java.lang.Object
- fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
- - fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule

All Implemented Interfaces:

Module

Direct Known Subclasses:

FilterAndMapReadsHadoopModule
```
public abstract class AbstractFilterAndMapReadsModule
extends AbstractModule
```
This class define an abstract module for read filtering, mapping and alignments filtering.

Since:

1.0

Author:

Laurent Jourdren

Field Summary

Fields
Modifier and Type	Field	Description
`protected static String`	`GENOME_DESCRIPTION_PORT_NAME`
`protected static int`	`HADOOP_TIMEOUT`
`protected static String`	`MAPPER_INDEX_PORT_NAME`
`static String`	`MODULE_NAME`
`protected static String`	`READS_PORT_NAME`

Constructor Summary

Constructors
Constructor Description

AbstractFilterAndMapReadsModule()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`configure(StepConfigurationContext context, Set<Parameter> stepParameters)`	Set the parameters of the step to configure the module.
`protected Map<String,String>`	`getAlignmentsFilterParameters()`	Get the parameters of the read alignments filters.
`protected String`	`getCounterGroup()`	Get the counter group to use for this module.
`String`	`getDescription()`	Get the description of the module
`InputPorts`	`getInputPorts()`	Get the input data format.
`protected fr.ens.biologie.genomique.kenetre.bio.readmapper.Mapper`	`getMapper()`	Get the mapper.
`protected String`	`getMapperArguments()`	Get the name of the mapper to use.
`protected String`	`getMapperFlavor()`	Get the flavor of the mapper to use.
`protected int`	`getMapperHadoopMemoryRequired()`	Get the amount in MB of memory required to execute the mapper.
`protected int`	`getMapperHadoopThreads()`	Get the name of the mapper to use.
`protected String`	`getMapperName()`	Get the name of the mapper to use.
`protected String`	`getMapperVersion()`	Get the version of the mapper to use.
`String`	`getName()`	Get the name of the module.
`OutputPorts`	`getOutputPorts()`	Get the output data format.
`protected Map<String,String>`	`getReadFilterParameters()`	Get the parameters of the read filters.
`protected int`	`getReducerTaskCount()`	Get the reducer task count.
`fr.ens.biologie.genomique.kenetre.util.Version`	`getVersion()`	Get version of the Module.
`protected boolean`	`isPairedEnd()`	Test if the step works in pair end mode.

Methods inherited from class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
getChecker, getParallelizationMode, getRequiredEoulsanVersion, getRequirements

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface fr.ens.biologie.genomique.eoulsan.core.Module
execute

- Field Detail
  - MODULE_NAME
```
public static final String MODULE_NAME
```
    See Also:
    
    Constant Field Values
  - READS_PORT_NAME
```
protected static final String READS_PORT_NAME
```
    See Also:
    
    Constant Field Values
  - MAPPER_INDEX_PORT_NAME
```
protected static final String MAPPER_INDEX_PORT_NAME
```
    See Also:
    
    Constant Field Values
  - GENOME_DESCRIPTION_PORT_NAME
```
protected static final String GENOME_DESCRIPTION_PORT_NAME
```
    See Also:
    
