C# Class Coon.Compass.ProteinHoarder.ProteinHoarder

Afficher le fichier Open project: dbaileychess/Compass Class Usage Examples

Méthodes publiques

Свойство Type Description
AnnotationType AnnotationType
CsvFiles List
DuplexQuantitation bool
FastaFile string
FilterQuantInterference bool
IgnorePeptideWithMissingData bool
IncludeNonFilteredResults bool
MaxFdr double
MaxMissedCleavages int
MinPeptidesPerGroup int
MinimumPeptideLength int
ModificationsToIgnore HashSet
OutputDirectory string
PScoreCalculationMethod PScoreCalculateionMethod
ParismonyPeptidesFiltered List>.Dictionary
ParsimonyPeptides List>.Dictionary
Proteases HashSet
ProteinsPerMinute bool
QuantInterferenceCutoff double
SemiDigestion bool
SequenceCoverageMap bool
UseConservativePScore bool
UseMedianForQuantitation bool
UseOnlyCompleteSets bool
UseQuant bool

Méthodes publiques

Méthode Description
Herd ( ) : void

Main algorithm for mapping peptides to proteins, and grouping proteins into protein groups

Log ( string message ) : void
ProgressUpdate ( double percent ) : void
ProteinHoarder ( IEnumerable csvFiles, string fastaFile, string outputDirectory, int minPeptidesPerGroup = 1, int maxMissedCleavages = 3, double maxFDR = 1, AnnotationType annotationType = AnnotationType.None, bool useConservativePScore = true, bool useQuant = false, bool useMedian = false, bool duplexQuantitation = false, bool useNoiseBandCap = false, HashSet modstoignore = null, bool filterquantInterference = true, double quantInterferenceCutoff = 0.25, bool includeUnfilteredResults = false, bool ignorePeptideWithMissingData = false, bool semiDigestion = false, bool proteinPerMinute = false, bool sequenceCoverageMap = false ) : System

Méthodes protégées

Méthode Description
OnUpdateLog ( StatusEventArgs e ) : void
OnUpdateProgress ( ProgressEventArgs e ) : void

Private Methods

Méthode Description
CleanUp ( ) : void

Free memory of data structures used and tell the main form to reactivate

ExtraInfo ( List proteinGroups, string outputDirectory ) : void
GetAllUniquePeptides ( IEnumerable csvFiles ) : Peptide>.Dictionary

Loads all the unique peptide sequences (L / I ambiguous) from the OMSSA csv files supplied. Keeps track of all the psms for those peptides as well.

GetMappedProteinsFromFasta ( string fastaFile, Peptide>.Dictionary uniquePeptides, IList proteases, bool semiDigestion = false ) : List

Performs an in silico digestion of all the proteins found within the fasta file.

GroupExperiments ( IEnumerable csvFiles, bool useQuant ) : ExperimentGroup>.Dictionary

Maps the peptide to all the protein groups that it is apart of

GroupProteins ( List proteins, bool printMessages = true ) : List

Groups proteins into groups based on the peptides in the proteins. Combines Proteins if they contain all the same peptide sequences (Indistinquishable) and removes groups that can be made up by other groups in its entirety (Subsumable). Lastly, it filters for false discovery.

WriteGroups ( ExperimentGroup>.Dictionary expgroups, string outputDirectory ) : void
WritePeptides ( ExperimentGroup>.Dictionary expgroups, string outputDirectory ) : void
WriteProteinsPerMinute ( List allPeptides, List proteins, string outputDirectory ) : void
WriteSequenceMaps ( List proteinGroups, string outputDirectory ) : void
WriteSummary ( ExperimentGroup>.Dictionary expgroups, string outputDirectory ) : void

Method Details

Herd() public méthode

Main algorithm for mapping peptides to proteins, and grouping proteins into protein groups
public Herd ( ) : void
Résultat void

Log() public méthode

public Log ( string message ) : void
message string
Résultat void

OnUpdateLog() protected méthode

protected OnUpdateLog ( StatusEventArgs e ) : void
e StatusEventArgs
Résultat void

