Add findall method

[CiaranOMara]

I reckon this PR fulfils the findall method requirements.

The findall method delegates to a Search iterator in the implementation. Let me know whether this approach suits and I'll add some docstrings.

Closes #217.

[codecov]

Codecov Report

Merging #218 (7a16f9d) into master (8d0080a) will increase coverage by 0.12%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #218      +/-   ##
==========================================
+ Coverage   88.45%   88.57%   +0.12%     
==========================================
  Files          31       31              
  Lines        2408     2425      +17     
==========================================
+ Hits         2130     2148      +18     
+ Misses        278      277       -1     

Flag	Coverage Δ
unittests	88.57% <100.00%> (+0.12%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
src/BioSequences.jl	94.11% <100.00%> (+94.11%)	⬆️
src/longsequences/seqview.jl	100.00% <100.00%> (ø)
src/biosequence/find.jl	61.29% <0.00%> (+3.22%)	⬆️

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[jakobnissen]

Great, thanks for contributing. Not sure about the signature though, it doesn't match Base. What signature would you prefer?

[CiaranOMara]

This PR is ready for another review pass.

I've added a convenience method that uses a view to limit the search range and map indices back to a parent. If it's not worthwhile, it can be removed.

BioSequences.jl/src/BioSequences.jl

Lines 259 to 263 in fd0f57f

	function Base.findall(pat, seq::BioSequence, rng::UnitRange{Int}; overlap::Bool = DEFAULT_OVERLAP)
	v = view(seq, rng)
	itr = search(pat, v; overlap)
	return map(x->parentindices(v)[1][x], itr)
	end

Also, is the PR code positioned where you'd like it to be within the project?

[jakobnissen]

I think everything looks good now.

[TransGirlCodes]

Looking good! Did you want to add some docstrings and or a paragraph in the search section of the manual? No immediate pressure as they can always be added before a release.

[CiaranOMara]

I reckon I can add some docstrings to this over the next couple of days.

[jakobnissen]

I'll just merge this, and then we can always add some docs later.