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Create an html file, paste in the following: <table class=""> <tr ng-repeat="item in items| filter:{ f1: (filters:f1 || ''), f2: (filters:f2 || ''), f3: (filters:f3 || '')}" > </tr> </table> <script type="text/javascript"> (function () { function foo() { $x = 2; } })(jQuery); </script> Run autoformat and all the javascript is left justified instead of being indented correctly. Remove one line so your text is like this: <table class=""> <tr ng-repeat="item in items| filter:{ f1: (filters:f1 || ''), f3: (filters:f3 || '')}" > </tr> </table> <script type="text/javascript"> (function () { function foo() { $x = 2; } })(jQuery); </script> and now the autoformatting works correctly.