Merge pull request #13 from sisl/abstract

added AbstractTrees compatibility to fix #8

README.md

@@ -6,18 +6,24 @@
 
 Flexible interactive visualization for large trees using [D3.js](d3js.org).
 
+![Tree](img/tree.png)
+
 ## Installation
 
 ```julia
 Pkg.add("D3Trees")
 ```
-or
-```julia
-Pkg.clone("https://github.com/sisl/D3Trees.jl.git")
-```
 
 ## Usage
 
+There are two ways to create a D3Tree object described below:
+
+### With AbstractTrees
+
+Any object that implements the interface from AbstractTrees can given to the constructor: `D3Tree(object)`.
+
+### Without AbstractTrees
+
 The structure of a D3Tree is specified with *lists of children for each node* stored in a `Vector` of `Int` `Vector`s. For example
 ```julia
 D3Tree([[2,3], [], [4], []])
@@ -31,8 +37,7 @@ t = D3Tree(children)
 
 inchrome(t)
 ```
-By clicking on the nodes, you can expand it to look like this:
-![Tree](img/tree.png)
+By clicking on the nodes, you can expand it to look like the image at the top of the page.
 
 Optional arguments control other aspects of the style (use `julia> ?D3Tree` for a complete list), for example
 ```julia
@@ -80,3 +85,8 @@ julia> t = D3Tree(children)
 ## Browser compatibility
 
 This package works best in the Google chrome or chromium browser.
+
+## Limitations
+
+- The tree is currently transmitted to the browser in one big json string, so it can be slow for large trees and cannot handle infinite trees.
+- This will not work offline because it downloads the D3 library on the fly (https://github.com/sisl/D3Trees.jl/issues/10)

REQUIRE

@@ -1,3 +1,4 @@
 julia 0.6
 JSON
 Blink
+AbstractTrees 0.1

src/D3Trees.jl

@@ -2,6 +2,8 @@ module D3Trees
 
 using JSON
 using Blink
+using AbstractTrees
+import AbstractTrees: printnode
 
 export
     D3Tree,
@@ -46,7 +48,7 @@ Construct a tree to be displayed using D3 in a browser or ipython notebook.
 - `init_duration::Number` - duration of the initial animation in ms.
 - `svg_height::Number` - height of the svg containing the tree in px.
 """
-function D3Tree(children; kwargs...)
+function D3Tree(children::AbstractVector{<:AbstractVector}; kwargs...)
     kwd = Dict(kwargs)
     n = length(children)
     return D3Tree(children,
@@ -58,17 +60,64 @@ function D3Tree(children; kwargs...)
                   convert(Dict{Symbol, Any}, kwd)
                  )
 end
-
+
+"""
+    D3Tree(node; detect_repeat=true)
+
+Construct a tree to be displayed using D3 in a browser or ipython notebook from any object that implements the AbstractTrees interface.
+
+# Arguments
+
+## Required
+
+- `node`: an object that has AbstractTrees.children(node) and AbstractTrees.printnode(io::IO, node)
+
+## Keyword
+
+- `detect_repeat`: if true, uses a dictionary to detect whether a node has appeared previously
+"""
+function D3Tree(node; detect_repeat::Bool=true)
+    t = D3Tree(Vector{Int}[])
+    if detect_repeat
+        node_dict = Dict{Any, Int}()
+        push_node!(t, node, node_dict)
+    else
+        push_node!(t, node)
+    end
+    return t
+end
+
+function push_node!(t, node, node_dict=nothing)
+    if !(node_dict isa Void) && haskey(node_dict, node)
+        return node_dict[node]
+    end
+
+    ind = length(t.children) + 1
+    if !(node_dict isa Void)
+        node_dict[node] = ind
+    end
+    if length(t.children) < ind
+        push!(t.children, Int[])
+        iob = IOBuffer()
+        printnode(iob, node)
+        push!(t.text, String(take!(iob)))
+    end
+    for c in children(node)
+        c_ind = push_node!(t, c, node_dict)
+        push!(t.children[ind], c_ind)
+    end
+    return ind
+end
+
 struct D3TreeNode
     tree::D3Tree
     index::Int
 end
 
-# this should be AbstractTrees.children
-children(n::D3TreeNode) = (D3TreeNode(n.tree, c) for c in n.tree.children[n.index])
+AbstractTrees.children(n::D3TreeNode) = (D3TreeNode(n.tree, c) for c in n.tree.children[n.index])
+AbstractTrees.children(t::D3Tree) = children(D3TreeNode(t, 1))
 n_children(n::D3TreeNode) = length(n.tree.children[n.index])
-# this should be AbstractTrees.printnode
-printnode(io::IO, n::D3TreeNode) = print(io, n.tree.text[n.index])
+AbstractTrees.printnode(io::IO, n::D3TreeNode) = print(io, n.tree.text[n.index])
 
 struct D3TreeView
     root::D3TreeNode

test/runtests.jl

@@ -8,15 +8,15 @@ text = ["one\n(second line)", "2", "III", "four"]
 style = ["", "fill:red", "r:14", "opacity:0.7"]
 link_style = ["", "stroke:blue", "", "stroke-width:10px"]
 tooltip = ["pops", "up", "on", "hover"]
-t = D3Tree(children,
+t1 = D3Tree(children,
            text=text,
            style=style,
            tooltip=tooltip,
            link_style=link_style)
 
-@show json(t)
+@show json(t1)
 
-stringmime(MIME("text/html"), t)
+stringmime(MIME("text/html"), t1)
 
 t2 = D3Tree(children,
             text=text,
@@ -31,8 +31,8 @@ t2 = D3Tree(children,
 # inchrome(t)
 # inchrome(t2)
 
-@show D3Trees.children(D3TreeNode(t, 1))
-show(STDOUT, MIME("text/plain"), t)
+@show D3Trees.children(D3TreeNode(t1, 1))
+show(STDOUT, MIME("text/plain"), t1)
 
 nbinclude("../examples/hello.ipynb")
 
@@ -48,3 +48,7 @@ println("creating tree object")
 
 println("html string")
 @time stringmime(MIME("text/html"), t)
+
+println("AbstractTrees constructor")
+@time t3 = D3Tree(t1)
+@time t4 = D3Tree(t1, detect_repeat=false)