Index

Symbols

--debug-logging mzspeclib command line option --format mzspeclib-convert command line option --header-file mzspeclib-convert command line option --input-format mzspeclib-convert command line option mzspeclib-describe command line option mzspeclib-index command line option mzspeclib-validate command line option --library-attribute mzspeclib-convert command line option --log-file mzspeclib command line option --profile mzspeclib-validate command line option

-d mzspeclib command line option -f mzspeclib-convert command line option -i mzspeclib-convert command line option mzspeclib-describe command line option mzspeclib-index command line option mzspeclib-validate command line option -K mzspeclib-convert command line option -k mzspeclib-convert command line option -l mzspeclib command line option -p mzspeclib-validate command line option

A

add() (mzspeclib.index.IndexBase method) (mzspeclib.index.MemoryIndex method) (mzspeclib.index.SQLIndex method) add_analyte() (mzspeclib.Interpretation method) (mzspeclib.Spectrum method) add_attribute() (mzspeclib.attributes.AttributeManager method) (mzspeclib.SpectrumLibrary method) add_attribute_group() (mzspeclib.attributes.AttributeManager method) add_cluster() (mzspeclib.index.IndexBase method) (mzspeclib.index.MemoryIndex method) (mzspeclib.index.SQLIndex method) add_interpretation() (mzspeclib.InterpretationCollection method) add_member_interpretation() (mzspeclib.Interpretation method) Analyte (class in mzspeclib) analyte_attribute_sets (mzspeclib.SpectrumLibrary property) analytes (mzspeclib.Interpretation attribute) (mzspeclib.InterpretationCollection property) append() (mzspeclib.backends.InMemorySpectrumLibrary method)

append_cluster() (mzspeclib.backends.InMemorySpectrumLibrary method) attribute (mzspeclib.attributes.AttributeManagedProperty attribute) AttributedEntity (class in mzspeclib.attributes) AttributeFacet (class in mzspeclib.attributes) AttributeGroupFacet (class in mzspeclib.attributes) AttributeListManagedProperty (class in mzspeclib.attributes) AttributeManagedProperty (class in mzspeclib.attributes) AttributeManager (class in mzspeclib.attributes) AttributeProxy (in module mzspeclib.attributes) AttributeProxyMeta (class in mzspeclib.attributes) attributes (mzspeclib.attributes.AttributeListManagedProperty attribute) (mzspeclib.SpectrumLibrary property) (mzspeclib.validate.ScopedSemanticRule attribute) AttributeSemanticPredicate (class in mzspeclib.validate) AttributeSemanticRule (class in mzspeclib.validate) AttributeSet (class in mzspeclib.attributes) AttributeSetRef (class in mzspeclib.attributes) AttributeSetTypes (class in mzspeclib.backends)

B

backend (mzspeclib.SpectrumLibrary attribute)

BibliospecSpectralLibrary (class in mzspeclib.backends)

C

chain() (mzspeclib.validate.ValidatorBase method) (mzspeclib.validate.ValidatorChain method) charge (mzspeclib.Analyte property) check_attributes() (mzspeclib.validate.ControlledVocabularyAttributeValidator method) (mzspeclib.validate.ValidatorBase method) (mzspeclib.validate.ValidatorChain method) check_names_unique() (mzspeclib.index.IndexBase method) clear() (mzspeclib.attributes.AttributeManager method) close() (mzspeclib.backends.JSONSpectralLibraryWriter method) (mzspeclib.backends.MSPSpectralLibraryWriter method) (mzspeclib.backends.SpectralLibraryWriterBase method) (mzspeclib.backends.TextSpectralLibraryWriter method) cluster_attribute_sets (mzspeclib.SpectrumLibrary property) cluster_records (mzspeclib.index.MemoryIndex attribute) combination_logic (mzspeclib.validate.ScopedSemanticRule attribute)

