/// <summary>
/// Creates a PeptideWithSetModifications object from a sequence string.
/// Useful for reading in MetaMorpheus search engine output into mzLib objects.
/// </summary>
public PeptideWithSetModifications(string sequence, Dictionary <string, Modification> allKnownMods, int numFixedMods = 0,
DigestionParams digestionParams = null, Protein p = null, int oneBasedStartResidueInProtein = int.MinValue,
int oneBasedEndResidueInProtein = int.MinValue, int missedCleavages = int.MinValue,
CleavageSpecificity cleavageSpecificity = CleavageSpecificity.Full, string peptideDescription = null)
: base(p, oneBasedStartResidueInProtein, oneBasedEndResidueInProtein, missedCleavages, cleavageSpecificity, peptideDescription)
{
if (sequence.Contains("|"))
{
throw new MzLibUtil.MzLibException("Ambiguous peptide cannot be parsed from string: " + sequence);
}
FullSequence = sequence;
GetModsAfterDeserialization(allKnownMods, out _baseSequence);
NumFixedMods = numFixedMods;
_digestionParams = digestionParams;
if (p != null)
{
ProteinAccession = p.Accession;
}
if (digestionParams != null)
{
DigestionParamString = digestionParams.ToString();
}
}
private ProteaseDictionary()
: base()
{
using (StreamReader proteases = new StreamReader(Path.Combine(Path.GetDirectoryName(Environment.GetCommandLineArgs()[0]), "proteases.tsv")))
{
proteases.ReadLine();
while (proteases.Peek() != -1)
{
string line = proteases.ReadLine();
string[] fields = line.Split('\t');
string name = fields[0];
string[] sequences_inducing_cleavage = fields[1].Split(new char[] { ',' }, StringSplitOptions.RemoveEmptyEntries);
string[] sequences_preventing_cleavage = fields[2].Split(new char[] { ',' }, StringSplitOptions.RemoveEmptyEntries);
Terminus cleavage_terminus = (Terminus)Enum.Parse(typeof(Terminus), fields[3], true);
CleavageSpecificity cleavage_specificity = (CleavageSpecificity)Enum.Parse(typeof(CleavageSpecificity), fields[4], true);
string psi_ms_accession_number = fields[5];
string psi_ms_name = fields[6];
string site_regexp = fields[7];
Protease protease = new Protease(name, sequences_inducing_cleavage, sequences_preventing_cleavage, cleavage_terminus, cleavage_specificity, psi_ms_accession_number, psi_ms_name, site_regexp);
Add(protease);
}
}
}
public Protease(string name, CleavageSpecificity cleavageSpecificity, string psiMSAccessionNumber, string psiMSName, List <DigestionMotif> motifList)
{
Name = name;
CleavageSpecificity = cleavageSpecificity;
PsiMsAccessionNumber = psiMSAccessionNumber;
PsiMsName = psiMSName;
DigestionMotifs = motifList ?? new List <DigestionMotif>();
}
public Protease(string name, IEnumerable<string> sequencesInducingCleavage, IEnumerable<string> sequencesPreventingCleavage, Terminus cleavageTerminus, CleavageSpecificity cleavageSpecificity)
{
Name = name;
SequencesInducingCleavage = sequencesInducingCleavage;
SequencesPreventingCleavage = sequencesPreventingCleavage;
CleavageTerminus = cleavageTerminus;
CleavageSpecificity = cleavageSpecificity;
}
public Protease(string name, string aminoAcidsInducingCleavage, string aminoAcidsPreventingCleavage, Terminus cleavageTerminus, CleavageSpecificity cleavageSpecificity)
