Move code in src/

Use browserify to build a single js
drpowell · Sep 25, 2016 · 356715f · 356715f
1 parent 04595d2
commit 356715f
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Showing 19 changed files with 101 additions and 84 deletions.
diff --git a/Makefile b/Makefile
@@ -16,7 +16,11 @@ help:
 
 compile:
 	@echo "### Compiling .coffee to .js ###"
-	coffee -c .
+	browserify -t coffeeify src/main.coffee -o build.js
+
+debug:
+	@echo "### Compiling .coffee to .js ###"
+	watchify -v --debug -t coffeeify src/main.coffee -o build.js
 
 demo: compile
 	@echo "### Copying .example files ###"
@@ -31,4 +35,4 @@ install: demo
 	@echo "http://$(HOSTNAME)/~$(USER)/fripan/pan.html"
 
 
-
+
diff --git a/README.md b/README.md
@@ -5,14 +5,19 @@ FriPan is a web-based tool for exploring the pan-genome of multiple bacterial ge
 
 ## Installation
 
-Ensure you have CoffeeScript >= 1.4 installed:
+Ensure you have CoffeeScript >= 1.4 & browserify installed:
 
     npm install -g coffee-script
+    npm install -g browserify
 
-Install the code and run the demo code:
+Install the code and build
 
     git clone https://github.com/drpowell/FriPan
     cd FriPan
+    npm install webworkify
+    make compile
+
+Run the demo code:
     make demo
     ./server.sh
     firefox http://localhost:8030/pan.html

diff --git a/mds-worker.coffee b/mds-worker.coffee
diff --git a/pan.html b/pan.html
@@ -7,23 +7,7 @@
   <link rel="stylesheet" type="text/css" href="pan.css">
   <link rel="stylesheet" href="//code.jquery.com/ui/1.10.4/themes/smoothness/jquery-ui.css">
 
-  <!-- jQuery -->
-  <script type="text/javascript" src="lib/jquery-1.8.2.min.js"></script>
-  <script type="text/javascript" src="lib/jquery-ui.js"></script>
-
-  <!-- D3 -->
-  <script type="text/javascript" src="lib/d3.v3.min.js"></script>
-  <script type="text/javascript" src="lib/colorbrewer.v1.min.js"></script>
-
-  <!-- numeric js -->
-  <script type="text/javascript" src="lib/numeric-1.2.6.js"></script>
-
-  <script type="text/javascript" src="util.js"></script>
-  <script type="text/javascript" src="pan.js"></script>
-  <script type="text/javascript" src="tree.js"></script>
-  <script type="text/javascript" src="mds-plot.js"></script>
-  <script type="text/javascript" src="gene-matrix.js"></script>
-
+  <script type="text/javascript" src="build.js"></script>
 </head>
 
 <body>

diff --git a/server.sh b/server.sh
@@ -1,6 +1,7 @@
 #!/bin/sh
 
-echo "Run: coffee -c -w . &"
+echo "Run: make compile"
+echo "      (or 'make debug' for development)"
 echo "http://localhost:8030/pan.html"
 python -mSimpleHTTPServer 8030
 
diff --git a/gene-matrix.coffee → src/gene-matrix.coffee b/gene-matrix.coffee → src/gene-matrix.coffee
@@ -167,4 +167,4 @@ class GeneMatrix
         @dispatch.order_changed() if @dispatch
 
