SearchDB (BioFSharp.Mz)

SearchDB Module

Namespace: BioFSharp.Mz
Assembly: BioFSharp.Mz.dll

Types and nested modules

Type/Module	Description
Db
ModCombinator
Table
LookUpResult<'a>
MassMode
PeptideContainer
PeptideWithFeature<'a, 'b>
ProteinContainer
SearchDbParams
SearchInfoIsotopic
SearchModSite
SearchModType
SearchModification

Functions and values

Function or value	Description
`connectOrCreateDB sdbParams` Full Usage: `connectOrCreateDB sdbParams` Parameters: sdbParams : `SearchDbParams` Returns: `SQLiteConnection`	sdbParams : `SearchDbParams` Returns: `SQLiteConnection`
`copyDBIntoMemory cn` Full Usage: `copyDBIntoMemory cn` Parameters: cn : `SQLiteConnection` Returns: `SQLiteConnection`	cn : `SQLiteConnection` Returns: `SQLiteConnection`
`createIsotopicMod infoIsotopic` Full Usage: `createIsotopicMod infoIsotopic` Parameters: infoIsotopic : `SearchInfoIsotopic` Returns: `Modification`	infoIsotopic : `SearchInfoIsotopic` Returns: `Modification`
`createLookUpResult modSequenceId pepSequenceId mass roundedMass stringSequence bioSequence globalMod` Full Usage: `createLookUpResult modSequenceId pepSequenceId mass roundedMass stringSequence bioSequence globalMod` Parameters: modSequenceId : `int` pepSequenceId : `int` mass : `float` roundedMass : `int64` stringSequence : `string` bioSequence : `'a list` globalMod : `int` Returns: `LookUpResult<'a>`	modSequenceId : `int` pepSequenceId : `int` mass : `float` roundedMass : `int64` stringSequence : `string` bioSequence : `'a list` globalMod : `int` Returns: `LookUpResult<'a>`
`createLookUpResultBy parseAAString (modSID, pepID, realMass, roundMass, seqs, gMod)` Full Usage: `createLookUpResultBy parseAAString (modSID, pepID, realMass, roundMass, seqs, gMod)` Parameters: parseAAString : `int -> string -> 'a list` modSID : `int` pepID : `int` realMass : `float` roundMass : `int64` seqs : `string` gMod : `int` Returns: `LookUpResult<'a>`	Creates a LookUpResult out of a entry in the ModSequence table parseAAString : `int -> string -> 'a list` modSID : `int` pepID : `int` realMass : `float` roundMass : `int64` seqs : `string` gMod : `int` Returns: `LookUpResult<'a>`
`createPeptideContainer peptideId sequence missCleavageStart missCleavageEnd missCleavageCount container` Full Usage: `createPeptideContainer peptideId sequence missCleavageStart missCleavageEnd missCleavageCount container` Parameters: peptideId : `int` sequence : `string` missCleavageStart : `int` missCleavageEnd : `int` missCleavageCount : `int` container : `PeptideWithFeature<string, float> list` Returns: `PeptideContainer`	peptideId : `int` sequence : `string` missCleavageStart : `int` missCleavageEnd : `int` missCleavageCount : `int` container : `PeptideWithFeature<string, float> list` Returns: `PeptideContainer`
`createPeptideWithFeature globalMod sequence feature` Full Usage: `createPeptideWithFeature globalMod sequence feature` Parameters: globalMod : `int` sequence : `'a` feature : `'b` Returns: `PeptideWithFeature<'a, 'b>`	Creates PeptideWithMass record globalMod : `int` sequence : `'a` feature : `'b` Returns: `PeptideWithFeature<'a, 'b>`
`createProteinContainer proteinId displayID sequence container` Full Usage: `createProteinContainer proteinId displayID sequence container` Parameters: proteinId : `int` displayID : `string` sequence : `string` container : `PeptideContainer list` Returns: `ProteinContainer`	proteinId : `int` displayID : `string` sequence : `string` container : `PeptideContainer list` Returns: `ProteinContainer`