{
Name = name;
CleavageTerminus = cleavageTerminus;
AminoAcidsInducingCleavage = aminoAcidsInducingCleavage;
AminoAcidsPreventingCleavage = aminoAcidsPreventingCleavage;
CleavageSpecificity = cleavageSpecificity;
}
public Protease(string name, CleavageSpecificity cleavageSpecificity, string psiMSAccessionNumber, string psiMSName, List <DigestionMotif> motifList, Modification modDetails = null)
{
Name = name;
CleavageSpecificity = cleavageSpecificity;
PsiMsAccessionNumber = psiMSAccessionNumber;
PsiMsName = psiMSName;
DigestionMotifs = motifList ?? new List <DigestionMotif>();
CleavageMod = modDetails;
}
internal ProteolyticPeptide(Protein protein, int oneBasedStartResidueInProtein, int oneBasedEndResidueInProtein, int missedCleavages, CleavageSpecificity cleavageSpecificityForFdrCategory, string peptideDescription = null, string baseSequence = null)
{
_protein = protein;
OneBasedStartResidueInProtein = oneBasedStartResidueInProtein;
OneBasedEndResidueInProtein = oneBasedEndResidueInProtein;
MissedCleavages = missedCleavages;
CleavageSpecificityForFdrCategory = cleavageSpecificityForFdrCategory;
PeptideDescription = peptideDescription;
_baseSequence = baseSequence;
}
public Protease(string name, IEnumerable <Tuple <string, FragmentationTerminus> > sequencesInducingCleavage, IEnumerable <Tuple <string, FragmentationTerminus> > sequencesPreventingCleavage, CleavageSpecificity cleavageSpecificity, string psiMSAccessionNumber, string psiMSName, string siteRegexp)
{
Name = name;
SequencesInducingCleavage = sequencesInducingCleavage;
SequencesPreventingCleavage = sequencesPreventingCleavage;
CleavageSpecificity = cleavageSpecificity;
PsiMsAccessionNumber = psiMSAccessionNumber;
PsiMsName = psiMSName;
SiteRegexp = siteRegexp;
}
public Protease(string name, IEnumerable <string> sequencesInducingCleavage, IEnumerable <string> sequencesPreventingCleavage, Terminus cleavageTerminus, CleavageSpecificity cleavageSpecificity, string psiMsAccessionNumber, string psiMsName, string siteRegexp)
{
Name = name;
SequencesInducingCleavage = sequencesInducingCleavage;
SequencesPreventingCleavage = sequencesPreventingCleavage;
CleavageTerminus = cleavageTerminus;
CleavageSpecificity = cleavageSpecificity;
PsiMsAccessionNumber = psiMsAccessionNumber;
PsiMsName = psiMsName;
SiteRegexp = siteRegexp;
}
public Protease(string name, IEnumerable<string> sequencesInducingCleavage, IEnumerable<string> sequencesPreventingCleavage, Terminus cleavageTerminus, CleavageSpecificity cleavageSpecificity, string psiMsAccessionNumber, string psiMsName, string siteRegexp)
{
Name = name;
SequencesInducingCleavage = sequencesInducingCleavage;
SequencesPreventingCleavage = sequencesPreventingCleavage;
CleavageTerminus = cleavageTerminus;
CleavageSpecificity = cleavageSpecificity;
PsiMsAccessionNumber = psiMsAccessionNumber;
PsiMsName = psiMsName;
SiteRegexp = siteRegexp;
}
private readonly string ProteinAccession; // used to get protein object after deserialization
/// <summary>
/// Creates a PeptideWithSetModifications object from a protein. Used when a Protein is digested.
