Merge pull request #53 from jakobnissen/master

Allow compact printing of alignments

Author: jakobnissen

Project.toml

@@ -4,18 +4,18 @@ authors = ["Kenta Sato <[email protected]>", "Ben J. Ward <benjward@protonma
 version = "2.0.0"
 
 [deps]
-BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea" # Note: required for distance function.
+BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea"
 BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
 BioSymbols = "3c28c6f8-a34d-59c4-9654-267d177fcfa9"
 IntervalTrees = "524e6230-43b7-53ae-be76-1e9e4d08d11b"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 
 [compat]
-julia = "1"
 BioGenerics = "0.1"
 BioSequences = "2"
 BioSymbols = "4"
 IntervalTrees = "1"
+julia = "1"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

src/pairwise/alignment.jl

@@ -132,9 +132,22 @@ aln2ref(aln::PairwiseAlignment, i::Integer) = aln2ref(aln.a, i)
 # Printers
 # --------
 
-function Base.show(io::IO, aln::PairwiseAlignment)
-    println(io, summary(aln), ':')
-    print(io, aln)
+function showshort(io::IO, aln::PairwiseAlignment)
+	print(io, summary(aln), "(lengths=(",
+		length(aln.a.seq), ", ", length(aln.b),
+		")/", length(aln), ')'
+	)
+end
+
+Base.show(io::IO, aln::PairwiseAlignment) = showshort(io, aln)
+
+function Base.show(io::IO, ::MIME"text/plain", aln::PairwiseAlignment)
+    if get(io, :compact, false)
+        showshort(io, aln)
+    else
+        println(io, summary(aln), ':')
+        print(io, aln)
+    end
 end
 
 function Base.print(io::IO, aln::PairwiseAlignment)

src/pairwise/result.jl

@@ -68,15 +68,24 @@ end
 # Printer
 # -------
 
+
 function Base.show(io::IO, aln::PairwiseAlignmentResult{T,S1,S2}) where {T,S1,S2}
-    println(io, summary(aln), ':')
-    if aln.isscore
-        print(io, "  score: ", aln.value)
+    print(io, summary(aln), '(', aln.isscore ? "score" : "distance", '=', aln.value, ')')
+end
+
+function Base.show(io::IO, ::MIME"text/plain", aln::PairwiseAlignmentResult{T,S1,S2}) where {T,S1,S2}
+    if get(io, :compact, false)
+        show(io, aln)
     else
-        print(io, "  distance: ", aln.value)
-    end
-    if hasalignment(aln)
-        println(io)
-        print(io, alignment(aln))
+        println(io, summary(aln), ':')
+        if aln.isscore
+            print(io, "  score: ", aln.value)
+        else
+            print(io, "  distance: ", aln.value)
+        end
+        if hasalignment(aln)
+            println(io)
+            print(io, alignment(aln))
+        end
     end
 end

test/runtests.jl

@@ -1014,7 +1014,9 @@ end
         seqtype = VERSION >= v"1.6" ?
             "BioSequences.LongAminoAcidSeq" :
             "BioSequences.LongSequence{BioSequences.AminoAcidAlphabet}"
-        @test sprint(show, aln) ==
+        buf = IOBuffer()
+        show(buf, MIME"text/plain"(), aln)
+        @test String(take!(buf)) ==
         """
         PairwiseAlignment{$(seqtype),$(VERSION >= v"1.6" ? " " : "")$(seqtype)}:
           seq:  1 EPVTSHPKAVSPTETK--PTEKGQHLPVSAPPKITQSLKAEASKDIAKLTCAVESSALCA 58
@@ -1039,6 +1041,12 @@ end
                   | |||| | |
           ref: 49 CVVESSVLRA 58
         """
+        buf = IOBuffer()
+        print(buf, (aln,))
+        @test String(take!(buf)) == (
+        	"""(PairwiseAlignment{$seqtype,$(VERSION >= v"1.6" ? " " : "")$(seqtype)}""" *
+        	"""(lengths=(58, 58)/60),)"""
+        )
         # Result from EMBOSS Needle:
         # EMBOSS_001         1 EPVTSHPKAVSPTETK--PTEKGQHLPVSAPPKITQSLKAEASKDIAKLT     48
         #                      ||  ||||||||||||  ||||.|||||||||||||.|||||||:|||||