Merge lp:~ma5/madanalysis5/v1.1.10beta into lp:madanalysis5

[Eric Conte]

=== modified file 'bin/ma5'
--- bin/ma5	2013-10-29 09:21:58 +0000
+++ bin/ma5	2014-05-17 19:51:11 +0000
@@ -24,6 +24,194 @@
 ################################################################################
 
 
+def MainSession():
+    
+    # Importing  MadAnalysis main class
+    from madanalysis.core.main import Main
+    main = Main()
+    main.ma5dir = ma5dir
+
+    # Release version
+    # Do not touch it !!!!!  
+    main.version = "1.1.10.35"
+    main.date = "2014/05/09"
+
+    # Checking arguments
+    import getopt
+    try:
+        optlist, arglist = getopt.getopt(sys.argv[1:], \
+                                     "PHReEvhfmsb", \
+                                     ["partonlevel","hadronlevel","recolevel",\
+                                      "expert","version","release","help",\
+                                      "forced","script","mg5","autocheck","build"])
+    except getopt.GetoptError, err:
+        logging.error(str(err))
+        usage()
+        sys.exit()
+
+    # Reading aguments
+    partonlevel = False
+    hadronlevel = False
+    recolevel   = False
+    expertmode  = False
+    forcedmode  = False
+    mg5mode     = False
+    scriptmode  = False
+    autocheck   = False
+    build       = False
+    for o,a in optlist:
+        if o in ("-P","--partonlevel"):
+            partonlevel=True
+        elif o in ("-H","--hadronlevel"):
+            hadronlevel=True
+        elif o in ("-R","--recolevel"):
+            recolevel=True
+        elif o in ("-E","-e","--expert"):
+            expertmode=True
+        elif o in ("-f","--forced"):
+            forcedmode=True
+        elif o in ("-m","--mg5"):
+            mg5mode=True
+        elif o in ("-s","--script"):
+            scriptmode=True
+        elif o in ("-v","--version","--release"):
+            logging.info("MA5 release : " + main.version + " " + main.date  + "\n")
+            sys.exit()
+        elif o in ("--autocheck"):
+            autocheck = True
+        elif o in ("-b","--build"):
+            build = True
+        elif o in ("-h","--help"):
+            usage()
+            sys.exit()
+
+    # Checking compatibility between arguments
+    if partonlevel and hadronlevel:
+       logging.error("Parton mode and hadron mode cannot be set in a same time.\n"
+                     "Please choose only one of these modes.")
+       sys.exit()
+    elif partonlevel and recolevel:
+       logging.error("Parton mode and reco mode cannot be set in a same time.\n"
+                     "Please choose only one of these modes.")
+       sys.exit()
+    
+    elif hadronlevel and recolevel:
+       logging.error("Hadron mode and reco mode cannot be set in a same time.\n"
+                     "Please choose only one of these modes.")
+       sys.exit()
+    if scriptmode:
+       forcedmode=True
+
+    # Setting argument in the main program 
+    from madanalysis.enumeration.ma5_running_type import MA5RunningType
+    if partonlevel:
+        main.mode=MA5RunningType.PARTON
+    elif hadronlevel:
+        main.mode=MA5RunningType.HADRON
+    elif recolevel:
+        main.mode=MA5RunningType.RECO
+        from madanalysis.enumeration.normalize_type import NormalizeType
+        main.normalize=NormalizeType.NONE
+
+    # Re-initializing the list of observables (hadron-level or reco-level)
+    if hadronlevel or recolevel:
+        main.InitObservables(main.mode)
+
+    main.forced = forcedmode
+    Main.forced = forcedmode
+    main.script = scriptmode
+    main.mg5    = mg5mode
+
+    # Setting batch mode for ROOT
+    #sys.argv.append('-b-')
+
+    # Displaying header
+    logging.info("")
+    logging.info(\
+    "*************************************************************\n" + \
+    "*                                                           *\n" + \
+    "*        W E L C O M E  to  M A D A N A L Y S I S  5        *\n" + \
+    "*                         ______  ______                    *\n" + \
+    "*                 /'\_/`\/\  __ \/\  ___\                   *\n" + \
+    "*                /\      \ \ \_\ \ \ \__/                   *\n" + \
+    "*                \ \ \__\ \ \  __ \ \___``\                 *\n" + \
+    "*                 \ \ \_/\ \ \ \/\ \/\ \_\ \                *\n" + \
+    "*                  \ \_\\\ \_\ \_\ \_\ \____/                *\n" + \
+    "*                   \/_/ \/_/\/_/\/_/\/___/                 *\n" + \
+    "*                                                           *\n" + \
+    "*   MA5 release : " + \
+             "%-24s" % main.version + "%+15s" % main.date  + "   *\n" + \
+    "*                                                           *\n" + \
+    "*         Comput. Phys. Commun. 184 (2013) 222-256          *\n" + \
+    "*                                                           *\n" + \
+    "*   The MadAnalysis Development Team - Please visit us at   *\n" + \
+    "*            https://launchpad.net/madanalysis5             *\n" + \
+    "*                                                           *\n" + \
+    "*              Type 'help' for in-line help.                *\n" + \
+    "*                                                           *\n" + \
+    "*************************************************************")
+
+    # Displaying special banner if auto-check mode is activated 
+    if autocheck:
+        logging.info("")
+        logging.info("                        AUTO-CHECK MODE")
+        logging.info("")
+
+    # Checking the present linux configuration
+    if not main.CheckLinuxConfig(detail=autocheck):
+        sys.exit()
+
+    # Building (if necesserary) the SampleAnalyzer library
+    if not main.BuildLibrary(forced=build):
+        sys.exit()	
+
+    logging.info("*************************************************************")
+
+
+    # Auto-check mode
+    if autocheck:
+        pass
+
+    # Expert mode
+    elif expertmode:
+        from madanalysis.core.expert_mode import ExpertMode
+        main.expertmode = True
+        expert = ExpertMode(main)
+        if not expert.CreateDirectory():
+            sys.exit()
+        if not expert.Copy():
+            sys.exit()
+        expert.GiveAdvice()
+        return False
+
+    # Normal mode
+    else:
+    
+        # Launching the interpreter
+        from madanalysis.interpreter.interpreter import Interpreter
+        interpreter = Interpreter(main)
+
+        # Looking for script
+        for arg in arglist:
+            filename=os.path.expanduser(arg)
+            filename=os.path.abspath(filename)
+            interpreter.load(filename)
+    
+        # Exit if script mode activated
+        if len(arglist)!=0 and main.script:
+            interpreter.run_cmd("quit")
+            return False
+    
+        # Interpreter loop
+        else:
+            interpreter.cmdloop()
+            if main.repeatSession==True:
+                return True
+            else:
+                return False
+        
+       
+
 def usage():
     logging.info("\nUsage of MadAnalysis 5")
     logging.info("------------------------")
@@ -50,6 +238,9 @@
     logging.info("This optional argument is a list of filenames containing a "+\
                  "set of MadAnalysis 5 commands. The file name are handled as "+\
                  "concatenated, and the commands are applied sequentially.\n")
+
+
+
     
 """This is the main executable, a simple frontend to set up the PYTHONPATH
 and call immediately the command line interface scripts"""
@@ -105,182 +296,16 @@
         readline.__doc__ = 'GNU'
         readline.parse_and_bind("tab: complete")
 
-
-# Importing  MadAnalysis main class
-from madanalysis.core.main import Main
-main = Main()
-main.ma5dir = ma5dir
-
-# Release version
-# Do not touch it !!!!!  
-main.version = "1.1.9"
-main.date = "2013/10/29"
-
-# Checking arguments
-import getopt
-try:
-    optlist, arglist = getopt.getopt(sys.argv[1:], \
-                                     "PHReEvhfmsb", \
-                                     ["partonlevel","hadronlevel","recolevel",\
-                                      "expert","version","release","help",\
-                                      "forced","script","mg5","autocheck","build"])
-except getopt.GetoptError, err:
-    logging.error(str(err))
-    usage()
-    sys.exit()
-
-# Reading aguments
-partonlevel = False
-hadronlevel = False
-recolevel   = False
-expertmode  = False
-forcedmode  = False
-mg5mode     = False
-scriptmode  = False
-autocheck   = False
-build       = False
-for o,a in optlist:
-    if o in ("-P","--partonlevel"):
-        partonlevel=True
-    elif o in ("-H","--hadronlevel"):
-        hadronlevel=True
-    elif o in ("-R","--recolevel"):
-        recolevel=True
-    elif o in ("-E","-e","--expert"):
-        expertmode=True
-    elif o in ("-f","--forced"):
-        forcedmode=True
-    elif o in ("-m","--mg5"):
-        mg5mode=True
-    elif o in ("-s","--script"):
-        scriptmode=True
-    elif o in ("-v","--version","--release"):
-        logging.info("MA5 release : " + main.version + " " + main.date  + "\n")
-        sys.exit()
-    elif o in ("--autocheck"):
-        autocheck = True
-    elif o in ("-b","--build"):
-        build = True
-    elif o in ("-h","--help"):
-        usage()
-        sys.exit()
-
-# Checking compatibility between arguments
-if partonlevel and hadronlevel:
-    logging.error("Parton mode and hadron mode cannot be set in a same time.\n"
-                  "Please choose only one of these modes.")
-    sys.exit()
-elif partonlevel and recolevel:
-    logging.error("Parton mode and reco mode cannot be set in a same time.\n"
-                  "Please choose only one of these modes.")
-    sys.exit()
-    
-elif hadronlevel and recolevel:
-    logging.error("Hadron mode and reco mode cannot be set in a same time.\n"
-                  "Please choose only one of these modes.")
-    sys.exit()
-if scriptmode:
-    forcedmode=True
-
-# Setting argument in the main program 
-from madanalysis.enumeration.ma5_running_type import MA5RunningType
-if partonlevel:
-    main.mode=MA5RunningType.PARTON
-elif hadronlevel:
-    main.mode=MA5RunningType.HADRON
-elif recolevel:
-    main.mode=MA5RunningType.RECO
-    from madanalysis.enumeration.normalize_type import NormalizeType
-    main.normalize=NormalizeType.NONE
-
-# Re-initializing the list of observables (hadron-level or reco-level)
-if hadronlevel or recolevel:
-    main.InitObservables(main.mode)
-
-
-main.forced = forcedmode
-Main.forced = forcedmode
-main.script = scriptmode
-main.mg5    = mg5mode
-
-# Setting batch mode for ROOT
-#sys.argv.append('-b-')
-
-# Displaying header
-logging.info("")
-logging.info(\
-"*************************************************************\n" + \
-"*                                                           *\n" + \
-"*        W E L C O M E  to  M A D A N A L Y S I S  5        *\n" + \
-"*                         ______  ______                    *\n" + \
-"*                 /'\_/`\/\  __ \/\  ___\                   *\n" + \
-"*                /\      \ \ \_\ \ \ \__/                   *\n" + \
-"*                \ \ \__\ \ \  __ \ \___``\                 *\n" + \
-"*                 \ \ \_/\ \ \ \/\ \/\ \_\ \                *\n" + \
-"*                  \ \_\\\ \_\ \_\ \_\ \____/                *\n" + \
-"*                   \/_/ \/_/\/_/\/_/\/___/                 *\n" + \
-"*                                                           *\n" + \
-"*   MA5 release : " + \
-         "%-24s" % main.version + "%+15s" % main.date  + "   *\n" + \
-"*                                                           *\n" + \
-"*         Comput. Phys. Commun. 184 (2013) 222-256          *\n" + \
-"*                                                           *\n" + \
-"*   The MadAnalysis Development Team - Please visit us at   *\n" + \
-"*            https://launchpad.net/madanalysis5             *\n" + \
-"*                                                           *\n" + \
-"*              Type 'help' for in-line help.                *\n" + \
-"*                                                           *\n" + \
-"*************************************************************")
-
-# Displaying special banner if auto-check mode is activated 
-if autocheck:
-    logging.info("")
-    logging.info("                        AUTO-CHECK MODE")
-    logging.info("")
-    
-
-# Checking the present linux configuration
-if not main.CheckLinuxConfig(detail=autocheck):
-    sys.exit()
-
-# Building (if necesserary) the SampleAnalyzer library
-if not main.BuildLibrary(forced=build):
-    sys.exit()	
-
-logging.info("*************************************************************")
-
-
-# Auto-check mode
-if autocheck:
-    pass
-
-# Expert mode
-elif expertmode:
-    from madanalysis.core.expert_mode import ExpertMode
-    expert = ExpertMode(main)
-    if not expert.CreateDirectory():
-        sys.exit()
-    if not expert.Copy():
-        sys.exit()
-    expert.GiveAdvice()
-
-# Normal mode
-else:
-    
-    # Launching the interpreter
-    from madanalysis.interpreter.interpreter import Interpreter
-    interpreter = Interpreter(main)
-
-    # Looking for script
-    for arg in arglist:
-        filename=os.path.expanduser(arg)
-        filename=os.path.abspath(filename)
-        interpreter.load(filename)
-    
-    # Exit if script mode activated
-    if len(arglist)!=0 and main.script:
-        interpreter.run_cmd("quit")
-    
-    # Interpreter loop
-    else:
-        interpreter.cmdloop()
+# Loop over MA5 sessions
+# Goal: allowing to restart
+while True:
+    repeat = MainSession()
+    if not repeat:
+        # Normal end
+        break
+    from madanalysis.core.string_tools import StringTools
+    logging.info("")
+    logging.info(StringTools.Fill('-',40))
+    logging.info(StringTools.Center('RESTART THE MADANALYSIS 5 SESSION',40))
+    logging.info(StringTools.Fill('-',40))
+    logging.info("")
 
=== added file 'madanalysis/IOinterface/delphes_migration.py'
--- madanalysis/IOinterface/delphes_migration.py	1970-01-01 00:00:00 +0000
+++ madanalysis/IOinterface/delphes_migration.py	2014-05-17 19:51:11 +0000
@@ -0,0 +1,81 @@
+################################################################################
+#  
+#  Copyright (C) 2012-2013 Eric Conte, Benjamin Fuks
+#  The MadAnalysis development team, email: <[e-mail]>
+#  
+#  This file is part of MadAnalysis 5.
+#  Official website: <https://launchpad.net/madanalysis5>
+#  
+#  MadAnalysis 5 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.
+#  
+#  MadAnalysis 5 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 MadAnalysis 5. If not, see <http://www.gnu.org/licenses/>
+#  
+################################################################################
+
+
+from madanalysis.selection.instance_name      import InstanceName
+from madanalysis.IOinterface.folder_writer    import FolderWriter
+from madanalysis.enumeration.ma5_running_type import MA5RunningType
+from madanalysis.core.string_tools            import StringTools
+import logging
+import shutil
+import os
+import commands
+import glob
+
+class DelphesMigration():
+
+    def __init__(self,main):
+        self.main = main
+
+    def Migrate(self):
+        self.ChangeTreeNames()
+        self.ApplyPatch()
+
+    def ApplyPatch(self):
+        os.system('cp '+self.main.ma5dir+'/tools/SampleAnalyzer/Detector/patch_delfes.tgz '+\
+                  self.main.ma5dir+'/tools/delfes/')
+        os.system('cd '+ self.main.ma5dir + '/tools/delfes/; tar xzf patch_delfes.tgz')
+
+
+    def ChangeTreeNames(self):
+        myfiles = glob.glob(self.main.ma5dir+'/tools/delfes/readers/Delphes*.cpp')
+        for myfile in myfiles:
+            self.ChangeTreeName(myfile)
+
+    def ChangeTreeName(self,filename):
+
+        try:
+            input = open(filename)
+        except:
+            return False
+
+        try:
+            output = open(filename+"~","w")
+        except:
+            return False
+
+        for line in input:
+            if line.find("treeWriter")!=-1 and line.find("ExRootTreeWriter")!=1:
+                line = line.replace('"Delphes"','"Delfes"')
+            output.write(line)
+                
+        output.close()
+        input.close()
+        os.system("mv "+filename+"~ "+filename)
+        return True
+
+        
+        
+        
+        
+        
 
=== modified file 'madanalysis/IOinterface/job_reader.py'
--- madanalysis/IOinterface/job_reader.py	2013-07-28 14:10:33 +0000
+++ madanalysis/IOinterface/job_reader.py	2014-05-17 19:51:11 +0000
@@ -293,9 +293,9 @@
                     beginTag.activate()
                 elif words[0].lower()=='</safheader>':
                     beginTag.desactivate()
-                if words[0].lower()=='<saffoot>':
+                if words[0].lower()=='<saffooter>':
                     endTag.activate()
-                elif words[0].lower()=='</saffoot>':
+                elif words[0].lower()=='</saffooter>':
                     endTag.desactivate()
                 if words[0].lower()=='<sampleglobalinfo>':
                     globalTag.activate()
@@ -573,7 +573,7 @@
             logging.error("SAF header <SAFheader> and </SAFheader> is not "+\
                           "found.")
         if endTag.Nactivated==0 or endTag.activated:
-            logging.error("SAF foot <SAFfoot> and </SAFfoot> is not "+\
+            logging.error("SAF footer <SAFfooter> and </SAFfooter> is not "+\
                           "found.")
         if globalTag.Nactivated==0 or globalTag.activated:
             logging.error("Information corresponding to the block "+\
 
=== modified file 'madanalysis/IOinterface/job_writer.py'
--- madanalysis/IOinterface/job_writer.py	2013-10-29 09:21:58 +0000
+++ madanalysis/IOinterface/job_writer.py	2014-05-17 19:51:11 +0000
@@ -26,6 +26,7 @@
 from madanalysis.IOinterface.folder_writer    import FolderWriter
 from madanalysis.enumeration.ma5_running_type import MA5RunningType
 from madanalysis.core.string_tools            import StringTools
+from madanalysis.IOinterface.shell_command    import ShellCommand
 import logging
 import shutil
 import os
@@ -40,6 +41,7 @@
         self.resubmit   = resubmit
         self.libZIP     = self.main.libZIP
         self.libDelphes = self.main.libDelphes
+        self.libDelfes  = self.main.libDelfes
         self.output     = self.main.output
         self.libFastjet = self.main.libFastJet
         self.fastsim    = self.main.fastsim
@@ -60,8 +62,6 @@
             return False
         elif not os.path.isdir(path+"/Build/SampleAnalyzer/Analyzer"):
             return False
-        elif not os.path.isdir(path+"/Build/SampleAnalyzer/Filter"):
-            return False
         elif not os.path.isdir(path+"/Build/Main"):
             return False
         elif not os.path.isdir(path+"/Output"):
@@ -99,11 +99,6 @@
             logging.error("Impossible to create the folder 'Build/SampleAnalyzer/Analyzer'")
             return False
         try:
-            os.mkdir(path+"/Build/SampleAnalyzer/Filter")
-        except:
-            logging.error("Impossible to create the folder 'Build/SampleAnalyzer/Filter'")
-            return False
-        try:
             os.mkdir(path+"/Build/Log")
         except:
             logging.error("Impossible to create the folder 'Build/Log'")
@@ -143,9 +138,6 @@
         elif not os.path.isdir(self.path+"/Build/SampleAnalyzer/Analyzer"):
             logging.error("folder '"+self.path+"/Build/SampleAnalyzer/Analyzer' is not found")
             return False
-        elif not os.path.isdir(self.path+"/Build/SampleAnalyzer/Filter"):
-            logging.error("folder '"+self.path+"/Build/SampleAnalyzer/Filter' is not found")
-            return False
         elif not os.path.isdir(self.path+"/Build/Main"):
             logging.error("folder '"+self.path+"/Build/Main' is not found")
             return False
@@ -170,19 +162,18 @@
 
     def CreateDelphesCard(self):
 
-        if self.fastsim.delphes.pileup=="":
-            if self.fastsim.delphes.detector=='cms':
-                cardname = 'delphes_card_CMS.tcl'
-            elif self.fastsim.delphes.detector=='atlas':
-                cardname ='delphes_card_ATLAS.tcl'
+        if self.main.fastsim.package=="delphes":
+            cardname = self.main.fastsim.delphes.card
+        elif self.main.fastsim.package=="delfes":
+            cardname = self.main.fastsim.delfes.card
+
+        if self.main.fastsim.package=="delfes":
+            cfg=self.main.fastsim.delfes
         else:
-            if self.fastsim.delphes.detector=='cms':
-                cardname = 'delphes_card_CMS_PileUp.tcl'
-            elif self.fastsim.delphes.detector=='atlas':
-                cardname ='delphes_card_ATLAS_PileUp.tcl'
+            cfg=self.main.fastsim.delphes
 
         try:
-            input = open(self.ma5dir+"/tools/SampleAnalyzer/"+cardname,'r')
+            input = open(self.ma5dir+"/tools/SampleAnalyzer/Detector/"+cardname,'r')
         except:
             pass
 
@@ -191,18 +182,18 @@
         except:
             pass
 
-        if self.main.fastsim.delphes.pileup!="":
+        if cfg.pileup!="":
             # Getting current dir
             theDir = os.getcwd()
 
             # Adding file
-            if self.main.fastsim.delphes.pileup.startswith('/'):
-                theFile = self.main.fastsim.delphes.pileup
+            if cfg.pileup.startswith('/'):
+                theFile = cfg.pileup
             else:    
-                theFile = os.path.normpath(theDir+"/"+self.main.fastsim.delphes.pileup)
+                theFile = os.path.normpath(theDir+"/"+cfg.pileup)
 
         for line in input:
-            if self.main.fastsim.delphes.pileup!="":
+            if cfg.pileup!="":
                 line=line.replace('MinBias.pileup',theFile)
             output.write(line)
 
@@ -234,22 +225,8 @@
         except:
             logging.error('Impossible to make executable the file "newAnalyzer"')
             return False
-        try:
-            shutil.copyfile\
-                      (\
-                      self.ma5dir+"/tools/SampleAnalyzer/newFilter.py",\
-                      self.path+"/Build/SampleAnalyzer/newFilter.py"\
-                      )
-        except:
-            logging.error('Impossible to copy the file "newFilter"')
-            return False
-        try:
-            os.chmod(self.path+"/Build/SampleAnalyzer/newFilter.py",0755)
-        except:
-            logging.error('Impossible to make executable the file "newFilter.py"')
-            return False
 
-        if self.main.fastsim.package=="delphes":
+        if self.main.fastsim.package in ["delphes","delfes"]:
             self.CreateDelphesCard()
 
         return True
@@ -267,7 +244,8 @@
 
     def PrintIncludes(self,file):
         file.write('// SampleHeader header\n')
-        file.write('#include \"SampleAnalyzer/Core/SampleAnalyzer.h\"\n')
+        file.write('#include "SampleAnalyzer/Core/SampleAnalyzer.h"\n')
+        file.write('#include "SampleAnalyzer/Analyzer/analysisList.h"\n') 
         file.write('using namespace MA5;\n\n')
         return
 
@@ -278,7 +256,9 @@
         file.write('int main(int argc, char *argv[])\n')
         file.write('{\n')
         file.write('  // Creating a manager\n')
-        file.write('  SampleAnalyzer manager;\n\n')
+        file.write('  SampleAnalyzer manager;\n')
+        file.write('  BuildUserTable(manager.AnalyzerList());\n')
+        file.write('\n')
 
         # Initializing
         file.write('  // ---------------------------------------------------\n')
@@ -286,7 +266,11 @@
         file.write('  // ---------------------------------------------------\n')
         file.write('  INFO << "    * Initializing all components" << endmsg;\n\n')
         file.write('  // Initializing the manager\n')
-        file.write('  if (!manager.Initialize(argc,argv,"pdg.ma5")) '+\
+        if self.main.expertmode:
+          file.write('  if (!manager.Initialize(argc,argv,"pdg.ma5",true)) '+\
+                   'return 1;\n\n')
+        else:
+          file.write('  if (!manager.Initialize(argc,argv,"pdg.ma5")) '+\
                    'return 1;\n\n')
         file.write('  // Creating data format for storing data\n')
         file.write('  EventFormat myEvent;\n')
@@ -314,39 +298,48 @@
 
         # Fast-Simulation detector
         # + Case Fastsim
-        if self.fastsim.package=="fastjet":
+        if self.main.fastsim.package=="fastjet":
             file.write('  //Getting pointer to the clusterer\n')
             file.write('  std::map<std::string, std::string> parametersC1;\n')
-            parameters = self.fastsim.SampleAnalyzerConfigString()
+            parameters = self.main.fastsim.SampleAnalyzerConfigString()
             for k,v in sorted(parameters.iteritems(),\
                               key=lambda (k,v): (k,v)):
                 file.write('  parametersC1["'+k+'"]="'+v+'";\n')
             file.write('  JetClustererBase* cluster1 = \n')
-            file.write('      manager.InitializeJetClusterer("'+self.fastsim.clustering.algorithm+'",parametersC1);\n')
+            file.write('      manager.InitializeJetClusterer("'+self.main.fastsim.clustering.algorithm+'",parametersC1);\n')
             file.write('  if (cluster1==0) return 1;\n\n')
             
