Merge lp:~ma5dev/madanalysis5/v1.7beta into lp:madanalysis5

[Benjamin Fuks]

=== modified file 'bin/ma5'
--- bin/ma5	2018-05-29 21:42:05 +0000
+++ bin/ma5	2019-02-13 11:05:44 +0000
@@ -62,8 +62,13 @@
 
 # Release version
 # Do not touch it !!!!!  
+<<<<<<< TREE
 version = "1.6.1"
 date = "2018/05/29"
+=======
+version = "1.7.21"
+date = "2019/02/07"
+>>>>>>> MERGE-SOURCE
 
 # Loading the MadAnalysis session
 import madanalysis.core.launcher

=== added directory 'doc'
=== added directory 'doc/expert_mode'
=== added file 'doc/expert_mode/main_expert.bib'
--- doc/expert_mode/main_expert.bib	1970-01-01 00:00:00 +0000
+++ doc/expert_mode/main_expert.bib	2019-02-13 11:05:44 +0000
@@ -0,0 +1,1151 @@
+@article{Dumont:2014tja,
+      author         = "Dumont, B. and Fuks, B. and Kraml, S. and Bein, S. and
+                        Chalons, G. and Conte, E. and Kulkarni, S. and Sengupta,
+                        D. and Wymant, C.",
+      title          = "{Toward a public analysis database for LHC new physics
+                        searches using MADANALYSIS 5}",
+      journal        = "Eur. Phys. J.",
+      volume         = "C75",
+      year           = "2015",
+      number         = "2",
+      pages          = "56",
+      doi            = "10.1140/epjc/s10052-014-3242-3",
+      eprint         = "1407.3278",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "CERN-PH-TH-2014-109, LAPTH-048-14, LPSC14143",
+      SLACcitation   = "%%CITATION = ARXIV:1407.3278;%%"
+}
+
+@article{deFavereau:2013fsa,
+      author         = "de Favereau, J. and Delaere, C. and Demin, P. and
+                        Giammanco, A. and Lemaître, V. and Mertens, A. and
+                        Selvaggi, M.",
+      title          = "{DELPHES 3, A modular framework for fast simulation of a
+                        generic collider experiment}",
+      collaboration  = "DELPHES 3",
+      journal        = "JHEP",
+      volume         = "02",
+      year           = "2014",
+      pages          = "057",
+      doi            = "10.1007/JHEP02(2014)057",
+      eprint         = "1307.6346",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ex",
+      SLACcitation   = "%%CITATION = ARXIV:1307.6346;%%"
+}
+
+@article{Skands:2003cj,
+      author         = "Skands, Peter Z. and others",
+      title          = "{SUSY Les Houches accord: Interfacing SUSY spectrum
+                        calculators, decay packages, and event generators}",
+      journal        = "JHEP",
+      volume         = "07",
+      year           = "2004",
+      pages          = "036",
+      doi            = "10.1088/1126-6708/2004/07/036",
+      eprint         = "hep-ph/0311123",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "LU-TP-03-39, SHEP-03-24, CERN-TH-2003-204, ZU-TH-15-03,
+                        LMU-19-03, DCPT-03-108, IPPP-03-54, CTS-IISC-2003-07,
+                        DESY-03-166, MPP-2003-111",
+      SLACcitation   = "%%CITATION = HEP-PH/0311123;%%"
+}
+
+@article{Allanach:2008qq,
+      author         = "Allanach, B. C. and others",
+      title          = "{SUSY Les Houches Accord 2}",
+      journal        = "Comput. Phys. Commun.",
+      volume         = "180",
+      year           = "2009",
+      pages          = "8-25",
+      doi            = "10.1016/j.cpc.2008.08.004",
+      eprint         = "0801.0045",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "FERMILAB-PUB-07-036-T, SLAC-PUB-12765,
+                        CERN-PH-TH-2007-148, DAMTP-2007-76, EDINBURGH-2007-31,
+                        KEK-TH-1170, LAPTH-1204-07, LPT-ORSAY-07-81, SHEP-07-13",
+      SLACcitation   = "%%CITATION = ARXIV:0801.0045;%%"
+}
+
+@article{Degrande:2011ua,
+      author         = "Degrande, Celine and Duhr, Claude and Fuks, Benjamin and
+                        Grellscheid, David and Mattelaer, Olivier and Reiter,
+                        Thomas",
+      title          = "{UFO - The Universal FeynRules Output}",
+      journal        = "Comput. Phys. Commun.",
+      volume         = "183",
+      year           = "2012",
+      pages          = "1201-1214",
+      doi            = "10.1016/j.cpc.2012.01.022",
+      eprint         = "1108.2040",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "CP3-11-25, IPHC-PHENO-11-04, IPPP-11-39, DCPT-11-78,
+                        MPP-2011-68",
+      SLACcitation   = "%%CITATION = ARXIV:1108.2040;%%"
+}
+
+@article{Conte:2014zja,
