Add getter methods (and forwarded getter methods) for alignment types

CHANGELOG.md

@@ -7,6 +7,10 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ## [Unreleased]
 
+### Added
+- Getter functions for `AlignedSequence`, `PairwiseAlignment`, and
+  `PairwiseAlignmentResult`
+
 ## [2.2.0]
 
 ### Added

docs/src/alignments.md

@@ -177,3 +177,24 @@ 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
+
+```

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

src/BioAlignments.jl

@@ -69,7 +69,8 @@ export
     score,
     distance,
     alignment,
-    hasalignment
+    hasalignment,
+    sequence
 
 using BioGenerics
 import BioGenerics: distance

src/alignedseq.jl

@@ -60,6 +60,21 @@ 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

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)

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
 # -------