         # + Case Delphes
-        if self.fastsim.package=="delphes":
+        if self.main.fastsim.package in ["delphes","delfes"]:
             file.write('  //Getting pointer to fast-simulation package\n')
             file.write('  std::map<std::string, std::string> parametersD1;\n')
-            parameters = self.fastsim.SampleAnalyzerConfigString()
+            if self.fastsim.package=="delfes":
+                cfg=self.main.fastsim.delfes
+            else:
+                cfg=self.main.fastsim.delphes
+            parameters = self.main.fastsim.SampleAnalyzerConfigString()
             for k,v in sorted(parameters.iteritems(),\
                               key=lambda (k,v): (k,v)):
                 file.write('  parametersD1["'+k+'"]="'+v+'";\n')
             file.write('  DetectorBase* fastsim1 = \n')
-            if self.fastsim.delphes.pileup=="":
-                if self.fastsim.delphes.detector=='cms':
-                    cardname = 'delphes_card_CMS.tcl'
-                elif self.fastsim.delphes.detector=='atlas':
-                    cardname ='delphes_card_ATLAS.tcl'
+
+            if self.main.fastsim.package=="delphes":
+                cardname = self.main.fastsim.delphes.card
+            elif self.main.fastsim.package=="delfes":
+                cardname = self.main.fastsim.delfes.card
+
+            if self.main.fastsim.package=="delphes":
+                file.write('      manager.InitializeDetector("delphes","../../Input/'+cardname+'",parametersD1);\n')
             else:
-                if self.fastsim.delphes.detector=='cms':
-                    cardname = 'delphes_card_CMS_PileUp.tcl'
-                elif self.fastsim.delphes.detector=='atlas':
-                    cardname ='delphes_card_ATLAS_PileUp.tcl'
-            file.write('      manager.InitializeDetector("delphes","../../Input/'+cardname+'",parametersD1);\n')
+                file.write('      manager.InitializeDetector("delfes","../../Input/'+cardname+'",parametersD1);\n')
+
             file.write('  if (fastsim1==0) return 1;\n\n')
 
+        # Post intialization (crating the output directory structure)
+        file.write('  // Post initialization (creates the new output directory structure)\n')
+        file.write('  if(!manager.PostInitialize()) return 1;\n\n')
+
+
         # Loop
         file.write('  // ---------------------------------------------------\n')
         file.write('  //                      EXECUTION\n')
@@ -377,9 +370,11 @@
         file.write('          manager.UpdateProgressBar();\n')
         if self.merging.enable:
             file.write('      analyzer2->Execute(mySample,myEvent);\n')
-        if self.fastsim.package=="fastjet":
+        if self.main.fastsim.package=="fastjet":
             file.write('      cluster1->Execute(mySample,myEvent);\n')
-        elif self.fastsim.package=="delphes":
+        elif self.main.fastsim.package=="delphes":
+            file.write('      fastsim1->Execute(mySample,myEvent);\n')
+        elif self.main.fastsim.package=="delfes":
             file.write('      fastsim1->Execute(mySample,myEvent);\n')
         file.write('      analyzer1->Execute(mySample,myEvent);\n')
         if self.output!="":
@@ -394,15 +389,6 @@
         file.write('  INFO << "    * Finalizing all components ..." << endmsg;\n\n')
         file.write('  // Finalizing all components\n')
         file.write('  manager.Finalize(mySamples,myEvent);\n')
-        
-#        file.write('  PHYSICS->mcConfig().AddInvisibleId(12);\n')
-#        file.write('  PHYSICS->mcConfig().AddInvisibleId(-12);\n')
-#        file.write('  PHYSICS->mcConfig().AddInvisibleId(14);\n')
-#        file.write('  PHYSICS->mcConfig().AddInvisibleId(-14);\n')
-#        file.write('  PHYSICS->mcConfig().AddInvisibleId(16);\n')
-#        file.write('  PHYSICS->mcConfig().AddInvisibleId(-16);\n')
-#        file.write('  PHYSICS->mcConfig().AddInvisibleId(1000022);\n\n')
-        
         file.write('  return 0;\n')
         file.write('}\n')
         return
@@ -425,23 +411,6 @@
         file.close()
         return True
 
-    def WriteEmptyFilterSource(self,main):
-        file = open(self.path+"/Build/SampleAnalyzer/Filter/filterList.cpp","w")
-        file.write('#include "SampleAnalyzer/Filter/FilterManager.h"\n')
-        file.write('using namespace MA5;\n')
-        file.write('#include <stdlib.h>\n\n')
-        file.write('// ------------------------------------------' +\
-                   '-----------------------------------\n')
-        file.write('// BuildUserTable\n')
-        file.write('// ------------------------------------------' +\
-                   '-----------------------------------\n')
-        file.write('void FilterManager::BuildUserTable()\n')
-        file.write('{\n')
-        file.write('}\n')
-        file.close()
-
-        return True
-
     def WriteSelectionSource(self,main):
         main.selection.RefreshStat();
         file = open(self.path+"/Build/SampleAnalyzer/Analyzer/user.cpp","w")
@@ -450,23 +419,22 @@
         job.WriteSource()
         file.close()
 
-        file = open(self.path+"/Build/SampleAnalyzer/Analyzer/analysisList.cpp","w")
+        file = open(self.path+"/Build/SampleAnalyzer/Analyzer/analysisList.h","w")
         file.write('#include "SampleAnalyzer/Analyzer/AnalyzerManager.h"\n')
         file.write('#include "SampleAnalyzer/Analyzer/user.h"\n')
         file.write('#include "SampleAnalyzer/Service/LogStream.h"\n')
-        file.write('using namespace MA5;\n')
-        file.write('#include <stdlib.h>\n\n')
+        file.write('\n')
         file.write('// ------------------------------------------' +\
                    '-----------------------------------\n')
         file.write('// BuildUserTable\n')
         file.write('// ------------------------------------------' +\
                    '-----------------------------------\n')
-        file.write('void AnalyzerManager::BuildUserTable()\n')
+        file.write('void BuildUserTable(MA5::AnalyzerManager& manager)\n')
         file.write('{\n')
-        file.write('  Add("MadAnalysis5job", new user);\n')
+        file.write('  using namespace MA5;\n')
+        file.write('  manager.Add("MadAnalysis5job", new user);\n')
         file.write('}\n')
         file.close()
-        self.WriteEmptyFilterSource(main)
         return True
 
     def CreateShowerDir(self,mode):
@@ -505,18 +473,20 @@
 
         # Compilators
         file.write('# Compilators\n')
-        file.write('GCC = g++\n')
+        file.write('CXX = g++\n')
         file.write('\n')
 
         # Options for compilation
         file.write('# Options for compilation\n')
         if self.libFastjet:
             file.write('CXXFASTJET = $(shell fastjet-config --cxxflags --plugins)\n')
-        file.write('CXXFLAGS = -Wall -O3 -I./ -I./../ -I' + '$(MA5_BASE)/tools/')
+        file.write('CXXFLAGS = -Wall -O3 -fPIC -I./ -I./../ -I' + '$(MA5_BASE)/tools/')
         if self.libZIP:
             file.write(' -DZIP_USE')
         if self.libDelphes:
-            file.write(' -DDELPHES_USE')
+            file.write(' -DROOT_USE -DDELPHES_USE')
+        if self.libDelfes:
+            file.write(' -DROOT_USE -DDELFES_USE')
         if self.libFastjet:
             file.write(' -DFASTJET_USE')
             file.write(' $(CXXFASTJET)')
@@ -530,16 +500,9 @@
         file.write('OBJS = $(SRCS:.cpp=.o)\n')
         file.write('\n')
 
-        # Files for filters
-        file.write('# Files for filters\n')
-        file.write('SRCS2 = $(wildcard Filter/*.cpp)\n')
-        file.write('HDRS2 = $(wildcard Filter/*.h)\n')
-        file.write('OBJS2 = $(SRCS2:.cpp=.o)\n')
-        file.write('\n')
-
         # Name of the library
         file.write('# Name of the library\n')
-        file.write('PROGRAM = SampleAnalyzerBld\n')
+        file.write('PROGRAM = UserPackage_for_ma5\n')
         file.write('\n')
 
         # All
@@ -549,21 +512,19 @@
 
         # Compilation
         file.write('# Compile target\n')
-        file.write('compile: $(OBJS) $(OBJS2)\n')
+        file.write('compile: $(OBJS)\n')
         file.write('\n')
         file.write('# Object file target\n')
         file.write('$(OBJS): $(HDRS)\n')
-        file.write('$(OBJS2): $(HDRS2)\n')
         file.write('\n')
 
         # Linking
         file.write('# Link target\n')
-        file.write('link: $(OBJS) $(OBJS2)\n')
-        file.write('\tcp ' +\
-            '$(MA5_BASE)/tools/SampleAnalyzer/Lib/libSampleAnalyzer.a ' +\
-            '../../Build/Lib/lib$(PROGRAM).a\n')
-        file.write('\tar -ruc ../../Build/Lib/lib$(PROGRAM).a $(OBJS) $(OBJS2)\n')
-        file.write('\tranlib ../../Build/Lib/lib$(PROGRAM).a\n')
+        file.write('link: $(OBJS)\n')
+        if self.main.isMAC:
+            file.write('\t$(CXX) -shared -flat_namespace -dynamiclib -undefined suppress -o ../../Build/Lib/lib$(PROGRAM).so $(OBJS)\n')
+        else:
+            file.write('\t$(CXX) -shared -o ../../Build/Lib/lib$(PROGRAM).so $(OBJS)\n')
         file.write('\n')
 
         # Phony target
@@ -577,7 +538,7 @@
         file.write('\n')
         file.write('# Do clean target\n')
         file.write('do_clean:\n')
-        file.write('\t@rm -f $(OBJS) $(OBJS2)\n')
+        file.write('\t@rm -f $(OBJS)\n')
         file.write('\n')
 
         # Mr Proper
@@ -586,7 +547,7 @@
         file.write('\n')
         file.write('# Do clean target\n')
         file.write('do_mrproper: do_clean\n')
-        file.write('\t@rm -f ../../Build/Lib/lib$(PROGRAM).a\n')
+        file.write('\t@rm -f ../../Build/Lib/lib$(PROGRAM).so\n')
         file.write('\t@rm -f *~ */*~ \n')
         file.write('\n')
         
@@ -615,9 +576,9 @@
     def WriteMakefiles(self,option=""):
 
         # Writing sub-Makefiles
-        self.WriteSampleAnalyzerMakefile(option)
-        if self.shwrmode!='':
-            self.WriteShoweringMakefile(option)
+        #self.WriteSampleAnalyzerMakefile(option)
+        #if self.shwrmode!='':
+        #    self.WriteShoweringMakefile(option)
 
         # Opening the main Makefile    
         file = open(self.path+"/Build/Makefile","w")
@@ -630,61 +591,79 @@
 
         # Compilators
         file.write('# Compilators\n')
-        file.write('GCC = g++\n')
+        file.write('CXX = g++\n')
         file.write('\n')
 
-        # Options for compilation
+        # Options for compilation : CXXFLAGS
         file.write('# Options for compilation\n')
-        if self.libFastjet:
-            file.write('CXXFASTJET = $(shell fastjet-config --cxxflags --plugins)\n')
-            
-            file.write('FASTJETLIB = $(shell fastjet-config --libs --plugins)\n')
-        file.write('CXXFLAGS = -Wall -O3 -I./ -I$(MA5_BASE)/tools/')
-        if self.shwrmode!='':
-            file.write(' -I$(MA5_BASE)' + \
-                '/tools/MCatNLO-utilities/MCatNLO/include')
+        options = []
+        options.extend(['-Wall','-O3','-I./','-I./SampleAnalyzer/','-I$(MA5_BASE)/tools/','-I'+self.main.configLinux.root_inc_path])
         if self.libZIP:
-            file.write(' -DZIP_USE')
+            options.extend(['-DZIP_USE'])
         if self.libDelphes:
-            file.write(' -DDELPHES_USE')
+            options.extend(['-DROOT_USE','-DDELPHES_USE'])
+        if self.libDelfes:
+            options.extend(['-DROOT_USE','-DDELFES_USE'])
         if self.libFastjet:
-            file.write(' -DFASTJET_USE')
-            file.write(' $(CXXFASTJET)')
+            options.extend(['-DROOT_USE','-DFASTJET_USE'])#,'$(shell fastjet-config --cxxflags --plugins)'])
+        file.write('CXXFLAGS = '+' '.join(options))
         file.write('\n')
-        file.write('LIBFLAGS = -LLib -lSampleAnalyzerBld -lGpad -lHist ' + 
-                   '-lGraf -lGraf3d ' +\
-                   '-lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lEG ' +\
-                   '-lRIO -lNet -lThread -lCore -lCint -pthread -lm -ldl '+\
-                   '-rdynamic')
+
+        # Options for compilation : LIBFLAGS
+
+        # - Root
+        libs=[]
+        libs.extend(['-L'+self.main.configLinux.root_lib_path, \
+                     '-lGpad','-lHist','-lGraf','-lGraf3d','-lTree', \
+                     '-lRint','-lPostscript','-lMatrix','-lPhysics', \
+                     '-lMathCore','-lEG', '-lRIO','-lNet','-lThread', \
+                     '-lCore','-lCint','-pthread','-lm','-ldl','-rdynamic'])
+
+        # - SampleAnalyzer
+        libs.extend(['-L$(MA5_BASE)/tools/SampleAnalyzer/Lib/','-lSampleAnalyzer'])
         if self.libZIP:
-            file.write(' -lz')
+            libs.extend(['-L'+self.main.configLinux.zlib_lib_path,'-lz','-lzlib_for_ma5'])
         if self.libDelphes:
-            file.write(' -lDelphes')
+            libs.extend(['-L'+self.main.configLinux.delphes_lib_paths[0],'-lDelphes','-ldelphes_for_ma5'])
+        if self.libDelfes:
+            libs.extend(['-L'+self.main.configLinux.delfes_lib_paths[0],'-lDelphes','-ldelfes_for_ma5'])
         if self.fortran:
-            file.write(' -lgfortran')
-        if self.libFastjet:
-            file.write(' $(FASTJETLIB)')
-        if self.shwrmode!='':
-            file.write(' -lShowering -lstdhep -lFmcfio')
-        file.write('\n\n')
-
-        # Files
-        file.write('# Files\n')
-        file.write('SRCS = $(wildcard Main/*.cpp)\n')
-        file.write('HDRS = $(wildcard Main/*.h)\n')
-        file.write('OBJS = $(SRCS:.cpp=.o)\n')
-        file.write('LIBS = Lib/libSampleAnalyzerBld.a')
-        if self.shwrmode!='':
-            file.write(' Lib/libShowering.a')
-        file.write('\n')
-        file.write('PRES = $(MA5_BASE)/tools/' +\
-                   'SampleAnalyzer/Lib/libSampleAnalyzer.a')
-        file.write('\n')
-
-        # Name of the executable
-        file.write('#Name of the executable\n')
-        file.write('PROGRAM = MadAnalysis5Job\n')
-        file.write('\n')
+            libs.extend(['-lgfortran'])
+        if self.libFastjet:
+            libs.extend(['$(shell fastjet-config --libs --plugins --rpath=no)','-lfastjet_for_ma5'])
+        file.write('LIBFLAGS = '+' '.join(libs)+'\n')
+        file.write('\n')
+
+        # Files to process
+        file.write('# Files to process\n')
+        file.write('SRCS  = $(wildcard Main/*.cpp)\n')
+        file.write('SRCS += $(wildcard SampleAnalyzer/Analyzer/*.cpp)\n')
+        file.write('HDRS  = $(wildcard Main/*.h)\n')
+        file.write('HDRS += $(wildcard SampleAnalyzer/Analyzer/*.h)\n')
+        file.write('\n')
+
+        # Files to generate
+        file.write('# Files to generate\n')
+        file.write('OBJS    = $(SRCS:.cpp=.o)\n')
+        file.write('PROGRAM = MadAnalysis5job\n')
+        file.write('\n')
+
+        # Lib to check
+        file.write('# Requirements to check before building\n')
+        libs=[]
+        libs.append('$(MA5_BASE)/tools/SampleAnalyzer/Lib/libSampleAnalyzer.so')
+        if self.libZIP:
+            libs.append('$(MA5_BASE)/tools/SampleAnalyzer/Lib/libzlib_for_ma5.so')
+        if self.libDelphes:
+            libs.append('$(MA5_BASE)/tools/SampleAnalyzer/Lib/libdelphes_for_ma5.so')
+        if self.libDelfes:
+            libs.append('$(MA5_BASE)/tools/SampleAnalyzer/Lib/libdelfes_for_ma5.so')
+        if self.libFastjet:
+            libs.append('$(MA5_BASE)/tools/SampleAnalyzer/Lib/libfastjet_for_ma5.so')
+        for ind in range(0,len(libs)):
+            file.write('REQUIRED'+str(ind+1)+' = '+libs[ind]+'\n')
+        file.write('\n')
+
 
         # Defining colours for shell
         file.write('# Defining colours\n')
@@ -703,16 +682,18 @@
         file.write('\n')
 
         # Check library
-        file.write('# Check library\n')
-        file.write('library_check:\n')
-        file.write('ifeq ($(wildcard $(PRES)),)\n')
-        file.write('\t@echo -e $(RED)"The static library "$(PRES)" is not found"\n')
-	file.write('\t@echo -e $(RED)" 1) Please check that MadAnalysis 5 is installed in the folder : "$(MA5_BASE)\n')
-        file.write('\t@echo -e $(RED)" 2) Launch MadAnalysis 5 in normal mode in order to build this library."\n')
-	file.write('\t@echo -e $(NORMAL)\n')
-	file.write('\t@false\n')
-        file.write('endif\n')
-        file.write('\n')
+        if len(libs)!=0:
+            file.write('# Check library\n')
+            file.write('library_check:\n')
+            for ind in range(0,len(libs)):
+                file.write('ifeq ($(wildcard $(REQUIRED'+str(ind+1)+')),)\n')
+                file.write('\t@echo -e $(RED)"The shared library "$(REQUIRED'+str(ind+1)+')" is not found"\n')
+	        file.write('\t@echo -e $(RED)" 1) Please check that MadAnalysis 5 is installed in the folder : "$(MA5_BASE)\n')
+                file.write('\t@echo -e $(RED)" 2) Launch MadAnalysis 5 in normal mode in order to build this library."\n')
+	        file.write('\t@echo -e $(NORMAL)\n')
+	        file.write('\t@false\n')
+                file.write('endif\n')
+            file.write('\n')
 
         # Header target
         file.write('# Header target\n')
@@ -756,7 +737,7 @@
 
         # Compile target
         file.write('# Compile target\n')
-        file.write('compile: $(LIBS) $(OBJS)\n')
+        file.write('compile: $(OBJS)\n')
         file.write('\n')
 
         # Object file target
@@ -766,34 +747,18 @@
 
         # Link target
         file.write('# Link target\n')
-        file.write('link: $(OBJS) $(LIBS)\n')
-        file.write('\t$(GCC) $(CXXFLAGS) $(OBJS) ')
+        file.write('link: $(OBJS)\n')
+        file.write('\t$(CXX) $(CXXFLAGS) $(OBJS) ')
         file.write('$(LIBFLAGS) -o $(PROGRAM)\n')
         file.write('\n')
 
-        # Library to build
-        file.write('# SampleAnalyzer library target\n')
-        file.write('$(LIBS):\n')
-        file.write('\t@(cd SampleAnalyzer/ && $(MAKE))\n')
-        file.write('\n')
-
-        # Library to build
-        if self.shwrmode!='':
-            file.write('# Showering library target\n')
-            file.write('Lib/libShowering.a:\n')
-            file.write('\t@(cd Showering/ && $(MAKE))\n')
-            file.write('\n')
-
         # Clean target
         file.write('# Clean target\n')
         file.write('clean: clean_header do_clean\n')
         file.write('\n')
         file.write('# Do clean target\n')
         file.write('do_clean: \n')
-        file.write('\t@(cd SampleAnalyzer/ && $(MAKE) $@)\n')
-        if self.shwrmode!='':
-            file.write('\t@(cd Showering/ && $(MAKE) $@)\n')
-        file.write('\t@rm -f $(OBJS) $(LIBS)\n')
+        file.write('\t@rm -f $(OBJS)\n')
         file.write('\n')
 
         # Mr Proper target
@@ -802,24 +767,21 @@
         file.write('\n')
         file.write('# Do Mr Proper target \n')
         file.write('do_mrproper: do_clean\n')
-        file.write('\t@(cd SampleAnalyzer/ && $(MAKE) $@)\n')
-        if self.shwrmode!='':
-            file.write('\t@(cd Showering/ && $(MAKE) $@)\n')
         file.write('\t@rm -f $(PROGRAM) Log/compilation.log' + \
-                   ' linking.log *~ */*~ \n')
+                   ' Log/linking.log Log/cleanup.log Log/mrproper.log *~ */*~ */*~ \n')
         file.write('\n')
 
         # Phony target
         file.write('# Phony target\n')
-        file.write('.PHONY: do_clean header link_header compile_header $(LIBS)\n')
+        file.write('.PHONY: do_clean header link_header compile_header\n')
         file.write('\n')
 
         # Closing the file
         file.close()
 
-        if not JobWriter.WriteSetupFile(True,self.path+'/Build/',self.ma5dir):
+        if not JobWriter.WriteSetupFile(True,self.path+'/Build/',self.ma5dir,True,self.main.configLinux,self.main.isMAC):
             return False
-        if not JobWriter.WriteSetupFile(False,self.path+'/Build/',self.ma5dir):
+        if not JobWriter.WriteSetupFile(False,self.path+'/Build/',self.ma5dir,True,self.main.configLinux,self.main.isMAC):
             return False
         
         return True
@@ -855,7 +817,10 @@
 
         
     @staticmethod
-    def WriteSetupFile(bash,path,ma5dir,MA5BASE=True):
+    def WriteSetupFile(bash,path,ma5dir,MA5BASE,configLinux,isMAC):
+
+        # Variable to check at the end
+        toCheck=[]
 
         # Opening file in write-only mode
         if bash:
@@ -904,59 +869,101 @@
             if bash:
                 file.write('export MA5_BASE=' + JobWriter.CleanPath(ma5dir)+'\n')
             else:
-                file.write('setenv MA5_BASE=' + JobWriter.CleanPath(ma5dir)+'\n')
+                file.write('setenv MA5_BASE ' + JobWriter.CleanPath(ma5dir)+'\n')
+            toCheck.append('MA5_BASE')
             file.write('\n')
 