+      author         = "Conte, Eric and Dumont, Béranger and Fuks, Benjamin and
+                        Wymant, Chris",
+      title          = "{Designing and recasting LHC analyses with MadAnalysis
+                        5}",
+      journal        = "Eur. Phys. J.",
+      volume         = "C74",
+      year           = "2014",
+      number         = "10",
+      pages          = "3103",
+      doi            = "10.1140/epjc/s10052-014-3103-0",
+      eprint         = "1405.3982",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "CERN-PH-TH-2014-088, LPSC-14-079, LAPTH-033-14,
+                        MCNET-14-11",
+      SLACcitation   = "%%CITATION = ARXIV:1405.3982;%%"
+}
+
+@article{Sirunyan:2017onm,
+      author         = "Sirunyan, Albert M and others",
+      title          = "{Search for dark matter and unparticles in events with a
+                        Z boson and missing transverse momentum in proton-proton
+                        collisions at $ \sqrt{s}=13 $ TeV}",
+      collaboration  = "CMS",
+      journal        = "JHEP",
+      volume         = "03",
+      year           = "2017",
+      pages          = "061",
+      doi            = "10.1007/JHEP09(2017)106, 10.1007/JHEP03(2017)061",
+      note           = "[Erratum: JHEP09,106(2017)]",
+      eprint         = "1701.02042",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ex",
+      reportNumber   = "CMS-EXO-16-010, CERN-EP-2016-309,
+                        FERMILAB-PUB-17-011-CMS",
+      SLACcitation   = "%%CITATION = ARXIV:1701.02042;%%"
+}
+
+@article{Abercrombie:2015wmb,
+      author         = "Abercrombie, Daniel and others",
+      editor         = "Boveia, Antonio and Doglioni, Caterina and Lowette,
+                        Steven and Malik, Sarah and Mrenna, Stephen",
+      title          = "{Dark Matter Benchmark Models for Early LHC Run-2
+                        Searches: Report of the ATLAS/CMS Dark Matter Forum     }",
+      year           = "2015",
+      eprint         = "1507.00966",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ex",
+      reportNumber   = "FERMILAB-PUB-15-282-CD",
+      SLACcitation   = "%%CITATION = ARXIV:1507.00966;%%"
+}
+
+@article{Georgi:2007ek,
+     author    = "Georgi, Howard",
+     title     = "{Unparticle Physics}",
+     journal   = "Phys. Rev. Lett.",
+     volume    = "98",
+     year      = "2007",
+     pages     = "221601",
+     eprint    = "hep-ph/0703260",
+     archivePrefix = "arXiv",
+     doi       = "10.1103/PhysRevLett.98.221601",
+     SLACcitation  = "%%CITATION = HEP-PH/0703260;%%"
+}
+
+@article{Georgi:2007si,
+     author    = "Georgi, Howard",
+     title     = "{Another Odd Thing About Unparticle Physics}",
+     journal   = "Phys. Lett.",
+     volume    = "B650",
+     year      = "2007",
+     pages     = "275-278",
+     eprint    = "0704.2457",
+     archivePrefix = "arXiv",
+     primaryClass  =  "hep-ph",
+     doi       = "10.1016/j.physletb.2007.05.037",
+     SLACcitation  = "%%CITATION = 0704.2457;%%"
+}
+
+@article{Alwall:2014hca,
+      author         = "Alwall, J. and Frederix, R. and Frixione, S. and Hirschi,
+                        V. and Maltoni, F. and Mattelaer, O. and Shao, H. -S. and
+                        Stelzer, T. and Torrielli, P. and Zaro, M.",
+      title          = "{The automated computation of tree-level and
+                        next-to-leading order differential cross sections, and
+                        their matching to parton shower simulations}",
+      journal        = "JHEP",
+      volume         = "07",
+      year           = "2014",
+      pages          = "079",
+      doi            = "10.1007/JHEP07(2014)079",
+      eprint         = "1405.0301",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "CERN-PH-TH-2014-064, CP3-14-18, LPN14-066, MCNET-14-09,
+                        ZU-TH-14-14",
+      SLACcitation   = "%%CITATION = ARXIV:1405.0301;%%"
+}
+
+@article{Sjostrand:2014zea,
+      author         = "Sjöstrand, Torbjörn and Ask, Stefan and Christiansen,
+                        Jesper R. and Corke, Richard and Desai, Nishita and Ilten,
+                        Philip and Mrenna, Stephen and Prestel, Stefan and
+                        Rasmussen, Christine O. and Skands, Peter Z.",
+      title          = "{An Introduction to PYTHIA 8.2}",
+      journal        = "Comput. Phys. Commun.",
+      volume         = "191",
+      year           = "2015",
+      pages          = "159-177",
