public TransitionLoss(StaticMod precursorMod, FragmentLoss loss, MassType massType)
: this()
{
PrecursorMod = precursorMod;
Loss = loss;
Mass = Loss.GetMass(massType);
}
private bool _showLoss = true; // Design mode with loss UI showing
#endregion Fields
#region Constructors
public EditStaticModDlg(StaticMod modEditing, IEnumerable<StaticMod> existing, bool heavy)
{
_existing = existing;
_editing = modEditing != null;
_heavy = heavy;
InitializeComponent();
// Amino acid characters and termini should not be localized
comboAA.Items.Add(string.Empty);
foreach (char aa in AminoAcid.All)
comboAA.Items.Add(aa.ToString(CultureInfo.InvariantCulture));
comboTerm.Items.Add(string.Empty);
comboTerm.Items.Add(ModTerminus.N.ToString());
comboTerm.Items.Add(ModTerminus.C.ToString());
//Formula Box
var location = heavy
? new Point(panelAtoms.Location.X + cb13C.Location.X, panelAtoms.Location.Y + cb13C.Location.Y)
: cbChemicalFormula.Location;
_formulaBox = new FormulaBox(Resources.EditStaticModDlg_EditStaticModDlg_Chemical_formula_,
Resources.EditMeasuredIonDlg_EditMeasuredIonDlg_A_verage_mass_,
Resources.EditMeasuredIonDlg_EditMeasuredIonDlg__Monoisotopic_mass_)
{
Location = location
};
Controls.Add(_formulaBox);
ComboNameVisible = !_editing;
TextNameVisible = _editing;
UpdateListAvailableMods();
cbVariableMod.Visible = !heavy;
_formulaBox.FormulaVisible = !heavy;
cbChemicalFormula.Visible = heavy;
cbChemicalFormula.Checked = !heavy || Settings.Default.ShowHeavyFormula;
if (heavy)
{
labelRelativeRT.Left = labelAA.Left;
comboRelativeRT.Left = comboAA.Left;
comboRelativeRT.Items.Add(RelativeRT.Matching.GetLocalizedString());
comboRelativeRT.Items.Add(RelativeRT.Overlapping.GetLocalizedString());
comboRelativeRT.Items.Add(RelativeRT.Preceding.GetLocalizedString());
comboRelativeRT.Items.Add(RelativeRT.Unknown.GetLocalizedString());
comboRelativeRT.SelectedIndex = 0;
}
else
{
labelRelativeRT.Visible = false;
comboRelativeRT.Visible = false;
}
ShowLoss = false;
if (heavy)
btnLoss.Visible = false;
Modification = _originalModification = modEditing;
}
public void MultiLabelExplicitSerialTest()
{
// Create a simple document and add two peptides
SrmDocument document = new SrmDocument(SrmSettingsList.GetDefault());
const string pepSequence1 = "QFVLSCVILR";
const string pepSequence2 = "DIEVYCDGAITTK";
var reader = new StringReader(string.Join("\n", new[] {">peptides1", pepSequence1, pepSequence2}));
IdentityPath path;
document = document.ImportFasta(reader, true, IdentityPath.ROOT, out path);
Assert.AreEqual(2, document.PeptideCount);
// Add some modifications in two new label types
var modCarb = new StaticMod("Carbamidomethyl Cysteine", "C", null, "C2H3ON");
var modOther = new StaticMod("Another Cysteine", "C", null, "CO8N2");
var staticMods = new[] {modCarb, modOther};
var mod15N = new StaticMod("All 15N", null, null, null, LabelAtoms.N15, null, null);
var modK13C = new StaticMod("13C K", "K", ModTerminus.C, null, LabelAtoms.C13, null, null);
var modR13C = new StaticMod("13C R", "R", ModTerminus.C, null, LabelAtoms.C13, null, null);
var modV13C = new StaticMod("Heavy V", "V", null, null, LabelAtoms.C13 | LabelAtoms.N15, null, null);
var heavyMods = new[] { mod15N, modK13C, modR13C, modV13C };
var labelTypeAA = new IsotopeLabelType("heavy AA", IsotopeLabelType.FirstHeavy);
var labelTypeAll = new IsotopeLabelType("heavy All", IsotopeLabelType.FirstHeavy + 1);
var settings = document.Settings;
settings = settings.ChangePeptideModifications(mods =>
new PeptideModifications(mods.StaticModifications,
new[]
{
new TypedModifications(labelTypeAA, new[] {modK13C, modR13C}),
new TypedModifications(labelTypeAll, new[] {mod15N})
}));
document = document.ChangeSettings(settings);
Assert.AreEqual(6, document.PeptideTransitionGroupCount);
// Add modifications to light and heavy AA in the first peptide
path = document.GetPathTo((int) SrmDocument.Level.Molecules, 0);
var nodePepMod = (PeptideDocNode) document.FindNode(path);
var explicitMod = new ExplicitMods(nodePepMod.Peptide,
new[] {new ExplicitMod(pepSequence1.IndexOf('C'), modOther)},
new[] {new TypedExplicitModifications(nodePepMod.Peptide, labelTypeAA, new ExplicitMod[0])});
document = document.ChangePeptideMods(path, explicitMod, staticMods, heavyMods);
Assert.AreEqual(5, document.PeptideTransitionGroupCount);
// Add a modification to heavy All in the second peptide
path = document.GetPathTo((int)SrmDocument.Level.Molecules, 1);
nodePepMod = (PeptideDocNode)document.FindNode(path);
explicitMod = new ExplicitMods(nodePepMod.Peptide, null,
new[] { new TypedExplicitModifications(nodePepMod.Peptide, labelTypeAll,
new[] {new ExplicitMod(pepSequence2.IndexOf('V'), modV13C)}) });
document = document.ChangePeptideMods(path, explicitMod, staticMods, heavyMods);
Assert.AreEqual(5, document.PeptideTransitionGroupCount);
AssertEx.Serializable(document, 3, AssertEx.DocumentCloned);
}
public ExplicitMod(int indexAA, StaticMod modification)
{
IndexAA = indexAA;
// In the document context, all static non-variable mods must have the explicit
// flag off to behave correctly for equality checks. Only in the
// settings context is the explicit flag necessary to destinguish
// between the global implicit modifications and the explicit modifications
// which do not apply to everything.