`createSearchDbParams name dbPath fastapath fastaHeaderToName protease minMissedCleavages maxMissedCleavages maxmass minPepLength maxPepLength globalMod massMode massFunction fixedMods variableMods varModThreshold` Full Usage: `createSearchDbParams name dbPath fastapath fastaHeaderToName protease minMissedCleavages maxMissedCleavages maxmass minPepLength maxPepLength globalMod massMode massFunction fixedMods variableMods varModThreshold` Parameters: name : `string` dbPath : `string` fastapath : `string` fastaHeaderToName : `string -> string` protease : `Protease` minMissedCleavages : `int` maxMissedCleavages : `int` maxmass : `float` minPepLength : `int` maxPepLength : `int` globalMod : `SearchInfoIsotopic list` massMode : `MassMode` massFunction : `IBioItem -> float` fixedMods : `SearchModification list` variableMods : `SearchModification list` varModThreshold : `int` Returns: `SearchDbParams`	name : `string` dbPath : `string` fastapath : `string` fastaHeaderToName : `string -> string` protease : `Protease` minMissedCleavages : `int` maxMissedCleavages : `int` maxmass : `float` minPepLength : `int` maxPepLength : `int` globalMod : `SearchInfoIsotopic list` massMode : `MassMode` massFunction : `IBioItem -> float` fixedMods : `SearchModification list` variableMods : `SearchModification list` varModThreshold : `int` Returns: `SearchDbParams`
`createSearchInfoIsotopic name sourceEl targetEl` Full Usage: `createSearchInfoIsotopic name sourceEl targetEl` Parameters: name : `string` sourceEl : `Element` targetEl : `Element` Returns: `SearchInfoIsotopic`	name : `string` sourceEl : `Element` targetEl : `Element` Returns: `SearchInfoIsotopic`
`createSearchModification name accession description isBiological composition site mType xModCode` Full Usage: `createSearchModification name accession description isBiological composition site mType xModCode` Parameters: name : `string` accession : `string` description : `string` isBiological : `bool` composition : `string` site : `SearchModSite list` mType : `SearchModType` xModCode : `string` Returns: `SearchModification`	name : `string` accession : `string` description : `string` isBiological : `bool` composition : `string` site : `SearchModSite list` mType : `SearchModType` xModCode : `string` Returns: `SearchModification`
`getDBConnection dbFilePath` Full Usage: `getDBConnection dbFilePath` Parameters: dbFilePath : `string` Returns: `SQLiteConnection`	Opens a new connection to the database in given path dbFilePath : `string` Returns: `SQLiteConnection`
`getDBConnectionBy sdbParams` Full Usage: `getDBConnectionBy sdbParams` Parameters: sdbParams : `SearchDbParams` Returns: `SQLiteConnection`	sdbParams : `SearchDbParams` Returns: `SQLiteConnection`
`getModBy smodi` Full Usage: `getModBy smodi` Parameters: smodi : `SearchModification` Returns: `Modification`	smodi : `SearchModification` Returns: `Modification`
`getPeptideLookUpBy sdbParams` Full Usage: `getPeptideLookUpBy sdbParams` Parameters: sdbParams : `SearchDbParams` Returns: `float -> float -> LookUpResult<AminoAcid> list`	Returns a LookUpResult list sdbParams : `SearchDbParams` Returns: `float -> float -> LookUpResult<AminoAcid> list`
`getPeptideLookUpFromFileBy sdbParams` Full Usage: `getPeptideLookUpFromFileBy sdbParams` Parameters: sdbParams : `SearchDbParams` Returns: `float -> float -> LookUpResult<AminoAcid> list`	Returns a LookUpResult list sdbParams : `SearchDbParams` Returns: `float -> float -> LookUpResult<AminoAcid> list`
`getPeptideLookUpWithMemBy calcIonSeries massFunction lookUpF lookUpCache lowerMass upperMass` Full Usage: `getPeptideLookUpWithMemBy calcIonSeries massFunction lookUpF lookUpCache lowerMass upperMass` Parameters: calcIonSeries : `'a -> AminoAcid list -> FragmentMasses` massFunction : `'a` lookUpF : `float -> float -> LookUpResult<AminoAcid> list` lookUpCache : `Cache<int64, (LookUpResult<AminoAcid> * FragmentMasses) list>` lowerMass : `float` upperMass : `float` Returns: `(LookUpResult<AminoAcid> * FragmentMasses) list`	calcIonSeries : `'a -> AminoAcid list -> FragmentMasses` massFunction : `'a` lookUpF : `float -> float -> LookUpResult<AminoAcid> list` lookUpCache : `Cache<int64, (LookUpResult<AminoAcid> * FragmentMasses) list>` lowerMass : `float` upperMass : `float` Returns: `(LookUpResult<AminoAcid> * FragmentMasses) list`
