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JAL-2996 JAL-3053 ~ | : [] {} () treated as gap characters.

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JAL-3095 account for sequence start when highlighting selections in trimmed VARNA model

JAL-3053 JAL-3061 JAL-3095 release notes

Merge branch 'bug/JAL-3061_RNA_secondary_structure_annotation_gap_character' into releases/Release_2_10_5_Branch

Merge branch 'releases/Release_2_10_5_Branch' of http://source.jalview.org/git/jalview into releases/Release_2_10_5_Branch

JAL-3095 release notes

java doc and fix for JAL-3095 - region of trimmed RNA model to highlight is indexed relative to SeuqenceI.getStart()

JAL-3003 remove redundant call to drawSelectionGroup

JAL-3092 release notes

JAL-3092 make sure base pair counter is always moved in loop that computes the helix count for a strand of RNA secondary structure

JAL-3091 release notes for JAL-3003 JAL-3059

JAL-3003 different coloured borders in demo annotation file

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JAL-247 release notes

JAL-3091 release 2.10.5 added to release notes

JAL-3061 / JAL-3053

Fixed broken StockholmFileTest tests



by adding " ." as a recognised Annotation.isWhiteSpace displayCharacter

(which happens for StockholmFile '.' RNA SS annotations)

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JAL-247 comment to clarify wrapped print algorithm

JAL-247 print/export wrapped uses common code to draw seq ids and annotation labels

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JAL-3087 include full alignment height in repeating wrapped height

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JAL-247 draw/print sequence ids now uses common code (unwrapped case)

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JAL-3059 use correct border colour for groups

JAL-3003 draw selection group outline on main graphics context

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JAL-3061 Added test StockholmFileTest.stockholmFileRnaSSSpaceChars() to read in RNA SS annotation with spaces, and check that StockholmFile print output converts these to '.'s. Also slight adjustment to StockholmFile.outputCharacter to avoid a nullPointer exception.

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Merge branch 'bug/JAL-3061_RNA_secondary_structure_annotation_gap_character' of https://source.jalview.org/git/jalview into bug/JAL-3061_RNA_secondary_structure_annotation_gap_character

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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Merge branch 'releases/Release_2_10_4_Branch' into bug/JAL-3061_RNA_secondary_structure_annotation_gap_character

Merge branch 'task/JAL-3047_clover2104b1_cherrypick' into releases/Release_2_10_4_Branch

Stockholm file for test

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Fixed bug ignoring "alpha" extended braces in RNA SS line in StockholmFile.java (loading a stockholm file with alpha braces in the SS_cons line)

JAL-3047 don't set classes unconditionally (forgot to delete it in earlier patch)

JAL-3047 don’t let the makedist task complete if a clover build was performed