+      doi            = "10.1016/j.cpc.2015.01.024",
+      eprint         = "1410.3012",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "LU-TP-14-36, MCNET-14-22, CERN-PH-TH-2014-190,
+                        FERMILAB-PUB-14-316-CD, DESY-14-178, SLAC-PUB-16122",
+      SLACcitation   = "%%CITATION = ARXIV:1410.3012;%%"
+}
+@article{Ball:2014uwa,
+      author         = "Ball, Richard D. and others",
+      title          = "{Parton distributions for the LHC Run II}",
+      collaboration  = "NNPDF",
+      journal        = "JHEP",
+      volume         = "04",
+      year           = "2015",
+      pages          = "040",
+      doi            = "10.1007/JHEP04(2015)040",
+      eprint         = "1410.8849",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "EDINBURGH-2014-15, IFUM-1034-FT, CERN-PH-TH-2013-253,
+                        OUTP-14-11P, CAVENDISH-HEP-14-11",
+      SLACcitation   = "%%CITATION = ARXIV:1410.8849;%%"
+}
+
+@article{Skands:2014pea,
+      author         = "Skands, Peter and Carrazza, Stefano and Rojo, Juan",
+      title          = "{Tuning PYTHIA 8.1: the Monash 2013 Tune}",
+      journal        = "Eur. Phys. J.",
+      volume         = "C74",
+      year           = "2014",
+      number         = "8",
+      pages          = "3024",
+      doi            = "10.1140/epjc/s10052-014-3024-y",
+      eprint         = "1404.5630",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "CERN-PH-TH-2014-069, MCNET-14-08, OUTP-14-05P",
+      SLACcitation   = "%%CITATION = ARXIV:1404.5630;%%"
+}
+
+@article{Alwall:2014bza,
+      author         = "Alwall, Johan and Duhr, Claude and Fuks, Benjamin and
+                        Mattelaer, Olivier and Öztürk, Deniz Gizem and Shen,
+                        Chia-Hsien",
+      title          = "{Computing decay rates for new physics theories with
+                        FeynRules  and MadGraph 5 _aMC@NLO}",
+      journal        = "Comput. Phys. Commun.",
+      volume         = "197",
+      year           = "2015",
+      pages          = "312-323",
+      doi            = "10.1016/j.cpc.2015.08.031",
+      eprint         = "1402.1178",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "CERN-PH-TH-2014-020, MCNET-14-03, IPPP-14-10, DCPT-14-20,
+                        CP3-14-11, CALT-68-2877, ZU-TH-02-14",
+      SLACcitation   = "%%CITATION = ARXIV:1402.1178;%%"
+}
+
+@article{Cacciari:2011ma,
+      author         = "Cacciari, Matteo and Salam, Gavin P. and Soyez, Gregory",
+      title          = "{FastJet User Manual}",
+      journal        = "Eur. Phys. J.",
+      volume         = "C72",
+      year           = "2012",
+      pages          = "1896",
+      doi            = "10.1140/epjc/s10052-012-1896-2",
+      eprint         = "1111.6097",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "CERN-PH-TH-2011-297",
+      SLACcitation   = "%%CITATION = ARXIV:1111.6097;%%"
+}
+@article{Cacciari:2008gp,
+      author         = "Cacciari, Matteo and Salam, Gavin P. and Soyez, Gregory",
+      title          = "{The Anti-k(t) jet clustering algorithm}",
+      journal        = "JHEP",
+      volume         = "04",
+      year           = "2008",
+      pages          = "063",
+      doi            = "10.1088/1126-6708/2008/04/063",
+      eprint         = "0802.1189",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "LPTHE-07-03",
+      SLACcitation   = "%%CITATION = ARXIV:0802.1189;%%"
+}
+
+@article{CMS:2016kkf,
+      author         = "{CMS Collaboration}",
+      title          = "{Identification of b quark jets at the CMS Experiment in
+                        the LHC Run 2}",
+      year           = "2016",
+      journal  = "CMS-PAS-BTV-15-001",
+      SLACcitation   = "%%CITATION = CMS-PAS-BTV-15-001;%%",
+      url = "http://cds.cern.ch/record/2138504"
+}
+
+@article{inspire,
+      key            = "1618045",
+      author         = "Fuks, Benjamin",
+      title          = "{MadAnalysis5 implementation of the mono-Z analysis of
+                        CMS with 2.3 fb-1 of data (CMS-EXO-16-010)}",
+      doi            = "10.7484/INSPIREHEP.DATA.RK53.S39D",
+      year           = "2017",
+      SLACcitation   = "%%CITATION = INSPIRE-1618045;%%"
+}
+
+@article{Read:2002hq,
+      author         = "Read, Alexander L.",
+      title          = "{Presentation of search results: The CL(s) technique}",
+      booktitle      = "{Advanced Statistical Techniques in Particle Physics.