 
-@GeneMatrix=GeneMatrix
+module.exports = GeneMatrix
diff --git a/lib/colorbrewer.v1.min.js → src/lib/colorbrewer.v1.min.js b/lib/colorbrewer.v1.min.js → src/lib/colorbrewer.v1.min.js
diff --git a/lib/d3.v3.min.js → src/lib/d3.v3.min.js b/lib/d3.v3.min.js → src/lib/d3.v3.min.js
diff --git a/lib/jquery-1.8.2.min.js → src/lib/jquery-1.8.2.min.js b/lib/jquery-1.8.2.min.js → src/lib/jquery-1.8.2.min.js
diff --git a/lib/jquery-ui.js → src/lib/jquery-ui.js b/lib/jquery-ui.js → src/lib/jquery-ui.js
diff --git a/lib/numeric-1.2.6.js → src/lib/numeric-1.2.6.js b/lib/numeric-1.2.6.js → src/lib/numeric-1.2.6.js
diff --git a/src/main.coffee b/src/main.coffee
@@ -0,0 +1,7 @@
+require('./lib/jquery-1.8.2.min.js')
+require('./lib/jquery-ui.js')
+require('./lib/d3.v3.min.js')
+# require('./lib/colorbrewer.v1.min.js')
+# require('./lib/numeric-1.2.6.js')
+
+require('./pan.coffee')
diff --git a/mds-plot.coffee → src/mds-plot.coffee b/mds-plot.coffee → src/mds-plot.coffee
@@ -239,5 +239,5 @@ class BarGraph
               .attr("height", (d) => @height - @y(d.val))
               .on('click', (d) => if @opts.click? then @opts.click(d))
 
-@ScatterPlot = ScatterPlot
-@BarGraph = BarGraph
+module.exports.ScatterPlot = ScatterPlot
+module.exports.BarGraph = BarGraph
diff --git a/src/mds-worker.coffee b/src/mds-worker.coffee
@@ -0,0 +1,34 @@
+
+# importScripts('util.js')
+# importScripts('lib/numeric-1.2.6.js')
+# importScripts('mds.js')
+# importScripts('gene-matrix.js')
+
+Util = require('./util.coffee')
+MDS = require('./mds.coffee')
+GeneMatrix = require('./gene-matrix.coffee')
+
+process = (ev) ->
+    #console.log ev.data
+    if ev.data.init?
+        #console.log "WORKER: Initialized!"
+        @matrix = GeneMatrix.from_hash(ev.data.init)
+    else if ev.data.msg?
+        msg = ev.data.msg
+        if msg.mds?
+            range = msg.mds
+            #our_log "WORKER: #{range}"
+            comp = MDS.MDS.pca_gene(@matrix, range)
+            postMessage(comp)
+        else if msg.dist?
+            range = msg.dist
+            #our_log "WORKER: #{range}"
+            dist_arr = MDS.Distance.distance(@matrix, range)
+            postMessage(dist_arr)
+        else
+            Util.our_log "WORKER:  Unknown method:",msg
+    else
+        Util.our_log "WORKER:  Unknown message:",ev.data
+
+module.exports =  (self) ->
+    self.addEventListener('message',(ev) -> process(ev))
diff --git a/mds.coffee → src/mds.coffee b/mds.coffee → src/mds.coffee
@@ -1,3 +1,6 @@
+numeric = require('./lib/numeric-1.2.6.js')
+Util = require('./util.coffee')
+
 class MDS
     # The "data" are rows, the "dimensions" are columns
     # Matrix has 1 row per "strain", 1 column per "cluster".  Each entry is a boolean
@@ -79,10 +82,9 @@ class Distance
         #console.log "matrix(c("+dist.map((r) -> ""+r)+"), byrow=T, nrow=#{dist.length}"
         #mat.strains().forEach((s1,i) -> mat.strains().map((s2,j) -> console.log s1,s2,dist[i][j]))
         #console.log mat.strains(),dist[0]
-        our_log "Distance took : #{new Date - t1}ms"
+        Util.our_log "Distance took : #{new Date - t1}ms"
 
         dist
 
-
-@MDS = MDS
-@Distance = Distance
+module.exports.MDS = MDS
+module.exports.Distance = Distance
diff --git a/pan.coffee → src/pan.coffee b/pan.coffee → src/pan.coffee
@@ -1,3 +1,8 @@
+work = require('webworkify');
+Util = require('./util.coffee')
+GeneMatrix = require('./gene-matrix.coffee')
+Tree = require('./tree.coffee')
+Plot = require('./mds-plot.coffee')
 
