private IEnumerable <TextSequence> GetTextSequencesForSelfAndChildren(
DisplayModificationOption displayModificationOption)
{
return(Enumerable.Range(0, UnmodifiedSequence.Length)
.Select(i => GetTextSequenceAtAaIndex(displayModificationOption, i))
.Concat(GetTextSequencesForLinkedPeptides(displayModificationOption)));
}
public IEnumerable <TextSequence> GetTextSequencesForLinkedPeptides(DisplayModificationOption displayModificationOption)
{
var result = new List <TextSequence>();
if (LinkedPeptides.Count == 0)
{
return(result);
}
result.Add(new TextSequence
{
Color = Color.Black,
Font = ModFontHolder.Plain,
Text = STR_WIDE_DASH
});
if (LinkedPeptides.Count > 1)
{
result.Add(new TextSequence
{
Color = Color.Black,
Font = ModFontHolder.Plain,
Text = @"["
});
}
bool first = true;
foreach (var linkedPeptide in LinkedPeptides.Values)
{
if (!first)
{
result.Add(new TextSequence
{
Color = Color.Black,
Font = ModFontHolder.Plain,
Text = @","
});
}
first = false;
result.AddRange(linkedPeptide.GetTextSequencesForSelfAndChildren(displayModificationOption));
}
if (LinkedPeptides.Count > 1)
{
result.Add(new TextSequence
{
Color = Color.Black,
Font = ModFontHolder.Plain,
Text = @"]"
});
}
return(result);
}
public TextSequence GetTextSequenceAtAaIndex(int residue)
{
Font font = ModFontHolder.Plain;
Color color = Color.Black;
String strAminoAcid = UnmodifiedSequence.Substring(residue, 1);
var modsAtResidue = GetModificationsAtResidue(residue).ToArray();
if (modsAtResidue.Length == 0)
{
return(new TextSequence
{
Color = color,
Font = font,
Text = strAminoAcid
});
}
var firstEntry = modsAtResidue[0];
color = ModFontHolder.GetModColor(firstEntry.Item1);
if (modsAtResidue.Skip(1).All(entry => entry.Item2.Equals(firstEntry.Item2)))
{
font = ModFontHolder.GetModFont(firstEntry.Item1);
return(new TextSequence
{
Color = color,
Font = font,
Text = strAminoAcid + DisplayModificationOption.GetModificationText(SrmSettings, firstEntry.Item2)
});
}
font = IsotopeLabelType.light.Equals(firstEntry.Item1)
? ModFontHolder.LightAndHeavy
: ModFontHolder.GetModFont(firstEntry.Item1);
string modText;
if (DisplayModificationOption == DisplayModificationOption.NOT_SHOWN)
{
modText = strAminoAcid;
}
else
{
modText = strAminoAcid + @"[*]";
}
return(new TextSequence
{
Color = color,
Font = font,
Text = modText
});
}
GetModificationsAtResidue(DisplayModificationOption displayModificationOption, int residue)
{
var mods = ImmutableList.ValueOf(_lightSequenceInfo.ModificationsByResidue[residue]);
if (displayModificationOption.IgnoreZeroMassMods)
{
mods = ImmutableList.ValueOf(mods.Where(mod => mod.MonoisotopicMass != 0 || mod.AverageMass != 0));
}
if (mods.Any())
{
yield return(Tuple.Create(IsotopeLabelType.light, mods));
}
foreach (var entry in _heavySequenceInfos)
{
mods = ImmutableList.ValueOf(entry.Item2.ModificationsByResidue[residue]);
if (mods.Any())
{
yield return(Tuple.Create(entry.Item1, mods));
}
}
}
public TextSequence GetTextSequenceAtAaIndex(DisplayModificationOption displayModificationOption, int residue)
{
Font font = ModFontHolder.Plain;
Color color = Color.Black;
string strAminoAcid = UnmodifiedSequence.Substring(residue, 1);
var modsAtResidue = GetModificationsAtResidue(displayModificationOption, residue).ToArray();
if (residue == CrosslinkedIndexAa ||
modsAtResidue.Any(labeledMod => labeledMod.Item2.Any(mod => mod.ExplicitMod.LinkedPeptide != null)) ||
_lightSequenceInfo.LooplinkSites.Contains(residue))
{
return(new TextSequence
{
Color = COLOR_CROSSLINK,
Font = ModFontHolder.LightAndHeavy,
Text = strAminoAcid
});
}
if (modsAtResidue.Length == 0)
{
return(new TextSequence
{
Color = color,
Font = font,
Text = strAminoAcid
});
}
var firstEntry = modsAtResidue[0];
color = ModFontHolder.GetModColor(firstEntry.Item1);
var firstMismatch = modsAtResidue.Skip(1).FirstOrDefault(entry => !entry.Item2.Equals(firstEntry.Item2));
if (firstMismatch == null)
{
font = ModFontHolder.GetModFont(firstEntry.Item1);
return(new TextSequence
{
Color = color,
Font = font,
Text = strAminoAcid + displayModificationOption.GetModificationText(SrmSettings, firstEntry.Item2)
});
}
if (IsotopeLabelType.light.Equals(firstEntry.Item1))
{
font = ModFontHolder.LightAndHeavy;
color = ModFontHolder.GetModColor(firstMismatch.Item1);
}
else
{
font = ModFontHolder.LightAndHeavy;
}
string modText;
if (displayModificationOption == DisplayModificationOption.NOT_SHOWN)
{
modText = strAminoAcid;
}
else
{
modText = strAminoAcid + @"[*]";
}
return(new TextSequence
{
Color = color,
Font = font,
Text = modText
});
}