Adobe Acrobat is not just a pdf reader. You can make an automatic script out of it based on JavaScript. This reading first come to mind when I was trying to find a way to copy highlighted text from pdf easily. I found out that I can use Acrobat JavaScript to extract highlighted text from a pdf file [2]!

To get started, you can read [2]. Furthermore, if you want to get source sample that is more applicable or even watch video training, you can check premium section in [3]. For list of Adobe Javascript API reference, you can read [4].

Sources:

[1] http://franciscomorales.org/2012/10/18/how-to-extract-highlighted-text-from-a-pdf-file/

[2] http://acrobatusers.com/tutorials/javascript_console

[3] http://www.pdfscripting.com/

[4] http://www.adobe.com/content/dam/Adobe/en/devnet/acrobat/pdfs/js_api_reference.pdf

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