         # Configuring PATH environment variable
-        file.write('# Configuring PATH environment variable\n')
-        if bash:
-            file.write('export PATH=' + JobWriter.CleanPath(os.environ['PATH'])+'\n')
-        else:
-            file.write('setenv PATH ' + JobWriter.CleanPath(os.environ['PATH'])+'\n')
-        file.write('\n')
-
-        # Configuring LD_LIBRARY_PATH environment variable
-        file.write('# Configuring LD_LIBRARY_PATH environment variable\n')
-        if bash:
-            file.write('export LD_LIBRARY_PATH=' + JobWriter.CleanPath(os.environ['LD_LIBRARY_PATH'])+'\n')
-        else:
-            file.write('setenv LD_LIBRARY_PATH ' + JobWriter.CleanPath(os.environ['LD_LIBRARY_PATH'])+'\n')
-        file.write('\n')
-
-        # Configuring LIBRARY_PATH environment variable
-        file.write('# Configuring LIBRARY_PATH environment variable\n')
-        if bash:
-            file.write('export LIBRARY_PATH=' + JobWriter.CleanPath(os.environ['LD_LIBRARY_PATH'])+'\n')
-        else:
-            file.write('setenv LIBRARY_PATH ' + JobWriter.CleanPath(os.environ['LD_LIBRARY_PATH'])+'\n')
-        file.write('\n')
-
-        # Configuring DYLD_LIBRARY_PATH environment variable
-        file.write('# Configuring DYLD_LIBRARY_PATH environment variable\n')
-        if bash:
-            file.write('export DYLD_LIBRARY_PATH='  + JobWriter.CleanPath(os.environ['DYLD_LIBRARY_PATH'])+'\n')
-        else:
-            file.write('setenv DYLD_LIBRARY_PATH '  + JobWriter.CleanPath(os.environ['DYLD_LIBRARY_PATH'])+'\n')
-        file.write('\n')
-
-        # Configuring CPLUS_INCLUDE_PATH environment variable
-        file.write('# Configuring CPLUS_INCLUDE_PATH environment variable\n')
-        if bash:
-            file.write('export CPLUS_INCLUDE_PATH=' + JobWriter.CleanPath(os.environ['CPLUS_INCLUDE_PATH'])+'\n')
-        else:
-            file.write('setenv CPLUS_INCLUDE_PATH ' + JobWriter.CleanPath(os.environ['CPLUS_INCLUDE_PATH'])+'\n')
-        file.write('\n')
+        if len(configLinux.toPATH)!=0:
+            file.write('# Configuring PATH environment variable\n')
+            if bash:
+                file.write('if [ $PATH ]; then\n')
+                file.write('export PATH=$PATH:' + JobWriter.CleanPath(':'.join(configLinux.toPATH))+'\n')
+                file.write('else\n')
+                file.write('export PATH=' + JobWriter.CleanPath(':'.join(configLinux.toPATH))+'\n')
+                file.write('fi\n')
+            else:
+                file.write('if ( $?PATH ) then\n')
+                file.write('setenv PATH "$PATH":' + JobWriter.CleanPath(':'.join(configLinux.toPATH))+'\n')
+                file.write('else\n')
+                file.write('setenv PATH ' + JobWriter.CleanPath(':'.join(configLinux.toPATH))+'\n')
+                file.write('endif\n')
+            toCheck.append('PATH')
+            file.write('\n')
+
+        if len(configLinux.toLDPATH)!=0:
+            
+            # Configuring LD_LIBRARY_PATH environment variable
+            file.write('# Configuring LD_LIBRARY_PATH environment variable\n')
+            if bash:
+                file.write('if [ $LD_LIBRARY_PATH ]; then\n')
+                file.write('export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:' + JobWriter.CleanPath(':'.join(configLinux.toLDPATH))+'\n')
+                file.write('else\n')
+                file.write('export LD_LIBRARY_PATH=' + JobWriter.CleanPath(':'.join(configLinux.toLDPATH))+'\n')
+                file.write('fi\n')
+            else:
+                file.write('if ( $?LD_LIBRARY_PATH ) then\n')
+                file.write('setenv LD_LIBRARY_PATH "$LD_LIBRARY_PATH":' + JobWriter.CleanPath(':'.join(configLinux.toLDPATH))+'\n')
+                file.write('else\n')
+                file.write('setenv LD_LIBRARY_PATH ' + JobWriter.CleanPath(':'.join(configLinux.toLDPATH))+'\n')
+                file.write('endif\n')
+            toCheck.append('LD_LIBRARY_PATH')
+            file.write('\n')
+
+            # Configuring LIBRARY_PATH environment variable
+            #file.write('# Configuring LIBRARY_PATH environment variable\n')
+            #if bash:
+            #    file.write('export LIBRARY_PATH=' + JobWriter.CleanPath(os.environ['LD_LIBRARY_PATH'])+'\n')
+            #else:
+            #    file.write('setenv LIBRARY_PATH ' + JobWriter.CleanPath(os.environ['LD_LIBRARY_PATH'])+'\n')
+            #file.write('\n')
+
+            # Configuring DYLD_LIBRARY_PATH environment variable
+            if isMAC:
+                file.write('# Configuring DYLD_LIBRARY_PATH environment variable\n')
+                if bash:
+                    file.write('if [ $DYLD_LIBRARY_PATH ]; then\n')
+                    file.write('export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:' + JobWriter.CleanPath(':'.join(configLinux.toLDPATH))+'\n')
+                    file.write('else\n')
+                    file.write('export DYLD_LIBRARY_PATH=' + JobWriter.CleanPath(':'.join(configLinux.toLDPATH))+'\n')
+                    file.write('fi\n')
+                else:
+                    file.write('if ( $?DYLD_LIBRARY_PATH ) then\n')
+                    file.write('setenv DYLD_LIBRARY_PATH "$DYLD_LIBRARY_PATH":' + JobWriter.CleanPath(':'.join(configLinux.toLDPATH))+'\n')
+                    file.write('else\n')
+                    file.write('setenv DYLD_LIBRARY_PATH ' + JobWriter.CleanPath(':'.join(configLinux.toLDPATH))+'\n')
+                    file.write('endif\n')
+                toCheck.append('DYLD_LIBRARY_PATH')
+                file.write('\n')
+
+            # Configuring CPLUS_INCLUDE_PATH environment variable
+            #file.write('# Configuring CPLUS_INCLUDE_PATH environment variable\n')
+            #if bash:
+            #    file.write('export CPLUS_INCLUDE_PATH=' + JobWriter.CleanPath(os.environ['CPLUS_INCLUDE_PATH'])+'\n')
+            #else:
+            #    file.write('setenv CPLUS_INCLUDE_PATH ' + JobWriter.CleanPath(os.environ['CPLUS_INCLUDE_PATH'])+'\n')
+            #file.write('\n')
 
         # Checking that all environment variables are defined
         file.write('# Checking that all environment variables are defined\n')
         if bash:
-            file.write('if [[ $PATH && $LD_LIBRARY_PATH && $LIBRARY_PATH && $DYLD_LIBRARY_PATH && $CPLUS_INCLUDE_PATH ]]; then\n')
+            file.write('if [[ ')
+            for ind in range(0,len(toCheck)):
+                if ind!=0:
+                    file.write(' && ')
+                file.write('$'+toCheck[ind])
+            file.write(' ]]; then\n')
             file.write('echo -e $YELLOW"'+StringTools.Fill('-',56)+'"\n')
 	    file.write('echo -e "'+StringTools.Center('Your environment is properly configured for MA5',56)+'"\n')
 	    file.write('echo -e "'+StringTools.Fill('-',56)+'"$NORMAL\n')
             file.write('fi\n')
         else:
-            file.write('if ( $?PATH && $?LD_LIBRARY_PATH && $?LIBRARY_PATH && $?DYLD_LIBRARY_PATH && $?CPLUS_INCLUDE_PATH) then\n')
+            file.write('if ( \n')
+            for ind in range(0,len(toCheck)):
+                if ind!=0:
+                    file.write(' && ')
+                file.write('$?'+toCheck[ind])
+            file.write(' ) then\n')
             file.write('echo $YELLOW"'+StringTools.Fill('-',56)+'"\n')
 	    file.write('echo "'+StringTools.Center('Your environment is properly configured for MA5',56)+'"\n')
 	    file.write('echo "'+StringTools.Fill('-',56)+'"$NORMAL\n')
@@ -972,33 +979,94 @@
 
         return True
 
+
     def CompileJob(self):
-        if self.resubmit:
-            res=commands.getstatusoutput("cd "\
-                                         +self.path+"/Build/;"\
-                                         +" make mrproper")
-            
-        res=commands.getstatusoutput("cd "\
-                                     +self.path+"/Build/;"\
-                                     +" make compile > Log/compilation.log 2>&1")
-        if res[0]==0:
-            return True
-        else:
-            logging.error("errors occured during compilation. " +\
-                          "For more details, see the file :")
-            logging.error(" "+self.path+"/Build/Log/compilation.log")
-            return False
+
+        # folder
+        folder = self.path+'/Build'
+
+        # log file name
+        logfile = folder+'/Log/compilation.log'
+        
+        # shell command
+        commands = ['make','compile']
+
+        # call
+        result, out = ShellCommand.ExecuteWithLog(commands,logfile,folder)
+
+        # return result
+        if not result:
+            logging.error('impossible to compile the project. For more details, see the log file:')
+            logging.error(logfile)
+            
+        return result
+
+
+    def MrproperJob(self):
+
+        # folder
+        folder = self.path+'/Build'
+
+        # log file name
+        logfile = folder+'/Log/mrproper.log'
+        
+        # shell command
+        commands = ['make','mrproper']
+
+        # call
+        result, out = ShellCommand.ExecuteWithLog(commands,logfile,folder)
+
+        # return result
+        if not result:
+            logging.error('impossible to clean the project. For more details, see the log file:')
+            logging.error(logfile)
+            
+        return result
+
+
+    def MrproperJob(self):
+
+        # folder
+        folder = self.path+'/Build'
+
+        # log file name
+        logfile = folder+'/Log/mrproper.log'
+        
+        # shell command
+        commands = ['make','mrproper']
+
+        # call
+        result, out = ShellCommand.ExecuteWithLog(commands,logfile,folder)
+
+        # return result
+        if not result:
+            logging.error('impossible to clean the project. For more details, see the log file:')
+            logging.error(logfile)
+            
+        return result
+
 
     def LinkJob(self):
-        res=commands.getstatusoutput("cd "\
-                                     +self.path+"/Build/;"\
-                                     +" make link > Log/linking.log 2>&1")
-        if res[0]==0:
-            return True
-        else:
-            logging.error("errors occured during compilation. For more details, see the file :")
-            logging.error(" "+self.path+"/Build/Log/linking.log")
-            return False
+
+        # folder
+        folder = self.path+'/Build'
+
+        # log file name
+        logfile = folder+'/Log/linking.log'
+        
+        # shell command
+        commands = ['make','link']
+
+        # call
+        result, out = ShellCommand.ExecuteWithLog(commands,logfile,folder)
+
+        # return result
+        if not result:
+            logging.error('impossible to link the project. For more details, see the log file:')
+            logging.error(logfile)
+            
+        return result
+
 
     def WriteHistory(self,history,firstdir):
         file = open(self.path+"/history.ma5","w")
@@ -1029,6 +1097,7 @@
             file.write("\n")
         file.close()    
 
+
     def RunJob(self,dataset):
 
         # Getting the dataset name    
@@ -1038,23 +1107,26 @@
         if not os.path.isdir(self.path+"/Output/"+name):
             os.mkdir(self.path+"/Output/"+name)
             
+        # folder where the program is launched
+        folder = self.path+'/Output/'+name
+
+        # shell command
+        commands = ['../../Build/MadAnalysis5job']
+
         # Weighted events
-        weighted_events=""
         if not dataset.weighted_events:
-            weighted_events=" --no_event_weight"
+            commands.append('--no_event_weight')
 
         # Release
-        release = ' --ma5_version="' + self.main.version + ';' + self.main.date + '"'
-
-        # Running SampleAnalyzer 
-        res=os.system('cd '\
-                      +self.path+'/Output/'+name+';'\
-                      +' ../../Build/'\
-                      +'MadAnalysis5Job '+weighted_events +\
-                      release +\
-                      ' ../../Input/'+name+'.list')
-
-        return True
+        commands.append('--ma5_version="'+self.main.version+';'+self.main.date+'"')
+
+        # Inputs
+        commands.append('../../Input/'+name+'.list')
+
+        # Running SampleAnalyzer
+        result = ShellCommand.Execute(commands,folder)
+
+        return result
 
         
         
 
=== modified file 'madanalysis/IOinterface/library_writer.py'
--- madanalysis/IOinterface/library_writer.py	2013-06-14 15:26:04 +0000
+++ madanalysis/IOinterface/library_writer.py	2014-05-17 19:51:11 +0000
@@ -26,22 +26,27 @@
 from madanalysis.IOinterface.folder_writer import FolderWriter
 from madanalysis.IOinterface.job_writer    import JobWriter
 from madanalysis.core.string_tools         import StringTools
+from madanalysis.IOinterface.shell_command import ShellCommand
 import logging
 import shutil
 import os
 import commands
+import subprocess
+
 
 class LibraryWriter():
 
-    def __init__(self,ma5dir,jobdir,libZIP,libFASTJET,forced,fortran,delphes):
+    def __init__(self,ma5dir,jobdir,libZIP,libFastJet,forced,fortran,delphes,delfes,main):
         self.ma5dir     = ma5dir
         self.jobdir     = jobdir
         self.path       = os.path.normpath(ma5dir+"/tools/")
         self.libZIP     = libZIP
-        self.libFASTJET = libFASTJET
+        self.libFastJet = libFastJet
         self.forced     = forced
         self.fortran    = fortran
         self.libDelphes = delphes
+        self.libDelfes  = delfes
+        self.main       = main
 
     def get_ncores(self):
         # Number of cores
@@ -72,9 +77,211 @@
                      str(ncores))
         return ncores
 
+    def get_ncores2(self):
+        # Number of cores
+        import multiprocessing
+        nmaxcores=multiprocessing.cpu_count()
+        logging.info("   How many cores for the compiling? default = max = " +\
+                     str(nmaxcores)+"")
+        
+        if not self.forced:
+            test=False
+            while(not test):
+                answer=raw_input("   Answer: ")
+                if answer=="":
+                    test=True
+                    ncores=nmaxcores
+                    break
+                try:
+                    ncores=int(answer)
+                except:    
+                    test=False
+                    continue
+                if ncores<=nmaxcores and ncores>0:
+                    test=True
+                    
+        else:
+            ncores=nmaxcores
+        logging.info("   => Number of cores used for the compilation = " +\
+                     str(ncores))
+        return ncores
+
+
     def Open(self):
         return FolderWriter.CreateDirectory(self.path,overwrite=True)
 
+    def WriteMakefileForInterfaces(self,package):
+
+        # Open the file
+        try:
+            file = open(self.path + "/SampleAnalyzer/Interfaces/Makefile_" + package,"w")
+        except:
+            logging.error('impossible to write the file '+ self.path + "/SampleAnalyzer/Makefile_" + package)
+            return False
+
+        # Header
+        file.write(StringTools.Fill('#',80)+'\n')
+        file.write('#'+StringTools.Center('MAKEFILE DEVOTED TO THE INTERFACE TO '+package.upper(),78)+'#\n')
+        file.write(StringTools.Fill('#',80)+'\n')
+        file.write('\n')
+
+        # Options for C++ compilation
+        file.write('# Options for C++ compilation\n')
+        file.write('CXX = g++\n')
+        if package=='fastjet':
+            file.write('CXXFASTJET = $(shell fastjet-config --cxxflags --plugins)\n')
+        file.write('CXXFLAGS = -Wall -O3 -DROOT_USE -fPIC -I'+self.main.configLinux.root_inc_path+' -I./../../')
+        if package=='zlib':
+            file.write(' -I'+self.main.configLinux.zlib_inc_path)
+        if package=='delphes':
+            for header in self.main.configLinux.delphes_inc_paths:
+                file.write(' -I'+header)
+        if package=='delfes':
+            for header in self.main.configLinux.delfes_inc_paths:
+                file.write(' -I'+header)
+        if package=='fastjet':
+            file.write(' $(CXXFASTJET)')
+        file.write('\n')
+
+        # Options for C++ compilation
+        if self.fortran:
+            file.write('# Options for Fortran compilation\n')
+            file.write('FC = gfortran\n')
+            file.write('FCFLAGS = -Wall -O3 -fPIC\n')
+            file.write('\n')
+
+        # Files for analyzers
+        file.write('# Files\n')
+        file.write('SRCS = $(wildcard '+package+'/*.cpp)\n')
+        file.write('HDRS = $(wildcard '+package+'/*.h)\n')
+        file.write('OBJS = $(SRCS:.cpp=.o)\n')
+        if self.fortran:
+            file.write('FORTRAN_SRCS = $(wildcard '+package+'/*.f)\n')
+            file.write('FORTRAN_OBJS = $(FORTRAN_SRCS:.f=.o)\n')
+        file.write('\n')
+
+        # Name of the library
+        file.write('# Name of the library\n')
+        file.write('PROGRAM = '+package+'_for_ma5\n')
+        file.write('\n')
+
+        # Defining colours for shell
+        file.write('# Defining colours\n')
+        file.write('GREEN  = "\\\\033[1;32m"\n')
+        file.write('RED    = "\\\\033[1;31m"\n')
+        file.write('PINK   = "\\\\033[1;35m"\n')
+        file.write('BLUE   = "\\\\033[1;34m"\n')
+        file.write('YELLOW = "\\\\033[1;33m"\n')
+        file.write('CYAN   = "\\\\033[1;36m"\n')
+        file.write('NORMAL = "\\\\033[0;39m"\n')
+        file.write('\n')
+
+        # All
+        file.write('# All target\n')
+        file.write('all: header compile_header compile link_header link\n')
+        file.write('\n')
+
+        # Header target
+        file.write('# Header target\n')
+        file.write('header:\n')
+        file.write('\t@echo -e $(YELLOW)"'+StringTools.Fill('-',50)+'"\n')
+	file.write('\t@echo -e "'+StringTools.Center('Building SampleAnalyzer library',50)+'"\n')
+	file.write('\t@echo -e "'+StringTools.Fill('-',50)+'"$(NORMAL)\n')
+        file.write('\n')
+
+        # Compile_header target
+        file.write('# Compile_header target\n')
+        file.write('compile_header:\n')
+        file.write('\t@echo -e $(YELLOW)"'+StringTools.Fill('-',50)+'"\n')
+	file.write('\t@echo -e "'+StringTools.Center('Compilation',50)+'"\n')
+	file.write('\t@echo -e "'+StringTools.Fill('-',50)+'"$(NORMAL)\n')
+        file.write('\n')
+
+        # Linking_header target
+        file.write('# Link_header target\n')
+        file.write('link_header:\n')
+        file.write('\t@echo -e $(YELLOW)"'+StringTools.Fill('-',50)+'"\n')
+	file.write('\t@echo -e "'+StringTools.Center('Final linking',50)+'"\n')
+	file.write('\t@echo -e "'+StringTools.Fill('-',50)+'"$(NORMAL)\n')
+        file.write('\n')
+
+        # Clean_header target
+        file.write('# clean_header target\n')
+        file.write('clean_header:\n')
+        file.write('\t@echo -e $(YELLOW)"'+StringTools.Fill('-',50)+'"\n')
+	file.write('\t@echo -e "'+StringTools.Center('Removing intermediate files from building',50)+'"\n')
+	file.write('\t@echo -e "'+StringTools.Fill('-',50)+'"$(NORMAL)\n')
+        file.write('\n')
+
+        # Mrproper_header target
+        file.write('# mrproper_header target\n')
+        file.write('mrproper_header:\n')
+        file.write('\t@echo -e $(YELLOW)"'+StringTools.Fill('-',50)+'"\n')
+	file.write('\t@echo -e "'+StringTools.Center('Cleaning all the project',50)+'"\n')
+	file.write('\t@echo -e "'+StringTools.Fill('-',50)+'"$(NORMAL)\n')
+        file.write('\n')
+
+        # Precompile
+        file.write('# Precompile target\n')
+        file.write('precompile:\n')
+        file.write('\n')
+
+        # Precompile
+        file.write('# Compile target\n')
+        if self.fortran:
+            file.write('compile: precompile $(OBJS) $(FORTRAN_OBJS)\n')
+        else:
+            file.write('compile: precompile $(OBJS)\n')
+        file.write('\n')
+
+        # Precompile
+        file.write('# Link target\n')
+        if self.fortran:
+            file.write('link: $(OBJS) $(FORTRAN_OBJS)\n')
+            if self.main.isMAC:
+                file.write('\t$(CXX) -shared -flat_namespace -dynamiclib -undefined suppress -o ../Lib/lib$(PROGRAM).so $(OBJS) $(FORTRAN_OBJS)\n')
+            else:
+                file.write('\t$(CXX) -shared -o ../Lib/lib$(PROGRAM).so $(OBJS) $(FORTRAN_OBJS)\n')
+        else:
+            file.write('link: $(OBJS)\n')
+            if self.main.isMAC:
+                file.write('\t$(CXX) -shared -flat_namespace -dynamiclib -undefined suppress -o ../Lib/lib$(PROGRAM).so $(OBJS)\n')
+            else:
+                file.write('\t$(CXX) -shared -o ../Lib/lib$(PROGRAM).so $(OBJS)\n')
+        file.write('\n')
+
+        # Phony target
+        file.write('# Phony target\n')
+        file.write('.PHONY: do_clean header compile_header link_header\n')
+        file.write('\n')
+
+        # Cleaning
+        file.write('# Clean target\n')
+        file.write('clean: clean_header do_clean\n')
+        file.write('\n')
+        file.write('# Do clean target\n')
+        file.write('do_clean: \n')
+        file.write('\t@rm -f $(OBJS)\n')
+        if self.fortran:
+            file.write('\t@rm -f $(FORTRAN_OBJS)\n')
+        file.write('\n')
+
+        # Mr Proper
+        file.write('# Mr Proper target \n')
+        file.write('mrproper: mrproper_header do_mrproper\n')
+        file.write('\n')
+        file.write('# Do Mr Proper target \n')
+        file.write('do_mrproper: do_clean\n')
+        file.write('\t@rm -f ../Lib/lib$(PROGRAM).so\n')
+        file.write('\t@rm -f compilation.log linking.log cleanup.log mrproper.log *~ */*~\n')
+        file.write('\n')
+
+        # Closing the file
+        file.close()
+
+        return True
+
+
     def WriteMakefile(self,option=""):
 
         # Open the file
@@ -88,23 +295,26 @@
 
         # Compilators
         file.write('# Compilators\n')
-        file.write('GCC = g++\n')
+        file.write('CXX = g++\n')
         if self.fortran:
             file.write('FC = gfortran\n')
         file.write('\n')
 
         # Options for compilation
         file.write('# Options for compilation\n')
-        if self.libFASTJET:
-            file.write('CXXFASTJET = $(shell fastjet-config --cxxflags --plugins)\n')
-        file.write('CXXFLAGS = -Wall -O3 $(shell root-config --cflags) -I./../')
+#        if self.libFastJet:
+#            file.write('CXXFASTJET = $(shell fastjet-config --cxxflags --plugins)\n')
+        # BENJ FIX file.write('CXXFLAGS = -Wall -O3 -fPIC $(shell root-config --cflags) -I./../')
+        file.write('CXXFLAGS = -Wall -O3 -DROOT_USE -fPIC -I'+self.main.configLinux.root_inc_path+' -I./../')
         if self.libZIP:
             file.write(' -DZIP_USE')
         if self.libDelphes:
             file.write(' -DDELPHES_USE')
-        if self.libFASTJET:
+        if self.libDelfes:
+            file.write(' -DDELFES_USE')
+        if self.libFastJet:
             file.write(' -DFASTJET_USE')
-            file.write(' $(CXXFASTJET)')
+ #           file.write(' $(CXXFASTJET)')
         file.write('\n')
         if self.fortran:
             file.write('FC = gfortran\n')
@@ -114,6 +324,7 @@
         # Files for analyzers
         file.write('# Files\n')
         file.write('SRCS = $(wildcard */*.cpp)\n')
+#        file.write('SRCS += $(wildcard */*/*.cpp)\n')
         file.write('HDRS = $(wildcard */*.h)\n')
         file.write('OBJS = $(SRCS:.cpp=.o)\n')
         if self.fortran:
@@ -199,10 +410,18 @@
         file.write('# Link target\n')
         if self.fortran:
             file.write('link: $(OBJS) $(FORTRAN_OBJS)\n')
-            file.write('\tar -ruc Lib/lib$(PROGRAM).a $(OBJS) $(FORTRAN_OBJS)\n')
+            if self.main.isMAC:
+                file.write('\t$(CXX) -shared -flat_namespace -dynamiclib -undefined suppress -o Lib/lib$(PROGRAM).so $(OBJS) $(FORTRAN_OBJS)\n')
+            else:
+                file.write('\t$(CXX) -shared -o Lib/lib$(PROGRAM).so $(OBJS) $(FORTRAN_OBJS)\n')
         else:
             file.write('link: $(OBJS)\n')
-            file.write('\tar -ruc Lib/lib$(PROGRAM).a $(OBJS)\n')
+            if self.main.isMAC:
+                file.write('\t$(CXX) -shared -flat_namespace -dynamiclib -undefined suppress -o Lib/lib$(PROGRAM).so $(OBJS)\n')
+            else:
+                file.write('\t$(CXX) -shared -o Lib/lib$(PROGRAM).so $(OBJS)\n')
+                
+#            file.write('\tar -ruc Lib/lib$(PROGRAM).a $(OBJS)\n')
         file.write('\n')
 
         # Phony target
@@ -216,7 +435,7 @@
         file.write('\n')
         file.write('# Do clean target\n')
         file.write('do_clean: \n')
-        file.write('\t@rm -f $(OBJS) Reader/FACdict.*\n')
+        file.write('\t@rm -f $(OBJS)\n')
         file.write('\n')
 
         # Mr Proper
@@ -225,54 +444,394 @@
         file.write('\n')
         file.write('# Do Mr Proper target \n')
         file.write('do_mrproper: do_clean\n')
-        file.write('\t@rm -f Lib/lib$(PROGRAM).a\n')
-        file.write('\t@rm -f compilation.log linking.log cleanup.log *~ */*~\n')
+        file.write('\t@rm -f Lib/lib$(PROGRAM).so\n')
+        file.write('\t@rm -f compilation.log linking.log cleanup.log mrproper.log *~ */*~\n')
         file.write('\n')
 