if (modification.IsUserSet)
modification = modification.ChangeExplicit(false);
Modification = modification;
}
public void NeutralLossListTest()
{
TestSmallMolecules = false; // No concept of neutral loss for small molecules
var phosphoLossMod = new StaticMod("Phospho Loss", "S, T, Y", null, false, "HPO3",
LabelAtoms.None, RelativeRT.Matching, null, null, new[] { new FragmentLoss("H3PO4"), });
SrmDocument document = new SrmDocument(SrmSettingsList.GetDefault().ChangePeptideModifications(mods =>
mods.ChangeStaticModifications(new List<StaticMod>(mods.StaticModifications) { phosphoLossMod })));
IdentityPath path = IdentityPath.ROOT;
SrmDocument docFasta = document.ImportFasta(new StringReader(TEXT_FASTA_YEAST_7), false, path, out path);
Assert.AreEqual(0, GetLossCount(docFasta, 1));
// Insert losses into the first transition group
var pathPeptide = docFasta.GetPathTo((int) SrmDocument.Level.Molecules, 0);
var nodePep = (PeptideDocNode) docFasta.FindNode(pathPeptide);
var nodeGroup = (TransitionGroupDocNode) nodePep.Children[0];
var listChildren = new List<DocNode>(nodeGroup.Children);
foreach (var nodeTran in nodeGroup.GetTransitions(docFasta.Settings,
nodePep.ExplicitMods, nodeGroup.PrecursorMz, null, null, null, false))
{
if (!nodeTran.HasLoss)
continue;
var tran = nodeTran.Transition;
int matchIndex = listChildren.IndexOf(node =>
Equals(tran, ((TransitionDocNode)node).Transition));
if (matchIndex == -1)
continue;
while (matchIndex < listChildren.Count &&
Equals(tran, ((TransitionDocNode)listChildren[matchIndex]).Transition))
{
matchIndex++;
}
listChildren.Insert(matchIndex, nodeTran);
}
var docLosses = (SrmDocument) docFasta.ReplaceChild(pathPeptide,
nodeGroup.ChangeChildren(listChildren));
int lossCount = GetLossCount(docLosses, 1);
Assert.IsTrue(lossCount > 0);
var docRoundTripped = AssertEx.RoundTripTransitionList(new ThermoMassListExporter(docLosses));
Assert.AreEqual(lossCount, GetLossCount(docRoundTripped, 1));
docRoundTripped = AssertEx.RoundTripTransitionList(new AgilentMassListExporter(docLosses));
Assert.AreEqual(lossCount, GetLossCount(docRoundTripped, 1));
}
/// <summary>
/// Checks if the given modification would impact the given peptides.
/// </summary>
/// <param name="mod">The modification to test</param>
/// <param name="structural">True if this is a structural modification</param>
/// <param name="includeUnmodVariable">True if variable modification should be counted</param>
/// <param name="nodePeps">The list of peptides to test</param>
/// <returns>True if the presence of this modification would change any of the peptides</returns>
public static bool ModAppliesToDoc(StaticMod mod, bool structural, bool includeUnmodVariable,
IEnumerable<PeptideDocNode> nodePeps)
{
// Enumerate all peptides where the modification matches the raw sequence. Obviously,
// it won't impact a peptide where the modification does not apply to the sequence.
foreach (var nodePep in nodePeps.Where(nodePep => mod.IsMod(nodePep.Peptide.Sequence)))
{
// If the peptide has no explicit modifications
if (!nodePep.HasExplicitMods)
{
// And the modification is not variable, or variable modifications
// are being included, then the modification affects this peptide.
if (!mod.IsVariable || includeUnmodVariable)
return true;
}
else
{
var expMods = nodePep.ExplicitMods;
// Otherwise, if this is a structural modification
if (structural)
{
// And there are no explicit structural modifications, or
// the structural modifications are variable and the test modification is not
// variable or the variable modifications contain this modification.
if (expMods.StaticModifications == null
|| (expMods.IsVariableStaticMods
&& (!mod.IsVariable
|| expMods.StaticModifications.Contains(expMod => Equals(expMod.Modification, mod)))))
{
return true;
}
}
// Not structural and no explicit heavy modifications are present
else if (!nodePep.ExplicitMods.HasHeavyModifications
|| nodePep.ExplicitMods.GetHeavyModifications().First() != null)
{
return true;
}
}
}
return false;
}
/// <summary>
/// Returns the number of StaticMod values in the dictionary that are equivalent to modToMatch.
/// </summary>
/// <param name="dict">Dictionary containing StaticMod values.</param>
/// <param name="modToMatch">StaticMod we're comparing to values in dictionary.</param>
/// <param name="equivMods">Dictionary we add count for StaticMods equivalent to modToMatch.</param>
/// <param name="index">Index of modToMatch in dict.</param>
/// <returns>Number of StaticMods equivalent to modToMatch. If there are no equivalent values, function will return 1.</returns>
public int CountEquivalent(KeyValuePair<string, StaticMod>[] dict, StaticMod modToMatch, SortedDictionary<string, int> equivMods, int index)
{
int totalCount = 0;
for (int i = 0; i < dict.Length; i++)
{
int count = 0;
StaticMod mod = dict[i].Value;
if (index != -1 && index == i)
Assert.IsTrue(mod.Equivalent(modToMatch));
if (mod.Equivalent(modToMatch))
count++;
if (!equivMods.ContainsKey(mod.Name))
equivMods.Add(mod.Name, count);
else
{
equivMods[mod.Name] += count;
}
totalCount += count;
}
return totalCount;
}
public bool IsModMatch(StaticMod mod)
{
return mod != null
&& (string.IsNullOrEmpty(mod.AAs) ||
mod.AminoAcids.ContainsAA(AA.ToString(CultureInfo.InvariantCulture)))
&& ((mod.Terminus == null) || Equals(mod.Terminus, Terminus));
}
public bool IsMassMatch(StaticMod mod, double mass)
{
return Equals(Math.Round(GetDefaultModMass(AA, mod), RoundedTo), mass)
&& IsModMatch(mod);
}
private bool IsInSettings(StaticMod staticMod)
{
return Settings.PeptideSettings.Modifications.HasModification(staticMod);
}
public StaticMod MatchVariableAndLossInclusion(StaticMod mod)
{
// Only allowed if the mods are equivalent
Assume.IsTrue(Equivalent(mod));
var result = this;
if (!Equals(result.IsVariable, mod.IsVariable))
result = result.ChangeVariable(mod.IsVariable);
if (result.Losses != null && !ArrayUtil.EqualsDeep(result.Losses, mod.Losses))
{
int len = result.Losses.Count;
var newLosses = new FragmentLoss[len];
for (int i = 0; i < len; i++)
{
newLosses[i] = result.Losses[i].ChangeInclusion(mod.Losses[i].Inclusion);
}
result = result.ChangeLosses(newLosses);
}
return result;
}
/// <summary>
/// Look up the modification in the conflicting mod array.
