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Using the delete duplicates tool is there a way in Mapbasic to have it run through a large number of tables, or do you have to manually select each table and run the tool?

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You can find the MapBasic source code for the Delete Duplicates tool in your MapBasic installations folder: ..\Samples\MAPBASIC\DeleteDuplicates

With this you can modify the code to loop thru all open tables or modify the dialog to let the user pick more than one table.

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