 # A worker that will only compute new values if the web worker is not busy
 # and the parameters have changed
@@ -50,7 +55,7 @@ class MDSHandler
     constructor: (@matrix, @think_elem) ->
         @dispatch = d3.dispatch("redraw")
         @_current_range = null
-        worker = new Worker('mds-worker.js')
+        worker = work(require('./mds-worker.coffee'))
         worker.postMessage(init: @matrix.as_hash())
         @latest_worker = new LatestWorker(worker, () => {mds: @_current_range})
         @latest_worker.on('updated', (comp) => @redraw(comp))
@@ -95,7 +100,7 @@ class MDSHandler
 class DendrogramWrapper
     constructor: (@widget, @matrix, @think_elem) ->
         @_current_range = null
-        worker = new Worker('mds-worker.js')
+        worker = work(require('./mds-worker.coffee'))
         worker.postMessage(init: @matrix.as_hash())
         @latest_worker = new LatestWorker(worker, () => {dist: @_current_range})
         @latest_worker.on('updated', (d) => @_calc_done(d))
@@ -119,7 +124,7 @@ class DendrogramWrapper
         @latest_worker.update()
 
     _calc_done: (dist_arr) ->
-        @tree = new TreeBuilder(dist_arr)
+        @tree = new Tree.TreeBuilder(dist_arr)
         @redraw()
 
     redraw: () ->
@@ -529,13 +534,13 @@ class Pan
         @matrix.on('order_changed', () => @redraw())
 
         @mdsDimension = 1
-        @mdsBarGraph = new BarGraph(
+        @mdsBarGraph = new Plot.BarGraph(
                          elem: '#mds-bargraph'
                          click: (d) =>
                             @mdsDimension=+d.lbl
                             @mds.redispatch()
                         )
-        @scatter = new ScatterPlot(
+        @scatter = new Plot.ScatterPlot(
                      elem: '#mds'
                      width: 500
                      height: 399
@@ -559,7 +564,7 @@ class Pan
         )
         @mds.update(null)
 
-        dendrogramWidget = new Dendrogram(
+        dendrogramWidget = new Tree.Dendrogram(
                         elem: '#dendrogram'
                         width: 600
                         height: 400
@@ -673,9 +678,9 @@ class Pan
             #console.log "domain size=#{domain.length}  sizes=#{sizes}.  Best=#{best}"
             scale.range(b[best])
             if domain.length>best
-                log_error("Not enough colours in #{scheme}, max=#{best}.  Need #{domain.length}")
+                Util.log_error("Not enough colours in #{scheme}, max=#{best}.  Need #{domain.length}")
         else
-            log_error("Bad colour scheme")
+            Util.log_error("Bad colour scheme")
 
         strain_colour = []
         for s in strains
@@ -755,7 +760,7 @@ parse_proteinortho = (tsv) ->
 # ------------------------------------------------------------
 #
 get_stem = () ->
-    get_url_params() || 'pan'
+    Util.get_url_params() || 'pan'
 
 process_gene_order = (matrix, json) ->
     strains = d3.keys(json).sort()
@@ -768,7 +773,7 @@ process_gene_order = (matrix, json) ->
 load_json = (matrix) ->
     d3.json("#{get_stem()}.json", (err, json) ->
         if (err)
-            log_warn("Missing '#{get_stem()}.json', trying deprecated .descriptions file")
+            Util.log_warn("Missing '#{get_stem()}.json', trying deprecated .descriptions file")
             load_desc(matrix)
         else
             process_gene_order(matrix,json.gene_order) if json.gene_order?
@@ -791,7 +796,7 @@ load_desc = (matrix) ->
             if match
                 matrix.set_desc(match[1], match[2])
             else
-                log_error "BAD LINE: #{l}"
+                Util.log_error "BAD LINE: #{l}"
         )
     )
 
@@ -826,7 +831,7 @@ class StrainInfo
     set_info: (@matrix) ->
         @columns = d3.keys(@matrix[0])
         if 'ID' != @columns.shift()
-            log_error("No ID column in #{get_stem()}.strains")
+            Util.log_error("No ID column in #{get_stem()}.strains")
             @columns = []
             return
 
@@ -835,23 +840,23 @@ class StrainInfo
             for c in @columns
                 s[c] = '_not-set_'
 
