Merge branch 'release-0.4.1'

Author: hdngr

Gruntfile.coffee

@@ -74,8 +74,6 @@ module.exports = (grunt) ->
     shell:
       commitBuild:
         command: "git add -A && git commit -am 'commit dist files for #{pkg.version}'"
-      docs:
-        command: 'grunt --gruntfile site/Gruntfile.coffee'
 
     # Watches files for changes and runs tasks based on the changed files
     watch:
@@ -499,10 +497,6 @@ module.exports = (grunt) ->
         cwd: "<%= yeoman.dist %>"
         src: "**"
 
-      litcoffee:
-        files:
-          'site/app/docs/_documentation/Annotated-Source.md':'.tmp/scripts/alchemysrc.coffee.md'
-
     concurrent:
       # Run some tasks in parallel to speed up build process
       server: ["compass:server", "coffee:dev",  "copy:styles"]
@@ -560,7 +554,7 @@ module.exports = (grunt) ->
   pullRequest = grunt.option('pr') 
   travis = grunt.option('travis')                         
   grunt.registerTask "default",
-    # release alchemy and build docs
+    # release alchemy
     if releaseFlag
       ["test:dist",
        "build",
@@ -572,7 +566,6 @@ module.exports = (grunt) ->
        "concat:s3", # squash vendor and alchemy files for cdn
        "concat:s3Version", # apply version numbers for cdn
        "s3:production" # publish files to s3 for cdn
-       "shell:docs", # publish docs
       ]
     # Travis-ci on a commit to the main repo branches
     else if travis

app/index.html

@@ -26,7 +26,6 @@
         <![endif]-->
 
         <div class="alchemy" id="alchemy"></div>
-        <div class="alchemy" id="chemistry"></div>
 
         <!-- build:js({.tmp,app}) scripts/vendor.js -->
         <!-- bower:js -->
@@ -39,9 +38,9 @@
 
         <script src="scripts/alchemy.js"></script>
         <script type="text/javascript">
+          
           var config = {
-            dataSource: "sample_data/contrib.json",
-            // curvedEdges: true
+            dataSource: "sample_data/contrib.json"
           }
 
           var alchemy = new Alchemy(config)

app/scripts/alchemy/API/create.coffee.md

@@ -14,7 +14,7 @@
     # You should have received a copy of the GNU Affero General Public License
     # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-    class Alchemy::create
+    class Alchemy::Create
         constructor: (instance)->
             @a = instance
         nodes: (nodeMap, nodeMaps...) ->
@@ -36,11 +36,12 @@
 
             nodeMaps = _.union nodeMaps, nodeMap
             # create the results set
-            results = []
             for n in nodeMaps
                 # check if the node already exists
                 registerNode n
-            results
+
+            @a.updateGraph() if @a.initial
+            
         edges: (edgeMap, edgeMaps...) ->
             a = this.a
             registerEdge = (edge) ->
@@ -73,8 +74,6 @@
                         aEdge = new a.models.Edge(edge, 0)
                         a._edges["#{edge.source}-#{edge.target}"] = [aEdge]
                         [aEdge]
-                        
-            if edgeMaps.length isnt 0
-                console.warn "Make sure this function supports multiple arguments"
-            else
-                registerEdge edgeMap
+             allEdges = _.uniq _.flatten arguments
+             _.each allEdges, (e)-> registerEdge e
+             @a.updateGraph() if @a.initial

app/scripts/alchemy/API/get.coffee.md

@@ -18,7 +18,7 @@
     # make js array method called ._state
     # @a.set.  nest set inside of get
 
-    Alchemy::get = (instance)->
+    Alchemy::Get = (instance) ->
         a: instance
         _el: []
         _elType: null
@@ -60,8 +60,8 @@
             elType = @_elType
             @_el = do (elType)->
                 switch elType
-                    when "node" then return _.values a._nodes
-                    when "edge" then return _.flatten _.map a._edges, (e)-> e
+                    when "node" then return a.elements.nodes.val
+                    when "edge" then return a.elements.edges.flat
             @_makeChain @_el
 