CombinationLogic (class in mzspeclib.validate) commit() (mzspeclib.index.IndexBase method) (mzspeclib.index.MemoryIndex method) (mzspeclib.index.SQLIndex method) compact_interpretation (mzspeclib.backends.TextSpectralLibraryWriter attribute) condition (mzspeclib.validate.ScopedSemanticRule attribute) ControlledVocabularyAttributeValidator (class in mzspeclib.validate) copy() (mzspeclib.attributes.AttributeManager method) create_index() (mzspeclib.backends.DIANNTSVSpectralLibrary method) (mzspeclib.backends.InMemorySpectrumLibrary method) (mzspeclib.backends.JSONSpectralLibrary method) (mzspeclib.backends.MSPSpectralLibrary method) (mzspeclib.backends.SpectralLibraryBackendBase method) (mzspeclib.backends.SpectronautTSVSpectralLibrary method) (mzspeclib.backends.TextSpectralLibrary method)

D

DIANNTSVSpectralLibrary (class in mzspeclib.backends)

DiaNNTSVSpectralLibrary (in module mzspeclib.backends)

E

EncyclopediaSpectralLibrary (class in mzspeclib.backends)

exists() (mzspeclib.index.IndexBase class method) (mzspeclib.index.SQLIndex class method)

F

filename (mzspeclib.backends.SpectralLibraryWriterBase attribute) (mzspeclib.SpectrumLibrary attribute) (mzspeclib.SpectrumLibrary property) find_spectra() (mzspeclib.SpectrumLibrary method) format (mzspeclib.SpectrumLibrary attribute)

FormatInferenceFailure from_backend() (mzspeclib.SpectrumLibrary class method) from_filename() (mzspeclib.index.IndexBase class method) (mzspeclib.index.MemoryIndex class method) (mzspeclib.index.SQLIndex class method)

G

get_analyte() (mzspeclib.Interpretation method) (mzspeclib.Spectrum method) get_attribute() (mzspeclib.attributes.AttributeManager method) (mzspeclib.SpectrumLibrary method) get_attribute_group() (mzspeclib.attributes.AttributeManager method) get_by_name() (mzspeclib.attributes.AttributeManager method) get_cluster() (mzspeclib.backends.InMemorySpectrumLibrary method) (mzspeclib.backends.JSONSpectralLibrary method) (mzspeclib.backends.SpectralLibraryBackendBase method) (mzspeclib.backends.TextSpectralLibrary method) (mzspeclib.SpectrumLibrary method) get_interpretation() (mzspeclib.InterpretationCollection method) get_member_interpretation() (mzspeclib.Interpretation method) get_next_group_identifier() (mzspeclib.attributes.AttributeManager method) get_object_validator_for() (in module mzspeclib.validate) get_spectrum() (mzspeclib.backends.BibliospecSpectralLibrary method) (mzspeclib.backends.EncyclopediaSpectralLibrary method) (mzspeclib.backends.InMemorySpectrumLibrary method) (mzspeclib.backends.JSONSpectralLibrary method) (mzspeclib.backends.MSPSpectralLibrary method) (mzspeclib.backends.SpectralLibraryBackendBase method) (mzspeclib.backends.TextSpectralLibrary method) (mzspeclib.SpectrumLibrary method)

get_validator_for() (in module mzspeclib.validate) guess_from_filename() (mzspeclib.backends.InMemorySpectrumLibrary class method) (mzspeclib.backends.JSONSpectralLibrary class method) (mzspeclib.backends.SpectralLibraryBackendBase class method) guess_from_header() (mzspeclib.backends.MSPSpectralLibrary class method) (mzspeclib.backends.SpectralLibraryBackendBase class method) (mzspeclib.backends.SPTXTSpectralLibrary class method) (mzspeclib.backends.TextSpectralLibrary class method) guess_implementation() (in module mzspeclib.backends) (mzspeclib.backends.SpectralLibraryBackendBase class method)

H

has_analyte() (mzspeclib.Interpretation method) has_attribute() (mzspeclib.attributes.AttributeManager method) (mzspeclib.SpectrumLibrary method)

has_index_preference() (mzspeclib.backends.BibliospecSpectralLibrary class method) (mzspeclib.backends.EncyclopediaSpectralLibrary class method) (mzspeclib.backends.SpectralLibraryBackendBase class method)