         # Closing the file
         file.close()
 
-        JobWriter.WriteSetupFile(True,self.path+'/SampleAnalyzer',self.ma5dir,False)
-        JobWriter.WriteSetupFile(False,self.path+'/SampleAnalyzer',self.ma5dir,False)
+        JobWriter.WriteSetupFile(True,self.path+'/SampleAnalyzer',self.ma5dir,False,self.main.configLinux,self.main.isMAC)
+        JobWriter.WriteSetupFile(False,self.path+'/SampleAnalyzer',self.ma5dir,False,self.main.configLinux,self.main.isMAC)
 
         return True
 
 
-    def Compile(self):
+    def Compile(self,ncores,package,folder):
+
+        # number of cores
         strcores=''
-        ncores = self.get_ncores()
         if ncores>1:
             strcores='-j'+str(ncores)
-        res=commands.getstatusoutput("cd "\
-                                     +self.path+"/SampleAnalyzer/;"\
-                                     +" make compile "+strcores+" > compilation.log 2>&1")
-        if res[0]==0:
-            return True
-        else:
-            logging.error("errors occured during compilation. For more details, see the file :")
-            logging.error(" "+self.path+"/SampleAnalyzer/compilation.log")
-            return False
-
-    def Link(self):
-        res=commands.getstatusoutput("cd "\
-                                     +self.path+"/SampleAnalyzer/;"\
-                                     +" make link > linking.log 2>&1")
-        if res[0]==0:
-            return True
-        else:
-            logging.error("errors occured during compilation. For more details, see the file :")
-            logging.error(" "+self.path+"/SampleAnalyzer/linking.log")
-            return False
-
-
-    def Clean(self):
-        res=commands.getstatusoutput("cd "\
-                                     +self.path+"/SampleAnalyzer/;"\
-                                     +" make clean > cleanup.log 2>&1")
-        return True
-
-    def MrProper(self):
-        res=commands.getstatusoutput("cd "\
-                                     +self.path+"/SampleAnalyzer/;"\
-                                     +" make mrproper > cleanup.log 2>&1")
-        return True
+
+        # log file name
+        if package == 'SampleAnalyzer':
+            logfile = folder+'/compilation.log'
+        else:
+            logfile = folder+'/compilation_'+package+'.log'
+
+        # makefile
+        if package == 'SampleAnalyzer':
+            makefile = 'Makefile'
+        else:
+            makefile = 'Makefile_'+package
+
+        # shell command
+        commands = ['make','compile',strcores,'--file='+makefile]
+
+        # call
+        result, out = ShellCommand.ExecuteWithLog(commands,logfile,folder)
+
+        # return result
+        if not result:
+            logging.error('impossible to compile the project. For more details, see the log file:')
+            logging.error(logfile)
+            
+        return result
+
+
+    def Link(self,package,folder):
+
+        # log file name
+        if package == 'SampleAnalyzer':
+            logfile = folder+'/linking.log'
+        else:
+            logfile = folder+'/linking_'+package+'.log'
+
+        # makefile
+        if package == 'SampleAnalyzer':
+            makefile = 'Makefile'
+        else:
+            makefile = 'Makefile_'+package
+
+        # shell command
+        commands = ['make','link','--file='+makefile]
+
+        # call
+        result, out = ShellCommand.ExecuteWithLog(commands,logfile,folder)
+
+        # return result
+        if not result:
+            logging.error('impossible to link the project. For more details, see the log file:')
+            logging.error(logfile)
+            
+        return result
+
+
+    def Clean(self,package,folder):
+
+        # log file name
+        if package == 'SampleAnalyzer':
+            logfile = folder+'/cleanup.log'
+        else:
+            logfile = folder+'/cleanup_'+package+'.log'
+
+        # makefile
+        if package == 'SampleAnalyzer':
+            makefile = 'Makefile'
+        else:
+            makefile = 'Makefile_'+package
+
+        # shell command
+        commands = ['make','clean','--file='+makefile]
+
+        # call
+        result, out = ShellCommand.ExecuteWithLog(commands,logfile,folder)
+
+        # return result
+        if not result:
+            logging.error('impossible to clean the project. For more details, see the log file:')
+            logging.error(logfile)
+            
+        return result
+
+
+    def MrProper(self,package,folder):
+
+        # log file name
+        if package == 'SampleAnalyzer':
+            logfile = folder+'/mrproper.log'
+        else:
+            logfile = folder+'/mrproper_'+package+'.log'
+
+        # makefile
+        if package == 'SampleAnalyzer':
+            makefile = 'Makefile'
+        else:
+            makefile = 'Makefile_'+package
+
+        # shell command
+        commands = ['make','mrproper','--file='+makefile]
+
+        # call
+        result, out = ShellCommand.ExecuteWithLog(commands,logfile,folder)
+
+        # return result
+        if not result:
+            logging.error('impossible to clean the project. For more details, see the log file:')
+            logging.error(logfile)
+            
+        return result
+
+
+    def Run(self,program,args,folder,silent=False):
+
+        # shell command
+        commands = ['./'+program]
+        commands.extend(args)
+
+        # logfile
+        logfile = folder+'/'+program+'.log'
+
+        # call
+        result, out = ShellCommand.ExecuteWithLog(commands,logfile,folder,silent)
+
+        # return result
+        if not result and not silent:
+            logging.error('impossible to run the project. For more details, see the log file:')
+            logging.error(logfile)
+            
+        return result
+
+
+    def CheckRun(self,logfile,silent=False):
+
+        # Open
+        try:
+            input = open(logfile)
+        except:
+            logging.error('impossible to open the file:'+logfile)
+            return False
+
+        end=False
+        begin=False
+        
+        # Loop over the logfile
+        for line in input:
+            line=line.lstrip()
+            line=line.rstrip()
+            if line=='BEGIN-SAMPLEANALYZER-TEST':
+                begin=True
+            elif line=='END-SAMPLEANALYZER-TEST':
+                end=True
+
+        # Close
+        try:
+            input.close()
+        except:
+            logging.error('impossible to close the file:'+logfile)
+            return False
+
+        # CrossCheck
+        if not (begin and end) and not silent:
+            logging.error('expected program output is not found. More details, see the log file:')
+            logging.error(logfile)
+            return False
+
+        return True
+
+
+    def WriteMakefileForTest(self):
+
+        # Open the file
+        filename = self.path + "/SampleAnalyzer/Test/Makefile_test"
+        try:
+            file = open(filename,"w")
+        except:
+            logging.error('impossible to write the file '+filenameself.path)
+            return False
+
+        # Writing header
+        file.write(StringTools.Fill('#',80)+'\n')
+        file.write('#'+StringTools.Center('MAKEFILE FOR SAMPLEANALYZER TEST',78)+'#\n')
+        file.write(StringTools.Fill('#',80)+'\n')
+        file.write('\n')
+
+        # Compilators
+        file.write('# Compilators\n')
+        file.write('CXX = g++\n')
+        file.write('\n')
+
+        # Options for compilation : CXXFLAGS
+        file.write('# Options for compilation\n')
+        options = []
+        options.extend(['-Wall','-O3','-I$(MA5_BASE)/tools/','-I'+self.main.configLinux.root_inc_path])
+        if self.libZIP:
+            options.extend(['-DZIP_USE'])
+        if self.libDelphes:
+            options.extend(['-DROOT_USE','-DDELPHES_USE'])
+        if self.libDelfes:
+            options.extend(['-DROOT_USE','-DDELFES_USE'])
+        if self.libFastJet:
+            options.extend(['-DROOT_USE','-DFASTJET_USE'])
+        file.write('CXXFLAGS = '+' '.join(options))
+        file.write('\n')
+
+        # Options for compilation : LIBFLAGS
+
+        # - Root
+        libs=[]
+        libs.extend(['-L'+self.main.configLinux.root_lib_path, \
+                     '-lGpad','-lHist','-lGraf','-lGraf3d','-lTree', \
+                     '-lRint','-lPostscript','-lMatrix','-lPhysics', \
+                     '-lMathCore','-lEG', '-lRIO','-lNet','-lThread', \
+                     '-lCore','-lCint','-pthread','-lm','-ldl','-rdynamic'])
+
+        # - SampleAnalyzer
+        libs.extend(['-L$(MA5_BASE)/tools/SampleAnalyzer/Lib/','-lSampleAnalyzer'])
+        if self.libZIP:
+            libs.extend(['-L'+self.main.configLinux.zlib_lib_path,'-lz','-lzlib_for_ma5'])
+        if self.libDelphes:
+            libs.extend(['-L'+self.main.configLinux.delphes_lib_paths[0],'-lDelphes','-ldelphes_for_ma5'])
+        if self.libDelfes:
+            libs.extend(['-L'+self.main.configLinux.delfes_lib_paths[0],'-lDelphes','-ldelfes_for_ma5'])
+        if self.fortran:
+            libs.extend(['-lgfortran'])
+        if self.libFastJet:
+            libs.extend(['$(shell fastjet-config --libs --plugins --rpath=no)','-lfastjet_for_ma5'])
+        file.write('LIBFLAGS = '+' '.join(libs)+'\n')
+        file.write('\n')
+
+        # Files to process
+        file.write('# Files to process\n')
+        file.write('SRCS  = $(wildcard Test.cpp)\n')
+        file.write('\n')
+
+        # Files to generate
+        file.write('# Files to generate\n')
+        file.write('OBJS    = $(SRCS:.cpp=.o)\n')
+        file.write('PROGRAM = SampleAnalyzerTest\n')
+        file.write('\n')
+
+        # Lib to check
+        file.write('# Requirements to check before building\n')
+        libs=[]
+        libs.append('$(MA5_BASE)/tools/SampleAnalyzer/Lib/libSampleAnalyzer.so')
+        if self.libZIP:
+            libs.append('$(MA5_BASE)/tools/SampleAnalyzer/Lib/libzlib_for_ma5.so')
+        if self.libDelphes:
+            libs.append('$(MA5_BASE)/tools/SampleAnalyzer/Lib/libdelphes_for_ma5.so')
+        if self.libDelfes:
+            libs.append('$(MA5_BASE)/tools/SampleAnalyzer/Lib/libdelfes_for_ma5.so')
+        if self.libFastJet:
+            libs.append('$(MA5_BASE)/tools/SampleAnalyzer/Lib/libfastjet_for_ma5.so')
+        for ind in range(0,len(libs)):
+            file.write('REQUIRED'+str(ind+1)+' = '+libs[ind]+'\n')
+        file.write('\n')
+
+
+        # Defining colours for shell
+        file.write('# Defining colours\n')
+        file.write('GREEN  = "\\\\033[1;32m"\n')
+        file.write('RED    = "\\\\033[1;31m"\n')
+        file.write('PINK   = "\\\\033[1;35m"\n')
+        file.write('BLUE   = "\\\\033[1;34m"\n')
+        file.write('YELLOW = "\\\\033[1;33m"\n')
+        file.write('CYAN   = "\\\\033[1;36m"\n')
+        file.write('NORMAL = "\\\\033[0;39m"\n')
+        file.write('\n')
+
+        # All target
+        file.write('# All target\n')
+        file.write('all: header library_check compile_header compile link_header link\n')
+        file.write('\n')
+
+        # Check library
+        if len(libs)!=0:
+            file.write('# Check library\n')
+            file.write('library_check:\n')
+            for ind in range(0,len(libs)):
+                file.write('ifeq ($(wildcard $(REQUIRED'+str(ind+1)+')),)\n')
+                file.write('\t@echo -e $(RED)"The shared library "$(REQUIRED'+str(ind+1)+')" is not found"\n')
+	        file.write('\t@echo -e $(RED)" 1) Please check that MadAnalysis 5 is installed in the folder : "$(MA5_BASE)\n')
+                file.write('\t@echo -e $(RED)" 2) Launch MadAnalysis 5 in normal mode in order to build this library."\n')
+	        file.write('\t@echo -e $(NORMAL)\n')
+	        file.write('\t@false\n')
+                file.write('endif\n')
+            file.write('\n')
+
+        # Header target
+        file.write('# Header target\n')
+        file.write('header:\n')
+        file.write('\t@echo -e $(YELLOW)"'+StringTools.Fill('-',50)+'"\n')
+	file.write('\t@echo -e "'+StringTools.Center('Building MA5 job',50)+'"\n')
+	file.write('\t@echo -e "'+StringTools.Fill('-',50)+'"$(NORMAL)\n')
+        file.write('\n')
+
+        # Compile_header target
+        file.write('# Compile_header target\n')
+        file.write('compile_header:\n')
+        file.write('\t@echo -e $(YELLOW)"'+StringTools.Fill('-',50)+'"\n')
+	file.write('\t@echo -e "'+StringTools.Center('Compilation',50)+'"\n')
+	file.write('\t@echo -e "'+StringTools.Fill('-',50)+'"$(NORMAL)\n')
+        file.write('\n')
+
+        # Linking_header target
+        file.write('# Link_header target\n')
+        file.write('link_header:\n')
+        file.write('\t@echo -e $(YELLOW)"'+StringTools.Fill('-',50)+'"\n')
+	file.write('\t@echo -e "'+StringTools.Center('Final linking',50)+'"\n')
+	file.write('\t@echo -e "'+StringTools.Fill('-',50)+'"$(NORMAL)\n')
+        file.write('\n')
+
+        # Clean_header target
+        file.write('# clean_header target\n')
+        file.write('clean_header:\n')
+        file.write('\t@echo -e $(YELLOW)"'+StringTools.Fill('-',50)+'"\n')
+	file.write('\t@echo -e "'+StringTools.Center('Removing intermediate files from building',50)+'"\n')
+	file.write('\t@echo -e "'+StringTools.Fill('-',50)+'"$(NORMAL)\n')
+        file.write('\n')
+
+        # Mrproper_header target
+        file.write('# mrproper_header target\n')
+        file.write('mrproper_header:\n')
+        file.write('\t@echo -e $(YELLOW)"'+StringTools.Fill('-',50)+'"\n')
+	file.write('\t@echo -e "'+StringTools.Center('Cleaning all the project',50)+'"\n')
+	file.write('\t@echo -e "'+StringTools.Fill('-',50)+'"$(NORMAL)\n')
+        file.write('\n')
+
+        # Compile target
+        file.write('# Compile target\n')
+        file.write('compile: $(OBJS)\n')
+        file.write('\n')
+
+        # Object file target
+        file.write('# Object file target\n')
+        file.write('$(OBJS): \n')
+        file.write('\n')
+
+        # Link target
+        file.write('# Link target\n')
+        file.write('link: $(OBJS)\n')
+        file.write('\t$(CXX) $(CXXFLAGS) $(OBJS) $(LIBFLAGS) -o $(PROGRAM)\n')
+        file.write('\n')
+
+        # Clean target
+        file.write('# Clean target\n')
+        file.write('clean: clean_header do_clean\n')
+        file.write('\n')
+        file.write('# Do clean target\n')
+        file.write('do_clean: \n')
+        file.write('\t@rm -f $(OBJS)\n')
+        file.write('\n')
+
+        # Mr Proper target
+        file.write('# Mr Proper target \n')
+        file.write('mrproper: mrproper_header do_mrproper\n')
+        file.write('\n')
+        file.write('# Do Mr Proper target \n')
+        file.write('do_mrproper: do_clean\n')
+        file.write('\t@rm -f $(PROGRAM) compilation_test.log' + \
+                   ' linking_test.log cleanup_test.log mrproper_test.log *~ */*~ */*~ \n')
+        file.write('\n')
+
+        # Phony target
+        file.write('# Phony target\n')
+        file.write('.PHONY: do_clean header link_header compile_header\n')
+        file.write('\n')
+
+        # Closing the file
+        file.close()
+
+        return True
+    
 
=== added file 'madanalysis/IOinterface/shell_command.py'
--- madanalysis/IOinterface/shell_command.py	1970-01-01 00:00:00 +0000
+++ madanalysis/IOinterface/shell_command.py	2014-05-17 19:51:11 +0000
@@ -0,0 +1,82 @@
+################################################################################
+#  
+#  Copyright (C) 2012-2013 Eric Conte, Benjamin Fuks
+#  The MadAnalysis development team, email: <[e-mail]>
+#  
+#  This file is part of MadAnalysis 5.
+#  Official website: <https://launchpad.net/madanalysis5>
+#  
+#  MadAnalysis 5 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.
+#  
+#  MadAnalysis 5 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 MadAnalysis 5. If not, see <http://www.gnu.org/licenses/>
+#  
+################################################################################
+
+
+import logging
+import shutil
+import os
+import commands
+import subprocess
+
+
+class ShellCommand():
+
+    @staticmethod
+    def ExecuteWithLog(theCommands,logfile,path,silent=False):
+
+        # Open the log file
+        try:
+            output = open(logfile,'w')
+        except:
+            if not silent:
+                logging.error('impossible to write the file '+logfile)
+            return False, None
+
+        # Launching the commands
+        try:
+            result=subprocess.Popen(theCommands, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, cwd=path)
+        except:
+            if not silent:
+                logging.error('impossible to execute the commands: '+' '.join(theCommands))
+            return False, None
+
+        # Getting stdout
+        out, err = result.communicate()
+        if out!=None:
+            for line in out:
+               output.write(line)
+
+        # Close the log file
+        output.close()
+            
+        # Return results
+        return (result.returncode==0), out
+    
+
+
+    @staticmethod
+    def Execute(theCommands,path):
+
+        # Launching the commands
+        try:
+            result=subprocess.Popen(theCommands, cwd=path)
+        except:
+            logging.error('impossible to execute the commands: '+' '.join(theCommands))
+            return False, None
+
+        # Getting stdout
+        out, err = result.communicate()
+            
+        # Return results
+        return (result.returncode==0)
+    
 
=== modified file 'madanalysis/UpdateNotes.txt'
--- madanalysis/UpdateNotes.txt	2013-10-29 09:21:58 +0000
+++ madanalysis/UpdateNotes.txt	2014-05-17 19:51:11 +0000
@@ -1,5 +1,89 @@
 Update notes for MadAnalysis 5 (in reverse time order)
 
+123  1.1.10.35 (2014/05/09) fuks:    Still a missing foot->footer replacement 
+
+122  1.1.10.34 (2014/05/07) fuks:    saffoot -> saffooter 
+
+116  1.1.10.33 (2014/04/30) fuks:    Moving ToRestFrame to the MCParticleFormat class 
+
+115  1.1.10.32 (2014/04/29) fuks:    Splitting the physics services in subcategories 
+
+114  1.1.10.31 (2014/04/22) fuks:    Renaming Daughter into daughter in sampleanalyzer 
+
+113  1.1.10.30 (2014/03/10) fuks:    Fixing bug in the mewanalyzer script 
+
+112  1.1.10.29 (2014/03/10) fuks:    updating the newanalyzer script 
+
+110  1.1.10.28 (2014/02/11) fuks:    Fixing minor bug when providing the wrong number of arguments to an 
+                                   observable (thanks to B.Dumont) 
+
+109  1.1.10.27 (2014/02/11) fuks:    Removing the old filter infrastructure 
+
+108  1.1.10.26 (2014/02/11) fuks:    Updating the expert mode: adding new analyses to an existing 
+                                   template directory 
+
+107  1.1.10.25 (2014/02/06) fuks:    Creation of an analysis template - changes in the file naming 
+
+106  1.1.10.24 (2014/02/06) fuks:    problems with wgetting fastjet on some machines 
+
+105  1.1.10.23 (2014/02/05) fuks:    Few bugs corrected in the mt2w implementation (thanks to Jeremy 
+                                   Bernon and Beranger Dumont) 
+
+104  1.1.10.22 (2014/01/31) fuks:    Implementation of the MT2W variable + sorting functions 
+
+103  1.1.10.21 (2014/01/29) fuks:    new methods :dphi_0_pi and sphi_0_2pi (both at the python and c++ 
+                                   levels) 
+
+102  1.1.10.20 (2014/01/28) fuks:    Cleaning conflicts between delfes and delphes 
+
+97   1.1.10.19 (2014/01/17) bfuks:   Beranger's suggestion for a IsSurviving function to be called from 
+                                   the manager 
+
+96   1.1.10.18 (2014/01/17) bfuks:   Beranger's suggestion for adding cuts/histos with one single RS: 
+                                   added 
+
+95   1.1.10.17 (2014/01/16) bfuks:   Bug with the "AllSurviving" function fixed 
+
+90   1.1.10.16 (2014/01/09) bfuks:   Charge is now a int and not a float anymore. Small related fixes 
+
+89   1.1.10.15 (2014/01/06) bfuks:   small bug fix 
+
+88   1.1.10.14 (2013/12/12) bfuks:   Check added in the case one wants to fill a histo for which some 
+                                   (but not all) SRs fails the cuts applied so far (thanks to Beranger) 
+
+87   1.1.10.13 (2013/12/12) bfuks:   Extended expert mode output: cleaning (cf. discussions with Chris) 
+
+86   1.1.10.12 (2013/12/11) bfuks:   Updating output format for the histo headers (extended expert mode) 
+
+85   1.1.10.11 (2013/12/05) bfuks:   Second Bug fix related to question #233529 
+
+84   1.1.10.10 (2013/12/04) bfuks:   Bug fix related to question #233529 
+
+83   1.1.10.9 (2013/12/03) bfuks:   Small bug in the MT2 routine (thanks to J. Bernon) 
+
+81   1.1.10.8 (2013/12/02) bfuks:   New output structure dedicated to multianalyses; few bug fixes 
+
+80   1.1.10.7 (2013/11/29) bfuks:   Bug in jetclustering + allowing for defining invisible particles via 
+                                   the invisible multiparticle in the reco mode 
+
+79   1.1.10.6 (2013/11/28) bfuks:   Problem with the MET in the simplified LHE format used by madgraph 
+                                   (question #239543) 
+
+78   1.1.10.5 (2013/11/28) bfuks:   Fixing clang issue (bug #1250337) 
+
+76   1.1.10.4 (2013/11/28) bfuks:   updating the versioning for the development version 
+
+75   1.1.10.3 (2013/11/28) bfuks:   MT2 variable + macos change of stdc++ library + cleaning of the 
+                                    welcome message 
+
+74   1.1.10.2 (2013/11/19) bfuks:   MultiAnalyses are now possible in the expert mode; output still to 
+                                    be implemented 
+
+72   1.1.10.1 (2013/11/14) bfuks:   small modifications in the view of including the signal region 
+                                    object 
+
+71   1.1.10.0 (2013/11/04) bfuks:   use of names with the counters 
+
 80   1.1.9  (2013/10/28) ma5team:   - adding Delphes interface + CMS/ATLAS cards
                                     - adding Delphes cards including pile-up
                                     - the electric charge is now an integer at the reco level 
 
=== added file 'madanalysis/configuration/delfes_configuration.py'
--- madanalysis/configuration/delfes_configuration.py	1970-01-01 00:00:00 +0000
+++ madanalysis/configuration/delfes_configuration.py	2014-05-17 19:51:11 +0000
@@ -0,0 +1,156 @@
+################################################################################
+#  
+#  Copyright (C) 2012-2013 Eric Conte, Benjamin Fuks
+#  The MadAnalysis development team, email: <[e-mail]>
+#  
+#  This file is part of MadAnalysis 5.
+#  Official website: <https://launchpad.net/madanalysis5>
+#  
+#  MadAnalysis 5 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.
+#  
+#  MadAnalysis 5 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 MadAnalysis 5. If not, see <http://www.gnu.org/licenses/>
+#  
+################################################################################
+
+
+from madanalysis.enumeration.ma5_running_type         import MA5RunningType
+import os
+import logging
+
+class DelfesConfiguration:
+
+    userVariables = { "detector" : ["cms","atlas"],\
+                      "output": ["true","false"],\
+                      "pileup": ["none"] }
+
+    def __init__(self):
+        self.detector  = "cms"
+        self.output    = True
+        self.pileup    = ""
+        self.card      = ""
+        self.SetCard()
+
+    def SetCard(self):
+        if self.detector=='cms' and self.pileup=="":
+            self.card = "delfes_card_CMS.tcl"
+        elif self.detector=='cms' and self.pileup!="":
+            self.card = "delfes_card_CMS_PileUp.tcl"
+        elif self.detector=='atlas' and self.pileup=="":
+            self.card = "delfes_card_ATLAS.tcl"
+        elif self.detector=='atlas' and self.pileup!="":
+            self.card = "delfes_card_ATLAS_PileUp.tcl"
+        
+    def Display(self):
+        self.user_DisplayParameter("detector")
+        self.user_DisplayParameter("output")
+        self.user_DisplayParameter("pileup")
+
+
+    def user_DisplayParameter(self,parameter):
+        if parameter=="detector":
+            logging.info(" detector : "+self.detector)
+            return
+        elif parameter=="output":
+            if self.output:
+                msg="true"
+            else:
+                msg="false"
+            logging.info(" ROOT output : "+msg)
+            return
+        elif parameter=="pileup":
+            if self.pileup=="":
+                msg="none"
+            else:
+                msg='"'+self.pileup+'"'
+            logging.info(" pile-up source = "+msg)
+
+    def SampleAnalyzerConfigString(self):
+            mydict = {}
+            if self.output:
+                mydict['output'] = '1'
+            else:
+                mydict['output'] = '0'
+            return mydict
+
+    def user_SetParameter(self,parameter,value,datasets,level):
+        
+        # algorithm
+        if parameter=="detector":
+
+            if value.lower()=="cms":
+                self.detector=value
+                self.SetCard()
+            elif value.lower()=="atlas":
+                self.detector=value
+                self.SetCard()
+            else:
+                logging.error("algorithm called '"+value+"' is not found.")
+            return
+
+        # output
+        elif parameter=="output":
+
+            if value.lower()=="true":
+                self.output = True
+            elif value.lower()=="false":
+                self.output = False
+            else:
+                logging.error("allowed values for output are: true false")
+            return
+        
+        # pileup
+        elif parameter=="pileup":
+            quoteTag=False
+            if value.startswith("'") and value.endswith("'"):
+                quoteTag=True
+            if value.startswith('"') and value.endswith('"'):
+                quoteTag=True
+            if quoteTag:
+                value=value[1:-1]
+            valuemin = value.lower()
+
+            # none
+            if valuemin=="none":
+                self.pileup = ""
+                self.SetCard()
+                
+            # .pileup
+            elif valuemin.endswith(".pileup"):
+                if not os.path.isfile(value):
+                    logging.error('File called "'+value+'" is not found')
+                    return
+                self.pileup = value
+                self.SetCard()
+                return
+
+            # other case: error
+            else:
+                logging.error("The file format for the pile-up source is not known. Only files with .pileup extension can be used.")
+                return False
+
+        else:
+            logging.error("parameter called '"+parameter+"' does not exist")
+            return
+
+        
+    def user_GetParameters(self):
+        return DelfesConfiguration.userVariables.keys()
+
+
+    def user_GetValues(self,variable):
+        table = []
+        try:
+            table.extend(DelfesConfiguration.userVariables[variable])
+        except:
+            pass
+        return table
+        
 
=== modified file 'madanalysis/configuration/delphes_configuration.py'
--- madanalysis/configuration/delphes_configuration.py	2013-10-27 21:05:18 +0000
+++ madanalysis/configuration/delphes_configuration.py	2014-05-17 19:51:11 +0000
@@ -36,7 +36,18 @@
         self.detector  = "cms"
         self.output    = True
         self.pileup    = ""
+        self.card      = ""
+        self.SetCard()
 
