When i was trying to run a program from the IDE, a window
pops up which has anagrams as a title and requests me to enter something
under "Your Guess" slot?

What is happening?

Where was the message from? The IDE or the program?

The title of the windows Anagrams is written next to the java mark.
then there is a menu space where only File is written.
on the next row is Scrambled Word in front of which is bartsartcoin
on next line is written Your Guess and there is an empty space prompting some entry
finally there are two buttons on the bottom left of the window one saying Guess and the other New Word.

Can you screen print it and post the image?
Nothing you're saying makes any sense.

What i mean is as follow:

when i try to run a program from IDE using the Run, Run File menu, a window appears and prompts me for some entries. On the bottom of the IDE there is a message which says OUTPUT AnagramGame1

Sounds like you've got a ghost or virus.

Better ask an IDE expert. I don't use an IDE.