I

id (mzspeclib.Interpretation attribute) (mzspeclib.validate.ScopedObjectRuleBase attribute) (mzspeclib.validate.ScopedSemanticRule attribute) IdentifiedAttributeManager (class in mzspeclib.attributes) identifier (mzspeclib.SpectrumLibrary attribute) (mzspeclib.SpectrumLibrary property) IndexBase (class in mzspeclib.index) InMemorySpectrumLibrary (class in mzspeclib.backends) INPATH mzspeclib-convert command line option mzspeclib-index command line option mzspeclib-validate command line option

Interpretation (class in mzspeclib) interpretation_attribute_sets (mzspeclib.SpectrumLibrary property) InterpretationCollection (class in mzspeclib) InterpretationMember (class in mzspeclib) items() (mzspeclib.InterpretationCollection method) iter_clusters() (mzspeclib.index.IndexBase method) (mzspeclib.index.MemoryIndex method) (mzspeclib.index.SQLIndex method) iter_spectra() (mzspeclib.index.IndexBase method) (mzspeclib.index.MemoryIndex method) (mzspeclib.index.SQLIndex method)

J

JSONSpectralLibrary (class in mzspeclib.backends)

JSONSpectralLibraryWriter (class in mzspeclib.backends)

K

keys() (mzspeclib.InterpretationCollection method)

L

LibraryFormatVersionFirstRule (class in mzspeclib.validate)

LibraryIterator (class in mzspeclib.backends) load_default_validator() (in module mzspeclib.validate)

M

member_interpretations (mzspeclib.Interpretation attribute) MemoryIndex (class in mzspeclib.index) metadata (mzspeclib.index.MemoryIndex attribute) modification_parser (mzspeclib.backends.MSPSpectralLibrary attribute) module mzspeclib mzspeclib.attributes mzspeclib.backends mzspeclib.index mzspeclib.validate MSPSpectralLibrary (class in mzspeclib.backends) MSPSpectralLibraryWriter (class in mzspeclib.backends) multiple (mzspeclib.attributes.AttributeManagedProperty attribute) mzspeclib module mzspeclib command line option --debug-logging --log-file -d -l mzspeclib-convert command line option --format --header-file --input-format --library-attribute -f -i -k -K INPATH OUTPATH

mzspeclib-describe command line option --input-format -i PATH mzspeclib-index command line option --input-format -i INPATH mzspeclib-validate command line option --input-format --profile -i -p INPATH mzspeclib.attributes module mzspeclib.backends module mzspeclib.index module mzspeclib.validate module

N

notes (mzspeclib.validate.ScopedSemanticRule attribute)

O

offset_for() (mzspeclib.index.IndexBase method) offset_for_cluster() (mzspeclib.index.IndexBase method)

OUTPATH mzspeclib-convert command line option

P

PATH mzspeclib-describe command line option path (mzspeclib.validate.ScopedObjectRuleBase attribute) (mzspeclib.validate.ScopedSemanticRule attribute)

peptide (mzspeclib.Analyte property) precursor_charge (mzspeclib.Spectrum property)

R

read() (mzspeclib.backends.BibliospecSpectralLibrary method) (mzspeclib.backends.EncyclopediaSpectralLibrary method) (mzspeclib.backends.InMemorySpectrumLibrary method) (mzspeclib.backends.JSONSpectralLibrary method) (mzspeclib.backends.SpectralLibraryBackendBase method) (mzspeclib.SpectrumLibrary method) read_header() (mzspeclib.backends.BibliospecSpectralLibrary method) (mzspeclib.backends.DIANNTSVSpectralLibrary method) (mzspeclib.backends.EncyclopediaSpectralLibrary method) (mzspeclib.backends.InMemorySpectrumLibrary method) (mzspeclib.backends.JSONSpectralLibrary method) (mzspeclib.backends.MSPSpectralLibrary method) (mzspeclib.backends.SpectralLibraryBackendBase method) (mzspeclib.backends.SpectronautTSVSpectralLibrary method) (mzspeclib.backends.SPTXTSpectralLibrary method) (mzspeclib.backends.TextSpectralLibrary method) (mzspeclib.SpectrumLibrary method)

