standardize and export getter names

docs/make.jl

@@ -16,7 +16,7 @@ makedocs(
         "Home" => "index.md",
         "Manual" => [
             "Installation" => "man/installation.md",
-            #"Network manipulation" => "man/netmanipulation.md",
+            "Network manipulation" => "man/netmanipulation.md",
             "Input Data for SNaQ" => "man/inputdata.md",
             "TICR pipeline" => "man/ticr_howtogetQuartetCFs.md",
             "Network estimation and display" => "man/snaq_plot.md",

docs/src/index.md

@@ -55,7 +55,7 @@ for network inference:
 ```@contents
 Pages = [
     "man/installation.md",
-    # "man/netmanipulation.md",
+    "man/netmanipulation.md",
     "man/inputdata.md",
     "man/ticr_howtogetQuartetCFs.md",
     "man/snaq_plot.md",

docs/src/lib/public.md

@@ -22,14 +22,36 @@ Private = false
 Order   = [:type]
 ```
 
-## utilities
+## basic utilities
 
 ```@docs
 tipLabels
-sorttaxa!
 printEdges
 printNodes
-summarizeDataCF
+getroot
+isrootof
+#isleaf
+#isexternal
+isparentof
+#ischildof
+hassinglechild
+getchild
+#getchildren
+#getchildedge
+getparent
+#getparents
+#getparentminor
+#getparentedge
+#getparentedgeminor
+getpartneredge
+getNodeAges
+pairwiseTaxonDistanceMatrix
+```
+
+## utilities to manipulate networks
+
+```@docs
+sorttaxa!
 directEdges!
 checkroot!
 preorder!
@@ -46,15 +68,9 @@ shrink2cycles!
 shrink3cycles!
 deleteHybridThreshold!
 rotate!
-getindex(::TraitSimulation, ::Symbol)
-getNodeAges
-pairwiseTaxonDistanceMatrix
 biconnectedComponents
 blobDecomposition
 treeedgecomponents
-getlabels
-nparams
-mapindividuals
 nni!
 ```
 
@@ -87,6 +103,7 @@ mapAllelesCFtable
 snaq!
 topologyMaxQPseudolik!
 topologyQPseudolik!
+summarizeDataCF
 fittedQuartetCF
 bootsnaq
 calibrateFromPairwiseDistances!
@@ -131,6 +148,7 @@ regressorShift
 regressorHybrid
 sharedPathMatrix
 vcv
+getindex(::TraitSimulation, ::Symbol)
 ```
 
 ## discrete trait evolution
@@ -143,7 +161,9 @@ randomTrait
 randomTrait!
 fitdiscrete
 maxParsimonyNet
+getlabels
 nstates
+nparams
 stationary
 empiricalDNAfrequencies
 ```

docs/src/man/netmanipulation.md

@@ -17,10 +17,17 @@ To traverse or learn something about a network, node or edge, see for example:
 - [`displayedTrees`](@ref), [`majorTree`](@ref),
   [`biconnectedComponents`](@ref), [`PhyloNetworks.blobInfo`](@ref)
 - [`hardwiredCluster`](@ref), [`hardwiredClusters`](@ref)
-- [`PhyloNetworks.getPartner`](@ref),
-  [`PhyloNetworks.getChild`](@ref), [`PhyloNetworks.getChildren`](@ref), [`PhyloNetworks.getChildEdge`](@ref)
-  [`PhyloNetworks.getParent`](@ref), [`PhyloNetworks.getParents`](@ref),
-  [`PhyloNetworks.getMajorParent`](@ref), [`PhyloNetworks.getMajorParentEdge`](@ref),
+- [`getroot`](@ref), [`isrootof`](@ref),
+  [`isleaf`](@ref PhyloNetworks.isrootof), [`isexternal`](@ref PhyloNetworks.isrootof),
+  [`isparentof`](@ref), [`ischildof`](@ref PhyloNetworks.isparentof),
+  [`hassinglechild`](@ref),
+- [`getchild`](@ref), [`getchildren`](@ref PhyloNetworks.getchild),
+  [`getchildedge`](@ref PhyloNetworks.getchild)
+  [`getparent`](@ref), [`getparents`](@ref PhyloNetworks.getparent),
+  [`getparentminor`](@ref PhyloNetworks.getparent),
+  [`getparentedge`](@ref PhyloNetworks.getparent),
+  [`getparentedgeminor`](@ref PhyloNetworks.getparent),
+  [`getpartneredge`](@ref)
 
