JAL-3053

JAL-3053
JAL-3061
two bugs with a similar theme (RNA secondary structure annotations)

JAL-3053
This fixes the reading in of Vienna extended dot-bracket notation for
RNA secondary structure annotations (which includes ALPHA/alpha braces).

To avoid (almost all) ambiguity with a protein secondary structure
annotation (Es and Hs), there's a whole-annotation regex match to ensure
some other RNA-based extended dot-bracket feature is present, and then
the reading in can assume an RNA feature set.

Test StockholmFileTest.stockholmFileRnaSSAlphaChars() compares the test
file examples/rna_ss_test.stk with a hard-coded Jalview equivalent. The
Annotation rnasecstr pairing is checked. I've added a sort Comparator
for SequenceFeature to help ensure that check is correct.
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JAL-3061
There is also a fix for the RNA Secondary Structure annotation output
that was preserving spaces in the output. This is not valid output in
this case, and so a '.' is used instead.

No test for this yet, will add later.