/// </summary>
public PeptideWithSetModifications(Protein protein, DigestionParams digestionParams, int oneBasedStartResidueInProtein,
int oneBasedEndResidueInProtein, CleavageSpecificity cleavageSpecificity, string peptideDescription, int missedCleavages,
Dictionary <int, Modification> allModsOneIsNterminus, int numFixedMods, string baseSequence = null)
: base(protein, oneBasedStartResidueInProtein, oneBasedEndResidueInProtein, missedCleavages, cleavageSpecificity, peptideDescription, baseSequence)
{
_allModsOneIsNterminus = allModsOneIsNterminus;
NumFixedMods = numFixedMods;
_digestionParams = digestionParams;
DetermineFullSequence();
ProteinAccession = protein.Accession;
UpdateCleavageSpecificity();
}
public static int GetMinNumberTermini(this CleavageSpecificity cleavageSpecifity)
{
switch (cleavageSpecifity)
{
case CleavageSpecificity.None:
return(0);
case CleavageSpecificity.Semi:
case CleavageSpecificity.SemiN:
case CleavageSpecificity.SemiC:
return(1);
case CleavageSpecificity.Full:
default:
return(2);
}
}
public DigestionParams(string protease = "trypsin", int maxMissedCleavages = 2, int minPeptideLength = 7, int maxPeptideLength = int.MaxValue,
int maxModificationIsoforms = 1024, InitiatorMethionineBehavior initiatorMethionineBehavior = InitiatorMethionineBehavior.Variable,
int maxModsForPeptides = 2, CleavageSpecificity searchModeType = CleavageSpecificity.Full, FragmentationTerminus fragmentationTerminus = FragmentationTerminus.Both,
bool generateUnlabeledProteinsForSilac = true)
{
Protease = ProteaseDictionary.Dictionary[protease];
MaxMissedCleavages = maxMissedCleavages;
MinPeptideLength = minPeptideLength;
MaxPeptideLength = maxPeptideLength;
MaxModificationIsoforms = maxModificationIsoforms;
InitiatorMethionineBehavior = initiatorMethionineBehavior;
MaxModsForPeptide = maxModsForPeptides;
SearchModeType = searchModeType;
FragmentationTerminus = fragmentationTerminus;
RecordSpecificProtease();
GeneratehUnlabeledProteinsForSilac = generateUnlabeledProteinsForSilac;
}
public static FdrCategory GetCleavageSpecificityCategory(CleavageSpecificity cleavageSpecificity)
{
if (cleavageSpecificity == CleavageSpecificity.Full)
{
return(FdrCategory.FullySpecific);
}
else if (cleavageSpecificity == CleavageSpecificity.Semi)
{
return(FdrCategory.SemiSpecific);
}
else if (cleavageSpecificity == CleavageSpecificity.None)
{
return(FdrCategory.NonSpecific);
}
else
{
throw new NotImplementedException("Cleavage specificity '" + cleavageSpecificity + "' has not been immplemented for local FDR calculations.");
}
}
private ProteaseDictionary()
: base()
{
using (StreamReader proteases = new StreamReader(Path.Combine(Path.GetDirectoryName(Environment.GetCommandLineArgs()[0]), "Configuration", "proteases.tsv")))
{
string header = proteases.ReadLine();
while (proteases.Peek() != -1)
{
string line = proteases.ReadLine();
string[] fields = line.Split('\t');
string name = fields[0];
string amino_acids_inducing_cleavage = fields[1];
string amino_acids_preventing_cleavage = fields[2];
Terminus cleavage_terminus = (Terminus)Enum.Parse(typeof(Terminus), fields[3]);
CleavageSpecificity cleavage_specificity = (CleavageSpecificity)Enum.Parse(typeof(CleavageSpecificity), fields[4]);
Protease protease = new Protease(name, amino_acids_inducing_cleavage, amino_acids_preventing_cleavage, cleavage_terminus, cleavage_specificity);
Add(protease);
}
}
}
private void SaveButton_Click(object sender, RoutedEventArgs e)
{
CleavageSpecificity searchModeType = CleavageSpecificity.Full; //classic and modern by default
if (semiSpecificSearchRadioButton.IsChecked.Value) //semi
{
searchModeType = CleavageSpecificity.Semi;
}
else if (nonSpecificSearchRadioButton.IsChecked.Value) //non
{
searchModeType = CleavageSpecificity.None;
}
//else it's the default of full
if (searchModeType != CleavageSpecificity.Full)
{
if (((Protease)proteaseComboBox.SelectedItem).Name.Contains("non-specific"))
{
searchModeType = CleavageSpecificity.None; //prevents an accidental semi attempt of a non-specific protease
if (cTerminalIons.IsChecked.Value)
{
Protease singleC = ProteaseDictionary.Dictionary["singleC"];
proteaseComboBox.SelectedItem = singleC;
}
else //we're not allowing no ion types. It must have N if it doesn't have C.
