I started with jquery and then bought some books in classic javascript (e.g. jony resig, jquery programmer!)
I thought javascript is hard to learn and with jquery you will learn what can be done with javascript! Then with books you will understand the insides of jquery. good luck
Also, if you need to choose between prototype and jquery, select jquery, I used the prototype for 4 months and did not recognize any javascript function.
Then, in just 1 week of javascript, I knew that setTimeout was used to
Just an example showing jquery to help you learn javascript from time to time
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