vidjil: vanity, bump year to 2017, welcome Aurélien in team

ab1a838f · Mathieu Giraud · 81eb736e · ab1a838f · ab1a838f · ab1a838f
Commit ab1a838f authored Jan 05, 2017 by Mathieu Giraud
35 changed files
--- a/README.org
+++ b/README.org
 #+TITLE: Vidjil -- High-throughput Analysis of V(D)J Immune Repertoire
-#+AUTHOR: The Vidjil team (Mathieu, Mikaël and Marc)
+#+AUTHOR: The Vidjil team (Mathieu, Mikaël, Aurélien, Florian, Marc, Ryan and Tatiana)

 [[https://travis-ci.org/vidjil/vidjil][https://img.shields.io/travis/vidjil/vidjil/master.svg]]
 [[http://opensource.org/licenses/GPL-3.0][http://img.shields.io/badge/license-GPLv3+-green.svg]]
@@ -7,7 +7,7 @@
 # https://coveralls.io/r/vidjil/vidjil http://img.shields.io/coveralls/vidjil/vidjil.svg

 # Vidjil -- V(D)J recombinations analysis -- [[http://www.vidjil.org]]
-# Copyright (C) 2011-2016 by Bonsai bioinformatics at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
+# Copyright (C) 2011-2017 by Bonsai bioinformatics at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
 # [[contact@vidjil.org]]

 V(D)J recombinations in lymphocytes are essential for immunological

--- a/algo/core/cluster-junctions.cpp
+++ b/algo/core/cluster-junctions.cpp
 /*
  This file is part of Vidjil <http://www.vidjil.org>
-  Copyright (C) 2011, 2012, 2013, 2014, 2015 by Bonsai bioinformatics 
+  Copyright (C) 2011-2017 by Bonsai bioinformatics
  at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
  Contributors: 
      Mathieu Giraud <mathieu.giraud@vidjil.org>

--- a/algo/core/compare-all.cpp
+++ b/algo/core/compare-all.cpp
 /*
  This file is part of Vidjil <http://www.vidjil.org>
-  Copyright (C) 2011, 2012, 2013, 2014, 2015 by Bonsai bioinformatics 
+  Copyright (C) 2011-2017 by Bonsai bioinformatics
  at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
  Contributors: 
      Mathieu Giraud <mathieu.giraud@vidjil.org>

--- a/algo/core/dynprog.cpp
+++ b/algo/core/dynprog.cpp
 /*
  This file is part of Vidjil <http://www.vidjil.org>
-  Copyright (C) 2011, 2012, 2013, 2014, 2015 by Bonsai bioinformatics 
+  Copyright (C) 2011-2017 by Bonsai bioinformatics
  at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
  Contributors: 
      Mathieu Giraud <mathieu.giraud@vidjil.org>

--- a/algo/core/fasta.cpp
+++ b/algo/core/fasta.cpp
 /*
  This file is part of Vidjil <http://www.vidjil.org>
-  Copyright (C) 2011, 2012, 2013, 2014, 2015 by Bonsai bioinformatics 
+  Copyright (C) 2011-2017 by Bonsai bioinformatics
  at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
  Contributors: 
      Mathieu Giraud <mathieu.giraud@vidjil.org>

--- a/algo/core/kmeraffect.cpp
+++ b/algo/core/kmeraffect.cpp
 /*
  This file is part of Vidjil <http://www.vidjil.org>
-  Copyright (C) 2011, 2012, 2013, 2014, 2015, 2016 by Bonsai bioinformatics
+  Copyright (C) 2011-2017 by Bonsai bioinformatics
  at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
  Contributors: 
      Mathieu Giraud <mathieu.giraud@vidjil.org>

--- a/algo/core/kmerstore.cpp
+++ b/algo/core/kmerstore.cpp
 /*
  This file is part of Vidjil <http://www.vidjil.org>
-  Copyright (C) 2011, 2012, 2013, 2014, 2015 by Bonsai bioinformatics 
+  Copyright (C) 2011-2017 by Bonsai bioinformatics
  at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
  Contributors: 
      Mathieu Giraud <mathieu.giraud@vidjil.org>

