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How to offer custom word processor like editing power from an application

I have a very complex Java application which renders spreadsheet tables and summary documents in a window.
These outputs are non standard in the sense that for instance the spreadsheet table isn’t really a spreadsheet indeed not every row is an instance of an entity and every column an attribute. Some rows might for instance be titles to sub tables.

Optimal data structure for binary data/Java

I have several input formats mostly restricted to geotiff and some proprietary binary formats. I import them into my program and then need to export them into various other data formats (also binary) but as two dimensional arrays.