How to config xbee s1 for sending data from arduino to PC with Xbee s1 ; Java program to read at the PC

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There is no configuration needed for the XBee modules to perform this function. This is more of a question on how you write your applications to send and receive data via a COM port. That is something that is not for this forum but for your Arduino processor forum and Microsoft’s forums for Java.

Do you mean I need to revert xbee’s to default settings without setting any parameters?
not even AT or API mode ?

I think what he means is that how you setup your XBee will likely depend on the program you use with the XBee, and its mode of operation. Does the java program expect to talk to an API interface? Then API mode would be needed on the XBee… Does the program talk to the XBee at a baud rate of 19200? Then appropriate settings would be needed to match the baud of the XBee serial interface, etc.