I'm not sure if this is what you're looking for or not, but here's how you do it by command line
REM These lines create the keystore
"C:\Program Files (x86)\Java\jdk1.6.0_23\bin\keytool" -genkey -keyalg rsa -alias netSSH
"C:\Program Files (x86)\Java\jdk1.6.0_23\bin\keytool" -certreq -alias netSSH
REM This line signs the Jar
"C:\Program Files (x86)\Java\jdk1.6.0_23\bin\jarsigner" -storepass <password> -signedjar "C:\Users\Jay\U\Workspace\U\Unification\SeaChange\war\java\seaChangeS.jar" "C:\Users\Jay\U\Workspace\U\Unification\SeaChange\war\java\seaChange.jar" netSSH