/// </summary>
private bool IsVariableMod(StaticMod mod)
{
if (string.IsNullOrEmpty(mod.AAs))
{
bool? conflict = IsAAConflict(null, mod.Terminus);
if (conflict.HasValue)
return conflict.Value;
}
else
{
foreach (char aa in mod.AminoAcids)
{
bool? conflict = IsAAConflict((byte) aa, mod.Terminus);
if (conflict.HasValue)
return conflict.Value;
}
}
return true;
}
public void AddModification(StaticMod mod, IsotopeLabelType labelType)
{
if (MatcherPepMods.GetModificationTypes().Contains(labelType))
{
var newMods = MatcherPepMods.GetModifications(labelType)
.Where(existingMod => !existingMod.Equivalent(mod)).ToList();
newMods.Add(mod);
MatcherPepMods = MatcherPepMods.ChangeModifications(labelType, newMods);
}
else if (labelType.IsLight)
{
MatcherPepMods =
new PeptideModifications(new List<StaticMod> { mod }, MatcherPepMods.GetHeavyModifications().ToArray());
}
else
{
var typedHeavyMods =
new List<TypedModifications>(MatcherPepMods.GetHeavyModifications())
{ new TypedModifications(labelType, new List<StaticMod> { mod }) };
MatcherPepMods = new PeptideModifications(MatcherPepMods.StaticModifications, typedHeavyMods);
}
MatchesUpdated = true;
}
public void OkDialog()
{
var helper = new MessageBoxHelper(this);
string name;
if (!helper.ValidateNameTextBox(_editing ? (Control) textName : comboMod, out name))
return;
// Allow updating the original modification
if (!_editing || !Equals(name, Modification.Name))
{
if(!ModNameAvailable(name))
{
helper.ShowTextBoxError(_editing ? (Control)textName : comboMod,
Resources.EditStaticModDlg_OkDialog_The_modification__0__already_exists, name);
return;
}
}
string aas = comboAA.Text;
if (string.IsNullOrEmpty(aas))
aas = null;
else
{
// Use the cleanest possible format.
var sb = new StringBuilder();
foreach (string aaPart in aas.Split(SEPARATOR_AA))
{
string aa = aaPart.Trim();
if (aa.Length == 0)
continue;
if (sb.Length > 0)
sb.Append(", "); // Not L10N
sb.Append(aa);
}
}
string termString = comboTerm.SelectedItem.ToString();
ModTerminus? term = null;
if (!string.IsNullOrEmpty(termString))
term = (ModTerminus) Enum.Parse(typeof (ModTerminus), termString);
if (cbVariableMod.Checked && aas == null && term == null)
{
MessageDlg.Show(this, Resources.EditStaticModDlg_OkDialog_Variable_modifications_must_specify_amino_acid_or_terminus);
comboAA.Focus();
return;
}
string formula = null;
double? monoMass = null;
double? avgMass = null;
LabelAtoms labelAtoms = LabelAtoms.None;
if (cbChemicalFormula.Checked)
formula = Formula;
else
labelAtoms = LabelAtoms;
// Get the losses to know whether any exist below
IList<FragmentLoss> losses = null;
if (listNeutralLosses.Items.Count > 0)
{
losses = Losses.ToArray();
}
if (!string.IsNullOrEmpty(formula))
{
try
{
SequenceMassCalc.ParseModMass(BioMassCalc.MONOISOTOPIC, formula);
}
catch (ArgumentException x)
{
_formulaBox.ShowTextBoxErrorFormula(helper, x.Message);
return;
}
}
else if (labelAtoms == LabelAtoms.None)
{
formula = null;
// Allow formula and both masses to be empty, if losses are present
if ( NotZero(_formulaBox.MonoMass) || NotZero(_formulaBox.AverageMass)|| losses == null)
{
// TODO: Maximum and minimum masses should be formalized and applied everywhere
double mass;
if (!_formulaBox.ValidateMonoText(helper, -1500, 5000, out mass))
return;
monoMass = mass;
if (!_formulaBox.ValidateAverageText(helper, -1500, 5000, out mass))
return;
avgMass = mass;
}
// Loss-only modifications may not be variable
else if (cbVariableMod.Checked)
{
MessageDlg.Show(this, Resources.EditStaticModDlg_OkDialog_The_variable_checkbox_only_applies_to_precursor_modification_Product_ion_losses_are_inherently_variable);
cbVariableMod.Focus();
return;
}
}
else if (aas == null && term.HasValue)
{
MessageDlg.Show(this, Resources.EditStaticModDlg_OkDialog_Labeled_atoms_on_terminal_modification_are_not_valid);
return;
}
RelativeRT relativeRT = RelativeRT.Matching;
if (comboRelativeRT.Visible && comboRelativeRT.SelectedItem != null)
{
relativeRT = RelativeRTExtension.GetEnum(comboRelativeRT.SelectedItem.ToString());
}
// Store state of the chemical formula checkbox for next use.
if (cbChemicalFormula.Visible)
Settings.Default.ShowHeavyFormula = _formulaBox.FormulaVisible;
var newMod = new StaticMod(name,
aas,
term,
cbVariableMod.Checked,
formula,
labelAtoms,
relativeRT,
monoMass,
avgMass,
losses);
foreach (StaticMod mod in _existing)
{
if (newMod.Equivalent(mod) && !(_editing && mod.Equals(_originalModification)))
{
if (DialogResult.OK == MultiButtonMsgDlg.Show(
this,
TextUtil.LineSeparate(Resources.EditStaticModDlg_OkDialog_There_is_an_existing_modification_with_the_same_settings,
string.Format("'{0}'.", mod.Name), // Not L10N
string.Empty,
Resources.EditStaticModDlg_OkDialog_Continue),
MultiButtonMsgDlg.BUTTON_OK))
{
Modification = newMod;
DialogResult = DialogResult.OK;
}
return;
}
}
var uniMod = UniMod.GetModification(name, IsStructural);
// If the modification name is not found in Unimod, check if there exists a modification in Unimod that matches
// the dialog modification, and prompt the user to to use the Unimod modification instead.
