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Test digest two xmls for same protein #824

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Test digest two xmls for same protein #824

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2b1e40e
supposedToBeDifferent
trishorts Jan 14, 2025
7de7d9c
dunno
trishorts Jan 14, 2025
088e2b1
correct protein accession now
trishorts Jan 15, 2025
00d87f0
j
trishorts Jan 15, 2025
7ccefd1
k
trishorts Jan 15, 2025
a15c4f8
added sort feature to GetModifiedPeptide4s using IComparable for Modi…
trishorts Jan 16, 2025
c61cffe
eliminate unused code
trishorts Jan 16, 2025
d71114a
Merge remote-tracking branch 'upstream/master' into testDigestTwoXmls…
trishorts Jan 16, 2025
20b2bc5
eliminate unused codfe
trishorts Jan 16, 2025
91515cc
eliminate icomparable and swtich to linq
trishorts Jan 16, 2025
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10 changes: 1 addition & 9 deletions mzLib/Omics/Digestion/DigestionProduct.cs
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Original file line number Diff line number Diff line change
@@ -1,10 +1,4 @@
using System;
using System.Collections.Generic;
using System.ComponentModel;
using System.Linq;
using System.Text;
using System.Threading.Tasks;
using Omics.Modifications;
using Omics.Modifications;

namespace Omics.Digestion
{
Expand Down Expand Up @@ -188,7 +182,5 @@ private static Dictionary<int, Modification> GetNewVariableModificationPattern(i

return modification_pattern;
}


}
}
57 changes: 29 additions & 28 deletions mzLib/Proteomics/ProteolyticDigestion/ProteolyticPeptide.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -97,48 +97,49 @@ internal IEnumerable<PeptideWithSetModifications> GetModifiedPeptides(IEnumerabl
}

// LOCALIZED MODS
foreach (var kvp in Protein.OneBasedPossibleLocalizedModifications)
foreach (var localizedMod in Protein.OneBasedPossibleLocalizedModifications
.SelectMany(kvp => kvp.Value.Select(value => (kvp.Key, value)))
.OrderBy(tuple => tuple.Key)
.ThenBy(tuple => tuple.value.IdWithMotif))
{
bool inBounds = kvp.Key >= OneBasedStartResidue && kvp.Key <= OneBasedEndResidue;
bool inBounds = localizedMod.Key >= OneBasedStartResidue && localizedMod.Key <= OneBasedEndResidue;
if (!inBounds)
{
continue;
}

int locInPeptide = kvp.Key - OneBasedStartResidueInProtein + 1;
foreach (Modification modWithMass in kvp.Value)
int locInPeptide = localizedMod.Key - OneBasedStartResidueInProtein + 1;

if (localizedMod.value is Modification variableModification)
{
if (modWithMass is Modification variableModification)
// Check if can be a n-term mod
if (locInPeptide == 1 && CanBeNTerminalMod(variableModification, peptideLength) && !Protein.IsDecoy)
{
// Check if can be a n-term mod
if (locInPeptide == 1 && CanBeNTerminalMod(variableModification, peptideLength) && !Protein.IsDecoy)
{
pepNTermVariableMods.Add(variableModification);
}
pepNTermVariableMods.Add(variableModification);
}

int r = locInPeptide - 1;
if (r >= 0 && r < peptideLength
&& (Protein.IsDecoy ||
(ModificationLocalization.ModFits(variableModification, Protein.BaseSequence, r + 1, peptideLength, OneBasedStartResidueInProtein + r)
&& variableModification.LocationRestriction == "Anywhere.")))
int r = locInPeptide - 1;
if (r >= 0 && r < peptideLength
&& (Protein.IsDecoy ||
(ModificationLocalization.ModFits(variableModification, Protein.BaseSequence, r + 1, peptideLength, OneBasedStartResidueInProtein + r)
&& variableModification.LocationRestriction == "Anywhere.")))
{
if (!twoBasedPossibleVariableAndLocalizeableModifications.TryGetValue(r + 2, out List<Modification> residueVariableMods))
{
if (!twoBasedPossibleVariableAndLocalizeableModifications.TryGetValue(r + 2, out List<Modification> residueVariableMods))
{
residueVariableMods = new List<Modification> { variableModification };
twoBasedPossibleVariableAndLocalizeableModifications.Add(r + 2, residueVariableMods);
}
else
{
residueVariableMods.Add(variableModification);
}
residueVariableMods = new List<Modification> { variableModification };
twoBasedPossibleVariableAndLocalizeableModifications.Add(r + 2, residueVariableMods);
}

// Check if can be a c-term mod
if (locInPeptide == peptideLength && CanBeCTerminalMod(variableModification, peptideLength) && !Protein.IsDecoy)
else
{
pepCTermVariableMods.Add(variableModification);
residueVariableMods.Add(variableModification);
}
}

// Check if can be a c-term mod
if (locInPeptide == peptideLength && CanBeCTerminalMod(variableModification, peptideLength) && !Protein.IsDecoy)
{
pepCTermVariableMods.Add(variableModification);
}
}
}

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