Index

_

__init__() (expectmine.io.adapters.cli_io_adapter.CliIoAdapter method) (expectmine.io.adapters.dict_io_adapter.DictIoAdapter method) (expectmine.io.base_io.BaseIo method) (expectmine.io.base_io_adapter.BaseIoAdapter method) (expectmine.io.io.cli_io.CliIo method) (expectmine.io.io.dict_io.DictIo method) (expectmine.logger.adapters.cli_logger_adapter.CliLoggerAdapter method) (expectmine.logger.base_logger.BaseLogger method) (expectmine.logger.base_logger_adapter.BaseLoggerAdapter method) (expectmine.logger.loggers.cli_logger.CliLogger method) (expectmine.steps.base_step.BaseStep method) (expectmine.storage.adapters.in_memory_adapter.InMemoryStoreAdapter method) (expectmine.storage.adapters.sqlite3_adapter.Sqlite3StoreAdapter method) (expectmine.storage.base_storage.BaseStore method) (expectmine.storage.base_storage_adapter.BaseStoreAdapter method) (expectmine.storage.stores.in_memory_store.InMemoryStore method) (expectmine.storage.stores.sqlite3_store.Sqlite3Store method)

A

ALL (expectmine.logger.base_logger.LogLevel attribute) all_answers() (expectmine.io.base_io.BaseIo method) (expectmine.io.io.cli_io.CliIo method) (expectmine.io.io.dict_io.DictIo method)

B

BaseIo (class in expectmine.io.base_io) BaseIoAdapter (class in expectmine.io.base_io_adapter) BaseLogger (class in expectmine.logger.base_logger) BaseLoggerAdapter (class in expectmine.logger.base_logger_adapter) BaseStep (class in expectmine.steps.base_step)

BaseStore (class in expectmine.storage.base_storage) BaseStoreAdapter (class in expectmine.storage.base_storage_adapter) boolean() (expectmine.io.base_io.BaseIo method) (expectmine.io.io.cli_io.CliIo method) (expectmine.io.io.dict_io.DictIo method)

C

can_run() (expectmine.steps.base_step.BaseStep class method) (expectmine.steps.steps.mzmine3.mzmine3.MZmine3 class method) (expectmine.steps.steps.shrink_mgf.ShrinkMgf class method) (expectmine.steps.steps.sirius_fingerprint.SiriusFingerprint class method) citation_and_disclaimer() (expectmine.steps.base_step.BaseStep class method) (expectmine.steps.steps.mzmine3.mzmine3.MZmine3 class method) (expectmine.steps.steps.shrink_mgf.ShrinkMgf class method) (expectmine.steps.steps.sirius_fingerprint.SiriusFingerprint class method)

CliIo (class in expectmine.io.io.cli_io) CliIoAdapter (class in expectmine.io.adapters.cli_io_adapter) CliLogger (class in expectmine.logger.loggers.cli_logger) CliLoggerAdapter (class in expectmine.logger.adapters.cli_logger_adapter)

D

DEBUG (expectmine.logger.base_logger.LogLevel attribute) debug() (expectmine.logger.base_logger.BaseLogger method) (expectmine.logger.loggers.cli_logger.CliLogger method) delete() (expectmine.storage.base_storage.BaseStore method) (expectmine.storage.stores.in_memory_store.InMemoryStore method) (expectmine.storage.stores.sqlite3_store.Sqlite3Store method)

DictIo (class in expectmine.io.io.dict_io) DictIoAdapter (class in expectmine.io.adapters.dict_io_adapter)

