FastqScreenGenomes (Aozan 3.1 API)

java.lang.Object
- fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreenGenomes

```
public class FastqScreenGenomes
extends Object
```
This class read the alias genome file. It make correspondence between genome name in Bcl2fastq samplesheet file and the genome name reference used for identified index of bowtie mapper.

Since:

1.3

Author:

Sandrine Perrin

Constructor Summary

Constructors
Constructor	Description
`FastqScreenGenomes(fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet samplesheet, String contaminantGenomeNames)`	Public constructor.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`Set<String>`	`getContaminantGenomes()`	Get the collection of genomes contaminants can be used for mapping.
`Set<String>`	`getSampleGenomes()`	Get the collection genomes name can be used for the mapping.
`static FastqScreenGenomes`	`newInstance(TestConfiguration testConfiguration)`	Private constructor of FastqScreenGenomeMapper.

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

- Constructor Detail
  - FastqScreenGenomes
```
public FastqScreenGenomes(fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet samplesheet,
                          String contaminantGenomeNames)
                   throws AozanException
```
    Public constructor.
    
    Parameters:
    
    samplesheet - sampleSheet file
    
    contaminantGenomeNames - a string with the list of the contaminant genomes
    
    Throws:
    
    AozanException - if an error occurs while creating the object
- Method Detail
  - getSampleGenomes
```
public Set<String> getSampleGenomes()
```
    Get the collection genomes name can be used for the mapping.
    
    Returns:
    
    collection genomes name for mapping
  - getContaminantGenomes
```
public Set<String> getContaminantGenomes()
```
    Get the collection of genomes contaminants can be used for mapping.
    
    Returns:
    
    collection of genomes contaminans
  - newInstance
```
public static FastqScreenGenomes newInstance(TestConfiguration testConfiguration)
                                      throws AozanException
```
    Private constructor of FastqScreenGenomeMapper.
    
    Parameters:
    
    testConfiguration - configuration properties
    
    Returns:
    
    a new instance of FastqScreenGenomes
    
    Throws:
    
    AozanException - if the initialization of instance fail.