record_for() (mzspeclib.index.IndexBase method) record_for_cluster() (mzspeclib.index.IndexBase method) records (mzspeclib.index.MemoryIndex attribute) remove_analyte() (mzspeclib.Interpretation method) (mzspeclib.Spectrum method) remove_attribute() (mzspeclib.attributes.AttributeManager method) (mzspeclib.SpectrumLibrary method) remove_member_interpretation() (mzspeclib.Interpretation method) requirement_level (mzspeclib.validate.ScopedObjectRuleBase attribute) (mzspeclib.validate.ScopedSemanticRule attribute) RequirementLevel (class in mzspeclib.validate) ROAttributeProxy (class in mzspeclib.attributes) RuleSet (class in mzspeclib.validate) RuleValidator (class in mzspeclib.validate)

S

ScopedObjectRuleBase (class in mzspeclib.validate) ScopedSemanticRule (class in mzspeclib.validate) search() (mzspeclib.index.IndexBase method) (mzspeclib.index.MemoryIndex method) (mzspeclib.index.SQLIndex method) search_clusters() (mzspeclib.index.IndexBase method) (mzspeclib.index.MemoryIndex method) (mzspeclib.index.SQLIndex method) session (mzspeclib.index.SQLIndex attribute) set_analyte() (mzspeclib.Interpretation method) set_interpretation() (mzspeclib.InterpretationCollection method) SpectralLibraryBackendBase (class in mzspeclib.backends)

SpectralLibraryWriterBase (class in mzspeclib.backends) SpectronautTSVSpectralLibrary (class in mzspeclib.backends) Spectrum (class in mzspeclib) spectrum_attribute_sets (mzspeclib.SpectrumLibrary property) SpectrumLibrary (class in mzspeclib) SpectrumPeakAnnotationRule (class in mzspeclib.validate) SPTXTSpectralLibrary (class in mzspeclib.backends) SQLIndex (class in mzspeclib.index) summarize_parsing_errors() (mzspeclib.backends.MSPSpectralLibrary method) (mzspeclib.backends.SpectralLibraryBackendBase method) (mzspeclib.SpectrumLibrary method) supported_file_extensions() (mzspeclib.SpectrumLibrary static method)

T

TextSpectralLibrary (class in mzspeclib.backends)

TextSpectralLibraryWriter (class in mzspeclib.backends)

U

unknown_attributes (mzspeclib.backends.MSPSpectralLibrary attribute)

V

validate() (mzspeclib.Interpretation method) ValidationError (class in mzspeclib.validate) ValidationWarning

ValidatorBase (class in mzspeclib.validate) ValidatorChain (class in mzspeclib.validate) values() (mzspeclib.InterpretationCollection method) version (mzspeclib.backends.TextSpectralLibraryWriter attribute)

W

write() (mzspeclib.Spectrum method) (mzspeclib.SpectrumLibrary method) write_cluster() (mzspeclib.backends.JSONSpectralLibraryWriter method) (mzspeclib.backends.SpectralLibraryWriterBase method) (mzspeclib.backends.TextSpectralLibraryWriter method) write_header() (mzspeclib.backends.JSONSpectralLibraryWriter method) (mzspeclib.backends.TextSpectralLibraryWriter method)

write_library() (mzspeclib.backends.JSONSpectralLibraryWriter method) (mzspeclib.backends.SpectralLibraryWriterBase method) write_spectrum() (mzspeclib.backends.JSONSpectralLibraryWriter method) (mzspeclib.backends.MSPSpectralLibraryWriter method) (mzspeclib.backends.SpectralLibraryWriterBase method) (mzspeclib.backends.TextSpectralLibraryWriter method)