OnUpdateProgress() protected méthode

protected OnUpdateProgress ( ProgressEventArgs e ) : void
e ProgressEventArgs
Résultat void

ProgressUpdate() public méthode

public ProgressUpdate ( double percent ) : void
percent double
Résultat void

ProteinHoarder() public méthode

public ProteinHoarder ( IEnumerable csvFiles, string fastaFile, string outputDirectory, int minPeptidesPerGroup = 1, int maxMissedCleavages = 3, double maxFDR = 1, AnnotationType annotationType = AnnotationType.None, bool useConservativePScore = true, bool useQuant = false, bool useMedian = false, bool duplexQuantitation = false, bool useNoiseBandCap = false, HashSet modstoignore = null, bool filterquantInterference = true, double quantInterferenceCutoff = 0.25, bool includeUnfilteredResults = false, bool ignorePeptideWithMissingData = false, bool semiDigestion = false, bool proteinPerMinute = false, bool sequenceCoverageMap = false ) : System
csvFiles IEnumerable
fastaFile string
outputDirectory string
minPeptidesPerGroup int
maxMissedCleavages int
maxFDR double
annotationType AnnotationType
useConservativePScore bool
useQuant bool
useMedian bool
duplexQuantitation bool
useNoiseBandCap bool
modstoignore HashSet
filterquantInterference bool
quantInterferenceCutoff double
includeUnfilteredResults bool
ignorePeptideWithMissingData bool
semiDigestion bool
proteinPerMinute bool
sequenceCoverageMap bool
Résultat System

Property Details

AnnotationType public_oe static_oe property

public static AnnotationType AnnotationType
Résultat AnnotationType

CsvFiles public_oe property

public List CsvFiles
Résultat List

DuplexQuantitation public_oe static_oe property

public static bool DuplexQuantitation
Résultat bool

FastaFile public_oe property

public string FastaFile
Résultat string

FilterQuantInterference public_oe static_oe property

public static bool FilterQuantInterference
Résultat bool

IgnorePeptideWithMissingData public_oe static_oe property

public static bool IgnorePeptideWithMissingData
Résultat bool

IncludeNonFilteredResults public_oe static_oe property

public static bool IncludeNonFilteredResults
Résultat bool

MaxFdr public_oe property

public double MaxFdr
Résultat double

MaxMissedCleavages public_oe property

public int MaxMissedCleavages
Résultat int

MinPeptidesPerGroup public_oe property

public int MinPeptidesPerGroup
Résultat int

MinimumPeptideLength public_oe property

public int MinimumPeptideLength
Résultat int

ModificationsToIgnore public_oe property

public HashSet ModificationsToIgnore
Résultat HashSet

OutputDirectory public_oe property

public string OutputDirectory
Résultat string

PScoreCalculationMethod public_oe static_oe property

public static PScoreCalculateionMethod PScoreCalculationMethod
Résultat PScoreCalculateionMethod

ParismonyPeptidesFiltered public_oe static_oe property

public static Dictionary> ParismonyPeptidesFiltered
Résultat List>.Dictionary

ParsimonyPeptides public_oe static_oe property

public static Dictionary> ParsimonyPeptides
Résultat List>.Dictionary

Proteases public_oe property

public HashSet Proteases
Résultat HashSet

ProteinsPerMinute public_oe static_oe property

public static bool ProteinsPerMinute
Résultat bool

QuantInterferenceCutoff public_oe static_oe property

public static double QuantInterferenceCutoff
Résultat double

SemiDigestion public_oe static_oe property

public static bool SemiDigestion
Résultat bool

SequenceCoverageMap public_oe static_oe property

public static bool SequenceCoverageMap
Résultat bool

UseConservativePScore public_oe static_oe property

public static bool UseConservativePScore
Résultat bool

UseMedianForQuantitation public_oe static_oe property

public static bool UseMedianForQuantitation
Résultat bool

UseOnlyCompleteSets public_oe static_oe property

public static bool UseOnlyCompleteSets
Résultat bool

UseQuant public_oe static_oe property

public static bool UseQuant
Résultat bool