+                        Proceedings, Conference, Durham, UK, March 18-22, 2002}",
+      journal        = "J. Phys.",
+      volume         = "G28",
+      year           = "2002",
+      pages          = "2693-2704",
+      doi            = "10.1088/0954-3899/28/10/313",
+      SLACcitation   = "%%CITATION = JPAGA,G28,2693;%%"
+}
+
+@article{Conte:2012fm,
+      author         = "Conte, Eric and Fuks, Benjamin and Serret, Guillaume",
+      title          = "{MadAnalysis 5, A User-Friendly Framework for Collider
+                        Phenomenology}",
+      journal        = "Comput. Phys. Commun.",
+      volume         = "184",
+      year           = "2013",
+      pages          = "222-256",
+      doi            = "10.1016/j.cpc.2012.09.009",
+      eprint         = "1206.1599",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "IPHC-PHENO-06",
+      SLACcitation   = "%%CITATION = ARXIV:1206.1599;%%"
+}
+
+@article{Arina:2016cqj,
+      author         = "Arina, Chiara and others",
+      title          = "{A comprehensive approach to dark matter studies:
+                        exploration of simplified top-philic models}",
+      journal        = "JHEP",
+      volume         = "11",
+      year           = "2016",
+      pages          = "111",
+      doi            = "10.1007/JHEP11(2016)111",
+      eprint         = "1605.09242",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      SLACcitation   = "%%CITATION = ARXIV:1605.09242;%%"
+}
+
+@article{Feng:2005gj,
+      author         = "Feng, Jonathan L. and Su, Shufang and Takayama, Fumihiro",
+      title          = "{Lower limit on dark matter production at the large
+                        hadron collider}",
+      journal        = "Phys. Rev. Lett.",
+      volume         = "96",
+      year           = "2006",
+      pages          = "151802",
+      doi            = "10.1103/PhysRevLett.96.151802",
+      eprint         = "hep-ph/0503117",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "UCI-TR-2005-11",
+      SLACcitation   = "%%CITATION = HEP-PH/0503117;%%"
+}
+
+@article{Bai:2010hh,
+      author         = "Bai, Yang and Fox, Patrick J. and Harnik, Roni",
+      title          = "{The Tevatron at the Frontier of Dark Matter Direct
+                        Detection}",
+      journal        = "JHEP",
+      volume         = "12",
+      year           = "2010",
+      pages          = "048",
+      doi            = "10.1007/JHEP12(2010)048",
+      eprint         = "1005.3797",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "FERMILAB-PUB-10-143-T",
+      SLACcitation   = "%%CITATION = ARXIV:1005.3797;%%"
+}
+
+@article{Fox:2011fx,
+      author         = "Fox, Patrick J. and Harnik, Roni and Kopp, Joachim and
+                        Tsai, Yuhsin",
+      title          = "{LEP Shines Light on Dark Matter}",
+      journal        = "Phys. Rev.",
+      volume         = "D84",
+      year           = "2011",
+      pages          = "014028",
+      doi            = "10.1103/PhysRevD.84.014028",
+      eprint         = "1103.0240",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "FERMILAB-PUB-11-039-T",
+      SLACcitation   = "%%CITATION = ARXIV:1103.0240;%%"
+}
+
+@article{Bell:2012rg,
+      author         = "Bell, Nicole F. and Dent, James B. and Galea, Ahmad J.