if (uniMod == null)
{
var matchingMod = UniMod.FindMatchingStaticMod(newMod, IsStructural);
if (matchingMod != null &&
(ModNameAvailable(matchingMod.Name) ||
(_editing && Equals(matchingMod.Name, Modification.Name))))
{
var result = MultiButtonMsgDlg.Show(
this,
TextUtil.LineSeparate(Resources.EditStaticModDlg_OkDialog_There_is_a_Unimod_modification_with_the_same_settings,
string.Empty,
string.Format(Resources.EditStaticModDlg_OkDialog_Click__Unimod__to_use_the_name___0___, matchingMod.Name),
string.Format(Resources.EditStaticModDlg_OkDialog_Click__Custom__to_use_the_name___0___, name)),
Resources.EditStaticModDlg_OkDialog_Unimod,
Resources.EditStaticModDlg_OkDialog_Custom,
true);
if (result == DialogResult.Yes)
newMod = matchingMod.MatchVariableAndLossInclusion(newMod); // Unimod
if (result == DialogResult.Cancel)
return;
}
}
else
{
// If the dialog modification matches the modification of the same name in Unimod,
// use the UnimodId.
if (newMod.Equivalent(uniMod))
newMod = uniMod.MatchVariableAndLossInclusion(newMod);
else
{
// Finally, if the modification name is found in Unimod, but the modification in Unimod does not
// match the dialog modification, prompt the user to use the Unimod modification definition instead.
if (DialogResult.OK != MultiButtonMsgDlg.Show(
this,
TextUtil.LineSeparate(string.Format(Resources.EditStaticModDlg_OkDialog_This_modification_does_not_match_the_Unimod_specifications_for___0___, name),
string.Empty,
Resources.EditStaticModDlg_OkDialog_Use_non_standard_settings_for_this_name),
MultiButtonMsgDlg.BUTTON_OK))
{
return;
}
}
}
_modification = newMod;
DialogResult = DialogResult.OK;
}
private static void CheckPeptideImplicitMods(XmlNode peptideNode, StaticMod[] staticMods, StaticMod[] heavyMods,
StaticMod[] heavy2Mods)
{
var modListStatic = peptideNode.SelectNodes(SrmDocument.EL.implicit_modifications + "/" +
SrmDocument.EL.implicit_static_modifications + "/" +
SrmDocument.EL.implicit_modification);
CheckImplicitMods(staticMods, modListStatic);
var modListHeavy = peptideNode.SelectNodes(SrmDocument.EL.implicit_modifications + "/" +
SrmDocument.EL.implicit_heavy_modifications +
"[not(@" + SrmDocument.ATTR.isotope_label + ")]/" +
SrmDocument.EL.implicit_modification);
CheckImplicitMods(heavyMods, modListHeavy);
var modListHeavy2 = peptideNode.SelectNodes(SrmDocument.EL.implicit_modifications + "/" +
SrmDocument.EL.implicit_heavy_modifications +
"[@" + SrmDocument.ATTR.isotope_label + " = 'heavy2']/" +
SrmDocument.EL.implicit_modification);
CheckImplicitMods(heavy2Mods, modListHeavy2);
}
private void AddMod(char aa, StaticMod mod, double[] modMasses, double[] modMassesExtra, string[] modFormulas)
{
modMasses[aa] = modMasses[char.ToLowerInvariant(aa)] += GetModMass(aa, mod);
// Deal with formulas and unexplained masses
double unexplainedMass;
string formula = GetModFormula(aa, mod, out unexplainedMass);
modFormulas[aa] = modFormulas[char.ToLowerInvariant(aa)] = CombineFormulas(modFormulas[aa], formula);
modMassesExtra[aa] = modMassesExtra[char.ToLowerInvariant(aa)] += unexplainedMass;
}
public string GetModFormula(char aa, StaticMod mod, out double unexplainedMass)
{
unexplainedMass = 0;
if (!string.IsNullOrEmpty(mod.Formula))
return mod.Formula;
else if (mod.LabelAtoms != LabelAtoms.None)
return GetHeavyFormula(aa, mod.LabelAtoms);
if (_massCalc.MassType == MassType.Monoisotopic)
{
if (mod.MonoisotopicMass.HasValue)
unexplainedMass = mod.MonoisotopicMass.Value;
}
else
{
if (mod.AverageMass.HasValue)
unexplainedMass = mod.AverageMass.Value;
}
return null;
}
public double GetModMass(char aa, StaticMod mod)
{
if (_massCalc.MassType == MassType.Monoisotopic)
{
if (mod.MonoisotopicMass.HasValue)
return mod.MonoisotopicMass.Value;
}
else
{
if (mod.AverageMass.HasValue)
return mod.AverageMass.Value;
}
if (!string.IsNullOrEmpty(mod.Formula))
return ParseModMass(mod.Formula);
else if (mod.LabelAtoms != LabelAtoms.None && AminoAcid.IsAA(aa))
return ParseModMass(GetHeavyFormula(aa, mod.LabelAtoms));
return 0;
}
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
}
}
/// <summary>
/// Equality minus <see cref="IsExplicit"/>, <see cref="UnimodId"/>, <see cref="IsVariable"/> and <see cref="XmlNamedElement.Equals(object)"/>.
/// Used checking for matches between user defined modifications and UniMod modifications.
