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Basically, Java script is a client side script which is used in web application. You can use it in verify a form in HTML, you can also use it in anything animation perposes. So obviously you can used Javas cripts in JS header in lotusscript agent.
Put a deeper view below-
3. As whatever you like to response, use the agent.
// Builds the XML variables
that will be sent to the agent.
var objDOM = new ActiveXObject
RootEl = objDOM.createNode(1,
objDOM.documentElement = RootEl
// add as many of these nodes as
// these variables will be accessible
via the agent.
objHeaders = objDOM.createNode
(1, "DocID", "")
objHeaders.text = document.all.