Merge pull request #12 from jangevaare/alpha

PhyloTrees rewrite using Dicts

README.md

@@ -13,30 +13,22 @@ To enable plotting, install [Plots.jl](https://github.com/tbreloff/Plots.jl) and
 
 ## Usage
 
-### Tree initialization
-To initialize a `Tree`, you must declare the data type of each `Node` and `Branch`:
-
-    > # Node data type
-    > N = Float64
-    >
-    > # Branch data type
-    > B = Void
-    >
+There are several ways to add nodes and branches to our `Tree`, see below for examples
+
     > # Initialize the tree
-    > exampletree = Tree{N, B}()
+    > exampletree = Tree()
 
     Phylogenetic tree with 0 nodes and 0 branches
 
-### The basics
-There are several ways to add nodes and branches to our `Tree`, see below for examples
-
     > # Add a node to the tree
     > addnode!(exampletree)
 
     Phylogenetic tree with 1 nodes and 0 branches
 
-    > # Add a node, connect it to node 1 with a branch
-    > branch!(exampletree, 1)
+Branches have `Float64` lengths
+
+    > # Add a node, connect it to node 1 with a branch 5.0 units in length
+    > branch!(exampletree, 1, 5.0)
 
     Phylogenetic tree with 2 nodes and 1 branches
 
@@ -45,81 +37,29 @@ There are several ways to add nodes and branches to our `Tree`, see below for ex
 
     Phylogenetic tree with 4 nodes and 1 branches
 
-    > # Connect node 3 to node 2
-    > addbranch!(exampletree, 2, 3)
+    > # Add a branch from node 2 to node 3 10.0 units in length
+    > addbranch!(exampletree, 2, 3, 10.0)
 
     Phylogenetic tree with 4 nodes and 2 branches
 
-### Nodes
-
 We can quickly look at the nodes present in our `Tree`:
 
-    > exampletree.nodes
-    4-element Array{PhyloTrees.Node{Float64},1}:
-    [root node]-->[branch 1]                                                               
+    > collect(exampletree.nodes)
+
+    [unattached node]
     [branch 1]-->[internal node]-->[branch 2]
-    [branch 2]-->[leaf node]                                                                    
-We can label nodes:
-
-    > # Set a label for node 1
-    > setlabel!(exampletree.nodes[1], "Test label")
+    [branch 2]-->[leaf node]                 
     [root node]-->[branch 1]
 
-    > # Test if node 1 now has a label
-    > haslabel(exampletree.nodes[1])
-    true
-
-    > # Get the label of node 1
-    > getlabel(exampletree.nodes[1])
-    "Test label"
-
-    > # Create a labelled node
-    > addnode!(exampletree, "Another test label")
-    Phylogenetic tree with 5 nodes and 2 branches
-
-Node data is contained in a `Nullable{N}` field named `data`:
-
-    > node 1
-    > exampletree.nodes[1].data
-    Nullable{Float64}()
-
-    > Get the data in node 1
-    > getdata(exampletree.nodes[1])
-    ERROR: NullException()     
-
-### Branches
-
-Branches have `Float64` lengths
-
-    > # Add a branch of length 10.0 from node 2 to 4
-    > addbranch!(exampletree, 2, 4, 10.0)
-    Phylogenetic tree with 5 nodes and 3 branches
-
-    > Retrieve the length of branch 3
-    > exampletree.branches[3].length
-    10.0
-
-Branches are not labelled, but they do have a `Nullable{B}` field named `data`:
-
-    > Get the data in branch 1
-    > getdata(exampletree.branches[1])
-    ERROR: NullException()
-
 ### Other capabilities
 
 Distance between nodes can be calculated using the `distance` function. A node visit ordering for postorder traversal of a tree can be found with `postorder`.
 
 Trees can be plotted using `plot`.
 
 There are many other functions available that are helpful when dealing with trees including:
-`addsubtree!`,
-`subtree`,
 `changesource!`,
 `changetarget!`,
-`validnode`,
-`validnodes`,
-`validbranch`,
-`validbranches`,
 `indegree`,
 `outdegree`,
 `isroot`,
@@ -140,10 +80,4 @@ There are many other functions available that are helpful when dealing with tree
 `descendantnodes`,
 `ancestorcount`,
 `ancestornodes`, and
-`nodetype`,
-`haslabel`,
-`setlabel!`,
-`getlabel`,
-`hasdata`,
-`setdata!`,
-`getdata`
+`nodetype`

src/PhyloTrees.jl

@@ -23,14 +23,10 @@ module PhyloTrees
     addnodes!,
     addbranch!,
     branch!,
-    addsubtree!,
-    subtree,
     changesource!,
     changetarget!,
-    validnode,
-    validnodes,
-    validbranch,
-    validbranches,
+    deletenode!,
+    deletebranch!,
     indegree,
     outdegree,
     isroot,
@@ -53,12 +49,6 @@ module PhyloTrees
     ancestorcount,
     ancestornodes,
     nodetype,
-    setlabel!,
-    haslabel,
-    getlabel,
-    setdata!,
-    hasdata,
-    getdata,
 
     # Distance
     distance,
@@ -67,8 +57,9 @@ module PhyloTrees
     postorder
 
   # Package files
-  include("core.jl")
+  include("structure.jl")
   include("show.jl")
+  include("construction.jl")
   include("utilities.jl")
   include("distance.jl")
   include("traversal.jl")