+                        and Jacques, Thomas D. and Krauss, Lawrence M. and Weiler,
+                        Thomas J.",
+      title          = "{Searching for Dark Matter at the LHC with a Mono-Z}",
+      journal        = "Phys. Rev.",
+      volume         = "D86",
+      year           = "2012",
+      pages          = "096011",
+      doi            = "10.1103/PhysRevD.86.096011",
+      eprint         = "1209.0231",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      SLACcitation   = "%%CITATION = ARXIV:1209.0231;%%"
+}
+@article{Petrov:2013nia,
+      author         = "Petrov, Alexey A. and Shepherd, William",
+      title          = "{Searching for dark matter at LHC with Mono-Higgs
+                        production}",
+      journal        = "Phys. Lett.",
+      volume         = "B730",
+      year           = "2014",
+      pages          = "178-183",
+      doi            = "10.1016/j.physletb.2014.01.051",
+      eprint         = "1311.1511",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "WSU-HEP-1308",
+      SLACcitation   = "%%CITATION = ARXIV:1311.1511;%%"
+}
+
+@article{Bai:2012xg,
+      author         = "Bai, Yang and Tait, Tim M. P.",
+      title          = "{Searches with Mono-Leptons}",
+      journal        = "Phys. Lett.",
+      volume         = "B723",
+      year           = "2013",
+      pages          = "384-387",
+      doi            = "10.1016/j.physletb.2013.05.057",
+      eprint         = "1208.4361",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "SLAC-PUB-15221, UCI-HEP-TR-2012-11",
+      SLACcitation   = "%%CITATION = ARXIV:1208.4361;%%"
+}
+@article{Birkedal:2004xn,
+      author         = "Birkedal, Andreas and Matchev, Konstantin and Perelstein,
+                        Maxim",
+      title          = "{Dark matter at colliders: A Model independent approach}",
+      journal        = "Phys. Rev.",
+      volume         = "D70",
+      year           = "2004",
+      pages          = "077701",
+      doi            = "10.1103/PhysRevD.70.077701",
+      eprint         = "hep-ph/0403004",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "UFIFT-HEP-04-3",
+      SLACcitation   = "%%CITATION = HEP-PH/0403004;%%"
+}
+
+
+@article{DAmbrosio:2002vsn,
+      author         = "D'Ambrosio, G. and Giudice, G. F. and Isidori, G. and
+                        Strumia, A.",
+      title          = "{Minimal flavor violation: An Effective field theory
+                        approach}",
+      journal        = "Nucl. Phys.",
+      volume         = "B645",
+      year           = "2002",
+      pages          = "155-187",
+      doi            = "10.1016/S0550-3213(02)00836-2",
+      eprint         = "hep-ph/0207036",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "CERN-TH-2002-147, IFUP-TH-2002-17",
+      SLACcitation   = "%%CITATION = HEP-PH/0207036;%%"
+}
+@article{Buras:2000dm,
+      author         = "Buras, A. J. and Gambino, P. and Gorbahn, M. and Jager,
+                        S. and Silvestrini, L.",
+      title          = "{Universal unitarity triangle and physics beyond the
+                        standard model}",
+      journal        = "Phys. Lett.",
+      volume         = "B500",
+      year           = "2001",
+      pages          = "161-167",
+      doi            = "10.1016/S0370-2693(01)00061-2",
+      eprint         = "hep-ph/0007085",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "TUM-HEP-379-00, CERN-TH-2000-190",
+      SLACcitation   = "%%CITATION = HEP-PH/0007085;%%"
+}
+
+@article{Aaboud:2016tnv,
+      author         = "Aaboud, Morad and others",
+      title          = "{Search for new phenomena in final states with an
+                        energetic jet and large missing transverse momentum in
+                        $pp$ collisions at $\sqrt{s}=13$??TeV using the ATLAS
+                        detector}",
+      collaboration  = "ATLAS",
+      journal        = "Phys. Rev.",
+      volume         = "D94",
+      year           = "2016",
+      number         = "3",
+      pages          = "032005",
+      doi            = "10.1103/PhysRevD.94.032005",
+      eprint         = "1604.07773",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ex",
+      reportNumber   = "CERN-EP-2016-075",
+      SLACcitation   = "%%CITATION = ARXIV:1604.07773;%%"
+}
+
+@article{Aaboud:2016zdn,
+      author         = "Aaboud, Morad and others",
+      title          = "{Search for squarks and gluinos in final states with jets
+                        and missing transverse momentum at $\sqrt{s} =$ 13 TeV
+                        with the ATLAS detector}",
+      collaboration  = "ATLAS",
+      journal        = "Eur. Phys. J.",
+      volume         = "C76",
+      year           = "2016",
+      number         = "7",
+      pages          = "392",
+      doi            = "10.1140/epjc/s10052-016-4184-8",
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+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ex",
+      reportNumber   = "CERN-EP-2016-080",
+      SLACcitation   = "%%CITATION = ARXIV:1605.03814;%%"
+}
+
+@article{Buchmueller:2015eea,
+      author         = "Buchmueller, Oliver and Malik, Sarah A. and McCabe,
