, this.options.RetentionTimeToleranceInSecond))
{
mrmPairs.RemoveAt(j);
break;
}
}
}
return(mrmPairs);
}
public SrmPairedPeptideItem(SrmPeptideItem light)
{
Enabled = true;
ProductIonPairs = (from p in light.ProductIons
select new SrmPairedProductIon(p)).ToList();
}
