Methods for organizing/showing algorithm that is coded in C or MATLAB
Is there any recommendations for how to show what your code is doing (C or MATLAB)?  Imagine if your code is really long and you have a lot of functions in your program, what is the best way to document the program?  I know Java IDEs have a way to ingest comments and spit them back out into a document that shows all the functions, and their inputs and outputs. I don't think C or MATLAB has this feature.  At this point, I am thinking comments are the only way to show what is going on in the code, but it may confuse the reader if they have to look through the raw code along side the comments.  The second option would be to write out the algorithm in a text editor such as Microsoft Word.  Is there an industry standard for doing this?

Thanks!  
Methods for organizing/showing algorithm that is coded in C or MATLAB
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Is there any recommendations for how to show what your code is doing (C or MATLAB)?  Imagine if your code is really long and you have a lot of functions in your program, what is the best way to document the program?  I know Java IDEs have a way to ingest comments and spit them back out into a document that shows all the functions, and their inputs and outputs. I don't think C or MATLAB has this feature.  At this point, I am thinking comments are the only way to show what is going on in the code, but it may confuse the reader if they have to look through the raw code along side the comments.  The second option would be to write out the algorithm in a text editor such as Microsoft Word.  Is there an industry standard for doing this?

Thanks!  