/// </summary>
public bool Equivalent(StaticMod obj)
{
if (!Equals(obj.AAs, AAs) ||
!obj.Terminus.Equals(Terminus) ||
!obj.AverageMass.Equals(AverageMass) ||
!obj.MonoisotopicMass.Equals(MonoisotopicMass) ||
!Equals(obj.RelativeRT, RelativeRT))
{
return false;
}
if (!ArrayUtil.EqualsDeep(obj._losses, _losses))
{
if (obj._losses != null && _losses != null)
{
if (obj._losses.Count != _losses.Count)
return false;
var losses1 = _losses.OrderBy(l => l.MonoisotopicMass).ToArray();
var losses2 = obj._losses.OrderBy(l => l.MonoisotopicMass).ToArray();
if (losses1.Where((t, i) => !EquivalentFormulas(t, losses2[i])).Any())
{
return false;
}
}
else if (obj._losses == null || _losses == null)
{
return false;
}
}
if (AAs != null)
{
foreach (var aa in AminoAcids)
{
if (!EquivalentFormulas(aa, obj))
return false;
}
}
else if (Terminus != null)
{
return EquivalentFormulas('\0', obj); // Not L10N
}
else
{
// Label all amino acids with this label
for (char aa = 'A'; aa <= 'Z'; aa++) // Not L10N
{
if (AminoAcid.IsAA(aa) && !EquivalentFormulas(aa, obj))
return false;
}
}
return true;
}
public ExplicitMod ChangeModification(StaticMod prop)
{
if (prop.IsExplicit)
prop = prop.ChangeExplicit(false);
return ChangeProp(ImClone(this), (im, v) => im.Modification = v, prop);
}
public void ChangeSettingsExplicitModTest()
{
SrmDocument docStudy7 = CreateStudy7Doc();
string transitionList = ExportCsv(docStudy7);
Assert.AreEqual(TestSmallMolecules ? 71: 69, transitionList.Split('\n').Length); // Did special test mode add a docnode to the end?
var settings = docStudy7.Settings.ChangeTransitionFilter(filter => filter.ChangeAutoSelect(false));
settings = settings.ChangePeptideModifications(mods => mods.ChangeHeavyModifications(ATOMIC_HEAVY_MODS));
docStudy7 = docStudy7.ChangeSettings(settings);
AssertEx.IsDocumentState(docStudy7, 1, 7, 11, 22, 66);
Assert.AreEqual(3, docStudy7.Peptides.Count(peptide => peptide.HasExplicitMods));
Assert.AreEqual(2, docStudy7.Peptides.Count(peptide => peptide.HasExplicitMods &&
peptide.ExplicitMods.StaticModifications.Count > 0 &&
peptide.ExplicitMods.StaticModifications[0].Modification.AAs[0] == 'C'));
Assert.AreEqual(2, docStudy7.Peptides.Count(peptide => peptide.HasExplicitMods &&
peptide.ExplicitMods.HeavyModifications[0].Modification.AAs[0] == 'V' &&
peptide.ExplicitMods.HeavyModifications[0].Modification.Label13C));
Assert.AreEqual(1, docStudy7.Peptides.Count(peptide => peptide.HasExplicitMods &&
peptide.ExplicitMods.HeavyModifications[0].Modification.AAs[0] == 'L' &&
peptide.ExplicitMods.HeavyModifications[0].Modification.Label13C));
AssertEx.NoDiff(transitionList, ExportCsv(docStudy7));
// Correct Heavy K
var listHeavyMods = new List<StaticMod>(ATOMIC_HEAVY_MODS);
listHeavyMods[0] = new StaticMod("Heavy K", "K", ModTerminus.C, null, LabelAtoms.C13|LabelAtoms.N15, null, null);
settings = settings.ChangePeptideModifications(mods => mods.ChangeHeavyModifications(listHeavyMods));
var docHeavyK = docStudy7.ChangeSettings(settings);
var peptidesOld = docStudy7.Peptides.ToArray();
var peptidesNew = docHeavyK.Peptides.ToArray();
Assert.AreEqual(peptidesOld.Length, peptidesNew.Length);
for (int i = 0; i < peptidesOld.Length; i++)
{
var peptideOld = peptidesOld[i];
var peptideNew = peptidesNew[i];
// Non-explicit cysteines should have changed, but no other peptides
string seq = peptideOld.Peptide.Sequence;
if (seq[seq.Length - 1] == 'K' && !peptideOld.HasExplicitMods)
Assert.AreNotSame(peptideOld, peptideNew);
else
Assert.AreSame(peptideOld, peptideNew);
}
// Change valine explicit only modification
listHeavyMods[2] = new StaticMod("13C V", "V", null, null, LabelAtoms.C13 | LabelAtoms.N15, null, null);
listHeavyMods[2] = listHeavyMods[2].ChangeExplicit(true);
settings = settings.ChangePeptideModifications(mods => mods.ChangeHeavyModifications(listHeavyMods));
var docHeavyV = docHeavyK.ChangeSettings(settings);
peptidesOld = docHeavyK.Peptides.ToArray();
peptidesNew = docHeavyV.Peptides.ToArray();
Assert.AreEqual(peptidesOld.Length, peptidesNew.Length);
for (int i = 0; i < peptidesOld.Length; i++)
{
var peptideOld = peptidesOld[i];
var peptideNew = peptidesNew[i];
// Explicit valines should have changed, but no other peptides
if (peptideOld.HasExplicitMods && peptideOld.ExplicitMods.HeavyModifications[0].Modification.AAs[0] == 'V')
Assert.AreNotSame(peptideOld, peptideNew);
else
Assert.AreSame(peptideOld, peptideNew);
}
// Remove implicit cysteine modification
var staticMods = new[] { settings.PeptideSettings.Modifications.StaticModifications[0].ChangeExplicit(true) };
settings = settings.ChangePeptideModifications(mods => mods.ChangeStaticModifications(staticMods));
var docNoStat = docHeavyV.ChangeSettings(settings);
peptidesOld = docHeavyV.Peptides.ToArray();
peptidesNew = docNoStat.Peptides.ToArray();
Assert.AreEqual(peptidesOld.Length, peptidesNew.Length);
for (int i = 0; i < peptidesOld.Length; i++)
{
var peptideOld = peptidesOld[i];
var peptideNew = peptidesNew[i];
// Non-explicit cysteines should have changed, but no other peptides
if (peptideOld.Peptide.Sequence.IndexOf('C') != -1 && !peptideOld.HasExplicitMods)
Assert.AreNotSame(peptideOld, peptideNew);
else
Assert.AreSame(peptideOld, peptideNew);
}
}
public void ModifyExplicitModTest()
{
SrmDocument docStudy7 = CreateStudy7Doc();