+                        Christopher and Penning, Bjoern",
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+
+@article{Buckley:2014ana,
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+
+@article{Mattelaer:2015haa,
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+
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+
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+
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+
+@article{Abe:1991ui,
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+
+@inproceedings{Blazey:2000qt,
+      author         = "Blazey, Gerald C. and others",
+      title          = "{Run II jet physics}",
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+
+@article{Salam:2007xv,
+      author         = "Salam, Gavin P. and Soyez, Gregory",
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+      journal        = "JHEP",
+      volume         = "05",
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+      doi            = "10.1088/1126-6708/2007/05/086",
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+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      SLACcitation   = "%%CITATION = ARXIV:0704.0292;%%"
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+
+@article{Patrignani:2016xqp,
+      author         = "Patrignani, C. and others",
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+
+
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+
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+      author         = "Boucheneb, Idir and Cacciapaglia, Giacomo and Deandrea,
+                        Aldo and Fuks, Benjamin",
+      title          = "{Revisiting monotop production at the LHC}",
+      journal        = "JHEP",
+      volume         = "01",
+      year           = "2015",
+      pages          = "017",
+      doi            = "10.1007/JHEP01(2015)017",
+      eprint         = "1407.7529",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "CERN-PH-TH-2014-140, LYCEN-2014-11",
+      SLACcitation   = "%%CITATION = ARXIV:1407.7529;%%"
+}
+
+@article{Agram:2013wda,
+      author         = "Agram, Jean-Laurent and Andrea, Jeremy and Buttignol,
+                        Michael and Conte, Eric and Fuks, Benjamin",
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+      eprint         = "1311.6478",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "CERN-PH-TH-2013-277",
+      SLACcitation   = "%%CITATION = ARXIV:1311.6478;%%"
+}
+
+@article{Andrea:2011ws,
+      author         = "Andrea, J. and Fuks, B. and Maltoni, F.",
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+      reportNumber   = "CP3-11-21, IPHC-PHENO-11-03",
+      SLACcitation   = "%%CITATION = ARXIV:1106.6199;%%"
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+
+@article{Davoudiasl:2011fj,
+      author         = "Davoudiasl, Hooman and Morrissey, David E. and Sigurdson,
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+
+@article{Kamenik:2011nb,
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+
+@article{Alvarez:2013jqa,
+      author         = "Alvarez, Ezequiel and Coluccio Leskow, Estefania and
+                        Drobnak, Jure and Kamenik, Jernej F.",
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+
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+
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+      SLACcitation   = "%%CITATION = ARXIV:1410.1149;%%"
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+      author         = "Chatrchyan, Serguei and others",
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+      year           = "2013",
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+
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+      author         = "Papucci, Michele and Sakurai, Kazuki and Weiler, Andreas
+                        and Zeune, Lisa",
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+      reportNumber   = "CERN-PH-TH-2014-019, DESY-14-010, KCL-PH-TH-2014-04,
+                        MCTP-14-03",
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+
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+                        Tattersall, Jamie and Kim, Jong Soo",
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+      reportNumber   = "ADP-13-29-T849, IFT-UAM-CSIC-13-133,
+                        ADP-13-29-T849-IFT-UAM-CSIC-13-133",
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+      eprint         = "1203.4813",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "SLAC-PUB-14897",
+      SLACcitation   = "%%CITATION = ARXIV:1203.4813;%%"
+}
+
+@article{Randall:2008rw,
+      author         = "Randall, Lisa and Tucker-Smith, David",
+      title          = "{Dijet Searches for Supersymmetry at the LHC}",
+      journal        = "Phys. Rev. Lett.",
+      volume         = "101",
+      year           = "2008",
+      pages          = "221803",
+      doi            = "10.1103/PhysRevLett.101.221803",
+      eprint         = "0806.1049",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      SLACcitation   = "%%CITATION = ARXIV:0806.1049;%%"
+}
+
+@article{Brun:1997pa,
+      author         = "Brun, R. and Rademakers, F.",
