Updating bioinfo.cristal.univ-lille.fr to bioinfo.univ-lille.fr

bonsai-team · Jun 22, 2023 · d541a78 · d541a78
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Showing 6 changed files with 14 additions and 14 deletions.
diff --git a/README b/README
@@ -5,7 +5,7 @@ tool is implemented in C++ and provided for research purposes only.
 
 Help on this program can be obtained with the --help (-h) parameter,
 or from the homepage :
-  http://bioinfo.cristal.univ-lille.fr/yass/iedera.php
+  http://bioinfo.univ-lille.fr/yass/iedera.php
 
 Several specific examples and papers are also provided on this
 webpage, depending on the specific usage you would need.

diff --git a/README.rst b/README.rst
@@ -10,15 +10,15 @@
     :target: https://app.codecov.io/gh/laurentnoe/iedera/branch/master
     :alt: Coverage
 
-.. image:: https://img.shields.io/website.svg?style=flat-square&label=Website&url=https%3A%2F%2Fbioinfo.cristal.univ-lille.fr
-    :target: https://bioinfo.cristal.univ-lille.fr/yass/iedera.php
+.. image:: https://img.shields.io/website.svg?style=flat-square&label=Website&url=https%3A%2F%2Fbioinfo.univ-lille.fr
+    :target: https://bioinfo.univ-lille.fr/yass/iedera.php
     :alt: Website
 
 
 iedera
 ======
 
-(more at  <http://bioinfo.cristal.univ-lille.fr/yass/iedera.php>)
+(more at  <http://bioinfo.univ-lille.fr/yass/iedera.php>)
 
 ``iedera`` is a tool to select and design *spaced seeds*, *transition
 constrained spaced seeds*, or more generally *subset seeds*, and
@@ -28,7 +28,7 @@ constrained spaced seeds*, or more generally *subset seeds*, and
 Installation
 ------------
 
-(more at  <http://bioinfo.cristal.univ-lille.fr/yass/iedera.php#downloadiedera>)
+(more at  <http://bioinfo.univ-lille.fr/yass/iedera.php#downloadiedera>)
 
 Binaries for Windows (x64) and OS X (x64) are available at <https://github.com/laurentnoe/iedera/releases>.
 
@@ -66,7 +66,7 @@ or copy the binary directly to your homedir::
 Command-line
 ------------
 
-(more at  <http://bioinfo.cristal.univ-lille.fr/yass/iedera.php#quick>)
+(more at  <http://bioinfo.univ-lille.fr/yass/iedera.php#quick>)
 
 
 **First, use** one of these two parameters :
@@ -114,7 +114,7 @@ consider the two following:
   to activate the hill-climbing algorithm on previous parameter -r
 
 
-(more at  <http://bioinfo.cristal.univ-lille.fr/yass/iedera.php#details>)
+(more at  <http://bioinfo.univ-lille.fr/yass/iedera.php#details>)
 
 
 Examples

diff --git a/configure b/configure
@@ -613,7 +613,7 @@ PACKAGE_TARNAME='iedera'
 PACKAGE_VERSION='1.07'
 PACKAGE_STRING='iedera 1.07'
 PACKAGE_BUGREPORT='laurent DT noe AT univ-lille DT fr'
-PACKAGE_URL='http://bioinfo.cristal.univ-lille.fr/yass/iedera'
+PACKAGE_URL='http://bioinfo.univ-lille.fr/yass/iedera'
 
 ac_unique_file="src/main.cc"
 # Factoring default headers for most tests.
@@ -1396,7 +1396,7 @@ Use these variables to override the choices made by `configure' or to help
 it to find libraries and programs with nonstandard names/locations.
 
 Report bugs to <laurent DT noe AT univ-lille DT fr>.
-iedera home page: <http://bioinfo.cristal.univ-lille.fr/yass/iedera>.
+iedera home page: <http://bioinfo.univ-lille.fr/yass/iedera>.
 _ACEOF
 ac_status=$?
 fi
@@ -4789,7 +4789,7 @@ Configuration commands:
 $config_commands
 
 Report bugs to <laurent DT noe AT univ-lille DT fr>.
-iedera home page: <http://bioinfo.cristal.univ-lille.fr/yass/iedera>."
+iedera home page: <http://bioinfo.univ-lille.fr/yass/iedera>."
 
 _ACEOF
 ac_cs_config=`printf "%s\n" "$ac_configure_args" | sed "$ac_safe_unquote"`

diff --git a/configure.ac b/configure.ac
@@ -181,7 +181,7 @@ AC_DEFUN([ACX_CHECK_TYPE_TRAITS_CXX11], [
 
 
 
