-et option (default factor threshold) and Hassan's factor thr file are (effectively) ignored.

[bryan-lunt]

Users should resolve by vote which order these get resolved in.

Currently, the factor thresholds will be input if they are provided in the .par file, but the other input locations are, in effect, ignored.

So we need to decide which order to resolve these in.

My preference is :
-ft (The factor threshold file) overwrites the input from
-et (The overall default factor threashold) which overwrites the input from
the .par file

The reason this is effectively ignored is that from neither of the first sources does it make its way into the parameters that get fed into the ExprPredictor (They do get used for the initial annotation.).
Unfortunately ExprPredictor re-annotates every sequence each time it's called on to make a prediction.
(That's fine if you want to learn the annotation threshold, but because it never got the values that were specified earlier, it means it starts at the default.)

[bryan-lunt]

Some more formal tests, and then we can close this issue.

[bryan-lunt]

Done.