Since a SharePoint application page references a master page file, all javascript needs to reside in the master page. However, when creating an application page to be used within your SharePoint environment, you’ll need to register a client script block.

To do so, add your own variation of javascript within the Page_Load() method of the aspx page that references a master page file:

<script runat="server" language="c#">
    private void Page_Load()
    {
        string myScript = string.Empty;
        myScript += "var showRow= true;";
        myScript += "function toggle(myTable) {";
        myScript += "  myTable.style.display = '';";
        myScript += "  var myTableRows = myTable.rows;";
        myScript += "  for (i = 0; i < myTableRows .length; i++) {";
        myScript += "    if (myTableRows [i].className != 'ChildGridHeaderRow') {";
        myScript += "      myTableRows [i].style.display = (showRow) ? 'none' : '';";
        myScript += "    }";
        myScript += "  }";
        myScript += "  showRow = !showRow;";
        myScript += "}";

        ClientScript.RegisterClientScriptBlock(this.GetType(), "MyOwnJavascriptTitle", myScript, true);
    }
</script>