--- a/algo/core/segment.cpp
+++ b/algo/core/segment.cpp
 /*
  This file is part of Vidjil <http://www.vidjil.org>
-  Copyright (C) 2011, 2012, 2013, 2014, 2015, 2016 by Bonsai bioinformatics
+  Copyright (C) 2011-2017 by Bonsai bioinformatics
  at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
  Contributors: 
      Mathieu Giraud <mathieu.giraud@vidjil.org>

--- a/algo/core/similarityMatrix.cpp
+++ b/algo/core/similarityMatrix.cpp
 /*
  This file is part of Vidjil <http://www.vidjil.org>
-  Copyright (C) 2011, 2012, 2013, 2014, 2015 by Bonsai bioinformatics 
+  Copyright (C) 2011-2017 by Bonsai bioinformatics
  at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
  Contributors: 
      Mathieu Giraud <mathieu.giraud@vidjil.org>

--- a/algo/vidjil.cpp
+++ b/algo/vidjil.cpp
 /*
  This file is part of Vidjil <http://www.vidjil.org>
-  Copyright (C) 2011, 2012, 2013, 2014, 2015, 2016 by Bonsai bioinformatics
+  Copyright (C) 2011-2017 by Bonsai bioinformatics
  at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
  Contributors: 
      Mathieu Giraud <mathieu.giraud@vidjil.org>
@@ -283,7 +283,7 @@ double atof_NO_LIMIT(char *optarg)
 int main (int argc, char **argv)
 {
  cout << "# Vidjil -- V(D)J recombinations analysis <http://www.vidjil.org/>" << endl
-       << "# Copyright (C) 2011, 2012, 2013, 2014, 2015, 2016 by the Vidjil team" << endl
+       << "# Copyright (C) 2011-2017 by the Vidjil team" << endl
       << "# Bonsai bioinformatics at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille" << endl 
       << endl
       << "# Vidjil is free software, and you are welcome to redistribute it" << endl

--- a/browser/index.html
+++ b/browser/index.html
 <!doctype html>

 <!-- 
-  This file is part of "Vidjil" <http://bioinfo.lille.inria.fr/vidjil>, V(D)J repertoire browsing and analysis
-  Copyright (C) 2013, 2014 by Marc Duez <marc.duez@lifl.fr> and the Vidjil Team
-  Bonsai bioinformatics at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
+  This file is part of Vidjil <http://www.vidjil.org>, High-throughput Analysis of V(D)J Immune Repertoire
+  Copyright (C) 2011-2017 by Bonsai bioinformatics
+  at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille

  "Vidjil" is free software: you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by

--- a/browser/js/axis.js
+++ b/browser/js/axis.js
 /*
 * This file is part of Vidjil <http://www.vidjil.org>,
 * High-throughput Analysis of V(D)J Immune Repertoire.
- * Copyright (C) 2013, 2014, 2015 by Bonsai bioinformatics 
+ * Copyright (C) 2013-2017 by Bonsai bioinformatics
 * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
 * Contributors: 
 *     Marc Duez <marc.duez@vidjil.org>

--- a/browser/js/clone.js
+++ b/browser/js/clone.js
 /*
 * This file is part of Vidjil <http://www.vidjil.org>,
 * High-throughput Analysis of V(D)J Immune Repertoire.
- * Copyright (C) 2013, 2014, 2015 by Bonsai bioinformatics 
+ * Copyright (C) 2013-2017 by Bonsai bioinformatics
 * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
 * Contributors: 
 *     Marc Duez <marc.duez@vidjil.org>

--- a/browser/js/com.js
+++ b/browser/js/com.js
 /*
 * This file is part of Vidjil <http://www.vidjil.org>,
 * High-throughput Analysis of V(D)J Immune Repertoire.
- * Copyright (C) 2013, 2014, 2015 by Bonsai bioinformatics 
+ * Copyright (C) 2013-2017 by Bonsai bioinformatics
 * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
 * Contributors: 
 *     Marc Duez <marc.duez@vidjil.org>

