vidjil: vanity, bump year to 2015, update department name, url and publication

The computer science department of the Université de Lille is is now CRIStAL

vidjil: vanity, bump year to 2015, update department name, url and publication
The computer science department of the Université de Lille is is now CRIStAL
8980f5da · Mathieu Giraud · 6efc8cbe · 8980f5da · 8980f5da · 8980f5da
Commit 8980f5da authored Jan 13, 2015 by Mathieu Giraud
--- a/algo/core/cluster-junctions.cpp
+++ b/algo/core/cluster-junctions.cpp
 /*
-  This file is part of "Vidjil" <http://bioinfo.lifl.fr/vidjil>
-  Copyright (C) 2011, 2012, 2013 by Bonsai bioinformatics at LIFL (UMR CNRS 8022, Université Lille) and Inria Lille
-  Contributors: Mathieu Giraud <mathieu.giraud@lifl.fr>, Mikaël Salson <mikael.salson@lifl.fr>, Marc Duez
+  This file is part of Vidjil <http://www.vidjil.org>
+  Copyright (C) 2011, 2012, 2013, 2014, 2015 by Bonsai bioinformatics 
+  at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
+  Contributors: 
+      Mathieu Giraud <mathieu.giraud@vidjil.org>
+      Mikaël Salson <mikael.salson@vidjil.org>
+      Marc Duez <marc.duez@vidjil.org>

  "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/algo/core/compare-all.cpp
+++ b/algo/core/compare-all.cpp
 /*
-  This file is part of "Vidjil" <http://bioinfo.lifl.fr/vidjil>
-  Copyright (C) 2011, 2012, 2013 by Bonsai bioinformatics at LIFL (UMR CNRS 8022, Université Lille) and Inria Lille
-  Contributors: Mathieu Giraud <mathieu.giraud@lifl.fr>, Mikaël Salson <mikael.salson@lifl.fr>
+  This file is part of Vidjil <http://www.vidjil.org>
+  Copyright (C) 2011, 2012, 2013, 2014, 2015 by Bonsai bioinformatics 
+  at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
+  Contributors: 
+      Mathieu Giraud <mathieu.giraud@vidjil.org>
+      Mikaël Salson <mikael.salson@vidjil.org>
+      Marc Duez <marc.duez@vidjil.org>

  "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/algo/core/dynprog.cpp
+++ b/algo/core/dynprog.cpp
 /*
-  This file is part of "Vidjil" <http://bioinfo.lifl.fr/vidjil>
-  Copyright (C) 2011, 2012, 2013 by Bonsai bioinformatics at LIFL (UMR CNRS 8022, Université Lille) and Inria Lille
-  Contributors: Mathieu Giraud <mathieu.giraud@lifl.fr>, Mikaël Salson <mikael.salson@lifl.fr>, Marc Duez
+  This file is part of Vidjil <http://www.vidjil.org>
+  Copyright (C) 2011, 2012, 2013, 2014, 2015 by Bonsai bioinformatics 
+  at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
+  Contributors: 
+      Mathieu Giraud <mathieu.giraud@vidjil.org>
+      Mikaël Salson <mikael.salson@vidjil.org>
+      Marc Duez <marc.duez@vidjil.org>

  "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/algo/core/fasta.cpp
+++ b/algo/core/fasta.cpp
 /*
-  This file is part of "Vidjil" <http://bioinfo.lifl.fr/vid>
-  Copyright (C) 2011, 2012, 2013 by Bonsai bioinformatics at LIFL (UMR CNRS 8022, Université Lille) and Inria Lille
-  Contributors: Mathieu Giraud <mathieu.giraud@lifl.fr>, Mikaël Salson <mikael.salson@lifl.fr>, David Chatel
+  This file is part of Vidjil <http://www.vidjil.org>
+  Copyright (C) 2011, 2012, 2013, 2014, 2015 by Bonsai bioinformatics 
+  at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
+  Contributors: 
+      Mathieu Giraud <mathieu.giraud@vidjil.org>
+      Mikaël Salson <mikael.salson@vidjil.org>
+      Marc Duez <marc.duez@vidjil.org>