`getProteinLookUpFromFileBy sdbParams` Full Usage: `getProteinLookUpFromFileBy sdbParams` Parameters: sdbParams : `SearchDbParams` Returns: `int32 -> (int * string * string) list`	Returns a list of proteins retrieved by PepsequenceID sdbParams : `SearchDbParams` Returns: `int32 -> (int * string * string) list`
`getProteinPeptideLookUpFromFileBy memoryDB` Full Usage: `getProteinPeptideLookUpFromFileBy memoryDB` Parameters: memoryDB : `SQLiteConnection` Returns: `int32 -> (string * string) list`	Prepares a function which returns a list of protein Accessions tupled with the peptide sequence whose ID they were retrieved by memoryDB : `SQLiteConnection` Returns: `int32 -> (string * string) list`
`getSDBParamsBy filePath` Full Usage: `getSDBParamsBy filePath` Parameters: filePath : `string` Returns: `SearchDbParams`	Returns SearchDbParams of a existing database by filePath filePath : `string` Returns: `SearchDbParams`
`getSDBParamsByCn cn` Full Usage: `getSDBParamsByCn cn` Parameters: cn : `SQLiteConnection` Returns: `SearchDbParams`	Returns SearchDbParams of a existing database by SQLiteConnection cn : `SQLiteConnection` Returns: `SearchDbParams`
`getThreadSafePeptideLookUpFromFileBy cn sdbParams` Full Usage: `getThreadSafePeptideLookUpFromFileBy cn sdbParams` Parameters: cn : `SQLiteConnection` sdbParams : `SearchDbParams` Returns: `float -> float -> LookUpResult<AminoAcid> list`	Returns a LookUpResult list cn : `SQLiteConnection` sdbParams : `SearchDbParams` Returns: `float -> float -> LookUpResult<AminoAcid> list`
`getThreadSafePeptideLookUpFromFileBySequenceAndGMod cn sdbParams` Full Usage: `getThreadSafePeptideLookUpFromFileBySequenceAndGMod cn sdbParams` Parameters: cn : `SQLiteConnection` sdbParams : `SearchDbParams` Returns: `string -> int -> LookUpResult<AminoAcid>`	Returns a LookUpResult cn : `SQLiteConnection` sdbParams : `SearchDbParams` Returns: `string -> int -> LookUpResult<AminoAcid>`
`initOfModAminoAcidString isotopMods fixedAndVarMods globalMod aaStr` Full Usage: `initOfModAminoAcidString isotopMods fixedAndVarMods globalMod aaStr` Parameters: isotopMods : `SearchInfoIsotopic list` fixedAndVarMods : `SearchModification list` globalMod : `int` aaStr : `string` Returns: `BioList<AminoAcid>`	Generates amino acid sequence of one-letter-code string containing modified AminoAcids indicated by 2 lowercase digits per modification. isotopMods : `SearchInfoIsotopic list` fixedAndVarMods : `SearchModification list` globalMod : `int` aaStr : `string` Returns: `BioList<AminoAcid>`
`listOfAA` Full Usage: `listOfAA` Returns: `AminoAcid list`	needed as input if element of SearchModSite is of UnionCase \| Any Returns: `AminoAcid list`
`massFBy massMode` Full Usage: `massFBy massMode` Parameters: massMode : `MassMode` Returns: `IBioItem -> float`	massMode : `MassMode` Returns: `IBioItem -> float`
`pepLengthLimitsBy maxExpCharge (arg2, arg3)` Full Usage: `pepLengthLimitsBy maxExpCharge (arg2, arg3)` Parameters: maxExpCharge : `int` arg1 : `float` arg2 : `float` Returns: `int * int`	maxExpCharge : `int` arg1 : `float` arg2 : `float` Returns: `int * int`
`xModToMods sMds` Full Usage: `xModToMods sMds` Parameters: sMds : `SearchModification list` Returns: `Map<string, Modification>`	Creates a mapping from the XModCode of a modification to the modification itself. sMds : `SearchModification list` Returns: `Map<string, Modification>`