Merge branch 'develop' for 1.0.5

Gruntfile.js

@@ -72,6 +72,7 @@ module.exports = function(grunt) {
 			jshint: {
 				options: {
 					undef: true,
+					esversion: 6,
 					globals: {
 						jQuery: true
 					}

LICENSES/LICENSE-contextMenu

@@ -1 +1 @@
-$.contextMenu is published under the [MIT license](http://www.opensource.org/licenses/mit-license) or [GPL v3](http://opensource.org/licenses/GPL-3.0) - which ever suits your needs best.
+$.contextMenu is published under the [MIT license](http://www.opensource.org/licenses/mit-license)

LICENSES/README.org

@@ -80,9 +80,9 @@ http://silviomoreto.github.io/bootstrap-select/
  - [[../d3/lib/jquery.min.js]]
 *** jQuery contextMenu
 **** Repository
-[[https://github.com/medialize/jQuery-contextMenu]]
+[[https://github.com/swisnl/jQuery-contextMenu]]
 **** Version
-1.6.6
+2.6.4
 **** LICENSE
 [[file:LICENSE-contextMenu][LICENSE-contextMenu]]
 **** Files

README.org

@@ -73,6 +73,9 @@ The licenses of included libraries might differ, please see [[LICENSES/README.or
 [[https://travis-ci.org/AliTVTeam/AliTV/][https://travis-ci.org/AliTVTeam/AliTV.svg?branch=master]]
 [[https://coveralls.io/github/AliTVTeam/AliTV?branch=master][https://coveralls.io/repos/github/AliTVTeam/AliTV/badge.svg?branch=master]]
 ** Changelog
+*** 1.0.5 <2018-05-15>
+ - Add experimental auto-ordering
+ - Fix context menu bug
 *** 1.0.4 <2018-01-05>
  - Use karyo names rather than ids in web interface
  - Add google analytics to collect usage stats (with opt-out possibility)

d3/AliTV.html

@@ -941,6 +941,7 @@ <h1><img src="css/AliTV_logo.png" alt="logo" width="200" height="160" style="mar
 
                 <li role="presentation"><a href="#tree" aria-controls="about" role="tab" data-toggle="tab"><b>Phylogenetic Tree</b></a></li>
                 <li role="presentation"><a href="#graphicalSettings" aria-controls="graphicalSettings" role="tab" data-toggle="tab"><b>Layout Settings</b></a></li>
+                <li role="presentation"><a href="#orderKaryos" aria-controls="orderKaryos" role="tab" data-toggle="tab"><b>Order</b></a></li>
                 <li role="presentation"><a href="#advancedSettings" aria-controls="advancedSettings" role="tab" data-toggle="tab"><b>Advanced Settings</b></a></li>
                 <li role="presentation"><a href="#importExport" aria-controls="importExport" role="tab" data-toggle="tab"><b>Import &amp; Export</b></a></li>
             </ul>
@@ -965,6 +966,30 @@ <h1><img src="css/AliTV_logo.png" alt="logo" width="200" height="160" style="mar
                     </div>
                 </div>
 
+                <div role="tabpanel" class="tab-pane" id="orderKaryos" style="margin:10px 10px">
+                    <div class="container-fluid">
+                        <div class="row">
+                            <div class="col-sm-12">
+                                <div class="col-sm-6">
+                                    <div class="form-group">
+                                        <mark class="bg-info">Auto-order (beta)</mark><br> Order chromosomes/contigs automatically by using the following heuristic:
+                                        <ol>
+                                            <li>Assume genome with longest chromosome is the reference</li>
+                                            <li>Reverse order of reference (if it was ordered by size, the largest chromosome comes first now)</li>
+                                            <li>Order each chromosome of non-reference genome by the position of the largest hit to the reference</li>
+                                            <li>Reverse each chromosome where the largest hit to the reference is twisted</li>
+                                        </ol>
+                                        Warning: The current order function is experimental and implemented in ES6 so if you are using an old browser it might not work.
+                                        <div style="margin: 10px 0px">
+                                            <button class="btn btn-info" onclick="ali.orderKaryosAutomatically()" style="font-size: 14px;">Auto-order</button>
+                                        </div>
+                                    </div>
+                                </div>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+
                 <div role="tabpanel" class="tab-pane fade" id="advancedSettings" style="margin:10px 10px">
                     <div class="container-fluid">
                         <div class="row">