+      title          = "{ROOT: An object oriented data analysis framework}",
+      booktitle      = "{New computing techniques in physics research V.
+                        Proceedings, 5th International Workshop, AIHENP '96,
+                        Lausanne, Switzerland, September 2-6, 1996}",
+      journal        = "Nucl. Instrum. Meth.",
+      volume         = "A389",
+      year           = "1997",
+      pages          = "81-86",
+      doi            = "10.1016/S0168-9002(97)00048-X",
+      SLACcitation   = "%%CITATION = NUIMA,A389,81;%%"
+}
+
+@article{Ambrogi:2017neo,
+      author         = "Ambrogi, Federico and Kraml, Sabine and Kulkarni, Suchita
+                        and Laa, Ursula and Lessa, Andre and Magerl, Veronika and
+                        Sonneveld, Jory and Traub, Michael and Waltenberger,
+                        Wolfgang",
+      title          = "{SModelS v1.1 user manual: Improving simplified model
+                        constraints with efficiency maps}",
+      journal        = "Comput. Phys. Commun.",
+      volume         = "227",
+      year           = "2018",
+      pages          = "72-98",
+      doi            = "10.1016/j.cpc.2018.02.007",
+      eprint         = "1701.06586",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "LPSC17001, HEPHY-PUB-981-17",
+      SLACcitation   = "%%CITATION = ARXIV:1701.06586;%%"
+}
+
+@inproceedings{Fuks:2018yku,
+      author         = "Fuks, Benjamin and others",
+      title          = "{Proceedings of the first MadAnalysis 5 workshop on LHC
+                        recasting in Korea}",
+      pages = "35-39",
+      year           = "2018",
+      eprint         = "1806.02537",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      SLACcitation   = "%%CITATION = ARXIV:1806.02537;%%"
+}

=== added file 'doc/expert_mode/main_expert.tex'
--- doc/expert_mode/main_expert.tex	1970-01-01 00:00:00 +0000
+++ doc/expert_mode/main_expert.tex	2019-02-13 11:05:44 +0000
@@ -0,0 +1,939 @@
+\documentclass[a4paper]{article}
+
+%% Language and font encodings
+\usepackage[english]{babel}
+\usepackage[utf8x]{inputenc}
+\usepackage[T1]{fontenc}
+\usepackage{url,slashed,multirow,cite,verbdef}
+\usepackage{hyperref}
+%% Sets page size and margins
+\usepackage[a4paper,top=3cm,bottom=2cm,left=3cm,right=3cm,marginparwidth=1.75cm]{geometry}
+
+%% Useful packages
+\usepackage{amsmath}
+\usepackage{graphicx}
+%\usepackage[colorlinks=true, allcolors=blue]{hyperref}
+\usepackage{xcolor}
+\definecolor{ao}{rgb}{0.0, 0.5, 0.0}
+% faire des boites
+\usepackage{framed,color}
+\definecolor{shadecolor}{rgb}{0.55, 0.71, 0.0}
+
+% Tools
+\newcommand{\MG}{\textsc{MadGraph}~5\_aMC@NLO}
+\newcommand{\PY}{\textsc{Pythia}~8}
+\newcommand{\MA}{\textsc{MadAnalysis}~5}
+\newcommand{\MW}{\textsc{MadWidth}}
+\newcommand{\MS}{\textsc{MadSpin}}
+\newcommand{\MAnorm}{{MadAnalysis}~5}
+\newcommand{\FJ}{\textsc{FastJet}}
+\newcommand{\FJnorm}{{FastJet}}
+\newcommand{\DEL}{\textsc{Delphes}}
+\newcommand{\DELnorm}{{Delphes}}
+\newcommand{\ROOT}{\textsc{Root}}
+\newcommand{\lhe}{\textsc{Lhe}}
+\newcommand{\lhco}{\textsc{Lhco}}
+\newcommand{\hepmc}{\textsc{HepMC}}
+\newcommand{\stdhep}{\textsc{StdHep}}
+\newcommand{\INSP}{\textsc{Inspire}}
+\newcommand{\python}{\textsc{Python}}
+\newcommand{\spla}{\textsc{SampleAnalyzer}}
+%latin
+\newcommand{\eg}{\textit{e.g.}}
+\newcommand{\ie}{\textit{i.e.}}
+\newcommand{\etc}{\textit{etc.}}
+
+% environments
+\def\be{\begin{equation}}
+\def\ee{\end{equation}}
+\def\bsp#1\esp{\begin{split}#1\end{split}}
+
+
+
+
+
+
+\begin{document}
+\begin{center} 
+{\color{ao} \huge \textbf{\textsc{MadAnalysis} 5 v1.6}} \\ \vspace{0.25cm}
+{\color{ao} \huge \textbf{Expert-Mode reference card}} \\ \vspace{0.25cm}
+\vspace{0.1cm} \textsl{\today}\\
+\vspace{0.1cm} \textsl{website: \url{http://madanalysis.irmp.ucl.ac.be/}}\\
+\vspace{0.1cm} \textsl{references: \href{https://arxiv.org/abs/1206.1599}{arXiv:1206.1599[hep-ph]}, \href{https://arxiv.org/abs/1405.3982}{arXiv:1405.3982[hep-ph]}, \href{https://arxiv.org/abs/1407.3278}{arXiv:1407.3278[hep-ph]}}
+\end{center}
+
+\hspace{0.5cm}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{shaded}
+\section{\Large Creating an analysis template in the expert mode}
+\end{shaded}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+For sophisticated analysis going beyond the capabilities of the normal mode of
+running of \MA, the user has to rely on the so-called expert mode, where
+analyses are implemented directly in the C++ framework of the platform. A blank
+template analysis can be generated by typing, in a shell,
+{\color{ao}\begin{verbatim}
+  bin/ma5 --expert      bin/ma5 -e      bin/ma5 -E
+\end{verbatim}}
+\MA\ then asks information about the name of the working directory to create, as
+well as information on the name of the analysis class that will have to be
+designed. Those two pieces of information can be provided as arguments when
+calling \MA\ from the shell,
+{\color{ao}\begin{verbatim}
+  bin/ma5 -E <dirname> <analysis>
+\end{verbatim}}
+where \verb+<dirname>+ consists in the working directory name, and
+\verb+analysis+ the name of the analysis class.
