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JAL-3210 Barebones gradle/buildship/eclipse. See README

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


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.



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.

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Stockholm file for test

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