Index

A

aaComp (in module maspy.constants) aaMass (in module maspy.constants) aaModComp (in module maspy.constants) aaModMass (in module maspy.constants) activation (maspy.core.MzmlPrecursor attribute) addLabel() (maspy.sil.LabelDescriptor method) addMsrunContainers() (in module maspy.core) addSiInfo() (maspy.core.SiiContainer method) addSiiToContainer() (in module maspy.reader)

addSpecfile() (maspy.core.FiContainer method) (maspy.core.MsrunContainer method) (maspy.core.SiiContainer method) applyArrayFilters() (in module maspy.auxiliary) applySiiQcValidation() (in module maspy.reader) applySiiRanking() (in module maspy.reader) arrayInfo (maspy.core.Ci attribute) (maspy.core.Sai attribute) arrays (maspy.core.Ci attribute) (maspy.core.Sai attribute) attrib (maspy.core.Ci attribute) attributes (maspy.core.Smi attribute) averagingData() (in module maspy.auxiliary)

B

binaryDataArrayTypes (in module maspy.xml)

C

calcDeviationLimits() (in module maspy.auxiliary) calcMassFromMz() (in module maspy.peptidemethods) calcMhFromMz() (in module maspy.peptidemethods) calcMz() (maspy.core.SiiContainer method) calcMzFromMass() (in module maspy.peptidemethods) calcMzFromMh() (in module maspy.peptidemethods) calcPeptideMass() (in module maspy.peptidemethods) calculateCoverage() (maspy.proteindb.ProteinDatabase method)

Ci (class in maspy.core) ciFromXml() (in module maspy.reader) clearParsedElements() (in module maspy.xml) clearTag() (in module maspy.xml) COMPOSITION (in module maspy.constants) convertMzml() (in module maspy.reader) corrArray() (maspy.auxiliary.DataFit method) cvParamFromDict() (in module maspy.xml)

D

DataFit (class in maspy.auxiliary) dataProcessingRef (maspy.core.Ci attribute) decodeBinaryData() (in module maspy.xml)

default() (maspy.auxiliary.MaspyJsonEncoder method) defaultFetchSiAttrFromSmi() (in module maspy.reader) digestInSilico() (in module maspy.peptidemethods)

E

encodeBinaryData() (in module maspy.xml) expasy_rules (in module maspy.constants) expectedLabelPosition() (in module maspy.sil)

extractBinaries() (in module maspy.xml) extractParams() (in module maspy.xml)

F

factorial (in module maspy.auxiliary) fastaParseSgd() (in module maspy.proteindb) fetchParentIon() (in module maspy.reader) fetchScanInfo() (in module maspy.reader) fetchSpectrumInfo() (in module maspy.reader) Fi (class in maspy.core)

FiContainer (class in maspy.core) FileFormatError findAllSubstrings() (in module maspy.auxiliary) findBinaryDataType() (in module maspy.xml) findParam() (in module maspy.xml)

G

generateSplines() (maspy.auxiliary.DataFit method) getArrays() (maspy.core.FiContainer method) (maspy.core.MsrunContainer method) (maspy.core.SiiContainer method) getItem() (maspy.core.FiContainer method) (maspy.core.MsrunContainer method)

getItems() (maspy.core.FiContainer method) (maspy.core.MsrunContainer method) (maspy.core.SiiContainer method) getParam() (in module maspy.xml) getValidItem() (maspy.core.SiiContainer method)

I

id (maspy.core.Ci attribute) (maspy.core.Sai attribute) (maspy.core.Smi attribute) importMsgfMzidResults() (in module maspy.reader) importMzml() (in module maspy.reader) importPeptideFeatures() (in module maspy.reader) importPercolatorResults() (in module maspy.reader)

importProteinDatabase() (in module maspy.proteindb) interpretBitEncoding() (in module maspy.xml) isolationWindow (maspy.core.MzmlPrecursor attribute) (maspy.core.MzmlProduct attribute) isUnique (maspy.proteindb.PeptideSequence attribute)

J

joinpath() (in module maspy.auxiliary)

jsonHook() (maspy.core.Ci static method) (maspy.core.Fi static method) (maspy.core.Sai static method) (maspy.core.Si static method) (maspy.core.Sii static method) (maspy.core.Smi static method) (maspy.proteindb.PeptideSequence static method) (maspy.proteindb.ProteinSequence static method)

L

LabelDescriptor (class in maspy.sil) length() (maspy.proteindb.PeptideSequence method) (maspy.proteindb.ProteinSequence method) listFiletypes() (in module maspy.auxiliary) load() (maspy.core.FiContainer method) (maspy.core.MsrunContainer method) (maspy.core.SiiContainer method) (maspy.proteindb.ProteinDatabase class method)

loadBinaryItemContainer() (in module maspy.auxiliary) loadMetadata() (maspy.xml.MzmlReader method) log10factorial (in module maspy.auxiliary)