+    def SetCard(self):
+        if self.detector=='cms' and self.pileup=="":
+            self.card = "delphes_card_CMS.tcl"
+        elif self.detector=='cms' and self.pileup!="":
+            self.card = "delphes_card_CMS_PileUp.tcl"
+        elif self.detector=='atlas' and self.pileup=="":
+            self.card = "delphes_card_ATLAS.tcl"
+        elif self.detector=='atlas' and self.pileup!="":
+            self.card = "delphes_card_ATLAS_PileUp.tcl"
         
     def Display(self):
         self.user_DisplayParameter("detector")
@@ -77,8 +88,10 @@
 
             if value.lower()=="cms":
                 self.detector=value
+                self.SetCard()
             elif value.lower()=="atlas":
                 self.detector=value
+                self.SetCard()
             else:
                 logging.error("algorithm called '"+value+"' is not found.")
             return
@@ -108,6 +121,7 @@
             # none
             if valuemin=="none":
                 self.pileup = ""
+                self.SetCard()
                 
             # .pileup
             elif valuemin.endswith(".pileup"):
@@ -115,6 +129,7 @@
                     logging.error('File called "'+value+'" is not found')
                     return
                 self.pileup = value
+                self.SetCard()
                 return
 
             # other case: error
 
=== modified file 'madanalysis/configuration/fastsim_configuration.py'
--- madanalysis/configuration/fastsim_configuration.py	2013-09-29 22:12:23 +0000
+++ madanalysis/configuration/fastsim_configuration.py	2014-05-17 19:51:11 +0000
@@ -22,18 +22,20 @@
 ################################################################################
 
 
-from madanalysis.enumeration.ma5_running_type import MA5RunningType
+from madanalysis.enumeration.ma5_running_type           import MA5RunningType
 from madanalysis.configuration.clustering_configuration import ClusteringConfiguration
-from madanalysis.configuration.delphes_configuration import DelphesConfiguration
+from madanalysis.configuration.delphes_configuration    import DelphesConfiguration
+from madanalysis.configuration.delfes_configuration     import DelfesConfiguration
 import logging
 
 class FastsimConfiguration:
 
-    userVariables = { "package" : ["fastjet","delphes","none"] }
+    userVariables = { "package" : ["fastjet","delphes","delfes","none"] }
 
     def __init__(self):
         self.clustering = 0
         self.delphes = 0
+        self.delfes = 0
         self.package    = "none"
 
         
@@ -43,6 +45,8 @@
             self.clustering.Display()
         elif self.package=="delphes":
             self.delphes.Display()
+        elif self.package=="delfes":
+            self.delfes.Display()
 
 
     def user_DisplayParameter(self,parameter):
@@ -53,6 +57,8 @@
             self.clustering.user_DisplayParameter(parameter)
         elif self.package=="delphes":
             self.delphes.user_DisplayParameter(parameter)
+        elif self.package=="delfes":
+            self.delfes.user_DisplayParameter(parameter)
 
 
     def SampleAnalyzerConfigString(self):
@@ -64,11 +70,15 @@
             mydict = {}
             mydict.update(self.delphes.SampleAnalyzerConfigString())
             return mydict
+        elif self.package=="delfes":
+            mydict = {}
+            mydict.update(self.delfes.SampleAnalyzerConfigString())
+            return mydict
         else:
             return {}
 
 
-    def user_SetParameter(self,parameter,value,datasets,level,fastjet,delphes):
+    def user_SetParameter(self,parameter,value,datasets,level,fastjet,delphes,delfes):
 
         # algorithm
         if parameter=="package":
@@ -89,11 +99,12 @@
                             test=False
                             break
                 if not test:
-                    logging.error("some datasets contain partonic/hadronic file format. Fast-simulation package cannot be switched off.")
+                    logging.error("some datasets contain partonic/hadronic file format. "+\
+                                  "Fast-simulation package cannot be switched off.")
                     return
 
             # Switch on the clustering
-            elif value in ["fastjet","delphes"]:
+            elif value in ["fastjet","delphes","delfes"]:
 
                 # Only in reco mode
                 if level!=MA5RunningType.RECO:
@@ -110,6 +121,11 @@
                     logging.error("delphes library is not installed. This fast-simulation package is not available.")
                     return
 
+                # Delfes ?
+                if value=='delfes' and not delfes:
+                    logging.error("delfes library is not installed. This fast-simulation package is not available.")
+                    return
+
                 test=True
                 for dataset in datasets:
                     if not test:
@@ -128,14 +144,22 @@
                 self.package="fastjet"
                 self.clustering = ClusteringConfiguration()
                 self.delphes = 0
+                self.delfes = 0
             elif value=="delphes":
                 self.package="delphes"
                 self.clustering = 0
                 self.delphes = DelphesConfiguration()
+                self.delfes = 0
+            elif value=="delfes":
+                self.package="delfes"
+                self.clustering = 0
+                self.delphes = 0
+                self.delfes = DelfesConfiguration()
             elif value=="none":
                 self.package="none"
                 self.clustering = 0
                 self.delphes = 0
+                self.delfes = 0
             else:
                 logging.error("parameter called '"+value+"' is not found.")
             return    
@@ -150,6 +174,8 @@
             return self.clustering.user_SetParameter(parameter,value,datasets,level)
         elif self.package=="delphes":
             return self.delphes.user_SetParameter(parameter,value,datasets,level)
+        elif self.package=="delfes":
+            return self.delfes.user_SetParameter(parameter,value,datasets,level)
 
         
     def user_GetParameters(self):
@@ -159,6 +185,9 @@
         elif self.package=="delphes":
             table = FastsimConfiguration.userVariables.keys()
             table.extend(self.delphes.user_GetParameters())
+        elif self.package=="delfes":
+            table = FastsimConfiguration.userVariables.keys()
+            table.extend(self.delfes.user_GetParameters())
         else:
             table = ["package"]
         return table
@@ -184,6 +213,15 @@
                 table.extend(self.delphes.user_GetValues(variable))
             except:
                 pass
+        elif self.package=="delfes":
+            try:
+                table.extend(FastsimConfiguration.userVariables[variable])
+            except:
+                pass
+            try:
+                table.extend(self.delfes.user_GetValues(variable))
+            except:
+                pass
         else:
             if variable=="package":
                 table.extend(FastsimConfiguration.userVariables["package"])
 
=== modified file 'madanalysis/core/config_checker.py'
--- madanalysis/core/config_checker.py	2013-10-27 21:36:24 +0000
+++ madanalysis/core/config_checker.py	2014-05-17 19:51:11 +0000
@@ -39,9 +39,10 @@
                 container.append(item)
         
 
-    def __init__(self,configLinux,ma5dir,script=False):
+    def __init__(self,configLinux,ma5dir,script=False,isMAC=False):
 
         # Getting parameter from the main program
+        self.isMAC=isMAC
         self.configLinux=configLinux
         self.ma5dir=ma5dir
         self.script=script
@@ -56,6 +57,74 @@
         self.fillHeaders()
 
 
+    def ReadUserOptions(self):
+
+        # Open the user options
+        filename = self.ma5dir+'/madanalysis/input/installation_options.dat'
+        try:
+            input = open(filename)
+        except:
+            logging.error('impossible to open the file: '+filename)
+            return False
+
+        # Loop over the file
+        for rawline in input:
+
+            if '#' in rawline:
+                line = rawline.split('#')[0]
+            if line=='':
+                continue
+            words=line.split('=')
+            if len(words)!=2:
+                logging.warning(filename+': the following line is incorrect and is skipped:')
+                logging.warning(line)
+            words[0]=words[0].lstrip()
+            words[0]=words[0].rstrip()
+            words[1]=words[1].lstrip()
+            words[1]=words[1].rstrip()
+
+            if words[0]=='root_includes':
+                self.configLinux.useroptions.root_includes==words[1]
+            elif words[0]=='root_libs':
+                self.configLinux.useroptions.root_libs=words[1]
+            elif words[0]=='delphes_veto':
+                self.configLinux.useroptions.delphes_veto=words[1]
+            elif words[0]=='delphes_includes':
+                self.configLinux.useroptions.delphes_includes=words[1]
+            elif words[0]=='delphes_libs':
+                self.configLinux.useroptions.delphes_libs=words[1]
+            elif words[0]=='delfes_veto':
+                self.configLinux.useroptions.delfes_veto=words[1]
+            elif words[0]=='delfes_includes':
+                self.configLinux.useroptions.delfes_includes=words[1]
+            elif words[0]=='delfes_libs':
+                self.configLinux.useroptions.delfes_libs=words[1]
+            elif words[0]=='zlib_veto':
+                self.configLinux.useroptions.zlib_veto=words[1]
+            elif words[0]=='zlib_includes':
+                self.configLinux.useroptions.zlib_includes=words[1]
+            elif words[0]=='zlib_libs':
+                self.configLinux.useroptions.zlib_libs=words[1]
+            elif words[0]=='fastjet_veto':
+                self.configLinux.useroptions.fastjet_veto=words[1]
+            elif words[0]=='fastjet_bin_path':
+                self.configLinux.useroptions.fastjet_bin_path=words[1]
+            elif words[0]=='pdflatex_veto':
+                self.configLinux.useroptions.pdflatex_veto=words[1]
+            elif words[0]=='latex_veto':
+                self.configLinux.useroptions.latex_veto=words[1]
+            elif words[0]=='dvipdf_veto':
+                self.configLinux.useroptions.dvipdf_veto=words[1]
+            else:
+                logging.warning(filename+': the options called "'+words[0]+'" is not found')
+
+        # Close the file
+        input.close()
+        
+        # Ok
+        return True
+    
+
     def FillMA5Path(self):
         os.environ['MA5_BASE']=self.ma5dir
 
@@ -89,6 +158,7 @@
                 
         
     def fillHeaders(self):
+
         # Filling container with paths included in CPLUS_INCLUDE_PATH
         try:
             cplus_include_path = os.environ['CPLUS_INCLUDE_PATH'].split(':')
@@ -146,76 +216,74 @@
         # Checking if ROOT is present
         self.PrintLibrary('Root')
 
+        # Does the user force the ROOT path
+        force1=False
+        force2=False
+        if self.configLinux.useroptions.root_includes!='0':
+            self.configLinux.root_inc_path=self.configLinux.useroptions.root_includes
+            force1=True
+        if self.configLinux.useroptions.root_libs!='0':
+            self.configLinux.root_lib_path=self.configLinux.useroptions.root_libs
+            force2=True
+        force=force1 and force2
+
         # Trying to call root-config
-        rootdirs = commands.getstatusoutput('root-config --libdir --incdir')
-        if rootdirs[0]>0:
-            self.PrintFAIL(warning=False)
-            logging.error('ROOT module called "root-config" is not detected.\n'\
-		          +'Two explanations :n'\
-		          +' - ROOT is not installed. You can download it '\
-		          +'from http://root.cern.ch\n'\
-		          +' - ROOT binary folder must be placed in the '\
-                          +'global environment variable $PATH')
-            return False
-
-        # Extracting ROOT library and header path
-        root_tmp = rootdirs[1].split() 
-        self.includes.append(root_tmp[1])
-        self.libs.append(root_tmp[0])
-        os.environ['LD_LIBRARY_PATH'] = os.environ['LD_LIBRARY_PATH'] + \
-                    		        ":" + root_tmp[0]
-        os.environ['DYLD_LIBRARY_PATH'] = os.environ['DYLD_LIBRARY_PATH'] + \
-                    		        ":" + root_tmp[0]
-        os.environ['LIBRARY_PATH'] = os.environ['LIBRARY_PATH'] + \
-                    		        ":" + root_tmp[0]
-        os.environ['CPLUS_INCLUDE_PATH'] = os.environ['CPLUS_INCLUDE_PATH'] + \
-                    		        ":" + root_tmp[1]
+        if not force:
+
+            # Using root-config
+            rootdirs = commands.getstatusoutput('root-config --libdir --incdir')
+            if rootdirs[0]>0:
+                self.PrintFAIL(warning=False)
+                logging.error('ROOT module called "root-config" is not detected.\n'\
+		              +'Two explanations :n'\
+		              +' - ROOT is not installed. You can download it '\
+		              +'from http://root.cern.ch\n'\
+		              +' - ROOT binary folder must be placed in the '\
+                              +'global environment variable $PATH')
+                return False
+
+            # Extracting ROOT library and header path
+            root_tmp = rootdirs[1].split()
+            self.configLinux.root_inc_path = root_tmp[1]
+            self.configLinux.root_lib_path = root_tmp[0]
 
         # Adding ROOT library path to Python path
-        sys.path.append(root_tmp[0])
-
-        # Looking for libPyROOT.so
-        find=False
-        for item in self.libs:
-            files=glob.glob(item+"/libPyROOT.so")
-            if len(files)!=0:
-	        self.configLinux.libraries['PyROOT']=files[0]+":"+str(os.stat(files[0]).st_mtime)
-    	        find=True
-   	        break
-        if not find:
-            self.PrintFAIL(warning=False)
-	    logging.error("ROOT library called 'libPyROOT.so' not found. Please check that ROOT is properly installed.")
-            return False
-
-        # Looking for ROOT.py
-        find=False
-        for item in self.libs:
-            files=glob.glob(item+"/ROOT.py")
-            if len(files)!=0:
-	        self.configLinux.libraries['ROOT']=files[0]+":"+str(os.stat(files[0]).st_mtime)
-	        find=True
-	        break
-        if not find:
-            self.PrintFAIL(warning=False)
-	    logging.error("ROOT file called 'ROOT.py' not found. Please check that ROOT is properly installed.")
-            return False
-
-        # Looking for TH1F.h
-        find=False
-        for item in self.includes:
-            files=glob.glob(item+"/TH1F.h")
-            if len(files)!=0:
-	        self.configLinux.headers['ROOT']=files[0]+":"+str(os.stat(files[0]).st_mtime)
-	        find=True
-	        break
-        if not find:
-            self.PrintFAIL(warning=False)
-	    logging.error("ROOT headers are not found. " +\
-		 "Please check that ROOT is properly installed.")
-            return False
+        sys.path.append(self.configLinux.root_lib_path)
+
+        # Check: looking for files
+        FilesToFind=[self.configLinux.root_lib_path+'/libPyROOT.so', \
+                     self.configLinux.root_inc_path+'/TH1F.h']
+        for file in FilesToFind:
+            if os.path.isfile(file):
+                self.configLinux.libraries[file.split('/')[-1]]=file+":"+str(os.stat(file).st_mtime)
+            else:
+                self.PrintFAIL(warning=False)
+	        logging.error("ROOT file called '"+file+"' is not found")
+                logging.error("Please check that ROOT is properly installed.")
+                return False
+            
+        # Check: looking for files
+        FilesToFind=[self.configLinux.root_lib_path+'/ROOT.py', \
+                     self.configLinux.root_lib_path+'/ROOT.pyc']
+        found=False
+        for file in FilesToFind:
+            if os.path.isfile(file):
+                self.configLinux.libraries[file.split('/')[-1]]=file+":"+str(os.stat(file).st_mtime)
+                found=True
+                break
+        if not found:
+            self.PrintFAIL(warning=False)
+            logging.error("ROOT file called 'ROOT.py' or 'ROOT.pyc' is not found")
+            logging.error("Please check that ROOT is properly installed.")
+            return False
+
+        # Root Install
         self.PrintOK()
-
-
+        return True
+
+
+    def checkPyROOT(self):
+    
         # Loading ROOT library
         self.PrintLibrary("PyRoot libraries")
         try :
@@ -272,6 +340,29 @@
             return True
 
 
+    def checkMake(self):
+        # Checking GNU Make
+        self.PrintLibrary('GNU Make')
+        make_version = commands.getstatusoutput('make --version')
+        if make_version[0]>0:
+            self.PrintFAIL(warning=False)
+            logging.error('GNU Make not found. Please install it before ' + \
+	             'using MadAnalysis 5')
+            return False
+        else:
+            self.PrintOK()
+            lines=make_version[1].split('\n')
+            if len(lines)==0:
+                logging.error('command "make --version" seems to not give the GNU Make version')
+                return False
+            line=lines[0]
+            line=line.replace(' ','')
+            line=line.lstrip()
+            line=line.rstrip()
+            self.configLinux.make_version = line
+            return True
+
+
     def checkGF(self):
         self.PrintLibrary("gfortran")
         gfortran_version = commands.getstatusoutput('gfortran -dumpversion')
@@ -285,14 +376,12 @@
                  gfortran_version = gfor.group(1)
              else:
                  self.PrintFAIL(warning=True)
-                 logging.warning('gfortran compiler not found.' + \
-                   ' aMCatNLO cannot be used.')
+                 logging.warning('gfortran compiler not found.')
                  return True
         ver = gfortran_version.split('.')
         if (int(ver[0])<4) or (int(ver[0])==4 and int(ver[1])<4):
             self.PrintFAIL(warning=True)
-            logging.warning('gfortran ' + gfortran_version + ' not recent enough (< 4.4.0).' +\
-                ' aMCatNLO cannot be used.')
+            logging.warning('gfortran ' + gfortran_version + ' older than 4.4.0.')
             return True
             
         self.configLinux.gfortran_version = gfortran_version
@@ -300,73 +389,112 @@
         return True
 
 
+    def FindLibraryWithPattern(self,pattern,files):
+        return self.FindFilesWithPattern(self.libs,pattern,files)
+
+    def FindHeader(self,file):
+        return self.FindFilesWithPattern(self.includes,file,[file])
+
+    def FindFilesWithPattern(self,paths,pattern,targets):
+        result_files=[]
+        result_paths=[]
+        for path in paths:
+            rawfiles=glob.glob(path+"/"+pattern)
+
+            filtered_files=[]
+            for file in rawfiles:
+                for target in targets:
+                    if file.endswith('/'+target):
+                        filtered_files.append(file)
+
+            if len(filtered_files)!=0:
+                result_files.extend(filtered_files)
+            for item in filtered_files:
+                result_paths.append(path)
+
+        if len(result_files)==0:
+            return "", ""
+        else:
+            return os.path.normpath(result_paths[0]), os.path.normpath(result_files[0])
+    
+
     def checkZLIB(self):
 
         self.PrintLibrary("zlib library")
-        
-        # Checking library libz.so
-        find=False
-        for item in self.libs:
-            files=glob.glob(item+"/libz.so")
-            files.extend(glob.glob(item+"/libz.a"))
-            files.extend(glob.glob(item+"/libz.dylib"))
-            if len(files)!=0:
-	        self.configLinux.libraries['ZLib']=files[0]+":"+str(os.stat(files[0]).st_mtime)
-   	        find=True
-                os.environ['LD_LIBRARY_PATH'] = os.environ['LD_LIBRARY_PATH'] + \
-                    		        ":" + item
-                os.environ['DYLD_LIBRARY_PATH'] = os.environ['DYLD_LIBRARY_PATH'] + \
-                    		        ":" + item
-                os.environ['LIBRARY_PATH'] = os.environ['LIBRARY_PATH'] + \
-                    		        ":" + item
-	        break
-
-        # If not, test if it is there locally 
-        if not find: 
-            item = self.ma5dir+'/tools/zlib/lib/'
-            files=glob.glob(item+"/libz.so")
-            files.extend(glob.glob(item+"/libz.a"))
-            files.extend(glob.glob(item+"/libz.dylib"))
-            if len(files)!=0:
-	        self.configLinux.libraries['ZLib']=files[0]+":"+str(os.stat(files[0]).st_mtime)
-   	        find=True
-                os.environ['LD_LIBRARY_PATH'] = os.environ['LD_LIBRARY_PATH'] + \
-                    		        ":" + item
-                os.environ['DYLD_LIBRARY_PATH'] = os.environ['DYLD_LIBRARY_PATH'] + \
-                    		        ":" + item
-                os.environ['LIBRARY_PATH'] = os.environ['LIBRARY_PATH'] + \
-                    		        ":" + item
-        # Not fail -> Warning
-        if not find:
-            self.PrintFAIL(warning=True)
-	    logging.warning("Library called 'libz' not found. Gzip format will be disabled.")
-            logging.warning("To enable this format, please type 'install zlib' package.")
-            return False
-
-	# Checking header file zlib.h
-        find=False
-        for item in self.includes:
-            files=glob.glob(item+"/zlib.h")
-            if len(files)!=0:
-  	        self.configLinux.headers['ZLib']=files[0]+":"+str(os.stat(files[0]).st_mtime)
-	        find=True
-                os.environ['CPLUS_INCLUDE_PATH'] = os.environ['CPLUS_INCLUDE_PATH'] + ":" + item
-   	        break
-
-        # If not, test if it is there locally 
-        if not find: 
-            find=os.path.isfile(self.ma5dir+'/tools/zlib/include/zlib.h')
-            if find:
-                os.environ['CPLUS_INCLUDE_PATH'] = os.environ['CPLUS_INCLUDE_PATH'] + ":" + \
-                                                   self.ma5dir+'/tools/zlib/include/'
-
-        if not find:
-            self.PrintFAIL(warning=True)
-	    logging.warning("Header file called 'zlib.h' not found. Gzip format will be disabled.")
-            logging.warning("To enable this format, please type 'install zlib' package.")
-            return False
-        else:
-            self.PrintOK()
+
+        # Name of the dynamic lib
+        libnames=['libz.so','libz.a']
+        if self.isMAC:
+            libnames.append('libz.dylib')
+        
+        # User veto
+        if self.configLinux.useroptions.zlib_veto=='1':
+            self.PrintFAIL(warning=True)
+	    logging.warning("Library called 'zlib' disabled. Gzip format will be disabled.")
+            return False
+
+        # Does the user force the paths?
+        force1=False
+        force2=False
+        if self.configLinux.useroptions.zlib_includes!="0":
+            self.configLinux.zlib_inc_path=self.configLinux.useroptions.zlib_includes
+            force1=True
+        if self.configLinux.useroptions.zlib_libs!="0":
+            self.configLinux.zlib_lib_path=self.configLinux.useroptions.zlib_libraries
+            force2=True
+        force=force1 and force2
+        
+        # Checking if zlib has been installed by MA5
+        ma5installation = False
+        if not force:
+            if os.path.isdir(self.ma5dir+'/tools/zlib'):
+                self.configLinux.zlib_inc_path=self.ma5dir+'/tools/zlib/include/'
+                self.configLinux.zlib_lib_path=self.ma5dir+'/tools/zlib/lib/'
+                ma5installation = True
+
+        # Check if the libraries and headers are available
+        if force or ma5installation:
+
+            # header
+            if not os.path.isfile(self.configLinux.zlib_inc_path+'/zlib.h'):
+                self.PrintFAIL(warning=True)
+	        logging.warning("Header file called '"+self.configLinux.zlib_inc_path+"'/zlib.h not found. Gzip format will be disabled.")
+                logging.warning("To enable this format, please type 'install zlib' package.")
+                return False
+
+            # lib
+            mypath, myfile = self.FindFilesWithPattern([self.configLinux.zlib_lib_path],"libz.*",libnames)
+            self.configLinux.zlib_lib=myfile
+            if self.configLinux.zlib_lib=="":
+                self.PrintFAIL(warning=True)
+	        logging.warning("Zlib library not found in "+self.configLinux.zlib_lib_path+" folder. Gzip format will be disabled.")
+                logging.warning("To enable this format, please type 'install zlib' package.")
+                return False
+
+        # Checking zlib can be found in other folders
+        if not force and not ma5installation:
+
+            # header
+            mypath, myfile = self.FindHeader('zlib.h')
+            self.configLinux.zlib_inc_path = mypath
+            if self.configLinux.zlib_inc_path=="":
+                self.PrintFAIL(warning=True)
+  	        logging.warning("Header file called 'zlib.h' not found. Gzip format will be disabled.")
+                logging.warning("To enable this format, please type 'install zlib' package.")
+                return False
+            
+            # lib
+            mypath, myfile = self.FindLibraryWithPattern('libz.*',libnames)
+            self.configLinux.zlib_lib_path = mypath
+            self.configLinux.zlib_lib      = myfile
+            if self.configLinux.zlib_lib_path=="":
+                self.PrintFAIL(warning=True)
+                logging.warning("Library called 'zlib' not found. Gzip format will be disabled.")
+                logging.warning("To enable this format, please type 'install zlib' package.")
+                return False
+
+        self.configLinux.libraries['ZLib']=self.configLinux.zlib_lib+":"+str(os.stat(self.configLinux.zlib_lib).st_mtime)
+        self.PrintOK()
  
         return True
 
@@ -374,72 +502,169 @@
     def checkDelphes(self):
 
