Remake JS and jQuery into AngularJS
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I suggest you to start with some tutorials (codescool offer the best one in my opinion)
Then google is my encyclopedia about single cases. If you post some case probably we can help you but your question is too general to have an answer
Angular1 is noting but organised JS, where you have controllers and related views and it can be totally written in the plain JS, you would however need to understand angular format of writing controllers.
Angular2 on the other hand should be written using typescript
Starts with some basic AngularJS tutorials like AngularJS Guide, get ramp-up on it and then starts desinging app in Architectural way in terms of Angular (MVC).
AngularJs provides MVC paltform where you can separate your Model, Views and Controller, so all your js related code goes in controller(Business logic) and model will be used in Views for data binding.
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