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R6 class representing ProlfquApp configuration

Source: R/R6_AppConfiguration.R
ProlfquAppConfig.Rd

R6 class representing ProlfquApp configuration

R6 class representing ProlfquApp configuration

See also

Other ProlfquAppConfig: ExternalReader, ProcessingOptions, ProjectSpec, make_DEA_config_R6(), set_list_to_R6()

Public fields

processing_options

ProcessingOption R6 class

project_spec

Project Spec R6 class

software

name of input software

prefix

either QC or DEA

zipdir_name

results should go to zipdir_name

flat_outdir

when TRUE, write results directly into `path` with no dated zipdir subdir (default FALSE keeps the dated layout)

path

path to working directory

group

group prefix

ext_reader

external reader configuration

Methods

Public methods

Method new()

Initialize ProlfquAppConfig with processing options, project spec, and external reader

Usage

ProlfquAppConfig$new(
  processing_options,
  project_spec,
  ext_reader,
  zipdir_name = ".",
  path = ".",
  software = "DIANN",
  prefix = "DEA",
  flat_outdir = FALSE
)

Arguments

processing_options

instance of ProcessingOptions

project_spec

instance of ProjectSpec

ext_reader

instance of ExternalReader

zipdir_name

where to store results

path

working directory path

software

name of input software

prefix

either QC or DEA

flat_outdir

write results directly into `path` without a dated subdir (default FALSE)

Method set_zipdir_name()

Set zip directory name based on project information and date

Usage

ProlfquAppConfig$set_zipdir_name()

Returns

the generated zip directory name

Method get_zipdir()

Get the full path to the zip directory

When `flat_outdir` is TRUE the dated zipdir subdir is skipped and results are written directly into `path`.

Usage

ProlfquAppConfig$get_zipdir()

Returns

full path to zip directory

Method get_result_dir()

Get the results directory path

Usage

ProlfquAppConfig$get_result_dir()

Returns

path to results directory

Method get_input_dir()

Get the input directory path

Usage

ProlfquAppConfig$get_input_dir()

Returns

path to input directory

Method as_list()

Convert R6 object to list

Usage

ProlfquAppConfig$as_list()

Returns

list representation of the R6 object

Method clone()

The objects of this class are cloneable with this method.

Usage

ProlfquAppConfig$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples



r6obj_config <- ProlfquAppConfig$new(
  ProcessingOptions$new(),
  ProjectSpec$new(),
  ExternalReader$new()
)
xx <- prolfqua::R6_extract_values(r6obj_config)
yaml::write_yaml(xx, file = file.path(tempdir(), "test.yaml"))
config <- yaml::read_yaml(file = file.path(tempdir(), "test.yaml"))

r6obj_config$set_zipdir_name()
#> [1] "DEA_20260623_vsn"

r6obj_config$get_zipdir()
#> [1] "./DEA_20260623_vsn"
r6obj_config$get_result_dir()
#> [1] "./DEA_20260623_vsn/Results_WU_"
r6obj_config$get_input_dir()
#> [1] "./DEA_20260623_vsn/Inputs_WU_"