    Constant Field Values
  - HADOOP_TIMEOUT
```
protected static final int HADOOP_TIMEOUT
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - AbstractFilterAndMapReadsModule
```
public AbstractFilterAndMapReadsModule()
```
- Method Detail
  - getCounterGroup
```
protected String getCounterGroup()
```
    Get the counter group to use for this module.
    
    Returns:
    
    the counter group of this module
  - isPairedEnd
```
protected boolean isPairedEnd()
```
    Test if the step works in pair end mode.
    
    Returns:
    
    true if the pair end mode is enable
  - getMapperName
```
protected String getMapperName()
```
    Get the name of the mapper to use.
    
    Returns:
    
    Returns the mapperName
  - getMapperVersion
```
protected String getMapperVersion()
```
    Get the version of the mapper to use.
    
    Returns:
    
    the version of the mapper to use
  - getMapperFlavor
```
protected String getMapperFlavor()
```
    Get the flavor of the mapper to use.
    
    Returns:
    
    the flavor of the mapper to use
  - getMapperArguments
```
protected String getMapperArguments()
```
    Get the name of the mapper to use.
    
    Returns:
    
    Returns the mapperName
  - getMapperHadoopThreads
```
protected int getMapperHadoopThreads()
```
    Get the name of the mapper to use.
    
    Returns:
    
    Returns the mapperName
  - getMapperHadoopMemoryRequired
```
protected int getMapperHadoopMemoryRequired()
```
    Get the amount in MB of memory required to execute the mapper. This value is required by Hadoop scheduler and if the mapper require more memory than declared the mapper process will be killed.
    
    Returns:
    
    the amount of memory required by the mapper in MB
  - getMapper
```
protected fr.ens.biologie.genomique.kenetre.bio.readmapper.Mapper getMapper()
```
    Get the mapper.
    
    Returns:
    
    the mapper object
  - getReducerTaskCount
```
protected int getReducerTaskCount()
```
    Get the reducer task count.
    
    Returns:
    
    the reducer task count
  - getReadFilterParameters
```
protected Map<String,String> getReadFilterParameters()
```
    Get the parameters of the read filters.
    
    Returns:
    
    a map with all the parameters of the filters
  - getAlignmentsFilterParameters
```
protected Map<String,String> getAlignmentsFilterParameters()
```
    Get the parameters of the read alignments filters.
    
    Returns:
    
    a map with all the parameters of the filters
  - getName
```
public String getName()
```
    Description copied from interface: Module
    
    Get the name of the module.
    
    Returns:
    
    the name of the module
  - getVersion
```
public fr.ens.biologie.genomique.kenetre.util.Version getVersion()
```
    Description copied from interface: Module
    
    Get version of the Module.
    
    Returns:
    
    a Version object with the version of the Module
  - getInputPorts
```
public InputPorts getInputPorts()
```
    Description copied from interface: Module
    
    Get the input data format.
    
    Specified by:
    
    getInputPorts in interface Module
    
    Overrides:
    
    getInputPorts in class AbstractModule
    
    Returns:
    
    a set with DataFormat or null if the module does not any need input format
  - getOutputPorts
```
public OutputPorts getOutputPorts()
```
    Description copied from interface: Module
    
    Get the output data format.
    
    Specified by:
    
    getOutputPorts in interface Module
    
    Overrides:
    
    getOutputPorts in class AbstractModule
    
    Returns:
    
    an set with DataFormat or null if the module does not produce any output data
  - getDescription
```
public String getDescription()
```
    Description copied from interface: Module
    
    Get the description of the module
    
    Specified by:
    
    getDescription in interface Module
    
    Overrides:
    
    getDescription in class AbstractModule
    
    Returns:
    
    the description of the module
  - configure
```
public void configure(StepConfigurationContext context,
                      Set<Parameter> stepParameters)
               throws EoulsanException
```
    Description copied from interface: Module
    
    Set the parameters of the step to configure the module.
    
    Specified by:
    
    configure in interface Module
    
    Overrides:
    
    configure in class AbstractModule
    
    Parameters:
    
    context - configuration context. The context can be null for generator steps
    
    stepParameters - parameters of the step
    
    Throws:
    
    EoulsanException - if a parameter is invalid

Class AbstractFilterAndMapReadsModule

Field Summary

Constructor Summary

Method Summary

Methods inherited from class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule

Methods inherited from class java.lang.Object

Methods inherited from interface fr.ens.biologie.genomique.eoulsan.core.Module

Field Detail

MODULE_NAME

READS_PORT_NAME

MAPPER_INDEX_PORT_NAME

GENOME_DESCRIPTION_PORT_NAME

HADOOP_TIMEOUT

Constructor Detail

AbstractFilterAndMapReadsModule

Method Detail

getCounterGroup

isPairedEnd

getMapperName

getMapperVersion

getMapperFlavor

getMapperArguments

getMapperHadoopThreads

getMapperHadoopMemoryRequired

getMapper

getReducerTaskCount

getReadFilterParameters

getAlignmentsFilterParameters

getName

getVersion

getInputPorts

getOutputPorts

getDescription

configure