{
Protease singleN = ProteaseDictionary.Dictionary["singleN"];
proteaseComboBox.SelectedItem = singleN;
}
}
if (!addCompIonCheckBox.IsChecked.Value)
{
MessageBox.Show("Warning: Complementary ions are strongly recommended when using this algorithm.");
}
//only use N or C termini, not both
if (cTerminalIons.IsChecked.Value)
{
nTerminalIons.IsChecked = false;
}
else
{
nTerminalIons.IsChecked = true;
}
}
if (!GlobalGuiSettings.CheckTaskSettingsValidity(precursorMassToleranceTextBox.Text, productMassToleranceTextBox.Text, missedCleavagesTextBox.Text,
maxModificationIsoformsTextBox.Text, MinPeptideLengthTextBox.Text, MaxPeptideLengthTextBox.Text, maxThreadsTextBox.Text, minScoreAllowed.Text,
peakFindingToleranceTextBox.Text, histogramBinWidthTextBox.Text, DeconvolutionMaxAssumedChargeStateTextBox.Text, NumberOfPeaksToKeepPerWindowTextBox.Text,
MinimumAllowedIntensityRatioToBasePeakTexBox.Text, WindowWidthThomsonsTextBox.Text, NumberOfWindowsTextBox.Text, numberOfDatabaseSearchesTextBox.Text, MaxModNumTextBox.Text, MaxFragmentMassTextBox.Text, QValueTextBox.Text))
{
return;
}
Protease protease = (Protease)proteaseComboBox.SelectedItem;
DissociationType dissociationType = GlobalVariables.AllSupportedDissociationTypes[dissociationTypeComboBox.SelectedItem.ToString()];
CustomFragmentationWindow.Close();
FragmentationTerminus fragmentationTerminus = FragmentationTerminus.Both;
if (nTerminalIons.IsChecked.Value && !cTerminalIons.IsChecked.Value)
{
fragmentationTerminus = FragmentationTerminus.N;
}
else if (!nTerminalIons.IsChecked.Value && cTerminalIons.IsChecked.Value)
{
fragmentationTerminus = FragmentationTerminus.C;
}
else if (!nTerminalIons.IsChecked.Value && !cTerminalIons.IsChecked.Value) //why would you want this
{
fragmentationTerminus = FragmentationTerminus.None;
MessageBox.Show("Warning: No ion types were selected. MetaMorpheus will be unable to search MS/MS spectra.");
}
//else both
int maxMissedCleavages = string.IsNullOrEmpty(missedCleavagesTextBox.Text) ? int.MaxValue : (int.Parse(missedCleavagesTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture));
int minPeptideLengthValue = (int.Parse(MinPeptideLengthTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture));
int maxPeptideLengthValue = string.IsNullOrEmpty(MaxPeptideLengthTextBox.Text) ? int.MaxValue : (int.Parse(MaxPeptideLengthTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture));
int MinVariantDepth = int.Parse(MinVariantDepthTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture);
int MaxHeterozygousVariants = int.Parse(MaxHeterozygousVariantsTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture);
int maxModificationIsoformsValue = (int.Parse(maxModificationIsoformsTextBox.Text, CultureInfo.InvariantCulture));
int maxModsForPeptideValue = (int.Parse(MaxModNumTextBox.Text, CultureInfo.InvariantCulture));
InitiatorMethionineBehavior initiatorMethionineBehavior = ((InitiatorMethionineBehavior)initiatorMethionineBehaviorComboBox.SelectedIndex);
DigestionParams digestionParamsToSave = new DigestionParams(
protease: protease.Name,
maxMissedCleavages: maxMissedCleavages,
minPeptideLength: minPeptideLengthValue,
maxPeptideLength: maxPeptideLengthValue,
maxModificationIsoforms: maxModificationIsoformsValue,
initiatorMethionineBehavior: initiatorMethionineBehavior,
maxModsForPeptides: maxModsForPeptideValue,
searchModeType: searchModeType,
fragmentationTerminus: fragmentationTerminus,
generateUnlabeledProteinsForSilac: CheckBoxQuantifyUnlabeledForSilac.IsChecked.Value);
Tolerance ProductMassTolerance;
