Merge branch 'release-v1.0.6'

AliTVTeam · Jun 8, 2018 · d09f51f · d09f51f
2 parents 0aec53e + c46a3ce
commit d09f51f
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diff --git a/AliTV-perl-interface b/AliTV-perl-interface
diff --git a/README.org b/README.org
@@ -73,6 +73,8 @@ 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
+*** 1.0.6 <2018-06-08>
+ - Update AliTV-perl-interface to v1.0.6
 *** 1.0.5 <2018-05-15>
  - Add experimental auto-ordering
  - Fix context menu bug

diff --git a/d3/doc/AliTV.html b/d3/doc/AliTV.html
@@ -14071,6 +14071,8 @@ <h4 class="name" id="orderKaryosAutomatically"><span class="type-signature"></sp
 
 <div class="description">
     This function re-orders the karyos in all genomes according to the longest hit to the reference genome (determined by globally longest sequence)
+This function is transpiled using babel to make tests with phantomJS work (does not support ES6)
+To see the original ES6 implementation you can check out fb68a0fb290ab38ccc381bfebd4323f267f97ca6
 </div>
 
 
@@ -14121,7 +14123,7 @@ <h4 class="name" id="orderKaryosAutomatically"><span class="type-signature"></sp
 
     <dt class="tag-source">Source:</dt>
     <dd class="tag-source"><ul class="dummy"><li>
-        <a href="AliTV.js.html">AliTV.js</a>, <a href="AliTV.js.html#line3541">line 3541</a>
+        <a href="AliTV.js.html">AliTV.js</a>, <a href="AliTV.js.html#line3543">line 3543</a>
     </li></ul></dd>
 
 
@@ -19490,7 +19492,7 @@ <h2><a href="index.html">Home</a></h2><h3>Classes</h3><ul><li><a href="AliTV.htm
 <br class="clear">
 
 <footer>
-    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Wed May 16 2018 09:46:34 GMT+0200 (CEST)
+    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Fri Jun 08 2018 16:49:31 GMT+0200 (CEST)
 </footer>
 
 <script> prettyPrint(); </script>

diff --git a/d3/doc/AliTV.js.html b/d3/doc/AliTV.js.html
@@ -36,7 +36,7 @@ <h1 class="page-title">Source: AliTV.js</h1>
 /* jshint funcscope:true */
 
 // use const instead of var as soon as EcmaScript 6 (ES6 is widely used)
-var AliTV_VERSION = "1.0.5";
+var AliTV_VERSION = "1.0.6";
 
 /**
  * Creates an object of type AliTV for drawing whole genome alignment visualizations
@@ -3564,6 +3564,8 @@ <h1 class="page-title">Source: AliTV.js</h1>
 
 /**
  * This function re-orders the karyos in all genomes according to the longest hit to the reference genome (determined by globally longest sequence)
+ * This function is transpiled using babel to make tests with phantomJS work (does not support ES6)
+ * To see the original ES6 implementation you can check out fb68a0fb290ab38ccc381bfebd4323f267f97ca6
  * @author Markus Ankenbrand
  */
 AliTV.prototype.orderKaryosAutomatically = function() {
@@ -3745,7 +3747,7 @@ <h2><a href="index.html">Home</a></h2><h3>Classes</h3><ul><li><a href="AliTV.htm
 <br class="clear">
 
 <footer>
-    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Wed May 16 2018 09:46:34 GMT+0200 (CEST)
+    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Fri Jun 08 2018 16:49:31 GMT+0200 (CEST)
 </footer>
 
 <script> prettyPrint(); </script>

diff --git a/d3/doc/index.html b/d3/doc/index.html
@@ -56,7 +56,7 @@ <h2><a href="index.html">Home</a></h2><h3>Classes</h3><ul><li><a href="AliTV.htm
 <br class="clear">
 
 <footer>
-    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Wed May 16 2018 09:46:34 GMT+0200 (CEST)
+    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Fri Jun 08 2018 16:49:31 GMT+0200 (CEST)
 </footer>
 
 <script> prettyPrint(); </script>

diff --git a/d3/js/AliTV.js b/d3/js/AliTV.js
@@ -8,7 +8,7 @@
 /* jshint funcscope:true */
 
 // use const instead of var as soon as EcmaScript 6 (ES6 is widely used)
-var AliTV_VERSION = "1.0.5";
+var AliTV_VERSION = "1.0.6";
 
 /**
  * Creates an object of type AliTV for drawing whole genome alignment visualizations

diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "AliTV",
-  "version": "1.0.5",
+  "version": "1.0.6",
   "scripts": {
     "test": "grunt travis --verbose"
   },
+9 −0		Changes
+9 −0		MANIFEST
+2 −0		Makefile.PL
+2 −2		README.md
+9 −178		bin/alitv.pl
+21 −0		data/vectors/run_test_input.yml
+10 −1		doc/alitv.md
+5 −7		lib/AliTV.pm
+1 −1		lib/AliTV/Base/Version.pm
+201 −0		lib/AliTV/Script.pm
+7 −0		t/301_AliTV-Script.t
+117 −0		t/302_AliTV-Script-generate_filenames.t
+476 −0		t/303_AliTV-Script-run-with-sequences.t
+439 −0		t/304_AliTV-Script-run-with-yml.t
+12 −19		t/505_AliTV-get_default_settings.t