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My suggestion: Do not add a flag, but a new type of alignment to the testcase. This alignment specifies correspondences that should be dropped during evaluation. Instead of setting the flag when sampling an input alignment, you can then set this alignment to the input alignment
You could name this alignment BlocklistAlignment, DropAlignment, or excludeAlignment.
TestCase gets an additional boolean to remove from the system alignment the input alignment during evaluation.
Possible names:
removeInputAlignment
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