         self.PrintLibrary("delphes library")
-        
-        # Checking library libDelphes.so
-        find=False
-        for item in self.libs:
-            files=glob.glob(item+"/libDelphes.so")
-            files.extend(glob.glob(item+"/libDelphes.a"))
-            files.extend(glob.glob(item+"/libDelphes.dylib"))
-            if len(files)!=0:
-	        self.configLinux.libraries['Delphes']=files[0]+":"+str(os.stat(files[0]).st_mtime)
-   	        find=True
-                os.environ['LD_LIBRARY_PATH'] = os.environ['LD_LIBRARY_PATH'] + \
-                    		        ":" + item
-                os.environ['DYLD_LIBRARY_PATH'] = os.environ['DYLD_LIBRARY_PATH'] + \
-                    		        ":" + item
-                os.environ['LIBRARY_PATH'] = os.environ['LIBRARY_PATH'] + \
-                    		        ":" + item
-	        break
-
-        # If not, test if it is there locally 
-        if not find: 
-            item = self.ma5dir+'/tools/delphes/'
-            files=glob.glob(item+"/libDelphes.so")
-            files.extend(glob.glob(item+"/libDelphes.a"))
-            files.extend(glob.glob(item+"/libDelphes.dylib"))
-            if len(files)!=0:
-	        self.configLinux.libraries['Delphes']=files[0]+":"+str(os.stat(files[0]).st_mtime)
-   	        find=True
-                os.environ['LD_LIBRARY_PATH'] = os.environ['LD_LIBRARY_PATH'] + \
-                    		        ":" + item
-                os.environ['DYLD_LIBRARY_PATH'] = os.environ['DYLD_LIBRARY_PATH'] + \
-                    		        ":" + item
-                os.environ['LIBRARY_PATH'] = os.environ['LIBRARY_PATH'] + \
-                    		        ":" + item
-        # Not fail -> Warning
-        if not find:
-            self.PrintFAIL(warning=True)
-	    logging.warning("Library called 'delphes' not found. Delphes ROOT format will be disabled.")
-            logging.warning("To enable this format, please type 'install delphes'.")
-            return False
-
-	# Checking header file 
-        find=False
-        for item in self.includes:
-            files=glob.glob(item+"/modules/ParticlePropagator.h")
-            if len(files)!=0:
-  	        self.configLinux.headers['Delphes']=files[0]+":"+str(os.stat(files[0]).st_mtime)
-	        find=True
-                os.environ['CPLUS_INCLUDE_PATH'] = os.environ['CPLUS_INCLUDE_PATH'] + ":" + item
-   	        break
-
-        # If not, test if it is there locally 
-        if not find: 
-            find=os.path.isfile(self.ma5dir+'/tools/delphes/modules/ParticlePropagator.h')
-            if find:
-                os.environ['CPLUS_INCLUDE_PATH'] = os.environ['CPLUS_INCLUDE_PATH'] + ":" + \
-                                                   self.ma5dir+'/tools/delphes/'
-                os.environ['CPLUS_INCLUDE_PATH'] = os.environ['CPLUS_INCLUDE_PATH'] + ":" + \
-                                                   self.ma5dir+'/tools/delphes/external/'
-
-        if not find:
-            self.PrintFAIL(warning=True)
-	    logging.warning("Header file called 'modules/ParticlePropagator.h' not found. Delphes ROOT format will be disabled.")
-            logging.warning("To enable this format, please type 'install delphes' package.")
-            return False
-        else:
-            self.PrintOK()
+
+        # Name of the dynamic lib
+        libnames=['libDelphes.so','libDelphes.a']
+        if self.isMAC:
+            libnames.append('libDelphes.dylib')
+
+        # User veto
+        if self.configLinux.useroptions.delphes_veto=='1':
+            self.PrintFAIL(warning=True)
+	    logging.warning("Library called 'delphes' disabled. Delphes ROOT format will be disabled.")
+            return False
+
+        # Does the user force the paths?
+        force1=False
+        force2=False
+        if self.configLinux.useroptions.delphes_includes!="0":
+            self.configLinux.delphes_inc_paths.append(self.configLinux.useroptions.delphes_includes)
+            self.configLinux.delphes_inc_paths.append(self.configLinux.useroptions.delphes_includes+'/external/')
+            force1=True
+        if self.configLinux.useroptions.delphes_libs!="0":
+            self.configLinux.delphes_lib_paths.append(self.configLinux.useroptions.delphes_libraries)
+            force2=True
+        force=force1 and force2
+
+        # Checking if Delphes has been installed by MA5
+        ma5installation = False
+        if not force:
+            if os.path.isdir(self.ma5dir+'/tools/delphes') and \
+               os.path.isdir(self.ma5dir+'/tools/delphes/external'):
+                self.configLinux.delphes_inc_paths.append(self.ma5dir+'/tools/delphes/')
+                self.configLinux.delphes_inc_paths.append(self.ma5dir+'/tools/delphes/external/')
+                self.configLinux.delphes_lib_paths.append(self.ma5dir+'/tools/delphes/')
+                ma5installation = True
+
+        # Check if the libraries and headers are available
+        if force or ma5installation:
+
+            # header
+            if not os.path.isfile(self.configLinux.delphes_inc_paths[0]+'/modules/ParticlePropagator.h'):
+                self.PrintFAIL(warning=True)
+	        logging.warning("Header file called '"+self.configLinux.delphes_inc_paths[0]+"/modules/ParticlePropagator.h' not found." +\
+                                "Delphes ROOT format will be disabled.")
+                logging.warning("To enable this format, please type 'install delphes' package.")
+                return False
+
+            # lib
+            mypath, myfile = self.FindFilesWithPattern(self.configLinux.delphes_lib_paths,"libDelphes.*",libnames)
+            self.configLinux.delphes_lib=myfile
+            if self.configLinux.delphes_lib=="":
+                self.PrintFAIL(warning=True)
+	        logging.warning("Delphes library not found in "+self.configLinux.delphes_lib_paths[0]+" folder. Delphes ROOT format will be disabled.")
+                logging.warning("To enable this format, please type 'install delphes' package.")
+                return False
+
+        # Checking Delphes can be found in other folders
+        if not force and not ma5installation:
+
+            # header
+            mypath, myfile = self.FindHeader('/modules/ParticlePropagator.h')
+            self.delphes_inc_path = mypath
+            if self.delphes_inc_path=="":
+                self.PrintFAIL(warning=True)
+  	        logging.warning("Header file called '/modules/ParticlePropagator.h' not found. Delphes ROOT format will be disabled.")
+                logging.warning("To enable this format, please type 'install delphes' package.")
+                return False
+            
+            # lib
+            mypath, myfile = self.FindLibraryWithPattern('libDelphes.*',libnames)
+            self.configLinux.delphes_lib_path = mypath
+            self.configLinux.delphes_lib      = myfile
+            if self.configLinux.delphes_lib_path=="":
+                self.PrintFAIL(warning=True)
+                logging.warning("Delphes library not found. Delphes format will be disabled.")
+                logging.warning("To enable this format, please type 'install delphes' package.")
+                return False
+
+        self.configLinux.libraries['Delphes']=self.configLinux.delphes_lib+":"+str(os.stat(self.configLinux.delphes_lib).st_mtime)
+        self.PrintOK()
+ 
+        return True
+
+
+    def checkDelfes(self):
+
+#        self.PrintLibrary("delfes library")
+
+        # Name of the dynamic lib
+        libnames=['libDelphes.so','libDelphes.a']
+        if self.isMAC:
+            libnames.append('libDelphes.dylib')
+
+        # User veto
+        if self.configLinux.useroptions.delfes_veto=='1':
+#            self.PrintFAIL(warning=True)
+#	    logging.warning("Library called 'delfes' disabled. Delfes ROOT format will be disabled.")
+            return False
+
+        # Does the user force the paths?
+        force1=False
+        force2=False
+        if self.configLinux.useroptions.delfes_includes!="0":
+            self.configLinux.delfes_inc_paths.append(self.configLinux.useroptions.delfes_includes)
+            self.configLinux.delfes_inc_paths.append(self.configLinux.useroptions.delfes_includes+'/external/')
+            force1=True
+        if self.configLinux.useroptions.delfes_libs!="0":
+            self.configLinux.delfes_lib_paths.append(self.configLinux.useroptions.delfes_libraries)
+            force2=True
+        force=force1 and force2
+
+        # Checking if delfes has been installed by MA5
+        ma5installation = False
+        if not force:
+            if os.path.isdir(self.ma5dir+'/tools/delfes') and \
+               os.path.isdir(self.ma5dir+'/tools/delfes/external'):
+                self.configLinux.delfes_inc_paths.append(self.ma5dir+'/tools/delfes/')
+                self.configLinux.delfes_inc_paths.append(self.ma5dir+'/tools/delfes/external/')
+                self.configLinux.delfes_lib_paths.append(self.ma5dir+'/tools/delfes/')
+                ma5installation = True
+
+        # Check if the libraries and headers are available
+        if force or ma5installation:
+
+            # header
+            if not os.path.isfile(self.configLinux.delfes_inc_paths[0]+'/modules/ParticlePropagator.h'):
+#                self.PrintFAIL(warning=True)
+#	        logging.warning("Header file called '"+self.configLinux.delfes_inc_paths[0]+"/modules/ParticlePropagator.h' not found." +\
+#                                "Delfes ROOT format will be disabled.")
+#                logging.warning("To enable this format, please type 'install delfes' package.")
+                return False
+
+            # lib
+            mypath, myfile = self.FindFilesWithPattern(self.configLinux.delfes_lib_paths,"libDelphes.*",libnames)
+            self.configLinux.delfes_lib=myfile
+            if self.configLinux.delfes_lib=="":
+#                self.PrintFAIL(warning=True)
+#	         logging.warning("Delfes library not found in "+self.configLinux.delfes_lib_paths[0]+" folder. Delfes ROOT format will be disabled.")
+#                logging.warning("To enable this format, please type 'install delfes' package.")
+                return False
+
+        # Checking Delfes can be found in other folders
+        if not force and not ma5installation:
+
+            # header
+            mypath, myfile = self.FindHeader('/modules/ParticlePropagator.h')
+            self.delfes_inc_path = mypath
+            if self.delfes_inc_path=="":
+#                self.PrintFAIL(warning=True)
+#                logging.warning("Header file called '/modules/ParticlePropagator.h' not found. Delfes ROOT format will be disabled.")
+#                logging.warning("To enable this format, please type 'install delfes' package.")
+                return False
+            
+            # lib
+            mypath, myfile = self.FindLibraryWithPattern('libDelphes.*',libnames)
+            self.configLinux.delfes_lib_path = mypath
+            self.configLinux.delfes_lib      = myfile
+            if self.configLinux.delfes_lib_path=="":
+#                self.PrintFAIL(warning=True)
+#                logging.warning("Delfes library not found. Delfes format will be disabled.")
+#                logging.warning("To enable this format, please type 'install delfes' package.")
+                return False
+
+        self.configLinux.libraries['Delfes']=self.configLinux.delfes_lib+":"+str(os.stat(self.configLinux.delfes_lib).st_mtime)
+#        self.PrintOK()
  
         return True
 
@@ -462,32 +687,58 @@
     def checkFastJet(self):
 
         self.PrintLibrary("FastJet")
-
         self.configLinux.fastjet_version = "none"
 
-        # Checking if fastjet is installed on the system
-        find = False
-        for item in self.paths:
-            files=glob.glob(item+"/fastjet-config")
-            files.extend(glob.glob(item+"/fastjet-config"))
-            if(len(files))!=0:
-               find = True
-               self.configLinux.fastjet_version = commands.getstatusoutput('fastjet-config --version')[1]
-
-        # If not, test if it is there locally 
-        if not find: 
-            find=os.path.isfile(self.ma5dir+'/tools/fastjet/bin/fastjet-config')
-
-        # If not there, print warning message; if there -> test it
-        if not find:
+        # User veto
+        if self.configLinux.useroptions.fastjet_veto=='1':
             self.PrintFAIL(warning=True)
-	    logging.warning("The fastJet package not found. JetClustering algorithms are disabled.")
-            logging.warning("To enable this functionnality, please type 'install fastjet'.")
+	    logging.warning("The FastJet package is disabled. JetClustering algorithms are disabled.")
             return False
-        else:
-            self.configLinux.fastjet_version = commands.getstatusoutput(self.ma5dir+'/tools/fastjet/bin/fastjet-config --version')[1]
-            os.environ['PATH'] = self.ma5dir+'/tools/fastjet/bin/:'+os.environ['PATH']
-            self.PrintOK()
+
+        # Does the user force the paths?
+        force=False
+        if self.configLinux.useroptions.fastjet_bin_path!="0":
+            self.configLinux.fastjet_bin_path.append(self.configLinux.useroptions.fastjet_bin_path)
+            force=True
+
+        # Checking if FastJet has been installed by MA5
+        ma5installation = False
+        if not force:
+            if os.path.isdir(self.ma5dir+'/tools/fastjet/bin'):
+                self.configLinux.fastjet_bin_path=self.ma5dir+'/tools/fastjet/bin/'
+                ma5installation = True
+
+        # Check if the libraries and headers are available
+        if force or ma5installation:
+
+            if not os.path.isfile(self.configLinux.fastjet_bin_path+'/fastjet-config'):
+                self.PrintFAIL(warning=True)
+	        logging.warning("The FastJet package not found. JetClustering algorithms are disabled.")
+                logging.warning("To enable this functionnality, please type 'install fastjet'.")
+                return False
+                
+        # Checking FastJet can be found in other folders
+        if not force and not ma5installation:
+
+            for item in self.paths:
+                files=glob.glob(item+"/fastjet-config")
+                files.extend(glob.glob(item+"/fastjet-config"))
+                if(len(files))!=0:
+                    self.configLinux.fastjet_bin_path=item
+                    break
+            if self.configLinux.fastjet_bin_path=='':
+                self.PrintFAIL(warning=True)
+	        logging.warning("The FastJet package not found. JetClustering algorithms are disabled.")
+                logging.warning("To enable this functionnality, please type 'install fastjet'.")
+                return False
+
+        self.configLinux.fastjet_version = commands.getstatusoutput(self.ma5dir+'/tools/fastjet/bin/fastjet-config --version')[1]
+        tmp = commands.getstatusoutput(self.ma5dir+'/tools/fastjet/bin/fastjet-config --libs --plugins')[1]
+        words = tmp.split()
+        for word in words:
+            if word.startswith('-L'):
+                self.configLinux.fastjet_lib_paths.append(word[2:])
+        self.PrintOK()
 
         return True
 
@@ -512,6 +763,11 @@
     def checkPdfLatex(self):
         self.PrintLibrary('pdflatex')
 
+        if self.configLinux.useroptions.pdflatex_veto=='1':
+            self.PrintFAIL(warning=True)
+	    logging.warning("pdflatex disabled. Reports under the pdf format will not be compiled.")
+            return False
+
         pdflatex_version = commands.getstatusoutput('pdflatex -version')
         if 'not found' in str(pdflatex_version) or 'no such file' in str(pdflatex_version):
             self.PrintFAIL(warning=True)
@@ -524,6 +780,11 @@
     def checkLatex(self):
         self.PrintLibrary('latex')
 
+        if self.configLinux.useroptions.latex_veto=='1':
+            self.PrintFAIL(warning=True)
+	    logging.warning("latex disabled. Reports under the dvi format will not be compiled.")
+            return False
+
         latex_version = commands.getstatusoutput('latex -version')
         if 'not found' in str(latex_version) or 'no such file' in str(latex_version):
             self.PrintFAIL(warning=True)
@@ -536,6 +797,11 @@
     def checkdvipdf(self):
         self.PrintLibrary('dvipdf')
 
+        if self.configLinux.useroptions.dvipdf_veto=='1':
+            self.PrintFAIL(warning=True)
+	    logging.warning("dvipdf disabled. DVI reports will not be converted to pdf files.")
+            return False
+
         dvipdf_version = commands.getstatusoutput('dvipdf')
         if 'not found' in str(dvipdf_version) or 'no such file' in str(dvipdf_version):
             self.PrintFAIL(warning=True)
 
=== modified file 'madanalysis/core/expert_mode.py'
--- madanalysis/core/expert_mode.py	2013-05-31 21:57:38 +0000
+++ madanalysis/core/expert_mode.py	2014-05-17 19:51:11 +0000
@@ -42,8 +42,10 @@
         
     def CreateDirectory(self):
         logging.info("\nWelcome to the expert mode of MadAnalysis")
-        logging.info("Please enter a folder for creating an empty SampleAnalyzer job")
+        logging.info("Please enter a folder name for creating an empty SampleAnalyzer job")
         answer=raw_input("Answer: ")
+        answer=answer.replace(' ','_');
+        answer=answer.replace('-','_');
         self.path = os.path.expanduser(answer)
         if not self.path.startswith('/'):
             self.path = self.main.currentdir+'/'+self.path
@@ -90,12 +92,17 @@
             return False
 
         # Writing an empty analysis
+        logging.info("Please enter a name for your analysis")
+        title=raw_input("Answer: ")
+        if title=="":
+            title="user"
+        title=title.replace(' ', '_');
+        title=title.replace('-', '_');
         logging.info("   Writing an empty analysis...")
-        jobber.WriteEmptyFilterSource(self.main)
-        os.system("cd "+self.path+"/Build/SampleAnalyzer; python newAnalyzer.py user")
+        os.system("cd "+self.path+"/Build/SampleAnalyzer; python newAnalyzer.py " + title + " 1")
 
         # Extracting analysis name
-        file = open(self.path+"/Build/SampleAnalyzer/Analyzer/analysisList.cpp")
+        file = open(self.path+"/Build/SampleAnalyzer/Analyzer/analysisList.h")
         title=""
         for line in file:
             if "Add" not in line:
@@ -105,9 +112,7 @@
                 title=words[1]
                 break
         file.close()
-        if title=="":
-            title="user"
-            
+
         # Writing a Makefile
         logging.info("   Writing a 'Makefile'...")
         if not jobber.WriteMakefiles():
 
=== modified file 'madanalysis/core/library_builder.py'
--- madanalysis/core/library_builder.py	2013-05-17 06:19:22 +0000
+++ madanalysis/core/library_builder.py	2014-05-17 19:51:11 +0000
@@ -31,11 +31,15 @@
 
 class LibraryBuilder:
 
-    def __init__(self,configLinux,ma5dir):
+    def __init__(self,configLinux,ma5dir,libZIP,libDelphes,libDelfes,libFastJet):
 
         self.configLinux=configLinux
         self.ma5dir=ma5dir
         self.configStore = LinuxArchitecture()
+        self.libZIP=libZIP
+        self.libDelphes=libDelphes
+        self.libDelfes=libDelfes
+        self.libFastJet=libFastJet
 
         
     def checkMA5(self):
@@ -53,19 +57,33 @@
                 logging.error(" "+name)
                 return False
 
-        # Look for shared library 'MadAnalysis' and 'config' file
-        if not os.path.isfile(self.ma5dir+'/tools/SampleAnalyzer/Lib/libSampleAnalyzer.a') \
+        # Look for the shared library 'MadAnalysis' and 'config' file
+        if not os.path.isfile(self.ma5dir+'/tools/SampleAnalyzer/Lib/libSampleAnalyzer.so') \
            or not os.path.isfile(self.ma5dir+'/tools/architecture.ma5'):
             FirstUse=True
+            return True, False
+
+        # Look for optional library
+        libraries = []
+        if self.libFastJet:
+            libraries.append(self.ma5dir+'/tools/SampleAnalyzer/Lib/libfastjet_for_ma5.so')
+        if self.libZIP:
+            libraries.append(self.ma5dir+'/tools/SampleAnalyzer/Lib/libzlib_for_ma5.so')
+        if self.libDelphes:
+            libraries.append(self.ma5dir+'/tools/SampleAnalyzer/Lib/libdelphes_for_ma5.so')
+        if self.libDelfes:
+            libraries.append(self.ma5dir+'/tools/SampleAnalyzer/Lib/libdelfes_for_ma5.so')
+        for library in libraries:
+            if not os.path.isfile(library):
+                return False, True
 
         # Importing the configuration stored with the library
         if not FirstUse:
             if not self.configStore.Import(self.ma5dir+'/tools/architecture.ma5'):
                 FirstUse=True
+                return True, False
 
-        if not FirstUse:
-             logging.info('  => MadAnalysis library found.')
-        return FirstUse
+        return FirstUse, False
     
         
     def compare(self):
 
=== modified file 'madanalysis/core/linux_architecture.py'
--- madanalysis/core/linux_architecture.py	2013-10-27 21:36:24 +0000
+++ madanalysis/core/linux_architecture.py	2014-05-17 19:51:11 +0000
@@ -23,14 +23,121 @@
 
 
 import logging
+
+class UserOptions:
+
+    def __init__(self):
+        self.root_includes    = '0'
+        self.root_libs        = '0'
+        self.delphes_veto     = '0'
+        self.delphes_includes = '0'
+        self.delphes_libs     = '0'
+        self.delfes_veto      = '0'
+        self.delfes_includes  = '0'
+        self.delfes_libs      = '0'
+        self.zlib_veto        = '0'
+        self.zlib_includes    = '0'
+        self.zlib_libs        = '0'
+        self.fastjet_veto     = '0'
+        self.fastjet_bin_path = '0'
+        self.pdflatex_veto    = '0'
+        self.latex_veto       = '0'
+        self.dvipdf_veto      = '0'
+        
+    def Dump(self):
+        logging.info(" ROOT header path     = " + str(self.root_includes))
+        logging.info(" ROOT library path    = " + str(self.root_libs))
+        logging.info(" DELPHES veto         = " + str(self.delphes_veto))
+        logging.info(" DELPHES header path  = " + str(self.delphes_includes))
+        logging.info(" DELPHES library path = " + str(self.delphes_libs))
+        logging.info(" DELFES veto          = " + str(self.delfes_veto))
+        logging.info(" DELFES header path   = " + str(self.delfes_includes))
+        logging.info(" DELFES library path  = " + str(self.delfes_libs))
+        logging.info(" ZLIB veto            = " + str(self.zlib_veto))
+        logging.info(" ZLIB header path     = " + str(self.zlib_includes))
+        logging.info(" ZLIB library path    = " + str(self.zlib_libs))
+        logging.info(" FASTJET veto         = " + str(self.fastjet_veto))
+        logging.info(" FASTJET bin path     = " + str(self.fastjet_bin_path))
+        logging.info(" PDFLATEX veto        = " + str(self.pdflatex_veto))
+        logging.info(" LATEX veto           = " + str(self.latex_veto))
+        logging.info(" DVIPDF veto          = " + str(self.dvipdf_veto))
+
+    def Export(self,file):
+        file.write(self.root_includes+"\n")
+        file.write(self.root_libs+"\n")
+        file.write(self.delphes_veto+"\n")
+        file.write(self.delphes_includes+"\n")
+        file.write(self.delphes_libs+"\n")
+        file.write(self.delfes_veto+"\n")
+        file.write(self.delfes_includes+"\n")
+        file.write(self.delfes_libs+"\n")
+        file.write(self.zlib_veto+"\n")
+        file.write(self.zlib_includes+"\n")
+        file.write(self.zlib_libs+"\n")
+        file.write(self.fastjet_veto+"\n")
+        file.write(self.fastjet_bin_path+"\n")
+        file.write(self.pdflatex_veto+"\n")
+        file.write(self.latex_veto+"\n")
+        file.write(self.dvipdf_veto+"\n")
+
+    def Import(self,file):
+        self.root_includes    = file.readline().replace('\n','')
+        self.root_libs        = file.readline().replace('\n','')
+        self.delphes_veto     = file.readline().replace('\n','')
+        self.delphes_includes = file.readline().replace('\n','')
+        self.delphes_libs     = file.readline().replace('\n','')
+        self.delfes_veto      = file.readline().replace('\n','')
+        self.delfes_includes  = file.readline().replace('\n','')
+        self.delfes_libs      = file.readline().replace('\n','')
+        self.zlib_veto        = file.readline().replace('\n','')
+        self.zlib_includes    = file.readline().replace('\n','')
+        self.zlib_libs        = file.readline().replace('\n','')
+        self.fastjet_veto     = file.readline().replace('\n','')
+        self.fastjet_bin_path = file.readline().replace('\n','')
+        self.pdflatex_veto    = file.readline().replace('\n','')
+        self.latex_veto       = file.readline().replace('\n','')
+        self.dvipdf_veto      = file.readline().replace('\n','')
+
+    def Compare(self,other):
+        if self.root_includes != other.root_includes:
+            return False
+        if self.root_libs != other.root_libs:
+            return False
+        if self.delphes_veto != other.delphes_veto:
+            return False
+        if self.delphes_includes != other.delphes_includes:
+            return False
+        if self.delphes_libs != other.delphes_libs:
+            return False
+        if self.delfes_veto != other.delfes_veto:
+            return False
+        if self.delfes_includes != other.delfes_includes:
+            return False
+        if self.delfes_libs != other.delfes_libs:
+            return False
+        if self.zlib_veto != other.zlib_veto:
+            return False
+        if self.zlib_includes != other.zlib_includes:
+            return False
+        if self.zlib_libs != other.zlib_libs:
+            return False
+        if self.fastjet_veto != other.fastjet_veto:
+            return False
+        if self.fastjet_bin_path != other.fastjet_bin_path:
+            return False
+        return True
+
 class LinuxArchitecture:
 
     def __init__(self):
+        self.useroptions      = UserOptions()
         self.platform         = ""
+        self.release          = ""
         self.ma5_version      = ""
         self.ma5_date         = ""
         self.python_version   = ""
         self.gcc_version      = ""
+        self.make_version     = ""
         self.gfortran_version = ""
         self.root_version     = ""
         self.fastjet_version  = ""
@@ -38,13 +145,35 @@
         self.headers          = {}
         self.editor           = ""
 