var settings = docStudy7.Settings.ChangeTransitionFilter(filter => filter.ChangeAutoSelect(false));
var listStaticMods = settings.PeptideSettings.Modifications.StaticModifications;
var listHeavyMods = new List<StaticMod>(settings.PeptideSettings.Modifications.HeavyModifications);
// Change an explicit heavy modification to something new
var modV = new StaticMod("Heavy V", "V", null, LabelAtoms.C13|LabelAtoms.N15);
listHeavyMods.Add(modV);
IdentityPath path = docStudy7.GetPathTo((int)SrmDocument.Level.Molecules, 0);
var peptideMod = (PeptideDocNode) docStudy7.FindNode(path);
var explicitMods = peptideMod.ExplicitMods;
explicitMods = explicitMods.ChangeHeavyModifications(new[] {explicitMods.HeavyModifications[0].ChangeModification(modV)});
var docHeavyV = docStudy7.ChangePeptideMods(path, explicitMods, listStaticMods, listHeavyMods);
var modSettings = docHeavyV.Settings.PeptideSettings.Modifications;
Assert.AreEqual(5, modSettings.HeavyModifications.Count);
Assert.AreEqual(4, modSettings.HeavyModifications.Count(mod => mod.Formula != null));
Assert.AreEqual(1, modSettings.HeavyModifications.Count(mod => mod.Label13C && mod.Label15N));
Assert.AreEqual(3, docHeavyV.Peptides.Count(peptide => peptide.HasExplicitMods));
Assert.AreEqual(1, docHeavyV.Peptides.Count(peptide => peptide.HasExplicitMods &&
peptide.ExplicitMods.HeavyModifications[0].Modification.AAs[0] == 'V' &&
peptide.ExplicitMods.HeavyModifications[0].Modification.Label13C));
Assert.AreEqual(1, docHeavyV.Peptides.Count(peptide => peptide.HasExplicitMods &&
peptide.ExplicitMods.HeavyModifications[0].Modification.AAs[0] == 'V' &&
peptide.ExplicitMods.HeavyModifications[0].Modification.Label13C &&
peptide.ExplicitMods.HeavyModifications[0].Modification.Label15N));
// Change an explicit heavy modification to something new
listHeavyMods = new List<StaticMod>(settings.PeptideSettings.Modifications.HeavyModifications);
modV = listHeavyMods[2] = ATOMIC_HEAVY_MODS[2];
explicitMods = peptideMod.ExplicitMods;
explicitMods = explicitMods.ChangeHeavyModifications(new[] { explicitMods.HeavyModifications[0].ChangeModification(modV) });
var doc13V = docStudy7.ChangePeptideMods(path, explicitMods, listStaticMods, listHeavyMods);
modSettings = doc13V.Settings.PeptideSettings.Modifications;
Assert.AreEqual(4, modSettings.HeavyModifications.Count);
Assert.AreEqual(3, modSettings.HeavyModifications.Count(mod => mod.Formula != null));
Assert.AreEqual(1, modSettings.HeavyModifications.Count(mod => mod.Label13C));
Assert.AreEqual(3, doc13V.Peptides.Count(peptide => peptide.HasExplicitMods));
Assert.AreEqual(2, doc13V.Peptides.Count(peptide => peptide.HasExplicitMods &&
peptide.ExplicitMods.HeavyModifications[0].Modification.AAs[0] == 'V' &&
peptide.ExplicitMods.HeavyModifications[0].Modification.Label13C));
// No change to the peptide, but change an orthoganal modification
path = docStudy7.GetPathTo((int)SrmDocument.Level.Molecules, docStudy7.Peptides.Count() - 1);
peptideMod = (PeptideDocNode)docStudy7.FindNode(path);
doc13V = docStudy7.ChangePeptideMods(path, peptideMod.ExplicitMods, listStaticMods, listHeavyMods);
modSettings = doc13V.Settings.PeptideSettings.Modifications;
Assert.AreEqual(4, modSettings.HeavyModifications.Count);
Assert.AreEqual(3, modSettings.HeavyModifications.Count(mod => mod.Formula != null));
Assert.AreEqual(1, modSettings.HeavyModifications.Count(mod => mod.Label13C));
Assert.AreEqual(3, doc13V.Peptides.Count(peptide => peptide.HasExplicitMods));
Assert.AreEqual(2, doc13V.Peptides.Count(peptide => peptide.HasExplicitMods &&
peptide.ExplicitMods.HeavyModifications[0].Modification.AAs[0] == 'V' &&
peptide.ExplicitMods.HeavyModifications[0].Modification.Label13C));
// No change to the peptide, but remove all other modifications from global lists
var docClear = docStudy7.ChangePeptideMods(path, peptideMod.ExplicitMods,
new StaticMod[0], new[] {listHeavyMods[3]});
Assert.AreSame(docClear, docStudy7);
// Remove explicit modifications from the global lists
listHeavyMods.RemoveRange(2, 2);
// Mimic the way PeptideSettingsUI would change the settings
var docRemoveExplicit = docStudy7.ChangeSettings(docStudy7.Settings.ChangePeptideModifications(
mods => mods.ChangeHeavyModifications(listHeavyMods)
.DeclareExplicitMods(docStudy7, listStaticMods, listHeavyMods)));
// Test expected changes
modSettings = docRemoveExplicit.Settings.PeptideSettings.Modifications;
Assert.AreEqual(2, modSettings.HeavyModifications.Count);
Assert.AreEqual(3, docRemoveExplicit.Peptides.Count(peptide => peptide.HasExplicitMods));
// Should leave no heavy modifications on the explicitly modified peptides
Assert.AreEqual(0, docRemoveExplicit.Peptides.Count(peptide => peptide.HasExplicitMods &&
peptide.ExplicitMods.HeavyModifications.Count > 0));
}
public bool Equals(StaticMod obj)
{
if (ReferenceEquals(null, obj)) return false;
if (ReferenceEquals(this, obj)) return true;
return EquivalentAll(obj) &&
obj.IsExplicit.Equals(IsExplicit);
}
private bool EquivalentFormulas(char aa, StaticMod obj)
{
SequenceMassCalc modCalc = new SequenceMassCalc(MassType.Monoisotopic);
double unexplainedMassThis, unexplainedMassObj;
string formulaThis = modCalc.GetModFormula(aa, this, out unexplainedMassThis);
string formulaObj = modCalc.GetModFormula(aa, obj, out unexplainedMassObj);
// If either is null, both must be null.
