FastQScreenSampleOvercontaminationCountProjectTest (Aozan 3.1 API)

java.lang.Object
- fr.ens.biologie.genomique.aozan.tests.project.AbstractProjectTest
- - fr.ens.biologie.genomique.aozan.tests.project.AbstractSimpleProjectTest
  - - fr.ens.biologie.genomique.aozan.tests.project.FastQScreenSampleOvercontaminationCountProjectTest

All Implemented Interfaces:

AozanTest, ProjectTest
```
public class FastQScreenSampleOvercontaminationCountProjectTest
extends AbstractSimpleProjectTest
```
The class define test on samples count on a project which exceed a contaminant threshold on percent mapped reads on dataset contaminants genomes. The default value of threshold is 0.10, can be redefine in configuration file.

Since:

1.4

Author:

Sandrine Perrin

Constructor Summary

Constructors
Constructor Description

FastQScreenSampleOvercontaminationCountProjectTest()
Public constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`List<String>`	`getCollectorsNamesRequiered()`	Get the name of the collectors required for the test.
`protected String`	`getKey(int projectId)`	Get the the key in the RunData object for the value to test.
`protected Class<?>`	`getValueType()`	Get the type of the value.

Methods inherited from class fr.ens.biologie.genomique.aozan.tests.project.AbstractSimpleProjectTest
configure, isValuePercent, test, testIndexedRead, transformValue

Methods inherited from class fr.ens.biologie.genomique.aozan.tests.project.AbstractProjectTest
getColumnName, getDescription, getName, getUnit, init

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

- Constructor Detail
  - FastQScreenSampleOvercontaminationCountProjectTest
```
public FastQScreenSampleOvercontaminationCountProjectTest()
```
    Public constructor.
- Method Detail
  - getCollectorsNamesRequiered
```
public List<String> getCollectorsNamesRequiered()
```
    Description copied from interface: AozanTest
    
    Get the name of the collectors required for the test.
    
    Returns:
    
    a list of String with the name of the required collectors
  - getKey
```
protected String getKey(int projectId)
```
    Description copied from class: AbstractSimpleProjectTest
    
    Get the the key in the RunData object for the value to test.
    
    Specified by:
    
    getKey in class AbstractSimpleProjectTest
    
    Parameters:
    
    projectId - the project Id
    
    Returns:
    
    a String with the required key
  - getValueType
```
protected Class<?> getValueType()
```
    Description copied from class: AbstractSimpleProjectTest
    
    Get the type of the value.
    
    Specified by:
    
    getValueType in class AbstractSimpleProjectTest
    
    Returns:
    
    a Class object with the type