--- a/browser/js/compare.js
+++ b/browser/js/compare.js
 /*
 * This file is part of Vidjil <http://www.vidjil.org>,
 * High-throughput Analysis of V(D)J Immune Repertoire.
- * Copyright (C) 2013, 2014, 2015 by Bonsai bioinformatics 
+ * Copyright (C) 2013-2017 by Bonsai bioinformatics
 * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
 * Contributors: 
 *     Antonette Carin <antonin.carette@etudiant.univ-lille1.fr>

--- a/browser/js/dbscan.js
+++ b/browser/js/dbscan.js
 /*
 * This file is part of Vidjil <http://www.vidjil.org>,
 * High-throughput Analysis of V(D)J Immune Repertoire.
- * Copyright (C) 2013, 2014, 2015 by Bonsai bioinformatics 
+ * Copyright (C) 2013-2017 by Bonsai bioinformatics
 * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
 * Contributors: 
 *     Antonette Carin <antonin.carette@etudiant.univ-lille1.fr>

--- a/browser/js/germline_builder.js
+++ b/browser/js/germline_builder.js
 /*
 * This file is part of Vidjil <http://www.vidjil.org>,
 * High-throughput Analysis of V(D)J Immune Repertoire.
- * Copyright (C) 2013, 2014, 2015 by Bonsai bioinformatics 
+ * Copyright (C) 2013-2017 by Bonsai bioinformatics
 * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
 * Contributors: 
 *     Marc Duez <marc.duez@vidjil.org>

--- a/browser/js/graph.js
+++ b/browser/js/graph.js
 /*
 * This file is part of Vidjil <http://www.vidjil.org>,
 * High-throughput Analysis of V(D)J Immune Repertoire.
- * Copyright (C) 2013, 2014, 2015 by Bonsai bioinformatics 
+ * Copyright (C) 2013-2017 by Bonsai bioinformatics
 * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
 * Contributors: 
 *     Marc Duez <marc.duez@vidjil.org>

--- a/browser/js/list.js
+++ b/browser/js/list.js
 /*
 * This file is part of Vidjil <http://www.vidjil.org>,
 * High-throughput Analysis of V(D)J Immune Repertoire.
- * Copyright (C) 2013, 2014, 2015 by Bonsai bioinformatics 
+ * Copyright (C) 2013-2017 by Bonsai bioinformatics
 * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
 * Contributors: 
 *     Marc Duez <marc.duez@vidjil.org>

--- a/browser/js/main.js
+++ b/browser/js/main.js
 /* This file is part of Vidjil <http://www.vidjil.org>,
 * High-throughput Analysis of V(D)J Immune Repertoire.
- * Copyright (C) 2013, 2014, 2015 by Bonsai bioinformatics
+ * Copyright (C) 2013-2017 by Bonsai bioinformatics
 * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
 * Contributors:
 *     Marc Duez <marc.duez@vidjil.org>

--- a/browser/js/menu.js
+++ b/browser/js/menu.js
 /*
 * This file is part of Vidjil <http://www.vidjil.org>,
 * High-throughput Analysis of V(D)J Immune Repertoire.
- * Copyright (C) 2013, 2014, 2015 by Bonsai bioinformatics 
+ * Copyright (C) 2013-2017 by Bonsai bioinformatics
 * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
 * Contributors: 
 *     Marc Duez <marc.duez@vidjil.org>

--- a/browser/js/model.js
+++ b/browser/js/model.js
 /*
 * This file is part of Vidjil <http://www.vidjil.org>,
 * High-throughput Analysis of V(D)J Immune Repertoire.
- * Copyright (C) 2013, 2014, 2015 by Bonsai bioinformatics 
+ * Copyright (C) 2013-2017 by Bonsai bioinformatics
 * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
 * Contributors: 
 *     Marc Duez <marc.duez@vidjil.org>

--- a/browser/js/model_loader.js
+++ b/browser/js/model_loader.js
 /*
 * This file is part of Vidjil <http://www.vidjil.org>,
 * High-throughput Analysis of V(D)J Immune Repertoire.
- * Copyright (C) 2013, 2014, 2015 by Bonsai bioinformatics 
+ * Copyright (C) 2013-2017 by Bonsai bioinformatics
 * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
 * Contributors: 
 *     Marc Duez <marc.duez@vidjil.org>

