Allow compact printing of alignments

[jakobnissen]

This changes printing of PairwiseAlignment and PairwiseAlignmentResult, such that they are displayed compactly in vectors and other structs. (I was getting annoyed by having my terminal wrecked when printing vectors of alignments).

When compact, they are now displayed like this:

julia> [aln]
1-element Vector{PairwiseAlignment{LongDNASeq, LongDNASeq}}:
 PairwiseAlignment{LongDNASeq, LongDNASeq}()

julia> [alnresult]
1-element Vector{PairwiseAlignmentResult{Int64, LongDNASeq, LongDNASeq}}:
 PairwiseAlignmentResult{Int64, LongDNASeq, LongDNASeq}(score=15)

This does violate the principle that the thing being printed should contain all the relevant information in the object, but in this case, I think there is no way to do this.

[codecov[bot]]

Codecov Report

Merging #53 (2c6f47f) into master (492cd58) will decrease coverage by 0.58%. The diff coverage is 36.84%.

@@            Coverage Diff             @@
##           master      #53      +/-   ##
==========================================
- Coverage   88.32%   87.73%   -0.59%     
==========================================
  Files          17       16       -1     
  Lines        1079     1052      -27     
==========================================
- Hits          953      923      -30     
- Misses        126      129       +3     

Impacted Files	Coverage Δ
src/pairwise/result.jl	43.47% <0.00%> (-9.16%)	:arrow_down:
src/pairwise/alignment.jl	98.21% <87.50%> (-0.86%)	:arrow_down:
src/operations.jl	85.71% <0.00%> (-4.61%)	:arrow_down:
src/pairwise/algorithms/banded_needleman_wunsch.jl	76.35% <0.00%> (-2.96%)	:arrow_down:
src/pairwise/algorithms/common.jl	90.32% <0.00%> (-0.86%)	:arrow_down:
src/pairwise/algorithms/needleman_wunsch.jl	84.29% <0.00%> (-0.38%)	:arrow_down:
src/BioAlignments.jl
src/submat.jl	98.07% <0.00%> (+0.01%)	:arrow_up:
src/alignment.jl	79.16% <0.00%> (+0.83%)	:arrow_up:
src/anchors.jl	100.00% <0.00%> (+16.66%)	:arrow_up:

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[BioTurboNick]

Is there some summary information that would be useful to print? aligned length, ungapped length of each sequence?

[CiaranOMara]

Does IOContext offer anything here?

[jakobnissen]

Does IOContext offer anything here?

Not 100% sure, but the docs for show states:

Checking the :compact IOContext property of io in such methods is recommended, since some containers show their elements by calling this method with :compact => true.

But yeah, good point @BioTurboNick , I'll add some more info. And also a few more tests of printing, just to make codecov happy :)

[jakobnissen]

Codecov is acting up, this is most definitely covered by the tests. Merging