-AC_INIT([iedera],[1.07],[laurent DT noe AT univ-lille DT fr],[iedera],[http://bioinfo.cristal.univ-lille.fr/yass/iedera])
+AC_INIT([iedera],[1.07],[laurent DT noe AT univ-lille DT fr],[iedera],[http://bioinfo.univ-lille.fr/yass/iedera])
 AC_CONFIG_SRCDIR([src/main.cc])
 AC_LANG([C++])
 AM_INIT_AUTOMAKE([subdir-objects

diff --git a/src/main.cc b/src/main.cc
@@ -11,7 +11,7 @@
  *
  * @section Download
  * Download the iedera source code and binaries on the following web page:\n
- * <A HREF="http://bioinfo.cristal.univ-lille.fr/yass/iedera.php">http://bioinfo.cristal.univ-lille.fr/yass/iedera.php</A>\n
+ * <A HREF="http://bioinfo.univ-lille.fr/yass/iedera.php">http://bioinfo.univ-lille.fr/yass/iedera.php</A>\n
  * A small tutorial to use iedera is also provided on this web page.\n
  *
  * @author <A HREF="http://www.cristal.univ-lille.fr/~noe" TARGET="_top">Laurent Noe</A>
@@ -420,7 +420,7 @@ void USAGE() {
   cerr << "      -b <dbl>,<dbl>,...      : set the Bernoulli/Markov background distribution (size |'A'|^k)" << endl;
   cerr << "      -f <dbl>,<dbl>,...      : set the Bernoulli/Markov foreground distribution (size |'A'|^k)" << endl;
   cerr << "      -fF <filename>          : set the foreground model (as a probabilistic NFA)" << endl;
-  cerr << "                                for more details, see http://bioinfo.cristal.univ-lille.fr/yass/iedera.php#fFFormat" << endl;
+  cerr << "                                for more details, see http://bioinfo.univ-lille.fr/yass/iedera.php#fFFormat" << endl;
   cerr << "      -l <int>                : set the alignment length (default = " <<  gv_alignment_length << ") " << endl;
   cerr << "      -ll <int>               : select the sub-align window computation and set its length (default = disabled)" << endl;
   cerr << "      -llf <function>         : set the sub-align function used to merge the results (default = \"min\")" << endl;

diff --git a/tests/iedera_gcov_test3 b/tests/iedera_gcov_test3
@@ -1,5 +1,5 @@
 #!/bin/sh
-# the protein non-tree-transitive from http://bioinfo.cristal.univ-lille.fr/yass/iedera_proteins/Makefile.sh
+# the protein non-tree-transitive from https://bioinfo.univ-lille.fr/yass/iedera_proteins/Makefile.sh
 ./iedera_gcov -z 1 -w 3,6 -j 0.05 -n 2 -r 100 -k -l 16 -s 1,7 -A 47 -B 22 -M \{\{1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1\},\{1,1,1,1,1,0,0,0,1,0,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,0,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1\},\{0,1,1,1,1,0,1,1,0,1,0,1,1,1,0,0,1,1,0,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1\},\{0,0,1,0,1,1,0,0,0,0,0,0,0,1,0,1,1,1,1,0,1,0,1,1,0,0,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1\},\{0,0,0,1,1,0,0,1,0,1,1,0,1,1,0,1,0,1,1,0,0,0,0,1,0,0,1,1,0,0,1,1,0,1,1,1,0,1,1,1,1,1,1,0,1,1,1\},\{0,0,0,0,0,1,1,1,1,0,1,1,1,1,1,0,1,1,1,1,0,1,1,1,0,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1\},\{0,0,0,0,0,0,0,0,1,1,1,0,0,1,1,0,1,1,0,1,1,0,1,1,0,1,0,0,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,1,1,1,0,0,1,1,0,0,1,1,1,1,0,0,0,0,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1,0,0,0,0,0,1,1,0,0,0,1,1,0,1,0,1,1,0,1,1,1,1,1,1,1,0,1,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,1,1,1,0,1,0,0,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1,0,0,0,0,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,0,1,0,0,1,0,1,1,0,1,1,1,1,1,1,1,1,1,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,1,0,1,1,0,1,1,1,1,1,1,1,1,1,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,0,1,1,1,0,1,1,1,1,1,1,1,1,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,0,1,1,1,1,0,1,1,1,0,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,1,1,1,0,1,1,0,0,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,0,1,0,0,1,0,0,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1,1,1,0,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1,0,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1\}\} -f 0.01612,0.01412,0.02288,0.00065,0.14347,0.00154,0.00168,0.01030,0.01514,0.01052,0.01076,0.01056,0.00419,0.00591,0.00192,0.00081,0.02840,0.05675,0.00273,0.00330,0.00029,0.01035,0.00191,0.03588,0.00030,0.02367,0.00466,0.00046,0.02768,0.00072,0.00759,0.01365,0.00286,0.01994,0.00964,0.00210,0.00983,0.04172,0.01117,0.00940,0.00744,0.00986,0.03641,0.00347,0.00708,0.00848,0.33169 -b 0.05108,0.03647,0.06770,0.00256,0.27712,0.00366,0.00485,0.01880,0.02941,0.01701,0.01457,0.01731,0.00757,0.00956,0.00389,0.00193,0.03584,0.07233,0.00571,0.00690,0.00064,0.01405,0.00281,0.04220,0.00068,0.02704,0.00418,0.00129,0.03316,0.00190,0.00860,0.01192,0.00234,0.01605,0.00704,0.00180,0.00583,0.02786,0.00752,0.00583,0.00479,0.00494,0.01591,0.00208,0.00372,0.00306,0.05849 || exit 99
 
 ./iedera_gcov -z 1 -j 0.05 -l 16  -A 64 -B 64 -m "#53;v3R,L34K" || exit 99