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I am a Computer Science major. I would like a note-taking program that will allow me a lot of versatility with math notation, allows me to format java code samples similarly to StackExchange and lets me drag pictures into the program. If it lets me save my notes in a common file-format such as pdf, odt, doc, or similar, that would be good too.

I understand this is a lot of requirements, so if it's not possible I apologize. Please, just suggest the best fits you can find.

I always say this on StackExchange websites. If you feel this post requires down-voting, please let me know why. I believe this is encouraged.

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Joplin is probably what you're looking for. It supports Markdown, and thus can be used to store code snippets. It also supports Math expressions using the Katex notation. Notes can be exported to PDF directly from Joplin. And of course, it supports images too.

Joplin is a free and open source note taking and to-do application available for Linux, Windows, macOS, Android and iOS. Its key features include end-to-end encryption, Markdown support, and synchronization via third-party services like NextCloud, Dropbox, OneDrive or WebDAV.

For me, Joplin is the perfect Evernote alternative, and more, since it supports encryption, is open source and supports synchronization using a cloud sync service of your choice.

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