give writemultinewick same options as writenewick (#244)

also:

* v1.3.1

* new method for getconnectingedge; existing (and new) method return nothing instead of an error if a connecting edge doesn't exists

Author: cecileane

Project.toml

@@ -1,7 +1,7 @@
 name = "PhyloNetworks"
 uuid = "33ad39ac-ed31-50eb-9b15-43d0656eaa72"
 license = "MIT"
-version = "1.3.0"
+version = "1.3.1"
 
 [deps]
 BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"

src/auxiliary.jl

@@ -458,8 +458,8 @@ end
 """
     getconnectingedge(node1::Node, node2::Node)
 
-Edge shared by (or connecting) `node1` and `node2`, that is: edge incident
-to both nodes. An error is thrown if the 2 nodes are not connected.
+Edge shared by (or connecting) `node1` and `node2`, that is, edge incident
+to both nodes; or `nothing` if the nodes are not adjacent (without error).
 
 See also [`isconnected`](@ref)
 """
@@ -469,15 +469,36 @@ function getconnectingedge(node1::Node, node2::Node)
             e1 === e2 && return e1
         end
     end
-    error("nodes not connected")
+    return nothing
+end
+"""
+    getconnectingedge(n1_number::Int, n2_number::Int, net::HybridNetwork)
+
+Edge in `net` that is incident to nodes `n1` and `n2` of specified numbers;
+or `nothing` if `n1` and `n2` are not adjacent and no such edge exists
+(without any error).
+
+Warning: if `net` has parallel edges, there might 2+ (hybrid and partner)
+edges connecting `n1` and `n2`. One of them is returned, arbitrarily.
+"""
+function getconnectingedge(n1num::Int, n2num::Int, net::HybridNetwork)
+    n1i = findfirst(n -> n.number == n1num, net.node)
+    isnothing(n1i) && error("no node numbered $n1num")
+    n1 = net.node[n1i]
+    for e in n1.edge
+        n2 = getOtherNode(e,n1)
+        if n2.number == n2num
+            return e
+        end
+    end
     return nothing
 end
 
 """
-    isconnected(node1::Node, node2::Node)
+    isconnected(n1::Node, n2::Node)
 
-Check if two nodes are connected by an edge. Return true if connected, false
-if not connected.
+`true` if nodes `n1` and `n2` are adjacent, that is, connected by an edge;
+`false` otherwise.
 
 See also [`getconnectingedge`](@ref)
 """

src/readwrite.jl

@@ -1202,18 +1202,30 @@ julia> writemultinewick(net, stdout)         # to write to the screen (standard
 (G,H,F);
 ```
 """
-function writemultinewick(n::Vector{HybridNetwork},file::AbstractString; append::Bool=false)
+function writemultinewick(
+    n::Vector{HybridNetwork},
+    file::AbstractString;
+    append::Bool=false,
+    kwargs...
+)
     mode = (append ? "a" : "w")
     open(file, mode) do s
-    writemultinewick(n,s)
+    writemultinewick(n,s; kwargs...)
     end # closes file safely
 end
 
-function writemultinewick(net::Vector{HybridNetwork},s::IO)
+function writemultinewick(
+    net::Vector{HybridNetwork},
+    s::IO;
+    round::Bool=false,
+    digits::Integer=3,
+    di::Bool=false,
+    internallabel::Bool=true,
+    support=nothing,
+)
     for i in 1:length(net)
       try
-        # writeTopologyLevel1(net[i],s,false,true,"none",false,false,3)
-        writenewick(net[i],s) # no rounding, not for dendroscope
+        writenewick(net[i],s,round,digits,di,internallabel,support)
         write(s,"\n")
       catch err
         if isa(err, RootMismatch) # continue writing other networks in list

test/test_auxiliary.jl

@@ -56,6 +56,9 @@ PhyloNetworks.EdgeT{PhyloNetworks.Node}:
 @test PhyloNetworks.getIndexNode(net0.edge[10], net0.node[8]) == 1
 @test PhyloNetworks.getIndexHybrid(net0.node[8], net) == 1
 @test PhyloNetworks.getconnectingedge(net0.node[8], net0.node[13]) === net0.edge[10]
+@test isnothing(PhyloNetworks.getconnectingedge(net0.node[8], net0.node[12]))
+@test PhyloNetworks.getconnectingedge(1, -4, net0) === net0.edge[1]
+@test isnothing(PhyloNetworks.getconnectingedge(2, -5, net0))
 PhyloNetworks.deleteIntNode!(net0, getroot(net0))
 @test net0.numedges == 19
 @test net0.numnodes == 18

test/test_relaxed_reading.jl

@@ -76,11 +76,11 @@ end
     @test_logs (:warn, r"^γ read") readnewick("(a:::.5);")
     @test_logs (:warn, r"^partners: 2 with no γ, 3 with γ>1.") readnewick("((b)#H1,#H1:::1.1);")
     @test_logs (:warn, r"^partners: 3 with no γ, 2 with γ>1.") readnewick("((b)#H1:::1.1,#H1);")
-    net = readnewick("(a, b):0.5;")
+    net = readnewick("(a, b:0.123:0.81);")
     tmpfile = "tmp.nwk"
-    writemultinewick([net], tmpfile)
-    writenewick(net, tmpfile; append=true, support=true)
-    @test readlines(tmpfile) == ["(a,b);","(a,b);"]
+    writemultinewick([net], tmpfile; round=true, digits=1, support=:y)
+    writenewick(net, tmpfile; append=true)
+    @test readlines(tmpfile) == ["(a,b:0.1:0.8);","(a,b:0.123);"]
     rm(tmpfile)
     @test_throws "not find or open tmp.nwk" readnewick(tmpfile)
     @test writenewick(readnewick("((a,(b)#H1)i1,(#H1,c))r;")) == "((a,(b)#H1)i1,(#H1,c))r;"