FileProcessor (irida 22.09 API)

All Known Implementing Classes:

AutomatedAnalysisFileProcessor, ChecksumFileProcessor, CoverageFileProcessor, FastqcFileProcessor, GzipFileProcessor
```
public interface FileProcessor
```
Responsible for processing a SequenceFile after the file has been uploaded to the server.

Method Summary

All Methods Instance Methods Abstract Methods Default Methods
Modifier and Type	Method	Description
`java.lang.Boolean`	`modifiesFile()`	If the `FileProcessor` throws a `FileProcessorException`, the `FileProcessor` should inform the caller whether or not proceeding with the remaining `FileProcessor` instances in the chain is safe.
`void`	`process(SequencingObject sequencingObject)`	Process the provided `SequenceFile`, then (optionally) proceed to the next processor in the chain.
`default boolean`	`shouldProcessFile(SequencingObject sequencingObject)`	This method asks the file processor whether it should act on this file.

- Method Detail
  - process
```
void process(SequencingObject sequencingObject)
```
    Process the provided SequenceFile, then (optionally) proceed to the next processor in the chain. Any modifications to the SequenceFile made by the FileProcessor should be persisted by the FileProcessor itself -- the FileProcessingChain *does not* handle persistence.
    
    Parameters:
    
    sequencingObject - the SequencingObject to process
    
    Throws:
    
    FileProcessorException - when processing fails.
  - modifiesFile
```
java.lang.Boolean modifiesFile()
```
    If the FileProcessor throws a FileProcessorException, the FileProcessor should inform the caller whether or not proceeding with the remaining FileProcessor instances in the chain is safe. If the FileProcessor modifies the file, then proceeding with the remaining FileProcessor in the chain is not safe.
    
    Returns:
    
    whether or not the FileProcessor modifies the SequenceFile.
  - shouldProcessFile
```
default boolean shouldProcessFile(SequencingObject sequencingObject)
```
    This method asks the file processor whether it should act on this file. The processor may have some settings that would not run on certain files.
    
    Parameters:
    
    sequencingObject - the SequencingObject to check
    
    Returns:
    
    true if the processor should act on the file