Merge branch 'develop'

README.org

@@ -1,15 +1,15 @@
-[[https://github.com/BioInf-Wuerzburg/AliTV/blob/master/LICENSE][https://img.shields.io/github/license/mashape/apistatus.svg]]
+[[https://github.com/AliTVTeam/AliTV/blob/master/LICENSE][https://img.shields.io/github/license/mashape/apistatus.svg]]
 
 ** Build
-[[https://travis-ci.org/BioInf-Wuerzburg/AliTV/][https://travis-ci.org/BioInf-Wuerzburg/AliTV.svg?branch=master]]
-[[https://coveralls.io/github/BioInf-Wuerzburg/AliTV?branch=master][https://coveralls.io/repos/github/BioInf-Wuerzburg/AliTV/badge.svg?branch=master]]
+[[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]]
 
 ** Homepage
-[[http://bioinf-wuerzburg.github.io/AliTV][AliTV]]
+[[http://alitvteam.github.io/AliTV][AliTV]]
 ** Installation
 
 #+BEGIN_EXAMPLE
-  git clone --recursive https://github.com/BioInf-Wuerzburg/AliTV
+  git clone --recursive https://github.com/AliTVTeam/AliTV
 #+END_EXAMPLE
 
 ** Dependencies
@@ -43,7 +43,7 @@ By default, AliTV generates ten files in the output folder:
 | <prefix>_query.fasta     | A copy of the query fasta with adjusted IDs                             |
 | <prefix>_reference.fasta | A copy of the reference fasta with adjusted IDs                         |
 
-A demo of the new interactive HTML/JavaScript output can be found [[http://bioinf-wuerzburg.github.io/AliTV/d3/AliTV.html][here]].
+A demo of the new interactive HTML/JavaScript output can be found [[http://alitvteam.github.io/AliTV/d3/AliTV.html][here]].
 
 ** Input
 Both the query and the reference file should be in fasta format.
@@ -52,7 +52,7 @@ Both the query and the reference file should be in fasta format.
 
 We have not yet submitted a manuscript.
 Please use this repository to cite AliTV if you use it in your project.
-[[https://zenodo.org/badge/latestdoi/12731/BioInf-Wuerzburg/AliTV][https://zenodo.org/badge/12731/BioInf-Wuerzburg/AliTV.svg]]
+[[https://zenodo.org/badge/latestdoi/12731/AliTVTeam/AliTV][https://zenodo.org/badge/12731/AliTVTeam/AliTV.svg]]
 
 Please also consider citing:
  - lastz or MUMmer
@@ -62,7 +62,7 @@ Please also consider citing:
 For a list of included libraries together with their respective licenses see the [[file:LICENSES/][LICENSES]] folder.
 ** Contact
 If you have any questions or encounter problems or potential bugs, don't
-hesitate to contact us. Either report [[https://github.com/BioInf-Wuerzburg/AliTV/issues][issues]] on github or write an email to:
+hesitate to contact us. Either report [[https://github.com/AliTVTeam/AliTV/issues][issues]] on github or write an email to:
 
 - Markus Ankenbrand - markus.ankenbrand@uni-wuerzburg.de
 
@@ -82,6 +82,8 @@ hesitate to contact us. Either report [[https://github.com/BioInf-Wuerzburg/AliT
 #+LaTeX_HEADER: \setlength{\parskip}{1.5ex}
 #+LATEX_HEADER: \renewcommand{\familydefault}{\sfdefault}
 ** Changelog
+*** 0.3.9 <2016-06-09 Do>
+ - Move to AliTVTeam organization
 *** 0.3.8 <2016-06-06 Mo>
  - Update bootstrap-select to version 1.10.0
  - Update colorpicker to version 2.3.2

bower.json

@@ -12,7 +12,7 @@
   "keywords": [
     "wga"
   ],
-  "homepage": "https://github.com/BioInf-Wuerzburg/AliTV",
+  "homepage": "https://github.com/AliTVTeam/AliTV",
   "ignore": [
     "**/.*",
     "node_modules",