--- a/browser/js/scatterPlot.js
+++ b/browser/js/scatterPlot.js
 /*
 * This file is part of Vidjil <http://www.vidjil.org>,
 * High-throughput Analysis of V(D)J Immune Repertoire.
- * Copyright (C) 2013, 2014, 2015 by Bonsai bioinformatics 
+ * Copyright (C) 2013-2017 by Bonsai bioinformatics
 * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
 * Contributors: 
 *     Marc Duez <marc.duez@vidjil.org>

--- a/browser/js/segmenter.js
+++ b/browser/js/segmenter.js
 /*
 * This file is part of Vidjil <http://www.vidjil.org>,
 * High-throughput Analysis of V(D)J Immune Repertoire.
- * Copyright (C) 2013, 2014, 2015 by Bonsai bioinformatics 
+ * Copyright (C) 2013-2017 by Bonsai bioinformatics
 * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
 * Contributors: 
 *     Marc Duez <marc.duez@vidjil.org>

--- a/browser/js/shortcut.js
+++ b/browser/js/shortcut.js
 /*
 * This file is part of Vidjil <http://www.vidjil.org>,
 * High-throughput Analysis of V(D)J Immune Repertoire.
- * Copyright (C) 2013, 2014, 2015 by Bonsai bioinformatics 
+ * Copyright (C) 2013-2017 by Bonsai bioinformatics
 * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
 * Contributors: 
 *     Antonin Carette <antonin.carette@etudiant.univ-lille1.fr>

--- a/browser/js/vidjil-style.js
+++ b/browser/js/vidjil-style.js
 /*
 * This file is part of Vidjil <http://www.vidjil.org>,
 * High-throughput Analysis of V(D)J Immune Repertoire.
- * Copyright (C) 2013, 2014, 2015 by Bonsai bioinformatics 
+ * Copyright (C) 2013-2017 by Bonsai bioinformatics
 * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
 * Contributors: 
 *     Marc Duez <marc.duez@vidjil.org>

--- a/browser/js/view.js
+++ b/browser/js/view.js
 /*
 * This file is part of Vidjil <http://www.vidjil.org>,
 * High-throughput Analysis of V(D)J Immune Repertoire.
- * Copyright (C) 2013, 2014, 2015 by Bonsai bioinformatics 
+ * Copyright (C) 2013-2017 by Bonsai bioinformatics
 * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
 * Contributors: 
 *     Marc Duez <marc.duez@vidjil.org>

--- a/doc/algo.org
+++ b/doc/algo.org
 #+TITLE: Vidjil Algorithm -- Command-line Manual
-#+AUTHOR: The Vidjil team (Mathieu, Mikaël, Marc, Tatiana and Rayan)
+#+AUTHOR: The Vidjil team (Mathieu, Mikaël, Aurélien, Florian, Marc, Tatiana and Rayan)
 #+HTML_HEAD: <link rel="stylesheet" type="text/css" href="org-mode.css" />

 # This manual can be browsed online:
@@ -7,7 +7,7 @@
 #     http://git.vidjil.org/blob/master/doc/algo.org    (development version)

 # Vidjil -- High-throughput Analysis of V(D)J Immune Repertoire -- [[http://www.vidjil.org]]
-# Copyright (C) 2011, 2012, 2013, 2014, 2015, 2016 by Bonsai bioinformatics
+# Copyright (C) 2011-2017 by Bonsai bioinformatics
 # at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
 # contact@vidjil.org


--- a/doc/credits.org
+++ b/doc/credits.org
@@ -6,11 +6,13 @@ developed by the Bonsai bioinformatics lab, at CRIStAL (UMR CNRS 9189, Universit
 Contact: Mathieu Giraud and Mikaël Salson <contact@vidjil.org>

 * Vidjil core development
- - Mathieu Giraud, 2011-2016
- - Mikaël Salson, 2011-2016
+ - Mathieu Giraud, 2011-2017
+ - Mikaël Salson, 2011-2017
 - Marc Duez, 2012-2016
- - Tatiana Rocher, 2014-2016
- - Florian Thonier, 2015-2016
+ - Tatiana Rocher, 2014-2017
+ - Florian Thonier, 2015-2017
+ - Ryan Herbert, 2015-2017
+ - Aurélien Béliard, 2016-2017

