Temperature and Secondary structure reference annotation not displayed when PDB + PAE loaded via structure chooser local file option

1. Need failing tests to check that adding a local structure, optionally with PAE file for a sequence actually adds annotation rows to the alignment honouring the current structure import settings.

See jalview.structure.StructureSelectionManagerTest.testAssociatedMappingToSubSeq() for example of how to do that (this one retrieves a structure via network..)

2. Fix tests.
3. Profit :)