if (formulaThis == null || formulaObj == null)
return formulaThis == null && formulaObj == null;
return unexplainedMassThis == unexplainedMassObj &&
ArrayUtil.EqualsDeep(GetFormulaModCounts(formulaThis).ToArray(),
GetFormulaModCounts(formulaObj).ToArray());
}
protected override void DoTest()
{
// Create modifications used in this test
var aquaMods = new[]
{
new StaticMod("Heavy K", "K", ModTerminus.C, null, LabelAtoms.C13|LabelAtoms.N15, null, null),
new StaticMod("Heavy R", "R", ModTerminus.C, null, LabelAtoms.C13|LabelAtoms.N15, null, null)
};
var explicitMod = new StaticMod("13C L", "L", null, null, LabelAtoms.C13, null, null);
var variableMod = new StaticMod("Methionine Oxidized", "M", null, true, "O",
LabelAtoms.None, RelativeRT.Matching, null, null, null);
Settings.Default.HeavyModList.Clear();
Settings.Default.HeavyModList.AddRange(aquaMods);
Settings.Default.HeavyModList.Add(explicitMod);
Settings.Default.StaticModList.Clear();
Settings.Default.StaticModList.AddRange(StaticModList.GetDefaultsOn());
var carbMod = Settings.Default.StaticModList[0];
Settings.Default.StaticModList.Add(variableMod);
// Clean-up before running the test
var settings = SrmSettingsList.GetDefault().ChangePeptideModifications(mod =>
mod.ChangeHeavyModifications(aquaMods));
RunUI(() => SkylineWindow.ModifyDocument("Set test settings",
doc => doc.ChangeSettings(settings)));
// Add FASTA sequence
RunUI(() => SkylineWindow.Paste(TEXT_FASTA_YEAST_39));
// Check and save original document information
var docOrig = WaitForProteinMetadataBackgroundLoaderCompletedUI();
var pathPeptide = docOrig.GetPathTo((int) SrmDocument.Level.Molecules, docOrig.PeptideCount - 3);
var peptideOrig = (PeptideDocNode) docOrig.FindNode(pathPeptide);
Assert.AreEqual(2, peptideOrig.Children.Count);
Assert.IsNull(peptideOrig.ExplicitMods);
// Add methionine oxidation variable modification
SetStaticModifications(names => new List<string>(names) { variableMod.Name });
var docVarMod = WaitForDocumentChange(docOrig);
// Check that variable modification worked, and that the peptide of
// interest is variably modified.
Assert.IsTrue(docOrig.PeptideCount < docVarMod.PeptideCount);
pathPeptide = docVarMod.GetPathTo((int)SrmDocument.Level.Molecules, docVarMod.PeptideCount - 4);
var peptideVarMod = (PeptideDocNode)docVarMod.FindNode(pathPeptide);
Assert.AreEqual(2, peptideVarMod.Children.Count);
Assert.IsTrue(peptideVarMod.HasVariableMods,
string.Format("No variable modifications found on the peptide {0}", peptideVarMod.Peptide.Sequence));
Assert.IsFalse(peptideVarMod.ExplicitMods.IsModified(IsotopeLabelType.heavy));
AssertPrecursorMzIsModified(peptideVarMod, 0, peptideVarMod, 1, -5, 0.2);
// Select the peptide of interest
RunUI(() => SkylineWindow.SequenceTree.SelectedPath = pathPeptide);
// Make sure the explicit modifications dialog does not modify the
// peptide when nothing is changed.
string sequence = peptideVarMod.Peptide.Sequence;
RunDlg<EditPepModsDlg>(SkylineWindow.ModifyPeptide, dlg =>
{
for (int i = 0; i < sequence.Length; i++)
{
dlg.SelectModification(IsotopeLabelType.light, i, "");
dlg.SelectModification(IsotopeLabelType.heavy, i, "");
}
dlg.ResetMods();
dlg.OkDialog();
});
Assert.AreSame(docVarMod, SkylineWindow.Document);
// Explicitly change the heavy modification
RunDlg<EditPepModsDlg>(SkylineWindow.ModifyPeptide, dlg =>
{
dlg.SelectModification(IsotopeLabelType.heavy, sequence.Length - 1, "");
dlg.SelectModification(IsotopeLabelType.heavy, sequence.LastIndexOf('L'),
explicitMod.Name);
dlg.OkDialog();
});
// Check for correct response to modification
var docExplicit = WaitForDocumentChange(docOrig);
var peptideExplicit = (PeptideDocNode) docExplicit.FindNode(pathPeptide);
Assert.AreEqual(2, peptideExplicit.Children.Count);
// Precursor m/z for light should be same
AssertPrecursorMzAreEqaul(peptideVarMod, 0, peptideExplicit, 0);
// Heavy should have changed
AssertPrecursorMzIsModified(peptideExplicit, 0, peptideExplicit, 1, -3, 0.2);
// Heavy should now be explicitly modified
Assert.IsTrue(peptideExplicit.ExplicitMods.IsModified(IsotopeLabelType.heavy));
// Remove carbamidomethyl cysteine implicit modification
SetStaticModifications(names => new[] { variableMod.Name });
var docNoImplicit = WaitForDocumentChange(docExplicit);
var peptideNoImplicit = (PeptideDocNode)docNoImplicit.FindNode(pathPeptide);
// Light should have gotten 57.0 lighter
const double modCarbMz = 57.0/2;
AssertPrecursorMzIsModified(peptideExplicit, 0, peptideNoImplicit, 0, modCarbMz, 0.1);
// Heavy delta should not have changed
AssertPrecursorMzIsModified(peptideNoImplicit, 0, peptideNoImplicit, 1, -3, 0.2);
// Reset should still return to implicit heavy mods without removing
// variable mods.