if (productMassToleranceComboBox.SelectedIndex == 0)
{
ProductMassTolerance = new AbsoluteTolerance(double.Parse(productMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
else
{
ProductMassTolerance = new PpmTolerance(double.Parse(productMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
Tolerance PrecursorMassTolerance;
if (precursorMassToleranceComboBox.SelectedIndex == 0)
{
PrecursorMassTolerance = new AbsoluteTolerance(double.Parse(precursorMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
else
{
PrecursorMassTolerance = new PpmTolerance(double.Parse(precursorMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
TheTask.SearchParameters.MaxFragmentSize = Double.Parse(MaxFragmentMassTextBox.Text, CultureInfo.InvariantCulture);
var listOfModsVariable = new List <(string, string)>();
foreach (var heh in VariableModTypeForTreeViewObservableCollection)
{
listOfModsVariable.AddRange(heh.Children.Where(b => b.Use).Select(b => (b.Parent.DisplayName, b.ModName)));
}
var listOfModsFixed = new List <(string, string)>();
foreach (var heh in FixedModTypeForTreeViewObservableCollection)
{
listOfModsFixed.AddRange(heh.Children.Where(b => b.Use).Select(b => (b.Parent.DisplayName, b.ModName)));
}
if (!GlobalGuiSettings.VariableModCheck(listOfModsVariable))
{
return;
}
bool TrimMs1Peaks = trimMs1.IsChecked.Value;
bool TrimMsMsPeaks = trimMsMs.IsChecked.Value;
int?numPeaksToKeep = null;
if (int.TryParse(NumberOfPeaksToKeepPerWindowTextBox.Text, out int numberOfPeaksToKeeep))
{
numPeaksToKeep = numberOfPeaksToKeeep;
}
double?minimumAllowedIntensityRatioToBasePeak = null;
if (double.TryParse(MinimumAllowedIntensityRatioToBasePeakTexBox.Text, out double minimumAllowedIntensityRatio))
{
minimumAllowedIntensityRatioToBasePeak = minimumAllowedIntensityRatio;
}
double?windowWidthThompsons = null;
if (double.TryParse(WindowWidthThomsonsTextBox.Text, out double windowWidth))
{
windowWidthThompsons = windowWidth;
}
int?numberOfWindows = null;
if (int.TryParse(NumberOfWindowsTextBox.Text, out int numWindows))
{
numberOfWindows = numWindows;
}
bool normalizePeaksAccrossAllWindows = normalizePeaksInWindowCheckBox.IsChecked.Value;
bool parseMaxThreadsPerFile = !maxThreadsTextBox.Text.Equals("") && (int.Parse(maxThreadsTextBox.Text) <= Environment.ProcessorCount && int.Parse(maxThreadsTextBox.Text) > 0);
CommonParameters commonParamsToSave = new CommonParameters(
taskDescriptor: OutputFileNameTextBox.Text != "" ? OutputFileNameTextBox.Text : "SearchTask",
maxThreadsToUsePerFile: parseMaxThreadsPerFile ? int.Parse(maxThreadsTextBox.Text, CultureInfo.InvariantCulture) : new CommonParameters().MaxThreadsToUsePerFile,
useDeltaScore: deltaScoreCheckBox.IsChecked.Value,
reportAllAmbiguity: allAmbiguity.IsChecked.Value,
deconvolutionMaxAssumedChargeState: int.Parse(DeconvolutionMaxAssumedChargeStateTextBox.Text, CultureInfo.InvariantCulture),
totalPartitions: int.Parse(numberOfDatabaseSearchesTextBox.Text, CultureInfo.InvariantCulture),
doPrecursorDeconvolution: deconvolutePrecursors.IsChecked.Value,
useProvidedPrecursorInfo: useProvidedPrecursor.IsChecked.Value,
scoreCutoff: double.Parse(minScoreAllowed.Text, CultureInfo.InvariantCulture),
listOfModsFixed: listOfModsFixed,
listOfModsVariable: listOfModsVariable,
dissociationType: dissociationType,
precursorMassTolerance: PrecursorMassTolerance,
productMassTolerance: ProductMassTolerance,
digestionParams: digestionParamsToSave,
trimMs1Peaks: TrimMs1Peaks,
trimMsMsPeaks: TrimMsMsPeaks,
numberOfPeaksToKeepPerWindow: numPeaksToKeep,