  "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/algo/core/kmeraffect.cpp
+++ b/algo/core/kmeraffect.cpp
 /*
-  This file is part of "Vidjil" <http://bioinfo.lifl.fr/vidjil>
-  Copyright (C) 2011, 2012, 2013 by Bonsai bioinformatics at LIFL (UMR CNRS 8022, Université Lille) and Inria Lille
-  Contributors: Mathieu Giraud <mathieu.giraud@lifl.fr>, Mikaël Salson <mikael.salson@lifl.fr>
+  This file is part of Vidjil <http://www.vidjil.org>
+  Copyright (C) 2011, 2012, 2013, 2014, 2015 by Bonsai bioinformatics 
+  at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
+  Contributors: 
+      Mathieu Giraud <mathieu.giraud@vidjil.org>
+      Mikaël Salson <mikael.salson@vidjil.org>
+      Marc Duez <marc.duez@vidjil.org>

  "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/algo/core/kmerstore.cpp
+++ b/algo/core/kmerstore.cpp
 /*
-  This file is part of "Vidjil" <http://bioinfo.lifl.fr/vidjil>
-  Copyright (C) 2011, 2012, 2013 by Bonsai bioinformatics at LIFL (UMR CNRS 8022, Université Lille) and Inria Lille
-  Contributors: Mathieu Giraud <mathieu.giraud@lifl.fr>, Mikaël Salson <mikael.salson@lifl.fr>, David Chatel
+  This file is part of Vidjil <http://www.vidjil.org>
+  Copyright (C) 2011, 2012, 2013, 2014, 2015 by Bonsai bioinformatics 
+  at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
+  Contributors: 
+      Mathieu Giraud <mathieu.giraud@vidjil.org>
+      Mikaël Salson <mikael.salson@vidjil.org>
+      Marc Duez <marc.duez@vidjil.org>

  "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/algo/core/labels.cpp
+++ b/algo/core/labels.cpp
-/*
-  This file is part of "Vidjil" <http://bioinfo.lifl.fr/vidjil>
-  Copyright (C) 2011, 2012, 2013 by Bonsai bioinformatics at LIFL (UMR CNRS 8022, Université Lille) and Inria Lille
-  Contributors: Mathieu Giraud <mathieu.giraud@lifl.fr>, Mikaël Salson <mikael.salson@lifl.fr>
-
-  "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/>
-*/

 #include "labels.h"
 #include <cmath>

--- a/algo/core/segment.cpp
+++ b/algo/core/segment.cpp
 /*
-  This file is part of "Vidjil" <http://bioinfo.lifl.fr/vidjil>
-  Copyright (C) 2011, 2012, 2013 by Bonsai bioinformatics at LIFL (UMR CNRS 8022, Université Lille) and Inria Lille
-  Contributors: Mathieu Giraud <mathieu.giraud@lifl.fr>, Mikaël Salson <mikael.salson@lifl.fr>, Marc Duez
+  This file is part of Vidjil <http://www.vidjil.org>
+  Copyright (C) 2011, 2012, 2013, 2014, 2015 by Bonsai bioinformatics 
+  at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
+  Contributors: 
+      Mathieu Giraud <mathieu.giraud@vidjil.org>
+      Mikaël Salson <mikael.salson@vidjil.org>
+      Marc Duez <marc.duez@vidjil.org>

  "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/algo/core/similarityMatrix.cpp
+++ b/algo/core/similarityMatrix.cpp
 /*
-  This file is part of "Vidjil" <http://bioinfo.lifl.fr/vidjil>
-  Copyright (C) 2011, 2012, 2013 by Bonsai bioinformatics at LIFL (UMR CNRS 8022, Université Lille) and Inria Lille
-  Contributors: Mathieu Giraud <mathieu.giraud@lifl.fr>, Mikaël Salson <mikael.salson@lifl.fr>
+  This file is part of Vidjil <http://www.vidjil.org>
+  Copyright (C) 2011, 2012, 2013, 2014, 2015 by Bonsai bioinformatics 
+  at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
+  Contributors: 
+      Mathieu Giraud <mathieu.giraud@vidjil.org>
+      Mikaël Salson <mikael.salson@vidjil.org>
+      Marc Duez <marc.duez@vidjil.org>