d3/AliTV.html

@@ -883,7 +883,7 @@ <h1><img src="css/AliTV_logo.png" alt="logo" width="200" height="160" style="mar
                                     <mark style="font-variant: small-caps;">AliTV (Alignment Toolbox and Visualization)</mark> is a software for visualizing Whole Genome Alignments. It generates publication-ready figures which can be used for the easy
                                     comparision of complete genomes. AliTV stands out due to its interactive functions for analyzing the alignments directly onto the figure.</p>
 
-                                <p>If you need help with AliTV, please checkout the official website <a href="http://bioinf-wuerzburg.github.io/AliTV/">http://bioinf-wuerzburg.github.io/AliTV/</a> or the gitHub page containing AliTVs repository <a href="https://github.com/BioInf-Wuerzburg/AliTV">https://github.com/BioInf-Wuerzburg/AliTV</a>.</p>
+                                <p>If you need help with AliTV, please checkout the official website <a href="http://alitvteam.github.io/AliTV/">http://alitvteam.github.io/AliTV/</a> or the gitHub page containing AliTVs repository <a href="https://github.com/AliTVTeam/AliTV">https://github.com/AliTVTeam/AliTV</a>.</p>
                             </div>
                         </div>
                     </div>

d3/doc/AliTV.html

@@ -18360,7 +18360,7 @@ <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 3.4.0</a> on Mon Jun 06 2016 16:47:45 GMT+0200 (CEST)
+    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.4.0</a> on Thu Jun 09 2016 13:37:17 GMT+0200 (CEST)
 </footer>
 
 <script> prettyPrint(); </script>

d3/doc/AliTV.js.html

@@ -35,7 +35,7 @@ <h1 class="page-title">Source: AliTV.js</h1>
 /* global bootbox: false */
 
 // use const instead of var as soon as EcmaScript 6 (ES6 is widely used)
-var AliTV_VERSION = "0.3.8";
+var AliTV_VERSION = "0.3.9";
 
 /**
  * Creates an object of type AliTV for drawing whole genome alignment visualizations
@@ -3440,7 +3440,7 @@ <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 3.4.0</a> on Mon Jun 06 2016 16:47:45 GMT+0200 (CEST)
+    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.4.0</a> on Thu Jun 09 2016 13:37:17 GMT+0200 (CEST)
 </footer>
 
 <script> prettyPrint(); </script>

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 3.4.0</a> on Mon Jun 06 2016 16:47:45 GMT+0200 (CEST)
+    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.4.0</a> on Thu Jun 09 2016 13:37:17 GMT+0200 (CEST)
 </footer>
 
 <script> prettyPrint(); </script>

d3/js/AliTV.js

@@ -7,7 +7,7 @@
 /* global bootbox: false */
 
 // use const instead of var as soon as EcmaScript 6 (ES6 is widely used)
-var AliTV_VERSION = "0.3.8";
+var AliTV_VERSION = "0.3.9";
 
 /**
  * Creates an object of type AliTV for drawing whole genome alignment visualizations

package.json

@@ -1,6 +1,6 @@
 {
   "name": "AliTV",
-  "version": "0.3.8",
+  "version": "0.3.9",
   "scripts": {
     "test": "grunt travis --verbose"
   },
@@ -24,14 +24,14 @@
   "dependencies": {},
   "repository": {
     "type": "git",
-    "url": "https://github.com/BioInf-Wuerzburg/AliTV.git"
+    "url": "https://github.com/AliTVTeam/AliTV.git"
   },
   "keywords": [
     "wga"
   ],
   "author": "Markus Ankenbrand",
   "license": "MIT",
   "bugs": {
-    "url": "https://github.com/BioInf-Wuerzburg/AliTV/issues"
+    "url": "https://github.com/AliTVTeam/AliTV/issues"
   }
 }