         elState: (state) ->
@@ -100,14 +100,13 @@
             clusterColoursObject
 
         ###### ALL METHODS BELOW THIS POINT WILL BE DEPRECATED UPON 1.0 ######
-        allEdges: ->
-            _.flatten _.map(@a._edges, (edgeArray) -> e for e in edgeArray)
+        allEdges: -> @a.elements.nodes.flat
 
         allNodes: (type) ->
             if type?
                 _.filter @a._nodes, (n) -> n if n._nodeType is type
             else
-                _.map @a._nodes, (n) -> n
+                @a.elements.nodes.val
 
         getNodes: (id, ids...)->
             a = @a
@@ -120,4 +119,4 @@
                 edge_id = "#{id}-#{target}"
                 @a._edges[edge_id]
             else if id? and not target?
-                @a._nodes[id]._adjacentEdges
+                @a._nodes[id]._adjacentEdges

app/scripts/alchemy/API/remove.coffee.md

@@ -14,8 +14,8 @@
     # You should have received a copy of the GNU Affero General Public License
     # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-    class Alchemy::remove
-        constructor: (instance)->
+    class Alchemy::Remove
+        constructor: (instance) ->
             @a = instance
 
         nodes: (nodeMap) ->

app/scripts/alchemy/API/set.coffee.md

@@ -14,5 +14,6 @@
     # You should have received a copy of the GNU Affero General Public License
     # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-    Alchemy::set =
-        state: (key, value) -> alchemy.state.key = value
+    Alchemy::Set = (instance)->
+        a    : instance
+        state: (key, value) -> @a.state.key = value

app/scripts/alchemy/Alchemy.coffee.md

@@ -29,9 +29,12 @@ title: Anotated Source
             @a = @
 
             @version  = "#VERSION#"
-            @get      = new @get @
-            @remove   = new @remove @
-            @create   = new @create @
+            # give access to default conf
+            @get      = new @Get    @
+            @remove   = new @Remove @
+            @create   = new @Create @
+            @set      = new @Set    @
+
             @drawing  =
                 DrawEdge : DrawEdge   @
                 DrawEdges: DrawEdges  @
@@ -63,10 +66,12 @@ title: Anotated Source
                 "layout": "default"
 
             @startGraph     = @startGraph @
+            @updateGraph    = @updateGraph @
             @generateLayout = @generateLayout @
             @svgStyles      = @svgStyles @
             @interactions   = @interactions @
             @search         = @search @
+            @plugins        = @plugins @
 
 	        # alchemy._nodes stores a node object as the value with the unique
             # id specified in the GraphJSON.
@@ -91,44 +96,35 @@ title: Anotated Source
 
         begin: (userConf) ->
             # overide configuration with user inputs
-            @setConf userConf
+            conf = @setConf userConf
             switch typeof @conf.dataSource
                 when 'string' then d3.json @a.conf.dataSource, @a.startGraph
                 when 'object' then @a.startGraph @a.conf.dataSource
-
+            
+            @plugins.init()
             Alchemy::instances.push @
 
             @
 
         setConf: (userConf) ->
             # apply base themes
             if userConf.theme?
-                userConf = _.merge _.cloneDeep(defaults), @a.themes["#{userConf.theme}"]
+                userConf = _.merge _.cloneDeep(@defaults), @a.themes["#{userConf.theme}"]
 
             for key, val of userConf
                 switch key
                     when "clusterColors"   then userConf["clusterColours"]   = val
                     when "backgroundColor" then userConf["backgroundColour"] = val
                     when "nodeColor"       then userConf[nodeColour]         = val
 
-            @a.conf = _.merge _.cloneDeep(defaults), userConf
+            @a.conf = _.merge _.cloneDeep(@defaults), userConf
 
         # All alchemy instances in order of creation.
         instances: []
 
-        getInst: (element)->
-            #Edge or Node
-            if element.a?
-                element.a
-
-            #_d3 packet
-            else if element.self?
-                element.self.a
-
-            #SVG element
-            else
-                Alchemy::instances[d3.select(element).attr("alchInst")]
-
+        getInst: (svg)->
+            instNumber = parseInt d3.select(svg).attr("alchInst")
+            Alchemy::instances[instNumber]
 
     root = exports ? this
     root.Alchemy = Alchemy

app/scripts/alchemy/clustering/clustering.coffee.md

@@ -52,8 +52,8 @@
                 gravity: (k) -> _gravity(k)
 
