Package task

Class ExecutorSequence

java.lang.Object

task.ExecutorSequence

public class ExecutorSequence
extends Object

The ExecutorSequence class is responsible for executing the sequence task to profile samples.

Constructor Summary

Constructors

Constructor	Description
ExecutorSequence(CLISequence cli)	Constructs an ExecutorSequence instance with the specified command-line interface.

Method Summary

Modifier and Type	Method	Description
void	run()	Executes the sequence generation task based on the specified content type.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

ExecutorSequence

public ExecutorSequence(CLISequence cli)
                 throws IOException,
MusialException

Constructs an ExecutorSequence instance with the specified command-line interface.

Parameters:

cli - The command-line interface for the sequence task.

Throws:

IOException - If an I/O error occurs while loading the storage.

MusialException - If a validation error occurs with the input parameters.

Method Details

run

public void run()
         throws IOException,
MusialException

Executes the sequence generation task based on the specified content type.

This method determines the type of sequence data to generate (amino acid or nucleotide) based on the cli.content value. It then processes the features and, if applicable, the contigs to generate the required sequence data. The sequence data is written to output files as specified in the command-line arguments.

Throws:

IOException - If an I/O error occurs during sequence generation or file writing.

MusialException - If an error occurs during sequence generation or validation.