OxfordNanoporeExperiment (Groovy Documentation)

life.qbic.datamodel.datasets.OxfordNanoporeExperiment

All Implemented Interfaces and Traits:

ExperimentFolder
```
final class OxfordNanoporeExperiment
```
Class that holds information about an Oxford Nanopore Experiment. @author: Sven Fillinger

Field Summary

Fields
Modifiers	Name	Description
`private static java.lang.String`	`FQDN_FILES`
`private static java.lang.String`	`FQDN_FOLDERS`
`private java.util.List<OxfordNanoporeMeasurement>`	`measurements`
`private static java.util.Set`	`nanoporeFileTypes`
`private static java.util.Set`	`nanoporeFolderTypes`
`private java.lang.String`	`sampleId`

Constructor Summary

Constructors
Constructor and description
`private OxfordNanoporeExperiment (java.lang.String sampleId, java.util.List<OxfordNanoporeMeasurement> measurements)`

Methods Summary

Methods
Type Params	Return Type	Name and description
	`static OxfordNanoporeExperiment`	`create(java.util.Map nanoPoreSequencerOutput)` Static factory method that creates a new instance from a Oxford Nanopore sequencer output.
	`private static java.lang.reflect.Method`	`determineMethod(java.lang.Class c)`
	`java.util.List<OxfordNanoporeMeasurement>`	`getMeasurements()` Provides a list of measurements contained within the experiment folder.
	`java.lang.String`	`getSampleCode()`
	`private static java.util.List`	`parseChildren(java.util.List<java.util.Map> children)`
	`private static DataFile`	`parseFile(java.util.Map fileTree)`
	`private static DataFolder`	`parseFolder(java.util.Map fileTree)`
	`private static java.util.List<?>`	`parseMeasurementItems(java.util.List<java.util.Map> items)`
	`private static java.util.List<OxfordNanoporeMeasurement>`	`parseMeasurements(java.util.Map nanoPoreSequencerOutput)` Helper method that creates the measurements from the sequencer output
	`private static java.lang.String`	`parseQbicIdFromRootFolder(java.util.Map nanoPoreSequencerOutput)` Helper method that parses the QBiC identifier from the root folder name
	`private static java.util.Optional<DataFolder>`	`tryToCreateDataFolder(java.lang.reflect.Method method, java.lang.String name, java.lang.String relativePath, java.util.List children)`

Inherited Methods Summary

Inherited Methods
Methods inherited from class	Name
`class java.lang.Object`	`java.lang.Object#wait(long), java.lang.Object#wait(long, int), java.lang.Object#wait(), java.lang.Object#equals(java.lang.Object), java.lang.Object#toString(), java.lang.Object#hashCode(), java.lang.Object#getClass(), java.lang.Object#notify(), java.lang.Object#notifyAll()`

- Field Detail
  - private static final java.lang.String FQDN_FILES
  - private static final java.lang.String FQDN_FOLDERS
  - private final java.util.List<OxfordNanoporeMeasurement> measurements
  - private static final java.util.Set nanoporeFileTypes
  - private static final java.util.Set nanoporeFolderTypes
  - private final java.lang.String sampleId
- Constructor Detail
  - private OxfordNanoporeExperiment(java.lang.String sampleId, java.util.List<OxfordNanoporeMeasurement> measurements)
- Method Detail
  - static OxfordNanoporeExperiment create(java.util.Map nanoPoreSequencerOutput)
    
    Static factory method that creates a new instance from a Oxford Nanopore sequencer output.
    Parameters:
    Map - nanoPoreSequencerOutput
    Returns:
    OxfordNanoporeExperiment A new instance of a nanopore experiment.
  - private static java.lang.reflect.Method determineMethod(java.lang.Class c)
  - java.util.List<OxfordNanoporeMeasurement> getMeasurements()
    
    Provides a list of measurements contained within the experiment folder.
    Returns:
  - @java.lang.Override java.lang.String getSampleCode()
  - private static java.util.List parseChildren(java.util.List<java.util.Map> children)
  - private static DataFile parseFile(java.util.Map fileTree)
  - private static DataFolder parseFolder(java.util.Map fileTree)
  - private static java.util.List<?> parseMeasurementItems(java.util.List<java.util.Map> items)
  - private static java.util.List<OxfordNanoporeMeasurement> parseMeasurements(java.util.Map nanoPoreSequencerOutput)
    
    Helper method that creates the measurements from the sequencer output
  - private static java.lang.String parseQbicIdFromRootFolder(java.util.Map nanoPoreSequencerOutput)
    
    Helper method that parses the QBiC identifier from the root folder name
  - private static java.util.Optional<DataFolder> tryToCreateDataFolder(java.lang.reflect.Method method, java.lang.String name, java.lang.String relativePath, java.util.List children)

Summary:
Field
Constructor
Method

| Detail:
Field
Constructor
Method

Groovy Documentation

[Groovy] Class OxfordNanoporeExperiment

Field Summary

Constructor Summary

Methods Summary

Inherited Methods Summary

Field Detail

private static final java.lang.String FQDN_FILES

private static final java.lang.String FQDN_FOLDERS

private final java.util.List<OxfordNanoporeMeasurement> measurements

private static final java.util.Set nanoporeFileTypes

private static final java.util.Set nanoporeFolderTypes

private final java.lang.String sampleId

Constructor Detail

private OxfordNanoporeExperiment(java.lang.String sampleId, java.util.List<OxfordNanoporeMeasurement> measurements)

Method Detail

static OxfordNanoporeExperiment create(java.util.Map nanoPoreSequencerOutput)

private static java.lang.reflect.Method determineMethod(java.lang.Class c)

java.util.List<OxfordNanoporeMeasurement> getMeasurements()

@java.lang.Override java.lang.String getSampleCode()

private static java.util.List parseChildren(java.util.List<java.util.Map> children)

private static DataFile parseFile(java.util.Map fileTree)

private static DataFolder parseFolder(java.util.Map fileTree)

private static java.util.List<?> parseMeasurementItems(java.util.List<java.util.Map> items)

private static java.util.List<OxfordNanoporeMeasurement> parseMeasurements(java.util.Map nanoPoreSequencerOutput)

private static java.lang.String parseQbicIdFromRootFolder(java.util.Map nanoPoreSequencerOutput)

private static java.util.Optional<DataFolder> tryToCreateDataFolder(java.lang.reflect.Method method, java.lang.String name, java.lang.String relativePath, java.util.List children)