RunDlg<EditPepModsDlg>(SkylineWindow.ModifyPeptide, dlg =>
{
dlg.ResetMods();
dlg.OkDialog();
});
var docReset = WaitForDocumentChange(docNoImplicit);
var peptideReset = (PeptideDocNode)docReset.FindNode(pathPeptide);
Assert.IsTrue(peptideReset.HasExplicitMods);
Assert.IsFalse(peptideReset.ExplicitMods.IsModified(IsotopeLabelType.heavy));
AssertPrecursorMzIsModified(peptideReset, 0, peptideReset, 1, -5, 0.2);
// Explicitly add back the Carbamidomethyl Cysteine
// Reset should still return to implicit heavy mods
RunDlg<EditPepModsDlg>(SkylineWindow.ModifyPeptide, dlg =>
{
dlg.SelectModification(IsotopeLabelType.light, sequence.IndexOf('C'), carbMod.Name);
dlg.OkDialog();
});
var docExCarb = WaitForDocumentChange(docReset);
var peptideExCarb = (PeptideDocNode)docExCarb.FindNode(pathPeptide);
Assert.IsTrue(peptideExCarb.HasExplicitMods);
Assert.IsFalse(peptideExCarb.HasVariableMods);
AssertPrecursorMzAreEqaul(peptideVarMod, 0, peptideExCarb, 0);
AssertPrecursorMzAreEqaul(peptideVarMod, 1, peptideExCarb, 1);
// Reset at this point should completely remove explicit modifications
// including oxidized M.
RunDlg<EditPepModsDlg>(SkylineWindow.ModifyPeptide, dlg =>
{
dlg.ResetMods();
dlg.OkDialog();
});
var docResetImplicit = WaitForDocumentChange(docExCarb);
var peptideResetImplicit = (PeptideDocNode) docResetImplicit.FindNode(pathPeptide);
Assert.IsFalse(peptideResetImplicit.HasExplicitMods);
AssertPrecursorMzIsModified(peptideOrig, 0, peptideResetImplicit, 0, modCarbMz, 0.1);
AssertPrecursorMzIsModified(peptideOrig, 1, peptideResetImplicit, 1, modCarbMz, 0.1);
// Turn off the variable modifications and explicitly modify using a variable mod
RunDlg<PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI, dlg =>
{
dlg.PickedStaticMods = new string[0];
dlg.OkDialog();
});
var docNoStaticMods = WaitForDocumentChange(docResetImplicit);
// Explicitly modify the first peptide
var pathPeptideFirst = docNoStaticMods.GetPathTo((int) SrmDocument.Level.Molecules, 0);
var peptideUnmod = (PeptideDocNode) docNoStaticMods.FindNode(pathPeptideFirst);
RunUI(() => SkylineWindow.SelectedPath = pathPeptideFirst);
RunDlg<EditPepModsDlg>(SkylineWindow.ModifyPeptide, dlg =>
{
var sequenceUnmod = peptideUnmod.Peptide.Sequence;
dlg.SelectModification(IsotopeLabelType.light, sequenceUnmod.IndexOf('M'), variableMod.Name);
dlg.OkDialog();
});
var docExplicitVarMod = WaitForDocumentChange(docNoStaticMods);
var peptideExplicitVarMod = (PeptideDocNode) docExplicitVarMod.FindNode(pathPeptideFirst);
Assert.IsTrue(peptideExplicitVarMod.HasExplicitMods);
if (peptideExplicitVarMod.ExplicitMods.StaticModifications == null)
{
Assert.IsNotNull(peptideExplicitVarMod.ExplicitMods.StaticModifications);
return; // For ReSharper
}
var varModPeptide = peptideExplicitVarMod.ExplicitMods.StaticModifications[0].Modification;
Assert.AreEqual(variableMod.Name, varModPeptide.Name);
// The modification instance on the peptide should not be marked as variable
Assert.IsFalse(varModPeptide.IsVariable);
var varModSettings = docExplicitVarMod.Settings.PeptideSettings.Modifications.StaticModifications[0];
Assert.AreEqual(variableMod.Name, varModSettings.Name);
Assert.IsTrue(varModSettings.IsExplicit);
Assert.IsFalse(varModSettings.IsVariable);
// Make sure this did not turn on the variable modification in the settings UI
RunDlg<PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI, dlg =>
{
Assert.AreEqual(0, dlg.PickedStaticMods.Length);
dlg.OkDialog();
});
Directory.CreateDirectory(TestContext.TestDir);
string saveFilePath = TestContext.GetTestPath("TestExplicitVariable.sky");
WaitForProteinMetadataBackgroundLoaderCompletedUI(); // make sure doc is complete before save
RunUI(() =>
{
Assert.IsTrue(SkylineWindow.SaveDocument(saveFilePath));
SkylineWindow.NewDocument();
Assert.IsTrue(SkylineWindow.OpenFile(saveFilePath));
});
WaitForProteinMetadataBackgroundLoaderCompletedUI();
var docRestored = SkylineWindow.Document;
var pathPeptideFirstNew = docRestored.GetPathTo((int) SrmDocument.Level.Molecules, 0);
var peptideExplicitVarModNew = docRestored.FindNode(pathPeptideFirstNew);
Assert.AreEqual(peptideExplicitVarMod, peptideExplicitVarModNew,
"Saved peptide with explicit variable modification was not restored correctly.");
Assert.IsTrue(Settings.Default.StaticModList.Contains(variableMod),
"Expected variable modification has been removed from the global list.");
}
public void RemoveModification(StaticMod mod, IsotopeLabelType labelType)
{
if (MatcherPepMods.GetModificationTypes().Contains(labelType))
{
var newMods = MatcherPepMods.GetModifications(labelType)
.Where(existingMod => !existingMod.Equivalent(mod)).ToArray();
MatcherPepMods = MatcherPepMods.ChangeModifications(labelType, newMods);
}
MatchesUpdated = true;
}
public static double GetDefaultModMass(char aa, StaticMod mod)
{
return CALC_DEFAULT.GetModMass(aa, mod);
}
private static string GetMatchString(AAModKey key, StaticMod staticMod, bool structural)
{
string formatString = structural ? "{0}[{1}{2}]" : "{0}{{{1}{2}}}"; // Not L10N
var modMass = Math.Round(GetDefaultModMass(key.AA, staticMod), key.RoundedTo);
return string.Format(formatString, key.AA, (modMass > 0 ? "+" : string.Empty), modMass); // Not L10N
}
/// <summary>
/// Equality minus the <see cref="IsExplicit"/> flag.
/// </summary>
public bool EquivalentAll(StaticMod obj)
{
return Equivalent(obj)
&& base.Equals(obj)
&& obj.IsVariable.Equals(IsVariable)
&& Equals(obj.UnimodId, UnimodId)
&& Equals(obj.ShortName, ShortName)
&& ArrayUtil.EqualsDeep(obj._losses, _losses);
}