E

ERROR (expectmine.logger.base_logger.LogLevel attribute) error() (expectmine.logger.base_logger.BaseLogger method) (expectmine.logger.loggers.cli_logger.CliLogger method) exists() (expectmine.storage.base_storage.BaseStore method) (expectmine.storage.stores.in_memory_store.InMemoryStore method) (expectmine.storage.stores.sqlite3_store.Sqlite3Store method) expectmine.io.adapters.cli_io_adapter module expectmine.io.adapters.dict_io_adapter module expectmine.io.base_io module expectmine.io.base_io_adapter module expectmine.io.io.cli_io module expectmine.io.io.dict_io module expectmine.io.utils module expectmine.logger.adapters.cli_logger_adapter module expectmine.logger.base_logger module expectmine.logger.base_logger_adapter module expectmine.logger.loggers.cli_logger module

expectmine.logger.utils module expectmine.pipeline.utils module expectmine.steps.base_step module expectmine.steps.steps.mzmine3.mzmine3 module expectmine.steps.steps.shrink_mgf module expectmine.steps.steps.sirius_fingerprint module expectmine.storage.adapters.in_memory_adapter module expectmine.storage.adapters.sqlite3_adapter module expectmine.storage.base_storage module expectmine.storage.base_storage_adapter module expectmine.storage.stores.in_memory_store module expectmine.storage.stores.sqlite3_store module expectmine.storage.utils module expectmine.utils.cmd module

F

filepath() (expectmine.io.base_io.BaseIo method) (expectmine.io.io.cli_io.CliIo method) (expectmine.io.io.dict_io.DictIo method)

filepaths() (expectmine.io.base_io.BaseIo method) (expectmine.io.io.cli_io.CliIo method) (expectmine.io.io.dict_io.DictIo method)

G

get() (expectmine.storage.base_storage.BaseStore method) (expectmine.storage.stores.in_memory_store.InMemoryStore method) (expectmine.storage.stores.sqlite3_store.Sqlite3Store method) get_instance() (expectmine.io.adapters.cli_io_adapter.CliIoAdapter method) (expectmine.io.adapters.dict_io_adapter.DictIoAdapter method) (expectmine.io.base_io_adapter.BaseIoAdapter method) (expectmine.logger.adapters.cli_logger_adapter.CliLoggerAdapter method) (expectmine.logger.base_logger_adapter.BaseLoggerAdapter method) (expectmine.storage.adapters.in_memory_adapter.InMemoryStoreAdapter method) (expectmine.storage.adapters.sqlite3_adapter.Sqlite3StoreAdapter method) (expectmine.storage.base_storage_adapter.BaseStoreAdapter method)

get_quickstart_config() (in module expectmine.pipeline.utils)

I

INFO (expectmine.logger.base_logger.LogLevel attribute) info() (expectmine.logger.base_logger.BaseLogger method) (expectmine.logger.loggers.cli_logger.CliLogger method) InMemoryStore (class in expectmine.storage.stores.in_memory_store)

InMemoryStoreAdapter (class in expectmine.storage.adapters.in_memory_adapter) install() (expectmine.steps.base_step.BaseStep method) (expectmine.steps.steps.mzmine3.mzmine3.MZmine3 method) (expectmine.steps.steps.shrink_mgf.ShrinkMgf method) (expectmine.steps.steps.sirius_fingerprint.SiriusFingerprint method)

L

list() (expectmine.storage.base_storage.BaseStore method) (expectmine.storage.stores.in_memory_store.InMemoryStore method) (expectmine.storage.stores.sqlite3_store.Sqlite3Store method)

log() (expectmine.logger.base_logger.BaseLogger method) (expectmine.logger.loggers.cli_logger.CliLogger method) LogLevel (class in expectmine.logger.base_logger)

M

metadata() (expectmine.steps.base_step.BaseStep method) (expectmine.steps.steps.mzmine3.mzmine3.MZmine3 method) (expectmine.steps.steps.shrink_mgf.ShrinkMgf method) (expectmine.steps.steps.sirius_fingerprint.SiriusFingerprint method) module expectmine.io.adapters.cli_io_adapter expectmine.io.adapters.dict_io_adapter expectmine.io.base_io expectmine.io.base_io_adapter expectmine.io.io.cli_io expectmine.io.io.dict_io expectmine.io.utils expectmine.logger.adapters.cli_logger_adapter expectmine.logger.base_logger expectmine.logger.base_logger_adapter expectmine.logger.loggers.cli_logger expectmine.logger.utils expectmine.pipeline.utils expectmine.steps.base_step expectmine.steps.steps.mzmine3.mzmine3 expectmine.steps.steps.shrink_mgf expectmine.steps.steps.sirius_fingerprint expectmine.storage.adapters.in_memory_adapter expectmine.storage.adapters.sqlite3_adapter expectmine.storage.base_storage expectmine.storage.base_storage_adapter expectmine.storage.stores.in_memory_store expectmine.storage.stores.sqlite3_store expectmine.storage.utils expectmine.utils.cmd

multiple_choice() (expectmine.io.base_io.BaseIo method) (expectmine.io.io.cli_io.CliIo method) (expectmine.io.io.dict_io.DictIo method) MZmine3 (class in expectmine.steps.steps.mzmine3.mzmine3)

