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Decide between Apex & Java

Hello All,

             I have a task that requires me to update our org's SF pages using data internal to our org. I have very little Apex development experience, but I've developed some small apex snippets as part of support. I am confused as to what would be the best bet in my case. I have to query a huge set of data from some tables and update certain objects in SF like Customer,Accounts,Contacts,Opportunity etc. Apex Reference document says that we should use Apex to,

 

"Process more than one record at a time efficiently, and with transactional correctness"

 

Apart from the "transactional correctness"I do not clearly understand the above statement. I am comfortable coding the entire piece in Java but I'd like to know the most efficient way of doing it to make the right architectural decision. Also, is there any governing limit that I should be concerned about? by going with Java or Apex? Please advice. Thanks all.