  "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/algo/vidjil.cpp
+++ b/algo/vidjil.cpp
 /*
-  This file is part of "Vidjil" <http://bioinfo.lifl.fr/vidjil>
-  Copyright (C) 2011, 2012, 2013, 2014 by Bonsai bioinformatics at LIFL (UMR CNRS 8022, Université Lille) and Inria Lille
-  Contributors: Mathieu Giraud <mathieu.giraud@lifl.fr>, Mikaël Salson <mikael.salson@lifl.fr>, Marc Duez <marc.duez@lifl.fr>
+  This file is part of Vidjil <http://www.vidjil.org>
+  Copyright (C) 2011, 2012, 2013, 2014, 2015 by Bonsai bioinformatics 
+  at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
+  Contributors: 
+      Mathieu Giraud <mathieu.giraud@vidjil.org>
+      Mikaël Salson <mikael.salson@vidjil.org>
+      Marc Duez <marc.duez@vidjil.org>

  "Vidjil" is free software: you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
@@ -222,13 +226,15 @@ void usage(char *progname)
 int main (int argc, char **argv)
 {
  cout << "# Vidjil -- V(D)J recombinations analysis <http://www.vidjil.org/>" << endl
-       << "# Copyright (C) 2011, 2012, 2013, 2014 by the Vidjil team" << endl
-       << "# Bonsai bioinformatics at LIFL (UMR CNRS 8022, Université Lille) and Inria Lille" << endl 
+       << "# Copyright (C) 2011, 2012, 2013, 2014, 2015 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
       << "# under certain conditions -- see http://git.vidjil.org/blob/master/doc/LICENSE" << endl
       << "# No lymphocyte was harmed in the making of this software," << endl
       << "# however this software is for research use only and comes with no warranty." << endl
+       << endl
+       << "# Please cite http://biomedcentral.com/1471-2164/15/409 if you use Vidjil." 
       << endl ;

  //$$ options: defaults

--- a/browser/js/axis.js
+++ b/browser/js/axis.js
 /*
-* This file is part of "Vidjil" <http://bioinfo.lifl.fr/vidjil>, V(D)J repertoire browsing and analysis
-* Copyright (C) 2013, 2014 by Marc Duez <marc.duez@lifl.fr>, Antonin Carette <antonin.carette@etudiant.univ-lille1.fr> and the Vidjil Team
-* Bonsai bioinformatics at LIFL (UMR CNRS 8022, 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) 2013, 2014, 2015 by Bonsai bioinformatics 
+ * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
+ * Contributors: 
+ *     Marc Duez <marc.duez@vidjil.org>
+ *     Antonin Carette <antonin.carette@etudiant.univ-lille1.fr>
+ *     The Vidjil Team <contact@vidjil.org>
+ * 
 * "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

--- a/browser/js/clone.js
+++ b/browser/js/clone.js
 /*
- * This file is part of "Vidjil" <http://bioinfo.lifl.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 LIFL (UMR CNRS 8022, 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) 2013, 2014, 2015 by Bonsai bioinformatics 
+ * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
+ * Contributors: 
+ *     Marc Duez <marc.duez@vidjil.org>
+ *     The Vidjil Team <contact@vidjil.org>
 *
 * "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/com.js
+++ b/browser/js/com.js
 /*
- * This file is part of "Vidjil" <http://bioinfo.lifl.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 LIFL (UMR CNRS 8022, 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) 2013, 2014, 2015 by Bonsai bioinformatics 
+ * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
+ * Contributors: 
+ *     Marc Duez <marc.duez@vidjil.org>
+ *     The Vidjil Team <contact@vidjil.org>
 *
 * "Vidjil" is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
@@ -62,7 +66,7 @@ function Com(flash_id, log_id, popup_id, data_id) {
        "welcome": " <h2>Vidjil <span class='logo'>(beta)</span></h2>"
 	    + "(c) 2011-2014, the Vidjil team" + "<br />Marc Duez, Mathieu Giraud and Mikaël Salson" 
 	    + " &ndash; <a href='http://www.vidjil.org'>http://www.vidjil.org/</a>" + "</br>" 
-	    + "</br>Vidjil is developed by the <a href='http://www.lifl.fr/bonsai'>Bonsai bioinformatics team</a> (LIFL, CNRS, U. Lille 1, Inria Lille), " 
+	    + "</br>Vidjil is developed by the <a href='http://cristal.univ-lille.fr/bonsai'>Bonsai bioinformatics team</a> (CRIStAL, CNRS, Univ. Lille, Inria Lille), " 
 	    + "in collaboration with the <a href='http://biologiepathologie.chru-lille.fr/organisation-fbp/91210.html'>department of Hematology</a> of CHRU Lille, " 
            + "the <a href='http://www.ircl.org/plate-forme-genomique.html'>Functional and Structural Genomic Platform</a> (U. Lille 2, IFR-114, IRCL)" 
 	    + " and the <a href='http://www.euroclonality.org/'>EuroClonality-NGS</a> working group." 