minimumAllowedIntensityRatioToBasePeak: minimumAllowedIntensityRatioToBasePeak,
windowWidthThomsons: windowWidthThompsons,
numberOfWindows: numberOfWindows, //maybe change this some day
normalizePeaksAccrossAllWindows: normalizePeaksAccrossAllWindows, //maybe change this some day
addCompIons: addCompIonCheckBox.IsChecked.Value,
qValueOutputFilter: QValueCheckBox.IsChecked.Value ? double.Parse(QValueTextBox.Text, CultureInfo.InvariantCulture) : 1.0,
assumeOrphanPeaksAreZ1Fragments: protease.Name != "top-down",
minVariantDepth: MinVariantDepth,
maxHeterozygousVariants: MaxHeterozygousVariants);
if (classicSearchRadioButton.IsChecked.Value)
{
TheTask.SearchParameters.SearchType = SearchType.Classic;
}
else if (modernSearchRadioButton.IsChecked.Value)
{
TheTask.SearchParameters.SearchType = SearchType.Modern;
}
else //both semi and nonspecific are termed "nonspecific", because they both contain at least one nonspecific cleavage and they share the same algorithm
{
TheTask.SearchParameters.SearchType = SearchType.NonSpecific;
}
TheTask.SearchParameters.DoParsimony = checkBoxParsimony.IsChecked.Value;
TheTask.SearchParameters.NoOneHitWonders = checkBoxNoOneHitWonders.IsChecked.Value;
TheTask.SearchParameters.DoQuantification = !checkBoxNoQuant.IsChecked.Value;
//SilacLabel deconvolution
{
if (StaticSilacLabelsObservableCollection.Count == 0)
{
TheTask.SearchParameters.SilacLabels = null;
}
else
{
List <Proteomics.SilacLabel> labelsToSave = new List <Proteomics.SilacLabel>();
foreach (SilacInfoForDataGrid info in StaticSilacLabelsObservableCollection)
{
Proteomics.SilacLabel labelToAdd = info.SilacLabel[0];
//This is needed to prevent double adding of additional labels.
//A quick test is to create a silac condition with two labels, save, reopen the task, save, and reopen again.
//Without this line, the second label will be doubled (K+8)&(R+10)&(R+10)
if (labelToAdd.AdditionalLabels != null)
{
labelToAdd.AdditionalLabels.Clear();
}
for (int infoIndex = 1; infoIndex < info.SilacLabel.Count; infoIndex++)
{
labelToAdd.AddAdditionalSilacLabel(info.SilacLabel[infoIndex]);
}
labelsToSave.Add(labelToAdd);
}
TheTask.SearchParameters.SilacLabels = labelsToSave;
}
}
TheTask.SearchParameters.Normalize = checkBoxNormalize.IsChecked.Value;
TheTask.SearchParameters.MatchBetweenRuns = checkBoxMatchBetweenRuns.IsChecked.Value;
TheTask.SearchParameters.ModPeptidesAreDifferent = modPepsAreUnique.IsChecked.Value;
TheTask.SearchParameters.QuantifyPpmTol = double.Parse(peakFindingToleranceTextBox.Text, CultureInfo.InvariantCulture);
TheTask.SearchParameters.SearchTarget = checkBoxTarget.IsChecked.Value;
TheTask.SearchParameters.WriteMzId = ckbMzId.IsChecked.Value;
TheTask.SearchParameters.WriteDecoys = writeDecoyCheckBox.IsChecked.Value;
TheTask.SearchParameters.WriteContaminants = writeContaminantCheckBox.IsChecked.Value;
//TheTask.SearchParameters.OutPepXML = ckbPepXML.IsChecked.Value;
if (checkBoxDecoy.IsChecked.Value)
{
if (radioButtonReverseDecoy.IsChecked.Value)
{
TheTask.SearchParameters.DecoyType = DecoyType.Reverse;
}
else //if (radioButtonSlideDecoy.IsChecked.Value)
{
TheTask.SearchParameters.DecoyType = DecoyType.Slide;
}
}
else
{
TheTask.SearchParameters.DecoyType = DecoyType.None;
}
if (massDiffAcceptExact.IsChecked.HasValue && massDiffAcceptExact.IsChecked.Value)
{
TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.Exact;
}
if (massDiffAccept1mm.IsChecked.HasValue && massDiffAccept1mm.IsChecked.Value)
{
TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.OneMM;
}
