Class BasecallingModelSelector
- java.lang.Object
-
- fr.ens.biologie.genomique.aozan.aozan3.nanopore.BasecallingModelSelector
-
public class BasecallingModelSelector extends Object
This class allow to select the model to use with Dorado from parameters like flowcell or kit references.- Since:
- 3.1
- Author:
- Laurent Jourdren
-
-
Constructor Summary
Constructors Constructor Description BasecallingModelSelector(Path modelsPath)
Public constructor.
-
Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static String
getChemistryType(String kit)
Get the chemistry type from the kit referencestatic String
getPoreType(String flowcellRef)
Get the pore type from the flowcell referencePath
select()
Select the right model.BasecallingModelSelector
withAnalyteType(String analyteType)
Add a filter based on the analyte type.BasecallingModelSelector
withChemistryType(String chemistryType)
Add a filter based on the chemistry type.BasecallingModelSelector
withFlowcellReference(String flowcell)
Add a filter based on the flowcell reference.BasecallingModelSelector
withKitReference(String kit)
Add a filter based on the kit reference.BasecallingModelSelector
withModelType(String modelType)
Add a filter based on the model type.BasecallingModelSelector
withModification(String modification)
Add a filter that allow models that handle a modification.BasecallingModelSelector
withNoModification()
Add a filter that reject models that handle modifications.BasecallingModelSelector
withPoreType(String poreType)
Add a filter based on the pore type.BasecallingModelSelector
withSamplingFrequency(String samplingFrequency)
Add a filter based on the sampling frequency.BasecallingModelSelector
withTranslocationSpeed(String translocationSpeed)
Add a filter based on the translocation speed.BasecallingModelSelector
withVersion(String version)
Add a filter based on the version of the model.
-
-
-
Constructor Detail
-
BasecallingModelSelector
public BasecallingModelSelector(Path modelsPath)
Public constructor.- Parameters:
modelsPath
- path of the Dorado models
-
-
Method Detail
-
getPoreType
public static String getPoreType(String flowcellRef)
Get the pore type from the flowcell reference- Parameters:
flowcellRef
- the flow cell reference- Returns:
- the pore type
-
getChemistryType
public static String getChemistryType(String kit)
Get the chemistry type from the kit reference- Parameters:
kit
- the kit reference- Returns:
- the chemistry type
-
withAnalyteType
public BasecallingModelSelector withAnalyteType(String analyteType)
Add a filter based on the analyte type.- Parameters:
analyteType
- the analyte type- Returns:
- the object
-
withPoreType
public BasecallingModelSelector withPoreType(String poreType)
Add a filter based on the pore type.- Parameters:
poreType
- the pore type- Returns:
- the object
-
withChemistryType
public BasecallingModelSelector withChemistryType(String chemistryType)
Add a filter based on the chemistry type.- Parameters:
chemistryType
- the chemistry type- Returns:
- the object
-
withTranslocationSpeed
public BasecallingModelSelector withTranslocationSpeed(String translocationSpeed)
Add a filter based on the translocation speed.- Parameters:
translocationSpeed
- the translocation speed- Returns:
- the object
-
withSamplingFrequency
public BasecallingModelSelector withSamplingFrequency(String samplingFrequency)
Add a filter based on the sampling frequency.- Parameters:
samplingFrequency
- the sampling frequency- Returns:
- the object
-
withModelType
public BasecallingModelSelector withModelType(String modelType)
Add a filter based on the model type.- Parameters:
modelType
- the model type- Returns:
- the object
-
withVersion
public BasecallingModelSelector withVersion(String version)
Add a filter based on the version of the model.- Parameters:
version
- the requested version of the model- Returns:
- the object
-
withFlowcellReference
public BasecallingModelSelector withFlowcellReference(String flowcell)
Add a filter based on the flowcell reference.- Parameters:
flowcell
- the flowcell reference- Returns:
- the object
-
withKitReference
public BasecallingModelSelector withKitReference(String kit)
Add a filter based on the kit reference.- Parameters:
kit
- the kit reference- Returns:
- the object
-
withNoModification
public BasecallingModelSelector withNoModification()
Add a filter that reject models that handle modifications.- Returns:
- the object
-
withModification
public BasecallingModelSelector withModification(String modification)
Add a filter that allow models that handle a modification.- Parameters:
modification
- required modification- Returns:
- the object
-
select
public Path select()
Select the right model.- Returns:
- the selected model
-
-