 To modify a network, for example:
 - [`rootonedge!`](@ref), [`rootatnode!`](@ref):

src/PhyloNetworks.jl

@@ -71,10 +71,25 @@ module PhyloNetworks
         readSnaqNetwork,
         topologyMaxQPseudolik!,
         topologyQPseudolik!,
+        ## getters
+        # fixit: add ancestors? getsibling? getdescendants (currently descendants)?
+        getroot,
+        isrootof,
+        isleaf,
+        isexternal,
+        isparentof,
+        ischildof,
+        hassinglechild,
+        getchild,
+        getchildren,
+        getchildedge,
+        getparent,
+        getparents,
+        getparentminor,
+        getparentedge,
+        getparentedgeminor,
+        getpartneredge,
         ## Network Manipulation
-        # getParent, getParents, getMajorParentEdge, getMinorParentEdge, getChildren,
-        # functions above: first rename them throughout to be consistent with other packages, like:
-        # parent child parents children parentmajor parentminor ancestor sibling offspring
         rootatnode!,
         rootonedge!,
         directEdges!,
@@ -96,7 +111,6 @@ module PhyloNetworks
         biconnectedComponents,
         blobDecomposition!,
         blobDecomposition,
-        mapindividuals,
         nni!,
         checkroot!,
         treeedgecomponents,

src/addHybrid.jl

@@ -48,7 +48,7 @@ julia> PhyloNetworks.addhybridedge!(net, true, true)
  name:H3
  hybrid node
  attached to 3 edges, numbered: 5 16 17
-, PhyloNetworks.Edge:
+, PhyloNetworks.EdgeT{PhyloNetworks.Node}:
  number:17
  length:0.01
  minor hybrid edge with gamma=0.32771460911632916
@@ -77,8 +77,8 @@ function addhybridedge!(net::HybridNetwork, nohybridladder::Bool, no3cycle::Bool
             continue           # if (e1,e2) was already attempted
         nattempts += 1
         ## check that constraints are met
-        p1 = getParent(edge1)
-        p2 = getParent(edge2)
+        p1 = getparent(edge1)
+        p2 = getparent(edge2)
         constraintsmet = true
         for con in constraints
             if con.type == 1 # forbid going out of (edge1) or into (edge2) the species group
@@ -97,7 +97,7 @@ function addhybridedge!(net::HybridNetwork, nohybridladder::Bool, no3cycle::Bool
         end
         ## check for no hybrid ladder, if requested:
          # edge2 cannot be a hybrid edge or the child of a hybrid node
-        if nohybridladder && (edge2.hybrid || getParent(edge2).hybrid)
+        if nohybridladder && (edge2.hybrid || getparent(edge2).hybrid)
             push!(blacklist, (e1,e2))
             continue
         end
@@ -151,7 +151,7 @@ julia> hybnode, hybedge = PhyloNetworks.addhybridedge!(net, net.edge[13], net.ed
  name:H3
  hybrid node
  attached to 3 edges, numbered: 8 16 17
-, PhyloNetworks.Edge:
+, PhyloNetworks.EdgeT{PhyloNetworks.Node}:
  number:17
  length:0.0
  minor hybrid edge with gamma=0.2
@@ -182,7 +182,7 @@ function addhybridedge!(net::HybridNetwork, edge1::Edge, edge2::Edge, hybridpart
             edgeabovee2.isMajor = false
         end
     else
-        c2 = getChild(edge2) # child of edge2 before we switch its direction
+        c2 = getchild(edge2) # child of edge2 before we switch its direction
         i2 = findfirst(isequal(c2), net.node)
         net.root = i2 # makes c2 the new root node
         edge2.hybrid = true
@@ -245,13 +245,13 @@ Output: `true` if a conflict would arise (non-DAG), `false` if no conflict.
 """
 function directionalconflict(net::HybridNetwork, parent::Node, edge2::Edge, hybridpartnernew::Bool)
     if hybridpartnernew # all edges would retain their directions: use isChild1 fields
-        c2 = getChild(edge2)
+        c2 = getchild(edge2)
         return parent === c2 || isdescendant(parent, c2)
     else # after hybrid addition, edge 2 would be reversed: "up" toward its own parent
         if !edge2.containRoot || edge2.hybrid
             return true # direction of edge2 cannot be reversed
         else # net would be a DAG with reversed directions, could even be rooted on edge2
-            p2 = getParent(edge2)
+            p2 = getparent(edge2)
             return parent === p2 || isdescendant_undirected(parent, p2, edge2)
         end
     end

src/addHybrid_snaq.jl

@@ -410,8 +410,8 @@ function addHybridBetweenClades!(hybnum::Number,sisnum::Number,net::HybridNetwor
     sisind = getIndexNode(sisnum,net)
 
     ## hybridization ed1->ed2
-    edge1 = getMajorParentEdge(net.node[sisind])
-    edge2 = getMajorParentEdge(net.node[hybind])
+    edge1 = getparentedge(net.node[sisind]) # major parent edges
+    edge2 = getparentedge(net.node[hybind])
 
     edge3,edge4 = parameters4createHybrid!(edge1, edge2,net)
     hybridnode = createHybrid!(edge1, edge2, edge3, edge4, net, 0.1) ## gamma=0.1, fixed later
@@ -434,9 +434,9 @@ function addHybridBetweenClades!(hybnum::Number,sisnum::Number,net::HybridNetwor
         edge2.isChild1 = false
     end
     ## used gamma=0.1 to make the new edge a minor edge, but we really do not have gamma value:
-    emaj = getMajorParentEdge(hybridnode)
+    emaj = getparentedge(hybridnode)
     emaj.gamma = -1
-    e = getMinorParentEdge(hybridnode)
+    e = getparentedgeminor(hybridnode)
     e.gamma = -1
     return e.number
 end