 * Other contributors
 - David Chatel, 2011-2012

--- a/doc/dev.org
+++ b/doc/dev.org
 #+TITLE: Vidjil -- Developer Documentation
-#+AUTHOR: The Vidjil team (Florian, Marc, Mathieu, Mikaël, Ryan and Tatiana)
+#+AUTHOR: The Vidjil team (Mathieu, Mikaël, Aurélien, Florian, Marc, Ryan and Tatiana)
 #+HTML_HEAD: <link rel="stylesheet" type="text/css" href="org-mode.css" />

 # This manual can be browsed online:
@@ -7,7 +7,7 @@
 #     http://git.vidjil.org/blob/master/doc/dev.org    (development version)

 # Vidjil -- High-throughput Analysis of V(D)J Immune Repertoire -- [[http://www.vidjil.org]]
-# Copyright (C) 2011, 2012, 2013, 2014, 2015, 2016 by Bonsai bioinformatics
+# Copyright (C) 2011-2017 by Bonsai bioinformatics
 # at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
 # contact@vidjil.org


--- a/doc/locus.org
+++ b/doc/locus.org
 #+TITLE: Vidjil -- Analyzed locus
-#+AUTHOR: The Vidjil team (Florian, Mathieu, Mikaël, Marc and Tatiana)
+#+AUTHOR: The Vidjil team (Mathieu, Mikaël, Aurélien, Florian, Marc, Ryan and Tatiana)
 #+HTML_HEAD: <link rel="stylesheet" type="text/css" href="org-mode.css" />
 #+OPTIONS: toc:nil


--- a/doc/user.org
+++ b/doc/user.org
 #+TITLE: Vidjil -- Web Application Manual
-#+AUTHOR: The Vidjil team (Mathieu, Mikaël, Florian, Marc, Ryan and Tatiana)
+#+AUTHOR: The Vidjil team (Mathieu, Mikaël, Aurélien, Florian, Marc, Ryan and Tatiana)
 #+HTML_HEAD: <link rel="stylesheet" type="text/css" href="org-mode.css" />

 Vidjil is an open-source platform for the analysis of high-throughput sequencing data from lymphocytes.
@@ -10,7 +10,7 @@ High-throughput sequencing (NGS/HTS) now enables the deep sequencing of a lympho
 This is the help of the [[http://app.vidjil.org/browser/][Vidjil web application]].
 Further help can always be asked to [[mailto:contact@vidjil.org][contact@vidjil.org]]. We can also arrange phone or Skype meeting.

-The Vidjil team (Mathieu, Mikaël, Florian, Marc, Ryan and Tatiana)
+The Vidjil team (Mathieu, Mikaël, Aurélien, Florian, Marc, Ryan and Tatiana)

 * Requirements


--- a/server/web2py/applications/vidjil/models/db.py
+++ b/server/web2py/applications/vidjil/models/db.py
 # -*- coding: utf-8 -*-

+#  This file is part of Vidjil <http://www.vidjil.org>,
+#  High-throughput Analysis of V(D)J Immune Repertoire.
+#  Copyright (C) 2014-2017 by Bonsai bioinformatics
+#  at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
+#
+#  "Vidjil" is free software: you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation, either version 3 of the License, or
+#  (at your option) any later version.
+#
+#  "Vidjil" is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with "Vidjil". If not, see <http://www.gnu.org/licenses/>
+
+
 import defs
 from gluon import current
 from gluon.custom_import import track_changes; track_changes(True)

--- a/tools/fuse.py
+++ b/tools/fuse.py
@@ -5,7 +5,7 @@

 #  This file is part of Vidjil <http://www.vidjil.org>,
 #  High-throughput Analysis of V(D)J Immune Repertoire.
-#  Copyright (C) 2011, 2012, 2013, 2014, 2015 by Bonsai bioinformatics 
+#  Copyright (C) 2011-2017 by Bonsai bioinformatics
 #  at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
 #  Contributors: 
 #      Marc Duez <marc.duez@vidjil.org>