+        self.root_inc_path=""
+        self.root_lib_path=""
+        self.zlib_inc_path=""
+        self.zlib_lib_path=""
+        self.zlib_lib=""
+        self.delphes_inc_paths=[]
+        self.delphes_lib_paths=[]
+        self.delphes_lib=""
+        self.delfes_inc_paths=[]
+        self.delfes_lib_paths=[]
+        self.delfes_lib=""
+        self.fastjet_bin_path=""
+        self.fastjet_lib_paths=[]
 
     def Dump(self):
-        logging.info(" Linux distrib    = " + self.platform)
+        logging.info(" User options")
+        logging.info(" ------------")
+        self.useroptions.Dump()
+        logging.info("")
+
+        logging.info(" Architecture")
+        logging.info(" ------------")
+        logging.info(" Platform         = " + self.platform)
+        logging.info(" Release platform = " + self.release)
         logging.info(" MA5 version      = " + self.ma5_version)
         logging.info(" MA5 date         = " + self.ma5_date)
         logging.info(" Python version   = " + self.python_version)
         logging.info(" gcc version      = " + self.gcc_version)
+        logging.info(" GNU Make version = " + self.make_version)
         logging.info(" gfortran version = " + self.gfortran_version)
         logging.info(" ROOT version     = " + self.root_version)
         logging.info(" FastJet version  = " + self.fastjet_version)
@@ -57,7 +186,6 @@
                 logging.info( " Header  '" + key + "' = " + \
                               value )
 
-
     def Export(self,filename):
         try:
             file = open(filename,"w")
@@ -65,11 +193,15 @@
             logging.error("impossible to write the configuration file '" + \
                           filename + "'")
             return False
+
+        self.useroptions.Export(file)
         file.write(self.platform+"\n")
+        file.write(self.release+"\n")
         file.write(self.ma5_version+"\n")
         file.write(self.ma5_date+"\n")
         file.write(self.python_version+"\n")
         file.write(self.gcc_version+"\n")
+        file.write(self.make_version+"\n")
         file.write(self.gfortran_version+"\n")
         file.write(self.root_version+"\n")
         file.write(self.fastjet_version+"\n")
@@ -92,12 +224,16 @@
             logging.error("impossible to read the configuration file '" + \
                           filename + "'")
             return False
+
         try:
+            self.useroptions.Import(file)
             self.platform         = file.readline().replace('\n','')
+            self.release          = file.readline().replace('\n','')
             self.ma5_version      = file.readline().replace('\n','')
             self.ma5_date         = file.readline().replace('\n','')
             self.python_version   = file.readline().replace('\n','')
             self.gcc_version      = file.readline().replace('\n','')
+            self.make_version     = file.readline().replace('\n','')
             self.gfortran_version = file.readline().replace('\n','')
             self.root_version     = file.readline().replace('\n','')
             self.fastjet_version  = file.readline().replace('\n','')
@@ -135,8 +271,13 @@
 
 
     def Compare(self, other):
+        if not self.useroptions.Compare(other.useroptions):
+            return False
+        
         if self.platform != other.platform:
             return False
+        if self.release != other.release:
+            return False
         if self.ma5_version != other.ma5_version:
             return False
         if self.ma5_date != other.ma5_date:
@@ -145,6 +286,8 @@
             return False
         if self.gcc_version != other.gcc_version:
             return False
+        if self.make_version != other.make_version:
+            return False
         if self.gfortran_version != other.gfortran_version:
             return False
         if self.root_version != other.root_version:
 
=== modified file 'madanalysis/core/main.py'
--- madanalysis/core/main.py	2013-10-27 21:36:24 +0000
+++ madanalysis/core/main.py	2014-05-17 19:51:11 +0000
@@ -43,7 +43,7 @@
 import logging
 import os
 import sys
-
+import platform
         
 class Main():
 
@@ -79,6 +79,7 @@
         self.mg5            = False
         self.libZIP         = False
         self.libDelphes     = False
+        self.libDelfes      = False
         self.pdflatex       = False
         self.latex          = False
         self.dvipdf         = False
@@ -86,9 +87,11 @@
         self.fortran        = False
         self.observables    = ObservableManager(self.mode)
         self.mcatnloutils   = False
+        self.expertmode     = False
+        self.isMAC          = False
+        self.repeatSession  = False 
         self.ResetParameters()
 
-
     def ResetParameters(self):
         self.merging        = MergingConfiguration()
         self.fastsim        = FastsimConfiguration()
@@ -128,7 +131,7 @@
         else:
             if self.fastsim.package=="none":
                 samples.append('.lhco')
-                if self.libDelphes:
+                if self.libDelphes or self.libDelfes:
                     samples.append('.root')
             else:
                 samples.append('.lhe')
@@ -405,8 +408,22 @@
         self.configLinux.ma5_version    = self.version
         self.configLinux.ma5_date       = self.date
         self.configLinux.python_version = sys.version.replace('\n','')
-        self.configLinux.platform       = sys.platform
-
+        self.configLinux.platform       = platform.system()
+        self.configLinux.release        = platform.release()
+
+        # Is Mac
+        sys.stdout.write("Platform: "+self.configLinux.platform+" "+self.configLinux.release+" ")
+        sys.stdout.flush()
+        if self.configLinux.platform.lower() in ['darwin','mac','macosx']:
+            self.isMAC = True
+            sys.stdout.write('\x1b[32m'+'[MAC/OSX mode]'+'\x1b[0m'+'\n')
+            sys.stdout.flush()
+        else:
+            self.isMAC = False
+            sys.stdout.write('\x1b[32m'+'[Linux mode]'+'\x1b[0m'+'\n')
+            sys.stdout.flush()
+
+        
         if detail:
             logging.info("General     Platform identifier : " + str(self.configLinux.platform))
             import multiprocessing
@@ -426,9 +443,13 @@
             logging.info("")
 
         # Initializing the config checker    
-        checker = ConfigChecker(self.configLinux,self.ma5dir,self.script)
+        checker = ConfigChecker(self.configLinux,self.ma5dir,self.script,self.isMAC)
         checker.checkTextEditor()
 
+        # Reading user options
+        if not checker.ReadUserOptions():
+            return False
+
         # Mandatory packages
         logging.info("Checking mandatory packages:")
         checker.PrintLibrary("python")
@@ -437,90 +458,239 @@
             return False
         if not checker.checkGPP():
             return False
+        if not checker.checkMake():
+            return False
         if not checker.checkROOT():
             return False
+        if not checker.checkPyROOT():
+            return False
 
         # Optional packages
         logging.info("Checking optional packages:")
-        if not checker.checkGF():
-            return False
-        self.libZIP = checker.checkZLIB()
+        self.libGF      = checker.checkGF()
+        self.libZIP     = checker.checkZLIB()
         self.libDelphes = checker.checkDelphes()
+        self.libDelfes  = checker.checkDelfes()
         self.libFastJet = checker.checkFastJet()
-        self.pdflatex = checker.checkPdfLatex()
-        self.latex = checker.checkLatex()
+        self.pdflatex   = checker.checkPdfLatex()
+        self.latex      = checker.checkLatex()
         if self.latex:
             self.dvipdf = checker.checkdvipdf()
-        self.mcatnloutils = checker.checkMCatNLOUtils()
-
+
+        # Set PATH variable
+        self.configLinux.toPATH=[]
+        self.configLinux.toLDPATH=[]
+        self.configLinux.toLDPATH.append(self.ma5dir+'/tools/SampleAnalyzer/Lib/')
+        self.configLinux.toLDPATH.append(self.configLinux.root_lib_path)
+        if self.libFastJet:
+            self.configLinux.toPATH.append(self.configLinux.fastjet_bin_path)
+            for path in self.configLinux.fastjet_lib_paths:
+                self.configLinux.toLDPATH.append(path)
+        if self.libZIP:
+            self.configLinux.toLDPATH.append(self.configLinux.zlib_lib_path)        
+        if self.libDelphes:
+            for path in self.configLinux.delphes_lib_paths:
+                self.configLinux.toLDPATH.append(path)        
+        if self.libDelfes:
+            for path in self.configLinux.delfes_lib_paths:
+                self.configLinux.toLDPATH.append(path)        
+
+        os.environ['PATH'] = os.environ['PATH'] + \
+                             ":" + ':'.join(self.configLinux.toPATH)
         os.environ['LD_LIBRARY_PATH'] = os.environ['LD_LIBRARY_PATH'] + \
-                                        ":" + self.ma5dir+'/tools/SampleAnalyzer/Lib/'
-        os.environ['LIBRARY_PATH'] = os.environ['LIBRARY_PATH'] + \
-                                        ":" + self.ma5dir+'/tools/SampleAnalyzer/Lib/'
+                                        ":" + ':'.join(self.configLinux.toLDPATH)
+        if self.isMAC:        
+            os.environ['DYLD_LIBRARY_PATH'] = os.environ['DYLD_LIBRARY_PATH'] + \
+                                        ":" + ':'.join(self.configLinux.toLDPATH)
 
-        if self.mcatnloutils:
-            os.environ['LD_LIBRARY_PATH'] = os.environ['LD_LIBRARY_PATH'] + \
-                      ":" + self.ma5dir+'/tools/MCatNLO-utilities/MCatNLO/lib/'
-            os.environ['LIBRARY_PATH'] = os.environ['LIBRARY_PATH'] + \
-                      ":" + self.ma5dir+'/tools/MCatNLO-utilities/MCatNLO/lib/'
-            
         return True 
    
+    def PrintOK(self):
+        sys.stdout.write('\x1b[32m'+'[OK]'+'\x1b[0m'+'\n')
+        sys.stdout.flush()
+
     def BuildLibrary(self,forced=False):
-        builder = LibraryBuilder(self.configLinux,self.ma5dir)
+        builder = LibraryBuilder(self.configLinux,self.ma5dir,self.libZIP,self.libDelphes,self.libDelfes,self.libFastJet)
+
         UpdateNeed=False
-        
-        FirstUse = builder.checkMA5()
-        if not FirstUse:
+        FirstUse, Missing = builder.checkMA5()
+        if not FirstUse and not Missing:
             UpdateNeed = not builder.compare()
 
-        rebuild = forced or FirstUse or UpdateNeed
-        if not rebuild:
+        rebuild = forced or FirstUse or UpdateNeed or Missing
+
+        if not rebuild:
+            if not os.path.isfile(self.ma5dir+'/tools/SampleAnalyzer/Lib/libSampleAnalyzer.so'):
+                FirstUse=True
+            rebuild = forced or FirstUse or UpdateNeed or Missing
+
+        if not rebuild:
+            logging.info('  => MadAnalysis libraries found.')
+
+            # Test the program
+            if not os.path.isfile(self.ma5dir+'/tools/SampleAnalyzer/Test/SampleAnalyzerTest'):
+                FirstUse=True
+
+            precompiler = LibraryWriter(self.ma5dir,'lib',self.libZIP,self.libFastJet,self.forced,self.fortran,self.libDelphes,self.libDelfes,self)
+            if not precompiler.Run('SampleAnalyzerTest',[],self.ma5dir+'/tools/SampleAnalyzer/Test',silent=True):
+                UpdateNeed=True
+
+            if not precompiler.CheckRun(self.ma5dir+'/tools/SampleAnalyzer/Test/SampleAnalyzerTest.log',silent=True):
+                UpdateNeed=True
+            rebuild = forced or FirstUse or UpdateNeed or Missing
+            
+        if not rebuild:
+            logging.info('  => MadAnalysis test program works.')
             return True
 
         # Compile library
         if FirstUse:
             logging.info("  => First use of MadAnalysis (or the library is missing).")
+        elif Missing:
+            logging.info("  => Libraries are missing or system configuration has changed. Need to rebuild the library.")
         elif UpdateNeed:
             logging.info("  => System configuration has changed since the last use. Need to rebuild the library.")
         elif forced:
             logging.info("  => The user forces to rebuild the library.")
 
         # Initializing the JobWriter
-        compiler = LibraryWriter(self.ma5dir,'lib',self.libZIP,self.libFastJet,self.forced,self.fortran,self.libDelphes)
+        compiler = LibraryWriter(self.ma5dir,'lib',self.libZIP,self.libFastJet,self.forced,self.fortran,self.libDelphes,self.libDelfes,self)
     
         # Dumping architecture
         if not self.configLinux.Export(self.ma5dir+'/tools/architecture.ma5'):
             sys.exit()
 
-        logging.info("   Creating a 'Makefile'...")
-        if not compiler.WriteMakefile('shared'):
-            logging.error("library building aborted.")
-            sys.exit()
-
-        if not compiler.MrProper():
-            logging.error("impossible to remove temporary files created during the building.")
-            sys.exit()
-
-        logging.info("   Compiling the MadAnalysis library...")
-        if not compiler.Compile():
-            logging.error("library building aborted.")
-            sys.exit()
-
-        logging.info("   Linking the MadAnalysis library...")
-        if not compiler.Link():
-            logging.error("library building aborted.")
-            sys.exit()
-
-        logging.info("   Checking the MadAnalysis library...")
-
-        if not os.path.isfile(self.ma5dir+'/tools/SampleAnalyzer/Lib/libSampleAnalyzer.a'):
-            logging.error("the library 'libSampleAnalyzer.a' is not produced.")
-            sys.exit()
-    
-        if not compiler.Clean():
-            logging.error("impossible to remove temporary files created during the building.")
-            sys.exit()
+        # Library to compiles
+        libraries = []
+        if self.libFastJet:
+            libraries.append(['FastJet', 'interface to FastJet', 'fastjet', self.ma5dir+'/tools/SampleAnalyzer/Lib/libfastjet_for_ma5.so',self.ma5dir+'/tools/SampleAnalyzer/Interfaces'])
+        if self.libZIP:
+            libraries.append(['zlib', 'interface to zlib', 'zlib', self.ma5dir+'/tools/SampleAnalyzer/Lib/libzlib_for_ma5.so',self.ma5dir+'/tools/SampleAnalyzer/Interfaces'])
+        if self.libDelphes:
+            libraries.append(['Delphes', 'interface to Delphes', 'delphes', self.ma5dir+'/tools/SampleAnalyzer/Lib/libdelphes_for_ma5.so',self.ma5dir+'/tools/SampleAnalyzer/Interfaces'])
+        if self.libDelfes:
+            libraries.append(['Delfes', 'interface to Delfes', 'delfes', self.ma5dir+'/tools/SampleAnalyzer/Lib/libdelfes_for_ma5.so',self.ma5dir+'/tools/SampleAnalyzer/Interfaces'])
+        libraries.append(['SampleAnalyzer', 'general SampleAnalyzer component', 'SampleAnalyzer', self.ma5dir+'/tools/SampleAnalyzer/Lib/libSampleAnalyzer.so',self.ma5dir+'/tools/SampleAnalyzer'])
+
+        # Writing the Makefiles
+        logging.info("")
+        logging.info("   **********************************************************")
+        logging.info("                Building SampleAnalyzer libraries     ")
+        logging.info("   **********************************************************")
+
+
+        # Getting number of cores
+        ncores = compiler.get_ncores2()
+
+        # Compiling the libraries
+        for ind in range(0,len(libraries)):
+            
+            logging.info("   **********************************************************")
+            logging.info("   Library "+str(ind+1)+"/"+str(len(libraries))+" - "+libraries[ind][1])
+
+            # Writing a Makefile
+            logging.info("     - Writing a Makefile ...")
+            if libraries[ind][0]=='SampleAnalyzer':
+                if not compiler.WriteMakefile():
+                    logging.error("library building aborted.")
+                    sys.exit()
+            else:
+                if not compiler.WriteMakefileForInterfaces(libraries[ind][2]):
+                    logging.error("library building aborted.")
+                    sys.exit()
+
+             # Cleaning the project
+            logging.info("     - Cleaning the project before building the library ...")
+            if not compiler.MrProper(libraries[ind][2],libraries[ind][4]):
+                logging.error("library building aborted.")
+                sys.exit()
+
+            # Compiling
+            logging.info("     - Compiling the source files ...")
+            if not compiler.Compile(ncores,libraries[ind][2],libraries[ind][4]):
+                logging.error("library building aborted.")
+                sys.exit()
+
+            # Linking
+            logging.info("     - Linking the library ...")
+            if not compiler.Link(libraries[ind][2],libraries[ind][4]):
+                logging.error("library building aborted.")
+                sys.exit()
+
+            # Checking
+            logging.info("     - Checking that the library is properly built ...")
+            if not os.path.isfile(libraries[ind][3]):
+                logging.error("the library '"+libraries[ind][3]+"' is not produced.")
+                sys.exit()
+
+             # Cleaning the project
+            logging.info("     - Cleaning the project after building the library ...")
+            if not compiler.Clean(libraries[ind][2],libraries[ind][4]):
+                logging.error("library building aborted.")
+                sys.exit()
+
+            # Print Ok
+            sys.stdout.write("     => Status: ")
+            self.PrintOK()
+
+        logging.info("   **********************************************************")
+        logging.info("   Test program ")
+
+        # Writing a Makefile
+        logging.info("     - Writing a Makefile ...")
+        if not compiler.WriteMakefileForTest():
+            logging.error("test program building aborted.")
+            sys.exit()
+
+        # Cleaning the project
+        logging.info("     - Cleaning the project before building the program ...")
+        if not compiler.MrProper('test',self.ma5dir+'/tools/SampleAnalyzer/Test'):
+            logging.error("test program building aborted.")
+            sys.exit()
+
+        # Compiling
+        logging.info("     - Compiling the source files ...")
+        if not compiler.Compile(ncores,'test',self.ma5dir+'/tools/SampleAnalyzer/Test'):
+            logging.error("test program building aborted.")
+            sys.exit()
+
+        # Linking
+        logging.info("     - Linking the program ...")
+        if not compiler.Link('test',self.ma5dir+'/tools/SampleAnalyzer/Test'):
+            logging.error("test program building aborted.")
+            sys.exit()
+
+        # Checking
+        logging.info("     - Checking that the program is properly built ...")
+        filename=self.ma5dir+'/tools/SampleAnalyzer/Test/SampleAnalyzerTest'
+        if not os.path.isfile(filename):
+            logging.error("the test program '"+filename+"' is not produced.")
+            sys.exit()
+
+        # Cleaning the project
+        logging.info("     - Cleaning the project after building the program ...")
+        if not compiler.Clean('test',self.ma5dir+'/tools/SampleAnalyzer/Test'):
+            logging.error("test program building aborted.")
+            sys.exit()
+
+        # Running the program test
+        logging.info("     - Running the test program ...")
+        if not compiler.Run('SampleAnalyzerTest',[],self.ma5dir+'/tools/SampleAnalyzer/Test'):
+            logging.error("the test is failed.")
+            sys.exit()
+
+        # Checking the program output
+        logging.info("     - Checking the program output...")
+        if not compiler.CheckRun(self.ma5dir+'/tools/SampleAnalyzer/Test/SampleAnalyzerTest.log'):
+            logging.error("the test is failed.")
+            sys.exit()
+
+        # Print Ok
+        sys.stdout.write("     => Status: ")
+        self.PrintOK()
+
+
+        logging.info("")
 
         return True    
         
 
=== modified file 'madanalysis/enumeration/observable_type.py'
--- madanalysis/enumeration/observable_type.py	2013-05-17 06:19:22 +0000
+++ madanalysis/enumeration/observable_type.py	2014-05-17 19:51:11 +0000
@@ -30,10 +30,10 @@
 	# name : accept_particles 
 	values = { 'UNKNOWN' : [False,'','','','',0,0,0,False,False],\
 		   'SQRTS' :   [False,'PHYSICS->SqrtS(event.mc())','PHYSICS->SqrtS(event.mc())','','GeV',100,0.,1000., True, False],\
-		   'TET' :     [False,'PHYSICS->EventTET(event.mc())','PHYSICS->EventTET(event.mc())','PHYSICS->EventTET(event.rec())','GeV',100,0.,1000., True,False],\
-		   'MET' :     [False,'PHYSICS->EventMET(event.mc())','PHYSICS->EventMET(event.mc())','PHYSICS->EventMET(event.rec())','GeV',100,0.,1000., True,False],\
-		   'THT' :     [False,'PHYSICS->EventTHT(event.mc())','PHYSICS->EventTHT(event.mc())','PHYSICS->EventTHT(event.rec())','GeV',100,0.,1000., True,False],\
-		   'MHT' :     [False,'PHYSICS->EventMHT(event.mc())','PHYSICS->EventMHT(event.mc())','PHYSICS->EventMHT(event.rec())','GeV',100,0.,1000.,True,False],\
+		   'TET' :     [False,'PHYSICS->Transverse->EventTET(event.mc())','PHYSICS->Transverse->EventTET(event.mc())','PHYSICS->Transverse->EventTET(event.rec())','GeV',100,0.,1000., True,False],\
+		   'MET' :     [False,'PHYSICS->Transverse->EventMET(event.mc())','PHYSICS->Transverse->EventMET(event.mc())','PHYSICS->Transverse->EventMET(event.rec())','GeV',100,0.,1000., True,False],\
+		   'THT' :     [False,'PHYSICS->Transverse->EventTHT(event.mc())','PHYSICS->Transverse->EventTHT(event.mc())','PHYSICS->Transverse->EventTHT(event.rec())','GeV',100,0.,1000., True,False],\
+		   'MHT' :     [False,'PHYSICS->Transverse->EventMHT(event.mc())','PHYSICS->Transverse->EventMHT(event.mc())','PHYSICS->Transverse->EventMHT(event.rec())','GeV',100,0.,1000.,True,False],\
 		   'NPID':     [False,'NPID','NPID','NPID','',100,0.,100.,False,False],\
 		   'NAPID':    [False,'NAPID','NAPID','NAPID','',100,0.,100.,False,False],\
 	           'E'   :     [True,'e()','e()','e()','GeV',100,0.,1000.,True,True],\
 
=== added file 'madanalysis/input/installation_options.dat'
--- madanalysis/input/installation_options.dat	1970-01-01 00:00:00 +0000
+++ madanalysis/input/installation_options.dat	2014-05-17 19:51:11 +0000
@@ -0,0 +1,35 @@
+# WARNING MA5 SHOULD DETECT AUTOMATICALLY YOUR CONFIGURATION
+# IF THIS AUTOMATED MODE FAILS, YOU CAN FORCE SOME 
+# OPTIONS THROUGH THIS FILE
+
+# -----ROOT-----
+# root_includes = /home/toto/root/include
+# root_libs     = /home/toto/root/lib
+
+# -----DELPHES----- 
+# delphes_veto     = 0 # 0=No, 1=Yes
+# delphes_includes = /home/toto/delphes/include
+# delphes_libs     = /home/toto/delphes/lib
+
+# -----DELFES----- 
+# delfes_veto     = 0 # 0=No, 1=Yes
+# delfes_includes = /home/toto/delfes/include
+# delfes_libs     = /home/toto/delfes/lib
+
+# -----ZLIB-----
+# zlib_veto     = 0 # 0=No, 1=Yes
+# zlib_includes = /home/toto/zlib/include
+# zlib_libs     = /home/toto/zlib/lib
+
+# -----FASTJET-----
+# fastjet_veto     = 0 # 0=No, 1=Yes
+# fastjet_bin_path = /home/toto/fastjet/include
+
+# -----PDFLATEX-----
+# pdflatex_veto = 0 # 0=No, 1=Yes
+
+# -----LATEX-----
+# latex_veto = 0 # 0=No, 1=Yes
+
+# -----DVIPDF-----
+# dvipdf_veto = 0 # 0=No, 1=Yes
 
=== modified file 'madanalysis/input/particles_name_default.txt'
--- madanalysis/input/particles_name_default.txt	2013-07-12 13:09:17 +0000
+++ madanalysis/input/particles_name_default.txt	2014-05-17 19:51:11 +0000
@@ -50,9 +50,8 @@
      23     z
      24     w+
     -24     w-
-# Note that we can't give a name to 25 here,
-# since it is different in SM and MSSM.
-# MSSM Higgs
+# The Higgs boson is called h1
+     25     h1
      35     h2
      36     h3
      37     h+
 
=== modified file 'madanalysis/interpreter/cmd_base.py'
--- madanalysis/interpreter/cmd_base.py	2013-05-17 06:19:22 +0000
+++ madanalysis/interpreter/cmd_base.py	2014-05-17 19:51:11 +0000
@@ -29,7 +29,7 @@
 class CmdBase():
     """Command CMDBase"""
 
-    reserved_words=["exit","quit","eof","history","shell","from","as","all","or","and"]
+    reserved_words=["exit","quit","eof","history","shell","from","as","all","or","and","main"]
 
     def __init__(self,main,cmd_name):
         self.reserved_words.append(cmd_name)
 
=== modified file 'madanalysis/interpreter/cmd_install.py'
--- madanalysis/interpreter/cmd_install.py	2013-10-27 21:05:18 +0000
+++ madanalysis/interpreter/cmd_install.py	2014-05-17 19:51:11 +0000
@@ -23,6 +23,7 @@
 
 
 from madanalysis.interpreter.cmd_base import CmdBase
+from madanalysis.IOinterface.delphes_migration import DelphesMigration
 import logging
 import os
 import sys
@@ -86,6 +87,8 @@
             return self.install_zlib()
         elif args[0]=='delphes':
             return self.install_delphes()
+        elif args[0]=='delfes':
+            return self.install_delfes()
         elif args[0]=='fastjet':
             return self.install_fastjet()
         elif args[0]=='MCatNLO-for-ma5':
@@ -99,7 +102,7 @@
     def help(self):
         logging.info("   Syntax: install <component>")
         logging.info("   Download and install a MadAnalysis component from the official site.")
-        logging.info("   List of available components : samples zlib fastjet MCatNLO-for-ma5 delphes")
+        logging.info("   List of available components : samples zlib fastjet MCatNLO-for-ma5 delphes delfes")
 
 
     def get_ncores(self):
@@ -219,8 +222,7 @@
         # End
         logging.info("Installation complete.")
 
