Merge pull request #85 from BioJulia/release/v2.3.0

Downstream tests are failing because the breaking change from #44 was merged here.
BioJulia · Oct 1, 2022 · b92ccf3 · b92ccf3
2 parents 782063c + eceafe6
commit b92ccf3
Show file tree

Hide file tree

Showing 8 changed files with 77 additions and 5 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,7 +10,13 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ### Added
 - Alignment position support (#44)
 
-## [2.2.0]
+## [2.3.0] - 2022-10-01
+
+### Added
+- Getter functions for `AlignedSequence`, `PairwiseAlignment`, and
+  `PairwiseAlignmentResult` (#83)
+
+## [2.2.0] - 2022-07-07
 
 ### Added- Compact printing of alignments (#53)
 - More SubstitutionMatrix operations (#60)
@@ -106,7 +112,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ## [0.1.0] - 2017-06-30
 - This initial release extracted the alignment utilities out from Bio.jl into this dedicated package.
 
-[Unreleased]: https://github.com/BioJulia/BioAlignments.jl/compare/v2.2.0...HEAD
+[Unreleased]: https://github.com/BioJulia/BioAlignments.jl/compare/v2.3.0...HEAD
+[2.2.1]: https://github.com/BioJulia/BioAlignments.jl/compare/v2.2.0...v2.3.0
 [2.2.0]: https://github.com/BioJulia/BioAlignments.jl/compare/v2.1.0...v2.2.0
 [2.1.0]: https://github.com/BioJulia/BioAlignments.jl/compare/v2.0.1...v2.1.0
 [2.0.1]: https://github.com/BioJulia/BioAlignments.jl/compare/v2.0.0...v2.0.1

diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "BioAlignments"
 uuid = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e"
 authors = ["Kenta Sato <bicycle1885@gmail.com>", "Sabrina J. Ward <sabrinajward@protonmail.com>"]
-version = "2.2.0"
+version = "2.3.0"
 
 [deps]
 BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea"

diff --git a/docs/src/alignments.md b/docs/src/alignments.md
@@ -180,3 +180,24 @@ julia> AlignedSequence(seq, ref)
 ACGT--AAT--
 
 ```
+
+You can get the underlying alignment and sequence back out of an
+`AlignedSequence` by using the `alignment` and `sequence` functions.
+
+```jldoctest
+julia> aln = AlignedSequence(dna"ACGT--AAT--", dna"ACGTTTAT-GG")
+········-··
+ACGT--AAT--
+
+julia> alignment(aln)
+Alignment:
+  aligned range:
+    seq: 0-7
+    ref: 0-10
+  CIGAR string: 4=2D1=1X1I2D
+
+julia> sequence(aln)
+7nt DNA Sequence:
+ACGTAAT
+
+```
diff --git a/docs/src/pairalign.md b/docs/src/pairalign.md
@@ -91,6 +91,9 @@ PairwiseAlignment{BioSequences.LongSequence{BioSequences.DNAAlphabet{4}}, BioSeq
            ||| ||      || |
   ref:  1 ACCT-GGTATGATAGCG 16
 
+julia> sequence(res)
+10nt DNA Sequence:
+CCTAGGAGGG
 
 julia> count_matches(aln)
 8

diff --git a/src/BioAlignments.jl b/src/BioAlignments.jl
@@ -75,7 +75,8 @@ export
     score,
     distance,
     alignment,
-    hasalignment
+    hasalignment,
+    sequence
 
 using BioGenerics
 import BioGenerics: distance

diff --git a/src/alignedseq.jl b/src/alignedseq.jl
@@ -62,6 +62,21 @@ function AlignedSequence(seq::BioSequences.BioSequence, seqpos::Integer,
     return AlignedSequence(newseq, anchors)
 end
 
+# Getter functions
+"""
+    alignment(aligned_sequence)
+
+Gets the [`Alignment`](@ref) of `aligned_sequence`.
+"""
+alignment(alnseq::AlignedSequence) = alnseq.aln
+
+"""
+    sequence(aligned_sequence)
+
+Return the sequence of `aligned_sequence`.
+"""
+sequence(alnseq::AlignedSequence) = alnseq.seq
+
 # First position in the reference sequence.
 function IntervalTrees.first(alnseq::AlignedSequence)
     return alnseq.aln.firstref

diff --git a/src/pairwise/alignment.jl b/src/pairwise/alignment.jl
@@ -14,6 +14,21 @@ mutable struct PairwiseAlignment{S1,S2}
     b::S2
 end
 
+# Getter functions
+"""
+    alignment(pairwise_alignment)
+
+Gets the underlying [`Alignment`](@ref) from `pairwise_alignment`.
+"""
+alignment(aln::PairwiseAlignment) = alignment(aln.a)
+
+"""
+    sequence(pairwise_alignment)
+
+Gets the query sequence of `pairwise_alignment`.
+"""
+sequence(aln::PairwiseAlignment) = sequence(aln.a)
+
 function Base.iterate(aln::PairwiseAlignment, ij=(2,1))
     i, j = ij
     if i > lastindex(aln.a.aln.anchors)

diff --git a/src/pairwise/result.jl b/src/pairwise/result.jl
@@ -53,7 +53,10 @@ hasalignment(aln::PairwiseAlignmentResult) = aln.aln !== nothing
 """
     alignment(alignment_result)
 
-Return alignment if any.
+Return the alignment if any as a [`PairwiseAlignment`](@ref). To get the
+[`Alignment`](@ref), nest the function, e.g. `alignment(alignment(alignment_result))`.
+This function returns a `PairwiseAlignment` instead of an `Alignment` for
+backwards-compatibility reasons.
 
 See also: `hasalignment`
 """
@@ -64,6 +67,13 @@ function alignment(aln::PairwiseAlignmentResult)
     return aln.aln
 end
 
+"""
+    sequence(alignment_result)
+
+Return the query sequence of `alignment_result`, if it exists.
+"""
+sequence(aln::PairwiseAlignmentResult) = sequence(alignment(aln))
+
 
 # Printer
 # -------