--- a/browser/js/compare.js
+++ b/browser/js/compare.js
 /*
-* This file is part of "Vidjil" <http://bioinfo.lifl.fr/vidjil>, V(D)J repertoire browsing and analysis
-* Copyright (C) 2014 by Carette Antonin <antonin.carette@etudiant.univ-lille1.fr> and the Vidjil Team
-* Bonsai bioinformatics at LIFL (UMR CNRS 8022, 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) 2013, 2014, 2015 by Bonsai bioinformatics 
+ * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
+ * Contributors: 
+ *     Antonette Carin <antonin.carette@etudiant.univ-lille1.fr>
+ *     The Vidjil Team <contact@vidjil.org>
+ *
 *
 * "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/dbscan.js
+++ b/browser/js/dbscan.js
 /*
-* This file is part of "Vidjil" <http://bioinfo.lifl.fr/vidjil>, V(D)J repertoire browsing and analysis
-* Copyright (C) 2014 by Carette Antonin <antonin.carette@etudiant.univ-lille1.fr> and the Vidjil Team
-* Bonsai bioinformatics at LIFL (UMR CNRS 8022, 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) 2013, 2014, 2015 by Bonsai bioinformatics 
+ * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
+ * Contributors: 
+ *     Antonette Carin <antonin.carette@etudiant.univ-lille1.fr>
+ *     The Vidjil Team <contact@vidjil.org>
+ *
 * "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

--- a/browser/js/germline_builder.js
+++ b/browser/js/germline_builder.js
 /*
- * This file is part of "Vidjil" <http://bioinfo.lifl.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 LIFL (UMR CNRS 8022, 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) 2013, 2014, 2015 by Bonsai bioinformatics 
+ * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
+ * Contributors: 
+ *     Marc Duez <marc.duez@vidjil.org>
+ *     The Vidjil Team <contact@vidjil.org>
 *
 * "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/graph.js
+++ b/browser/js/graph.js
 /*
- * This file is part of "Vidjil" <http://bioinfo.lifl.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 LIFL (UMR CNRS 8022, 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) 2013, 2014, 2015 by Bonsai bioinformatics 
+ * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
+ * Contributors: 
+ *     Marc Duez <marc.duez@vidjil.org>
+ *     The Vidjil Team <contact@vidjil.org>
 *
 * "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/list.js
+++ b/browser/js/list.js
 /*
- * This file is part of "Vidjil" <http://bioinfo.lifl.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 LIFL (UMR CNRS 8022, 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) 2013, 2014, 2015 by Bonsai bioinformatics 
+ * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
+ * Contributors: 
+ *     Marc Duez <marc.duez@vidjil.org>
+ *     The Vidjil Team <contact@vidjil.org>
 *
 * "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/menu.js
+++ b/browser/js/menu.js
 /*
-* This file is part of "Vidjil" <http://bioinfo.lifl.fr/vidjil>, V(D)J repertoire browsing and analysis
-* Copyright (C) 2013, 2014 by Marc Duez <marc.duez@lifl.fr>, Antonin Carette <antonin.carette@etudiant.univ-lille1.fr> and the Vidjil Team
-* Bonsai bioinformatics at LIFL (UMR CNRS 8022, 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) 2013, 2014, 2015 by Bonsai bioinformatics 
+ * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
+ * Contributors: 
+ *     Marc Duez <marc.duez@vidjil.org>
+ *     The Vidjil Team <contact@vidjil.org>
+ *
 * "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

--- a/browser/js/model.js
+++ b/browser/js/model.js
 /*
- * This file is part of "Vidjil" <http://bioinfo.lifl.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 LIFL (UMR CNRS 8022, 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) 2013, 2014, 2015 by Bonsai bioinformatics 
+ * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
+ * Contributors: 
+ *     Marc Duez <marc.duez@vidjil.org>
+ *     The Vidjil Team <contact@vidjil.org>
 *
 * "Vidjil" is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by