-
-        return True
+        return 'restart'
 
 
     def install_delphes(self):
@@ -244,9 +246,11 @@
         installdir = self.main.ma5dir + '/tools/delphes/'
 
         # List of files
-        files = { "delphes.tar.gz" : "http://cp3.irmp.ucl.ac.be/downloads/Delphes-3.0.10.tar.gz" }
+        #files = { "delphes.tar.gz" : "http://cp3.irmp.ucl.ac.be/downloads/Delphes-3.0.12.tar.gz" }
+        files = { "delphes.tar.gz" : "http://cp3.irmp.ucl.ac.be/downloads/Delphes-3.1.1.tar.gz"}
         
         # Launching wget
+        logging.info("Configuring the package ...")
         if not self.wget(files,'delphes',installdir):
             return False
 
@@ -287,8 +291,85 @@
         # End
         logging.info("Installation complete.")
 
-
-        return True
+        return 'restart'
+
+
+    def install_delfes(self):
+
+        # Asking for number of cores
+        ncores = self.get_ncores()
+        
+        # Checking connection with MA5 web site
+        if not self.check_ma5site():
+            return False
+    
+        # Creating tools folder
+        if not self.create_tools_folder():
+            return False
+
+        # Creating package folder
+        if not self.create_package_folder('delfes'):
+            return False
+
+        # Directory to install
+        installdir = self.main.ma5dir + '/tools/delfes/'
+
+        # List of files
+#       files = { "delfes.tar.gz" : "http://cp3.irmp.ucl.ac.be/downloads/Delphes-3.0.12.tar.gz" }
+        files = { "delfes.tar.gz" : "http://cp3.irmp.ucl.ac.be/downloads/Delphes-3.1.1.tar.gz"}
+        
+        # Launching wget
+        if not self.wget(files,'delfes',installdir):
+            return False
+
+        # Detarring package
+        packagedir = self.untar(installdir,'delfes.tar.gz','delfes')
+        if packagedir == "":
+            return False
+
+        # Changing the name of the directory
+        os.system("mv "+packagedir+"/* "+self.main.ma5dir+"/tools/delfes/")
+        packagedir = self.main.ma5dir+"/tools/delfes/"
+       
+        # Migration
+        logging.info("Applying the MadAnalysis 5 patch to the package ...")
+        migrator = DelphesMigration(self.main)
+        migrator.Migrate()
+
+        # Configuring
+        logging.info("Configuring the package ...")
+        os.system("cd "+packagedir+" ; ./configure > "+self.main.ma5dir+"/tools/delfes/"+"configuration.log 2>&1")
+
+        # Compiling
+        logging.info("Compiling the package ...")
+        os.system("cd "+packagedir+" ; make -j"+str(ncores)+" > "+self.main.ma5dir+"/tools/delfes/"+"compilation.log 2>&1")
+
+        # Final check
+        logging.info("Checking installation ...")
+        if (not os.path.isdir(self.main.ma5dir+"/tools/delfes/modules")):
+            logging.error('package modules are missing.')
+            self.display_log('delfes')
+            return False
+
+        if not os.path.isfile(self.main.ma5dir+'/tools/delfes/modules/ParticlePropagator.h'):
+            logging.error("header labeled 'modules/ParticlePropagator.h' is missing.")
+            self.display_log('delfes')
+            return False
+
+        if not os.path.isfile(self.main.ma5dir+'/tools/delfes/libDelphes.so'):
+            logging.error("library labeled 'libdelphes.so' is missing.")
+            self.display_log('delfes')
+            return False
+
+        if not os.path.isfile(self.main.ma5dir+'/tools/delfes/DelphesSTDHEP'):
+            logging.error("library labeled 'DelphesSTDHEP' is missing.")
+            self.display_log('delfes')
+            return False
+        
+        # End
+        logging.info("Installation complete.")
+
+        return 'restart'
 
 
     def install_mcatnlo(self):
@@ -423,7 +504,7 @@
         for file,url in files.items():
             ind+=1
             result="OK"
-            logging.info(' * ' + str(ind)+"/"+str(len(files.keys()))+" Downloading the file '"+file+"' ...")
+            logging.info(' * ' + str(ind)+"/"+str(len(files.keys()))+" Downloading the file "+url+" ...")
 
             try:
                 urllib.urlretrieve(url,installdir+'/'+file,CmdInstall.reporthook)
@@ -473,7 +554,7 @@
             return False
 
         # List of files
-        files = { "fastjet.tar.gz" : "https://madanalysis.irmp.ucl.ac.be/raw-attachment/wiki/WikiStart/fastjet-3.0.3.tar.gz" }
+        files = { "fastjet.tar.gz" : "http://madanalysis.irmp.ucl.ac.be/raw-attachment/wiki/WikiStart/fastjet-3.0.6.tar.gz" }
 
         # Launching wget
         if not self.wget(files,'fastjet',installdir):
@@ -521,11 +602,10 @@
             self.display_log('fastjet')
             return False
         
-        
         # End
         logging.info("Installation complete.")
 
-        return True
+        return 'restart'
 
 
     def install_samples(self):
@@ -593,7 +673,7 @@
         if nargs>2:
             return []
         else:
-            output = ["samples","zlib","fastjet", "MCatNLO-for-ma5", "delphes" ]
+            output = ["samples","zlib","fastjet", "MCatNLO-for-ma5", "delphes", "delfes" ]
             return self.finalize_complete(text,output)
     
 
 
=== modified file 'madanalysis/interpreter/cmd_plot.py'
--- madanalysis/interpreter/cmd_plot.py	2013-05-17 06:19:22 +0000
+++ madanalysis/interpreter/cmd_plot.py	2014-05-17 19:51:11 +0000
@@ -54,7 +54,6 @@
 
         # Getting reference to observable
         obsRef=self.main.observables.get(obsName)
-
         foundArguments = False
         foundOptions   = False
         foundBinning   = False 
@@ -80,7 +79,7 @@
                 Nbracket2-=1
                 if i==(len(args)-1):
                     foundOptions=True
-                
+
         if Nbracket1!=0:
             logging.error("number of opening-bracket '(' and number of " +\
                           "closing-braket ')' does not match.")
@@ -168,6 +167,11 @@
             arguments=self.extract_arguments(args[2:endArguments],obsName,obsRef)
             if arguments==None:
                 return
+        elif len(obsRef.args) !=0: # checks whether arguments should have been provided
+          logging.error("the observable '"+obsName+"' requires "+
+                str(len(obsRef.args))+" arguments whereas no arguments have been specified.")
+          return
+        
 
         # Creating histo
         histo = Histogram(obsRef,arguments,nbins,xmin,xmax)
 
=== modified file 'madanalysis/interpreter/cmd_set.py'
--- madanalysis/interpreter/cmd_set.py	2013-09-26 12:30:50 +0000
+++ madanalysis/interpreter/cmd_set.py	2014-05-17 19:51:11 +0000
@@ -102,7 +102,7 @@
         elif len(objs)==3 and objs[0].lower()=='main' and objs[1].lower()=='merging':
             self.main.merging.user_SetParameter(objs[2],args[2],self.main.mode,self.main.libFastJet)
         elif len(objs)==3 and objs[0].lower()=='main' and objs[1].lower()=='fastsim':
-            self.main.fastsim.user_SetParameter(objs[2],args[2],self.main.datasets,self.main.mode,self.main.libFastJet,self.main.libDelphes) 
+            self.main.fastsim.user_SetParameter(objs[2],args[2],self.main.datasets,self.main.mode,self.main.libFastJet,self.main.libDelphes,self.main.libDelfes) 
         elif len(objs)==3 and objs[0].lower()=='main' and objs[1].lower()=='shower':
             self.main.shower.user_SetParameter(objs[2],args[2],self.main.mode,self.main.mcatnloutils)
         else:
 
=== modified file 'madanalysis/interpreter/cmd_submit.py'
--- madanalysis/interpreter/cmd_submit.py	2013-10-27 21:36:24 +0000
+++ madanalysis/interpreter/cmd_submit.py	2014-05-17 19:51:11 +0000
@@ -335,16 +335,10 @@
         if answer=="no" or answer=="n":
             return
         else:
-            if self.main.fastsim.delphes.pileup=="":
-                if self.main.fastsim.delphes.detector=='cms':
-                    cardname = 'delphes_card_CMS.tcl'
-                elif self.main.fastsim.delphes.detector=='atlas':
-                    cardname ='delphes_card_ATLAS.tcl'
-            else:
-                if self.main.fastsim.delphes.detector=='cms':
-                    cardname = 'delphes_card_CMS_PileUp.tcl'
-                elif self.main.fastsim.delphes.detector=='atlas':
-                    cardname ='delphes_card_ATLAS_PileUp.tcl'
+            if self.main.fastsim.package=="delphes":
+                cardname = self.main.fastsim.delphes.card
+            elif self.main.fastsim.package=="delfes":
+                cardname = self.main.fastsim.delfes.card
             os.system(self.main.configLinux.editor+" "+dirname+"/Input/"+cardname)
 
 
@@ -408,9 +402,15 @@
                 return False
 
         #edit the delphes cards
-        if self.main.fastsim.package=="delphes":
+        if self.main.fastsim.package in ["delphes","delfes"]:
             self.editDelphesCard(dirname)
 
+        if self.resubmit:
+            logging.info("   Cleaning 'SampleAnalyzer'...")
+            if not jobber.MrproperJob():
+                logging.error("job submission aborted.")
+                return False
+
         logging.info("   Compiling 'SampleAnalyzer'...")
         if not jobber.CompileJob():
             logging.error("job submission aborted.")
 
=== modified file 'madanalysis/interpreter/interpreter.py'
--- madanalysis/interpreter/interpreter.py	2013-05-31 21:57:38 +0000
+++ madanalysis/interpreter/interpreter.py	2014-05-17 19:51:11 +0000
@@ -26,6 +26,7 @@
    Uses the cmd package for command interpretation and tab completion.
 """
 
+import logging
 import readline
 import os
 
@@ -174,6 +175,38 @@
     def complete_import(self,text,line,begidx,endidx):
         return self.cmd_import.complete(text,line,begidx,endidx)
 
+     # Restart
+    def do_restart(self, line):
+        """ sending a signal allowing to restart the interpreter """
+        if self.main.script:
+            logging.warning("'restart' command is not allowed in script mode.")
+        else:
+            YES=False
+            # Asking the safety question
+            if not Main.forced:
+                logging.warning("Are you sure to restart the MadAnalysis 5 session? (Y/N)")
+                allowed_answers=['n','no','y','yes']
+                answer=""
+                while answer not in  allowed_answers:
+                   answer=raw_input("Answer: ")
+                   answer=answer.lower()
+                   if answer=="no" or answer=="n":
+                       YES=False
+                       break
+                   elif answer=='yes' or answer=='y':
+                       YES=True
+                       break
+            if YES:
+                self.main.repeatSession=True
+                return True
+            else:
+                pass
+
+    def help_restart(self):
+        logging.info("   Syntax: restart ")
+        logging.info("   Quit the current MadAnalysis sessiona and open a new one.")
+        logging.info("   All the information will be discarded.")
+
     def do_remove(self,line):
         self.cmd_remove.do(self.split_arg(line))
 
@@ -193,7 +226,11 @@
         return self.cmd_swap.complete(text,line,begidx,endidx)
 
     def do_install(self,line):
-        self.cmd_install.do(self.split_arg(line))
+        result = self.cmd_install.do(self.split_arg(line))
+        if result=='restart':
+            logging.info(" ")
+            logging.info("MadAnalysis 5 must be restarted for taking into account the present installation.")
+            return self.do_restart('restart')
 
     def help_install(self):
         self.cmd_install.help()
 
=== modified file 'madanalysis/interpreter/interpreter_base.py'
--- madanalysis/interpreter/interpreter_base.py	2013-05-24 13:05:09 +0000
+++ madanalysis/interpreter/interpreter_base.py	2014-05-17 19:51:11 +0000
@@ -190,7 +190,7 @@
         """ exit the mainloop() """
         logging.info("")
         return True
- 
+
     # Aliases
     do_EOF = do_quit
     do_exit = do_quit
 
=== modified file 'madanalysis/job/job_candidate_cut.py'
--- madanalysis/job/job_candidate_cut.py	2013-05-17 06:19:22 +0000
+++ madanalysis/job/job_candidate_cut.py	2014-05-17 19:51:11 +0000
@@ -212,7 +212,7 @@
             # Bracket for begin 
             file.write('    {\n')
 
-            file.write('      '+container2+'=PHYSICS->rankFilter('+\
+            file.write('      '+container2+'=SORTER->rankFilter('+\
                         newcontainer2+','+str(other_part[0].PTrank)+','+\
                         'PTordering'+');\n\n')
             
@@ -305,8 +305,14 @@
     # Case of one particle/multiparticle
     if len(combi1)==1:
         file.write('    if (')
+        if main.mode == MA5RunningType.PARTON:
+          TheObs=obs.code_parton[:-2]
+        elif main.mode == MA5RunningType.HADRON:
+          TheObs=obs.code_hadron[:-2]
+        else:
+          TheObs=obs.code_reco[:-2]
         file.write(containers1[0]+'[a]->' +\
-                   'dr('+container+'[muf])' +\
+                   TheObs+'('+container+'[muf])' +\
                    OperatorType.convert2cpp(condition.operator) +\
                    str(condition.threshold) +\
                    ') {'+tagName+'['+str(tagIndex)+']=true; break;}\n')
@@ -338,8 +344,14 @@
 
         # Result    
         file.write('    if (q1.')
-        if obs.name in ['DELTAR','vDELTAR']:
-            file.write('dr('+container+'[muf])'+ OperatorType.convert2cpp(condition.operator) + \
+        if obs.name in ['DELTAR','vDELTAR','DPHI_0_PI','DPHI_0_2PI']:
+            if main.mode == MA5RunningType.PARTON:
+              TheObs=obs.code_parton[:-2]
+            elif main.mode == MA5RunningType.HADRON:
+              TheObs=obs.code_hadron[:-2]
+            else:
+              TheObs=obs.code_reco[:-2]
+            file.write(TheObs+'('+container+'[muf])'+ OperatorType.convert2cpp(condition.operator) + \
                    str(condition.threshold) +   \
                    ') {'+tagName+'['+str(tagIndex)+']=true; break;}\n')
         else:
 
=== modified file 'madanalysis/job/job_event_cut.py'
--- madanalysis/job/job_event_cut.py	2013-05-17 06:19:22 +0000
+++ madanalysis/job/job_event_cut.py	2014-05-17 19:51:11 +0000
@@ -243,9 +243,15 @@
 
     # Case of one particle/multiparticle
     if len(combi1)==1 and len(combi2)==1:
+        if main.mode == MA5RunningType.PARTON:
+          TheObs=obs.code_parton[:-2]
+        elif main.mode == MA5RunningType.HADRON:
+          TheObs=obs.code_hadron[:-2]
+        else:
+          TheObs=obs.code_reco[:-2]
         file.write('    if (')
         file.write(containers1[0]+'['+iterator1+'[0]]->' +\
-                   'dr('+containers2[0]+'['+iterator2+'[0]])' +\
+                   TheObs+'('+containers2[0]+'['+iterator2+'[0]])' +\
                    OperatorType.convert2cpp(condition.operator) +\
                    str(condition.threshold) +\
                    ') {'+tagName+'['+str(tagIndex)+']=true; break;}\n')
@@ -279,7 +285,13 @@
                        'momentum();\n')
 
         # Result    
-        file.write('    if (q1.dr(q2)'+\
+        if main.mode == MA5RunningType.PARTON:
+          TheObs=obs.code_parton[:-2]
+        elif main.mode == MA5RunningType.HADRON:
+          TheObs=obs.code_hadron[:-2]
+        else:
+          TheObs=obs.code_reco[:-2]
+        file.write('    if (q1.'+TheObs+'(q2)'+\
                    ''+ OperatorType.convert2cpp(condition.operator) + \
                    str(condition.threshold) +   \
                    ') {'+tagName+'['+str(tagIndex)+']=true; break;}\n')
 
=== modified file 'madanalysis/job/job_execute.py'
--- madanalysis/job/job_execute.py	2013-10-03 16:02:40 +0000
+++ madanalysis/job/job_execute.py	2014-05-17 19:51:11 +0000
@@ -69,7 +69,7 @@
 
     file.write('  // Sorting particle collection according to '+rank+'\n')
     file.write('  // for getting '+str(part.PTrank)+'th particle\n')
-    file.write('  '+container+'=PHYSICS->rankFilter('+\
+    file.write('  '+container+'=SORTER->rankFilter('+\
                newcontainer+','+str(part.PTrank)+','+rank+');\n\n')
 
 
@@ -206,13 +206,13 @@
     # Put isolated negative muon
     if part.particle.Find(130):
         file.write('      if ( (event.rec()->muons()[i].charge()<0) &&'+\
-               ' PHYSICS->IsIsolatedMuon(event.rec()->muons()[i],event.rec()) ) '+\
+               ' PHYSICS->Id->IsIsolatedMuon(event.rec()->muons()[i],event.rec()) ) '+\
                container+'.push_back(&(event.rec()->muons()[i]));\n')
 
     # Put isolated positive muon
     if part.particle.Find(-130):
         file.write('      if ( (event.rec()->muons()[i].charge()>0) &&'+\
-               ' PHYSICS->IsIsolatedMuon(event.rec()->muons()[i],event.rec()) ) '+\
+               ' PHYSICS->Id->IsIsolatedMuon(event.rec()->muons()[i],event.rec()) ) '+\
                container+'.push_back(&(event.rec()->muons()[i]));\n')
 
 
 
=== modified file 'madanalysis/job/job_header.py'
--- madanalysis/job/job_header.py	2013-05-17 06:19:22 +0000
+++ madanalysis/job/job_header.py	2014-05-17 19:51:11 +0000
@@ -139,11 +139,11 @@
 
     # FinalSate
     if status=="finalstate":
-        file.write("     if ( !PHYSICS->IsFinalState(part) ) return false;\n")
+        file.write("     if ( !PHYSICS->Id->IsFinalState(part) ) return false;\n")
     elif status=="initialstate":
-        file.write("     if ( !PHYSICS->IsInitialState(part) ) return false;\n")
+        file.write("     if ( !PHYSICS->Id->IsInitialState(part) ) return false;\n")
     elif status=="interstate":
-        file.write("     if ( !PHYSICS->IsInterState(part) ) return false;\n")
+        file.write("     if ( !PHYSICS->Id->IsInterState(part) ) return false;\n")
 
     # Id
     file.write('     if ( ')
 
=== modified file 'madanalysis/job/job_initialize.py'
--- madanalysis/job/job_initialize.py	2013-07-12 13:09:17 +0000
+++ madanalysis/job/job_initialize.py	2014-05-17 19:51:11 +0000
@@ -428,6 +428,9 @@
         file.write('  PHYSICS->mcConfig().AddInvisibleId(16);\n')
         file.write('  PHYSICS->mcConfig().AddInvisibleId(1000022);\n')
         file.write('  PHYSICS->mcConfig().AddInvisibleId(1000039);\n')
+        for item in main.multiparticles.Get("invisible"):
+          if item not in [-16,-14,-12,12,14,16,1000022,1000039]:
+            file.write('  PHYSICS->mcConfig().AddInvisibleId('+str(item)+');\n')
         file.write('\n')
 
 
@@ -456,7 +459,12 @@
     # Initializing array of cuts     
     if Ncuts!=0:
         file.write('  // Initializing cut array\n')
-        file.write('  cuts_.Initialize('+str(Ncuts)+');\n')
+    icut=1
+    for item in main.selection.table:
+      if item.__class__.__name__=="Cut":
+        file.write("  cuts_.InitCut(\""+item.conditions.GetStringDisplay()+"\");\n")
+    if Ncuts!=0:
+        file.write('\n')
 
     # Initializing each item
     ihisto  = 0
 
=== modified file 'madanalysis/job/job_plot.py'
--- madanalysis/job/job_plot.py	2013-10-29 05:48:23 +0000
+++ madanalysis/job/job_plot.py	2014-05-17 19:51:11 +0000
@@ -72,11 +72,11 @@
         file.write('  for (unsigned int i=0;i<event.mc()->particles().size();i++)\n')
         file.write('  {\n')
         if main.selection[iabs].statuscode=="finalstate":
-            file.write('    if (!PHYSICS->IsFinalState(event.mc()->particles()[i])) continue;\n')
+            file.write('    if (!PHYSICS->Id->IsFinalState(event.mc()->particles()[i])) continue;\n')
         elif main.selection[iabs].statuscode=="initialstate":
-            file.write('    if (!PHYSICS->IsInitialState(event.mc()->particles()[i])) continue;\n')
+            file.write('    if (!PHYSICS->Id->IsInitialState(event.mc()->particles()[i])) continue;\n')
         elif main.selection[iabs].statuscode=="interstate":
-            file.write('    if (!PHYSICS->IsInterState(event.mc()->particles()[i])) continue;\n')
+            file.write('    if (!PHYSICS->Id->IsInterState(event.mc()->particles()[i])) continue;\n')
         if npid:
             file.write('    H'+str(ihisto)+'_' +\
                    '->Fill(event.mc()->particles()[i].pdgid(),__event_weight__);\n')
@@ -245,8 +245,14 @@
 
         # Case of one particle/multiparticle
         if len(combi2)==1:
+            if main.mode == MA5RunningType.PARTON:
+              TheObs=obs.code_parton[:-2]
+            elif main.mode == MA5RunningType.HADRON:
+              TheObs=obs.code_hadron[:-2]
+            else:
+              TheObs=obs.code_reco[:-2]
             file.write('      H'+str(ihisto)+'_->Fill('\
-                       'q1.dr('+containers2[0]+\
+                       'q1.'+TheObs+'('+containers2[0]+\
                        '[b[0]]),__event_weight__);\n')
 
         # Operation : sum or diff
@@ -275,8 +281,14 @@
                                'momentum();\n')
 
                 # Result    
+                if main.mode == MA5RunningType.PARTON:
+                  TheObs=obs.code_parton[:-2]
+                elif main.mode == MA5RunningType.HADRON:
+                  TheObs=obs.code_hadron[:-2]
+                else:
+                  TheObs=obs.code_reco[:-2]
                 file.write('    H'+str(ihisto)+'_->Fill('+\
-                               'q1.dr(q2),__event_weight__);\n')
+                               'q1.'+TheObs+'(q2),__event_weight__);\n')
 
         # End Loop
         WriteEndLoop(file,iabs,ihisto,combi2,main)
@@ -317,8 +329,14 @@
 
         # Case of one particle/multiparticle
         if len(combi1)==1:
+            if main.mode == MA5RunningType.PARTON:
+              TheObs=obs.code_parton[:-2]
+            elif main.mode == MA5RunningType.HADRON:
+              TheObs=obs.code_hadron[:-2]
+            else:
+              TheObs=obs.code_reco[:-2]
             file.write('      H'+str(ihisto)+'_->Fill('\
-                       'q2.dr('+containers1[0]+\
+                       'q2.'+TheObs+'('+containers1[0]+\
                        '[a[0]]),__event_weight__);\n')
 
         # Operation : sum or diff
@@ -347,8 +365,14 @@
                                'momentum();\n')
 
                 # Result    
+                if main.mode == MA5RunningType.PARTON:
+                  TheObs=obs.code_parton[:-2]
+                elif main.mode == MA5RunningType.HADRON:
+                  TheObs=obs.code_hadron[:-2]
+                else:
+                  TheObs=obs.code_reco[:-2]
                 file.write('    H'+str(ihisto)+'_->Fill('+\
-                               'q1.dr(q2),__event_weight__);\n')
+                               'q1.'+TheObs+'(q2),__event_weight__);\n')
 
         # End Loop
         WriteEndLoop(file,iabs,ihisto,combi1,main)
@@ -389,7 +413,13 @@
         WriteEndLoop(file,ihisto,iabs,combi2,main)
 
         # After the two loops 
-        file.write('    H'+str(ihisto)+'_->Fill(q1.dr(q2),__event_weight__);\n')
+        if main.mode == MA5RunningType.PARTON:
+          TheObs=obs.code_parton[:-2]
+        elif main.mode == MA5RunningType.HADRON:
+          TheObs=obs.code_hadron[:-2]
+        else:
+          TheObs=obs.code_reco[:-2]
+        file.write('    H'+str(ihisto)+'_->Fill(q1.'+TheObs+'(q2),__event_weight__);\n')
         
 
 def WriteBeforeLoop(file,iabs,ihisto,combination,main,value='value',q='q'):
@@ -567,9 +597,15 @@
 
     # Case of one particle/multiparticle
     if len(combi1)==1 and len(combi2)==1:
+        if main.mode == MA5RunningType.PARTON:
+          TheObs=obs.code_parton[:-2]
+        elif main.mode == MA5RunningType.HADRON:
+          TheObs=obs.code_hadron[:-2]
+        else:
+          TheObs=obs.code_reco[:-2]
         file.write('      H'+str(ihisto)+'_->Fill('+\
                    containers1[0]+'['+iterator1+'[0]]->'+\
-                   'dr('+containers2[0]+'['+iterator2+'[0]]),__event_weight__);\n')
+                   TheObs+'('+containers2[0]+'['+iterator2+'[0]]),__event_weight__);\n')
         return