Can we call run method directly?

Yes, we can call run method directly. Only difference is that when start method is called it creates a separate call stack for that thread but in case when run method is called directly from main method it will not create a new call stack. Run method is goes into current call stack. i.e. No new thread will be created and it is the responsibility of the main thread to complete the job.

Example:

ThreadExample.java

/**
 * This program is used to show that 
 * we can call run method directly.
 * @author w3spoint
 */
class Test extends Thread{
	public void run(){
		System.out.println("thread started.");
	}
}
 
public class ThreadExample {
	public static void main(String args[]){
		//creating thread.
		Test thrd = new Test();
 
		//call run method.
		thrd.run();
	}
}

Output:

thread started.

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