N

number() (expectmine.io.base_io.BaseIo method) (expectmine.io.io.cli_io.CliIo method) (expectmine.io.io.dict_io.DictIo method)

O

output_filetypes() (expectmine.steps.base_step.BaseStep class method) (expectmine.steps.steps.mzmine3.mzmine3.MZmine3 class method) (expectmine.steps.steps.shrink_mgf.ShrinkMgf class method) (expectmine.steps.steps.sirius_fingerprint.SiriusFingerprint class method)

P

parse_number() (in module expectmine.io.utils) parse_path() (in module expectmine.io.utils)

put() (expectmine.storage.base_storage.BaseStore method) (expectmine.storage.stores.in_memory_store.InMemoryStore method) (expectmine.storage.stores.sqlite3_store.Sqlite3Store method)

R

run() (expectmine.steps.base_step.BaseStep method) (expectmine.steps.steps.mzmine3.mzmine3.MZmine3 method) (expectmine.steps.steps.shrink_mgf.ShrinkMgf method) (expectmine.steps.steps.sirius_fingerprint.SiriusFingerprint method)

run_cmd() (in module expectmine.utils.cmd)

S

setup() (expectmine.steps.base_step.BaseStep method) (expectmine.steps.steps.mzmine3.mzmine3.MZmine3 method) (expectmine.steps.steps.shrink_mgf.ShrinkMgf method) (expectmine.steps.steps.sirius_fingerprint.SiriusFingerprint method) ShrinkMgf (class in expectmine.steps.steps.shrink_mgf) single_choice() (expectmine.io.base_io.BaseIo method) (expectmine.io.io.cli_io.CliIo method) (expectmine.io.io.dict_io.DictIo method) SiriusFingerprint (class in expectmine.steps.steps.sirius_fingerprint)

Sqlite3Store (class in expectmine.storage.stores.sqlite3_store) Sqlite3StoreAdapter (class in expectmine.storage.adapters.sqlite3_adapter) step_name() (expectmine.steps.base_step.BaseStep class method) (expectmine.steps.steps.mzmine3.mzmine3.MZmine3 class method) (expectmine.steps.steps.shrink_mgf.ShrinkMgf class method) (expectmine.steps.steps.sirius_fingerprint.SiriusFingerprint class method) string() (expectmine.io.base_io.BaseIo method) (expectmine.io.io.cli_io.CliIo method) (expectmine.io.io.dict_io.DictIo method)

V

validate_adapter_init() (in module expectmine.logger.utils) (in module expectmine.storage.utils) validate_add_step() (in module expectmine.pipeline.utils) validate_arguments() (in module expectmine.io.utils) validate_choice() (in module expectmine.io.utils) validate_cmd() (in module expectmine.utils.cmd) validate_init() (in module expectmine.logger.utils) (in module expectmine.pipeline.utils) validate_input_files() (in module expectmine.pipeline.utils)

validate_key() (in module expectmine.storage.utils) validate_output_directory() (in module expectmine.pipeline.utils) validate_pipeline() (in module expectmine.storage.utils) validate_pipeline_store_init() (in module expectmine.storage.utils) validate_step_can_run() (in module expectmine.pipeline.utils) validate_step_name() (in module expectmine.io.utils) (in module expectmine.storage.utils) validate_storage_init() (in module expectmine.storage.utils) validate_value() (in module expectmine.storage.utils)

W

WARN (expectmine.logger.base_logger.LogLevel attribute)

warn() (expectmine.logger.base_logger.BaseLogger method) (expectmine.logger.loggers.cli_logger.CliLogger method)