-        log_info "Read info on #{@matrix.length}.  Columns=#{@columns}"
+        Util.log_info "Read info on #{@matrix.length}.  Columns=#{@columns}"
         for row in @matrix
             s = @find_strain_by_name(row['ID'])
             if !s?
-                log_error "Unable to find strain for #{row['ID']}"
+                Util.log_error "Unable to find strain for #{row['ID']}"
             else
                 for c in @columns
                     s[c] = row[c]
 
 setup_download = (sel) ->
     d3.selectAll(".svg-download")
-          .on("mousedown", (e) -> download_svg(d3.event.target))
+          .on("mousedown", (e) -> Util.download_svg(d3.event.target))
 
 init = () ->
     document.title = "FriPan : #{get_stem()}"
     $(".hdr .title").append("<span class='title'>: #{get_stem()}</span>")
-    setup_nav_bar()
+    Util.setup_nav_bar()
 
     url = "#{get_stem()}.proteinortho"
     d3.tsv(url, (data) ->
@@ -878,4 +883,4 @@ init = () ->
         setup_download(".svg_download")
     )
 
-$(document).ready(() -> add_browser_warning() ; init() )
+$(document).ready(() -> Util.add_browser_warning() ; init() )
diff --git a/test-tree.coffee → src/test-tree.coffee b/test-tree.coffee → src/test-tree.coffee
diff --git a/tree.coffee → src/tree.coffee b/tree.coffee → src/tree.coffee
@@ -333,6 +333,6 @@ class Dendrogram
             @opts.callback[typ](args)
 
 
-window.Dendrogram = Dendrogram
 
-window.TreeBuilder = TreeBuilder
+module.exports.Dendrogram = Dendrogram
+module.exports.TreeBuilder = TreeBuilder
diff --git a/util.coffee → src/util.coffee b/util.coffee → src/util.coffee
@@ -1,13 +1,15 @@
-@our_log = (o) ->
+root = module.exports
+
+root.our_log = (o) ->
     if console? && console.log?
         console.log.apply(console, if !!arguments.length then arguments else [this])
     else if opera? && opera.postError?
         opera.postError(o || this)
 
-@log_info = (o) -> log_msg("INFO", arguments)
-@log_warn = (o) -> log_msg("WARN", arguments)
-@log_error = (o) -> log_msg("ERROR", arguments)
-@log_debug = (o) ->
+root.log_info = (o) -> log_msg("INFO", arguments)
+root.log_warn = (o) -> log_msg("WARN", arguments)
+root.log_error = (o) -> log_msg("ERROR", arguments)
+root.log_debug = (o) ->
     log_msg("DEBUG", arguments) if window.debug?
 
 # Our internal log allowing a log type
@@ -33,15 +35,15 @@ html_warning = """
     </div>
     """
 
-@setup_nav_bar = () ->
+root.setup_nav_bar = () ->
     #about = $(require("../templates/about.hbs")(version: degust_version))
     #$('#about-modal').replaceWith(about)
     $("a.log-link").click(() -> $('.log-list').toggle())
 
     #window.debug ?= get_url_vars()["debug"]
 
 # Display a popup warning, or fill in a warning box if using IE
-@add_browser_warning = () ->
+root.add_browser_warning = () ->
     if window.navigator.userAgent.indexOf("MSIE ")>=0
         outer = $('.browser-warning-outer')
         if outer.length==0
@@ -50,11 +52,10 @@ html_warning = """
             outer = $('.browser-warning-outer')
         outer.append(html_warning)
 
-@get_url_params = () ->
+root.get_url_params = () ->
     hash = window.location.search
     hash.substring(1)               # remove '?'
 
-
 # ------------------------------------------------------------
 # SVG Downloading
 #
@@ -107,5 +108,5 @@ class SVG
           .attr("href-lang", "image/svg+xml")
           .attr("href", "data:image/svg+xml;base64,\n" + btoa(html))
 
-@download_svg = SVG.download_svg
+root.download_svg = SVG.download_svg
 # ------------------------------------------------------------