if (massDiffAccept2mm.IsChecked.HasValue && massDiffAccept2mm.IsChecked.Value)
{
TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.TwoMM;
}
if (massDiffAccept3mm.IsChecked.HasValue && massDiffAccept3mm.IsChecked.Value)
{
TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.ThreeMM;
}
if (massDiffAccept187.IsChecked.HasValue && massDiffAccept187.IsChecked.Value)
{
TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.ModOpen;
}
if (massDiffAcceptOpen.IsChecked.HasValue && massDiffAcceptOpen.IsChecked.Value)
{
TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.Open;
}
if (massDiffAcceptCustom.IsChecked.HasValue && massDiffAcceptCustom.IsChecked.Value)
{
try
{
MassDiffAcceptor customMassDiffAcceptor = SearchTask.GetMassDiffAcceptor(null, MassDiffAcceptorType.Custom, customkMdacTextBox.Text);
}
catch (Exception ex)
{
MessageBox.Show("Could not parse custom mass difference acceptor: " + ex.Message, "Error", MessageBoxButton.OK, MessageBoxImage.Error);
return;
}
TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.Custom;
TheTask.SearchParameters.CustomMdac = customkMdacTextBox.Text;
}
//determine if semi or nonspecific with a specific protease.
if (searchModeType == CleavageSpecificity.Semi || protease.CleavageSpecificity == CleavageSpecificity.Semi)
{
TheTask.SearchParameters.LocalFdrCategories = new List <FdrCategory> {
FdrCategory.FullySpecific, FdrCategory.SemiSpecific
};
}
else if (searchModeType == CleavageSpecificity.None && protease.CleavageSpecificity != CleavageSpecificity.None)
{
TheTask.SearchParameters.LocalFdrCategories = new List <FdrCategory> {
FdrCategory.FullySpecific, FdrCategory.SemiSpecific, FdrCategory.NonSpecific
};
}
else
{
TheTask.SearchParameters.LocalFdrCategories = new List <FdrCategory> {
FdrCategory.FullySpecific
};
}
// displays warning if classic search is enabled with an open search mode
if (TheTask.SearchParameters.SearchType == SearchType.Classic &&
(TheTask.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.ModOpen || TheTask.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.Open))
{
MessageBoxResult result = MessageBox.Show("Modern Search mode is recommended when conducting open precursor mass searches to reduce search time.\n\n" +
"Continue anyway?", "Modern search recommended", MessageBoxButton.OKCancel);
if (result == MessageBoxResult.Cancel)
{
return;
}
}
TheTask.SearchParameters.DoHistogramAnalysis = checkBoxHistogramAnalysis.IsChecked.Value;
TheTask.SearchParameters.HistogramBinTolInDaltons = double.Parse(histogramBinWidthTextBox.Text, CultureInfo.InvariantCulture);
TheTask.SearchParameters.WritePrunedDatabase = writePrunedDBCheckBox.IsChecked.Value;
SetModSelectionForPrunedDB();
TheTask.CommonParameters = commonParamsToSave;
DialogResult = true;
}
private readonly string ProteinAccession; // used to get protein object after deserialization
public InSilicoPeptide(Protein protein, DigestionParams digestionParams, int oneBasedStartResidueInProtein, int oneBasedEndResidueInProtein, CleavageSpecificity cleavageSpecificity,
string peptideDescription, int missedCleavages, Dictionary <int, Modification> allModsOneIsNterminus, int numFixedMods, string baseSeqeunce, bool isPeptideUnique) : base(protein, digestionParams, oneBasedStartResidueInProtein, oneBasedEndResidueInProtein,
cleavageSpecificity, peptideDescription, missedCleavages, allModsOneIsNterminus, numFixedMods, baseSeqeunce)
{
_allModsOneIsNterminus = allModsOneIsNterminus;
_digestionParams = digestionParams;
ProteinAccession = protein.Accession;
UniquePeptide = isPeptideUnique;
}
