Package task

Class ExecutorProfile

java.lang.Object

task.ExecutorProfile

public class ExecutorProfile
extends Object

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

This class initializes the CLI profile, loads the storage, and manages the storage table. It provides functionality to apply queries, populate the storage table based on the content type, and either print or write the output to a file.

Constructor Summary

Constructors

Constructor	Description
ExecutorProfile(CLIProfile cli)	Constructs an instance of the ExecutorProfile class.

Method Summary

Modifier and Type	Method	Description
void	run()	Executes the main logic of the ExecutorProfile class.

Methods inherited from class java.lang.Object

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

Constructor Details

ExecutorProfile

public ExecutorProfile(CLIProfile cli)
                throws IOException

Constructs an instance of the ExecutorProfile class.

This constructor initializes the CLI profile, loads the storage from the input path, and creates a storage table for managing data.

Parameters:

cli - The CLIProfile object containing user input and options.

Throws:

IOException - If an error occurs while loading the storage.

Method Details

run

public void run()

Executes the main logic of the ExecutorProfile class.

This method applies query filters if provided, populates the storage table based on the content type, and either prints the table to the console or writes it to the specified output file.

The method performs the following steps:

• Checks if the query is not empty and applies the filters to the storage table.
• Profiles the storage table based on the content type (VARIANTS, ALLELES, or PROTEOFORMS).
• Prints the table to the console if no output file is specified, or writes it to the output file.

If the content type is unexpected, an IllegalStateException is thrown.