M

maspy (module) maspy.auxiliary (module) maspy.constants (module) maspy.core (module) maspy.errors (module) maspy.featuremethods (module) maspy.mit_stats (module) maspy.peptidemethods (module) maspy.proteindb (module) maspy.reader (module) maspy.sil (module) maspy.writer (module) maspy.xml (module)

MaspyJsonEncoder (class in maspy.auxiliary) mass() (maspy.proteindb.PeptideSequence method) (maspy.proteindb.ProteinSequence method) matchingFilePaths() (in module maspy.auxiliary) matchToFeatures() (in module maspy.featuremethods) Memoize (class in maspy.auxiliary) missedCleavage (maspy.proteindb.PeptideSequence attribute) modAminoacidsFromLabelInfo() (in module maspy.sil) modSymbolsFromLabelInfo() (in module maspy.sil) MsrunContainer (class in maspy.core) MzmlPrecursor (class in maspy.core) MzmlProduct (class in maspy.core) MzmlReader (class in maspy.xml) MzmlScan (class in maspy.core)

N

next() (maspy.xml.MzmlReader method)

O

open() (maspy.auxiliary.PartiallySafeReplace method)

openSafeReplace() (in module maspy.auxiliary)

P

params (maspy.core.Ci attribute) (maspy.core.MzmlScan attribute) (maspy.core.Smi attribute) parseSpectra() (maspy.xml.MzmlReader method) PartiallySafeReplace (class in maspy.auxiliary) PeptideSequence (class in maspy.proteindb) precursor (maspy.core.Ci attribute) precursorList (maspy.core.Smi attribute) prepareSiiImport() (in module maspy.reader)

processInput() (maspy.auxiliary.DataFit method) product (maspy.core.Ci attribute) productList (maspy.core.Smi attribute) ProteinDatabase (class in maspy.proteindb) proteinPositions (maspy.proteindb.PeptideSequence attribute) proteins (maspy.proteindb.PeptideSequence attribute) ProteinSequence (class in maspy.proteindb)

R

readMsgfMzidResults() (in module maspy.reader) readPercolatorResults() (in module maspy.reader) recClearTag() (in module maspy.xml) recCopyElement() (in module maspy.xml) recRemoveTreeFormating() (in module maspy.xml) refParamGroupFromDict() (in module maspy.xml) removeAnnotation() (maspy.core.FiContainer method) removeData() (maspy.core.MsrunContainer method) removeModifications() (in module maspy.peptidemethods)

removeSpecfile() (maspy.core.FiContainer method) (maspy.core.MsrunContainer method) (maspy.core.SiiContainer method) returnArrayFilters() (in module maspy.auxiliary) returnLabelState() (in module maspy.sil) returnLabelStateMassDifferences() (in module maspy.sil) returnModPositions() (in module maspy.peptidemethods) returnSplineList() (in module maspy.auxiliary) rtCalibration() (in module maspy.featuremethods) runningMean() (in module maspy.mit_stats) runningMedian() (in module maspy.mit_stats)

S

Sai (class in maspy.core) save() (maspy.core.FiContainer method) (maspy.core.MsrunContainer method) (maspy.core.SiiContainer method) (maspy.proteindb.ProteinDatabase method) scanList (maspy.core.Smi attribute) scanListParams (maspy.core.Smi attribute) scanWindowList (maspy.core.MzmlScan attribute) searchFileLocation() (in module maspy.auxiliary) selectedIonList (maspy.core.MzmlPrecursor attribute) sequence (maspy.proteindb.PeptideSequence attribute) setPath() (maspy.core.FiContainer method) (maspy.core.MsrunContainer method) (maspy.core.SiiContainer method)

Si (class in maspy.core) Sii (class in maspy.core) SiiContainer (class in maspy.core) Smi (class in maspy.core) smiFromXmlSpectrum() (in module maspy.reader) specfile (maspy.core.Ci attribute) (maspy.core.Sai attribute) (maspy.core.Smi attribute) spectrumRef (maspy.core.MzmlPrecursor attribute) sublistReader() (in module maspy.xml)

T

tolerantArrayMatching() (in module maspy.auxiliary)

toList() (in module maspy.auxiliary)

U

userParamFromDict() (in module maspy.xml)

W

writeBinaryItemContainer() (in module maspy.auxiliary) writeJsonZipfile() (in module maspy.auxiliary)

writeMzml() (in module maspy.writer)

X

xmlAddParams() (in module maspy.xml) xmlChromatogramFromCi() (in module maspy.writer) xmlGenBinaryDataArrayList() (in module maspy.writer) xmlGenPrecursorList() (in module maspy.writer)

xmlGenProductList() (in module maspy.writer) xmlGenScanList() (in module maspy.writer) xmlSpectrumFromSmi() (in module maspy.writer)