JAL-3053JAL-3061 two bugs with a similar theme (RNA secondary structure annotations)JAL-3053This fixes the reading in of Vienna extended dot-bracket notation forRNA secondary structure annotations (which includes ALPHA/alpha braces).To avoid (almost all) ambiguity with a protein secondary structureannotation (Es and Hs), there's a whole-annotation regex match to ensuresome other RNA-based extended dot-bracket feature is present, and thenthe reading in can assume an RNA feature set.Test StockholmFileTest.stockholmFileRnaSSAlphaChars() compares the testfile examples/rna_ss_test.stk with a hard-coded Jalview equivalent. TheAnnotation rnasecstr pairing is checked. I've added a sort Comparatorfor SequenceFeature to help ensure that check is correct.--JAL-3061There is also a fix for the RNA Secondary Structure annotation outputthat was preserving spaces in the output. This is not valid output inthis case, and so a '.' is used instead.No test for this yet, will add later.