         identifyClusters: (a)->
-            nodes = a.get.allNodes()
-            clusters = _.uniq _.map(_.values(nodes), (node)-> node.getProperties()[a.conf.clusterKey])
+            nodes = a.elements.nodes.val
+            clusters = _.uniq _.map(nodes, (node)-> node.getProperties()[a.conf.clusterKey])
             @clusterMap = _.zipObject clusters, [0..clusters.length]
         
         getClusterColour: (clusterValue) ->

app/scripts/alchemy/core/index.coffee.md

@@ -0,0 +1,38 @@
+    
+    Alchemy::Index = (instance, all)->
+        a = instance
+
+        # Index maintains an index of common mappings/selections of
+        # nodes and edges to reduce iteration during non-creative/destructive
+        # operation of alchemy.
+        
+        # a.elements is set with base iterations that other iterations are made
+        # from.  These are seperated out so that other indexes can use them
+        # during creation instead of recreating them during index.
+
+        # ORDERING IS IMPORTANT!
+        # Before reordering or adding a new index, see if you can
+        # use a previous index in it's creation.
+        
+        elements =
+            nodes:
+                val: do -> _.values a._nodes
+            edges:
+                val: do -> _.values a._edges
+        
+        nodes = elements.nodes
+        edges = elements.edges
+
+        elements.edges.flat = do -> _.flatten edges.val
+
+        elements.nodes.d3 = do -> _.map nodes.val, (n)-> n._d3
+        elements.edges.d3 = do -> _.map edges.flat, (e)-> e._d3
+
+        a.elements = elements
+
+        () ->
+
+            # Auxiliary indexes.
+            a.elements.nodes.svg = do -> a.vis.selectAll 'g.node'
+
+            a.elements.edges.svg  = do -> a.vis.selectAll 'g.edge'

app/scripts/alchemy/core/interactions.coffee.md

@@ -18,17 +18,20 @@
         a = instance
 
         edgeClick: (d) ->
-            a = d.self.a
-
+            # Don't consider drag a click
+            return if d3.event.defaultPrevented
+            # Don't tell alchemy about the click
             d3.event.stopPropagation()
+            # Convert d3.edge to alchemy.edge
             edge = d.self
+
+            if typeof a.conf.edgeClick is 'function'
+                a.conf.edgeClick(edge)
             if edge._state != "hidden"
                 edge._state = do ->
                     return "active" if edge._state is "selected"
                     "selected"
                 edge.setStyles()
-            if typeof a.conf.edgeClick? is 'function'
-                a.conf.edgeClick()
 
         edgeMouseOver: (d) ->
             edge = d.self
@@ -70,17 +73,19 @@
         nodeClick: (n) ->
             # Don't consider drag a click
             return if d3.event.defaultPrevented
-
+            # Don't tell alchemy about the click
             d3.event.stopPropagation()
+            # Convert d3.node to alchemy.node
             node = n.self
 
+            if typeof a.conf.nodeClick is 'function'
+                a.conf.nodeClick(node)
+
             if node._state != "hidden"
                 node._state = do ->
                     return "active" if node._state is "selected"
                     "selected"
                 node.setStyles()
-            if typeof a.conf.nodeClick is 'function'
-                a.conf.nodeClick(n)
 
         zoom: (extent) ->
                     if not @_zoomBehavior?
@@ -113,16 +118,16 @@
                         @._zoomBehavior.scale(scale)
                                        .translate([x,y])
 
-        toggleControlDash: () ->
-            #toggle off-canvas class on click
-            offCanvas = a.dash.classed("off-canvas") or
-                        a.dash.classed("initial")
-            a.dash
-                   .classed {
-                        "off-canvas": !offCanvas,
-                        "initial"   : false,
-                        "on-canvas" : offCanvas
-                    }
+        # toggleControlDash: () ->
+        #     #toggle off-canvas class on click
+        #     offCanvas = a.dash.classed("off-canvas") or
+        #                 a.dash.classed("initial")
+        #     a.dash
+        #            .classed {
+        #                 "off-canvas": !offCanvas,
+        #                 "initial"   : false,
+        #                 "on-canvas" : offCanvas
+        #             }
 
         nodeDragStarted: (d, i) ->
             d3.event.preventDefault