I have been trying to guard the signature of a method by adding 
"//GEN-LINE:" in the beginning of the body just after the beginning
brace. I get the content of the method and prefix it with "//GEN-LINE:"
and then set the body with setBody() of MethodElement.

This works a fine when I create a new Method as shown below:
String body = ...
MethodElement method = new MethodElement();
method.setBody("//GEN-LINE:\n" + body);

Then I see the method written as below:

public void success() {//GEN-LINE:
   //body
}

But the issue is when I try to modify an existing
method from a source file.

MethodElement method = ... // get existing method
String body = methd.getBody();
method.setBody("GEN-LINE:\n" + body);

In this case an existing method:

publid void failed() {}

will be modified as:

public void failed() {
   //GEN-LINE:
}

I am expecting this guarded comment
to appear on the same line of the method
signature as shown below so that I can guard the signature.

public void failed() {//GEN-LINE:
}

I am not able to figure out where this new line
is being added while modifying an existing method.

Any help in this regard is greatly appreciated.