How can I add a Google apps script to a spreadsheet created using the API?

Question

After reading up a lot on the Google Spreadsheet API I have come to the conclusion that formatting (such as merging cells, changing fonts etc) is only avail

Answer 1

(Aug 2016) There is no way programmatic way to link a Google Sheet and Apps Script code other than manually. Based on what it seems you want ("create and fill the spreadsheets with data programatically using Java"), you can now do it without Apps Script.

TL;DR: Above, @Henrique has answered multiple questions and even questions that weren't asked! The good news is that today, we have more answers representing alternate possible solutions to what you're seeking.

1. It's now possible to "upload" Apps Script code programmatically with the import/export system, say with Eclipse since you're a Java developer (2013 announcement).
2. I agree with Henrique's suggestion that if you create a spreadsheet template, i.e., Excel file, you can use the Google Drive API to programmatically import/create identical Google Sheets with all your desired formatting.
3. "Formatting (such as merging cells, changing fonts etc)" can now be done outside of Apps Script, as there is a "new" Google Sheets API v4 (not GData).

In order to use the new API, you need to get the Google APIs Client Library for Java and use the latest Sheets API, which is much more powerful and flexible than any previous API. Here's one code sample to help get you started. If you're not "allergic" to Python, I also made a video with a different, slightly longer example introducing the new API and gave a deeper dive into its code via a blogpost that you can learn from.

Note the v4 API allows you to create spreadsheets & sheets, upload & download data, as well as, in the general sense, programmatically access a Sheet as if you were using the user interface (create frozen rows, perform cell formatting, resizing rows/columns, adding pivot tables, creating charts, etc.), but to perform file-level access such as uploads & downloads, imports & exports (same as uploads & downloads but conversion to/from Google Apps formats), you would use the Drive API instead.