From fdf88072fd7630f9e7721682dc475272a2418a48 Mon Sep 17 00:00:00 2001
From: Seth Bromberger <seth@ncisecurity.com>
Date: Fri, 19 Dec 2014 09:58:26 -0800
Subject: [PATCH 1/3] fixed indexing issue when vertices are <:Integer

---
 src/graph.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/graph.jl b/src/graph.jl
index 47fa6449..e0a62869 100644
--- a/src/graph.jl
+++ b/src/graph.jl
@@ -55,7 +55,7 @@ vertices(g::GenericGraph) = g.vertices
 num_edges(g::GenericGraph) = length(g.edges)
 edges(g::GenericGraph) = g.edges
 
-vertex_index{V<:ProvidedVertexType}(v::V, g::GenericGraph{V}) = vertex_index(v)
+vertex_index{V<:ProvidedVertexType}(v::V, g::GenericGraph{V}) = vertex_index(v,vertices(g))
 edge_index{V,E}(e::E, g::GenericGraph{V,E}) = edge_index(e)
 
 out_edges{V}(v::V, g::GenericGraph{V}) = g.finclist[vertex_index(v, g)]

From fe2b228b587820b344d246e52a7078bbfdeefbe8 Mon Sep 17 00:00:00 2001
From: Seth Bromberger <seth@ncisecurity.com>
Date: Fri, 19 Dec 2014 23:09:22 -0800
Subject: [PATCH 2/3] SimpleGraph now is O(1) vertex indexing, and does not
 take vertices for add_vertex\!()

deprecated add_vertex\!(g::SimpleGraph, v)
---
 src/graph.jl | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/src/graph.jl b/src/graph.jl
index e0a62869..cd58991b 100644
--- a/src/graph.jl
+++ b/src/graph.jl
@@ -55,6 +55,7 @@ vertices(g::GenericGraph) = g.vertices
 num_edges(g::GenericGraph) = length(g.edges)
 edges(g::GenericGraph) = g.edges
 
+vertex_index(v::Integer, g::SimpleGraph) = (v <= g.vertices[end]? v: 0)
 vertex_index{V<:ProvidedVertexType}(v::V, g::GenericGraph{V}) = vertex_index(v,vertices(g))
 edge_index{V,E}(e::E, g::GenericGraph{V,E}) = edge_index(e)
 
@@ -69,6 +70,16 @@ in_neighbors{V}(v::V, g::GenericGraph{V}) = SourceIterator(g, in_edges(v, g))
 
 # mutation
 
+function add_vertex!(g::SimpleGraph)
+    v = g.vertices[end] + 1
+    g.vertices = 1:v
+    push!(g.finclist, Int[])
+    push!(g.binclist, Int[])
+    v
+end
+
+@deprecate add_vertex!(g::SimpleGraph,v) add_vertex!(g::SimpleGraph)
+
 function add_vertex!{V}(g::GenericGraph{V}, v::V)
     push!(g.vertices, v)
     push!(g.finclist, Int[])

From ceb7b4c8ff348aee05330bd57c3a2ee977c51257 Mon Sep 17 00:00:00 2001
From: Seth Bromberger <github@bromberger.com>
Date: Sun, 21 Dec 2014 08:55:27 -0800
Subject: [PATCH 3/3] added @mlubin's suggestions for indexing to preserve
 KeyIndex and others O(1)

---
 src/common.jl |  2 --
 src/graph.jl  | 11 ++++++++++-
 2 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/src/common.jl b/src/common.jl
index ebf1a840..7e35cae8 100644
--- a/src/common.jl
+++ b/src/common.jl
@@ -8,8 +8,6 @@ typealias AttributeDict Dict{UTF8String, Any}
 #
 ################################################
 
-vertex_index(v::Integer) = v
-
 immutable KeyVertex{K}
     index::Int
     key::K
diff --git a/src/graph.jl b/src/graph.jl
index cd58991b..1492aeaf 100644
--- a/src/graph.jl
+++ b/src/graph.jl
@@ -56,7 +56,15 @@ num_edges(g::GenericGraph) = length(g.edges)
 edges(g::GenericGraph) = g.edges
 
 vertex_index(v::Integer, g::SimpleGraph) = (v <= g.vertices[end]? v: 0)
-vertex_index{V<:ProvidedVertexType}(v::V, g::GenericGraph{V}) = vertex_index(v,vertices(g))
+
+function vertex_index{V<:ProvidedVertexType}(v::V, g::GenericGraph{V})
+    if applicable(vertex_index, v)  # use O(1) if possible
+        return vertex_index(v)
+    else                            # use O(n)
+        return vertex_index(v,vertices(g))
+    end
+end
+
 edge_index{V,E}(e::E, g::GenericGraph{V,E}) = edge_index(e)
 
 out_edges{V}(v::V, g::GenericGraph{V}) = g.finclist[vertex_index(v, g)]
@@ -71,6 +79,7 @@ in_neighbors{V}(v::V, g::GenericGraph{V}) = SourceIterator(g, in_edges(v, g))
 # mutation
 
 function add_vertex!(g::SimpleGraph)
+    # ensure SimpleGraph indices are consecutive, allowing O(1) indexing
     v = g.vertices[end] + 1
     g.vertices = 1:v
     push!(g.finclist, Int[])