+
+For a proper use of the program, the user has to setup some environment
+variables accordingly. This can be done by entering the \verb+Build+ subfolder
+of the working directory and typing in a shell,
+{\color{ao}\begin{verbatim}
+  source setup.sh         source setup.csh
+\end{verbatim}}
+depending on the shell nature. The \verb+Build+ folder also contains a makefile
+allowing for standard \verb+make+ commands,
+{\color{ao}\begin{verbatim}
+  make clean       make proper       make
+\end{verbatim}}
+The first command allows one to remove all intermediate object and backup
+files whilst the second command yields the removal of all files that have been
+created by the make action. Finally, the last command allows to build the code.
+
+The code can then be run from the \verb+Build+
+directory by typing,
+{\color{ao}\begin{verbatim}
+  MadAnalysis5Job [options] [inputfile]
+\end{verbatim}}
+The file {\color{ao}\verb?[inputfile]?} consists in a text file with a list of paths
+pointing to the event samples to analyze, with one filename per line. Several
+options are available, as summarized in the table below.
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{l p{8.4cm}}
+\hline
+Option & Description\\
+\hline
+\color{ao}\verb?--check_event?      & Sanity check of the input file.\\
+\color{ao}\verb?--no_event_weight?  & Ignores the event weights.\\
+\color{ao}\verb?--ma5_version=XXXX? & Allows to specify which version of the \MA\ console
+  to use.\\
+\hline
+\end{tabular}
+\end{center}
+\newpage
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{shaded}
+\section{\Large Portable datatypes}
+\end{shaded}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\noindent The \spla\ data format includes several portable data types, that we
+show in the table below together with the corresponding bit width.
+\renewcommand{\arraystretch}{1.1}%
+\begin{center}\begin{tabular}{l l p{8.0cm}}
+\hline
+Name & Bit width & Description\\
+\hline
+\color{ao} \verb?MAbool?    & 1  & Boolean.\\
+\hline
+\color{ao}\verb?MAint8?    & 8  & Byte integer.\\
+\color{ao}\verb?MAint16?   & 16 & Short integer.\\
+\color{ao}\verb?MAint32?   & 32 & Integer.\\
+\color{ao}\verb?MAint64?   & 64 & Long integer.\\
+\hline
+\color{ao}\verb?MAuint8?   & 8  & Unsigned byte integer.\\
+\color{ao}\verb?MAuint16?  & 16 & Unsigned short integer.\\
+\color{ao}\verb?MAuint32?  & 32 & Unsigned integer.\\
+\color{ao}\verb?MAuint64?  & 64 & Unsigned long integer.\\
+\hline
+\color{ao} \verb?MAfloat32? & 32 & Single-precision floating-point number.\\
+{\color{ao} \verb?MAfloat64?} or {\color{ao} \verb?MAdouble64?}  & 64 & Double-precision
+   floating-point number.\\
+\hline
+\end{tabular}
+\end{center}
+Moreover, four-vectors can be implemented as instances of the
+{\color{ao}\verb+MALorentzVector+} class that contains the same methods as the \ROOT\
+{\color{ao}\verb+TLorentzVector+} class~\cite{Brun:1997pa}.
+
+\vspace{2cm}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{shaded}
+\section{\Large Data format for an event sample}
+\end{shaded}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\noindent The analysis class contains an {\color{ao}\verb+Initialize+}, an {\color{ao}\verb+Execute+} and a
+{\color{ao}\verb+Finalize+} method that are respectively executed before starting to read an
+event sample, on each event and after having read all events. The {\color{ao}\verb+Execute+}
+method requires two arguments, an instance of the {\color{ao}\verb+SampleFormat+} class and
+an event passed as an {\color{ao}\verb+EventFormat+} instance (see the next subsection).
+Monte Carlo event samples are generally accompanied with global information on
+the sample, such as the identifier of the parton density set that has been used
+or the total cross section associated with the described process. Those pieces
+of information are stored as attributes of the above-mentioned
+{\color{ao}\verb+SampleFormat+} object, and can be retrieved through the methods given in
+the table below (in particular through attributes of the {\color{ao}\verb+mc()+} and
+{\color{ao}\verb+rec()+} objects) on run time.
+\verbdef{\expa}{const std::vector<std::string>& header() const}
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{l p{6.2cm}}
+\hline
+Method name and type & Description\\
+\hline
+\color{ao}\verb+MCSampleFormat* mc()+            & Monte Carlo information (see below).\\
+\color{ao}\verb+RecSampleFormat* rec()+          & Reconstruction information (see below).
+    \\
+\color{ao}\verb+const std::string name()+        & Sample name.\\
+\color{ao}\verb+const MAuint64& nevents() const+ & Number of events in the sample.\\
+\multicolumn{2}{l}{\color{ao}\expa}\\    &  Sample header.\\
+\hline
+\end{tabular}
+\end{center}
+The Monte Carlo information is available through the {\color{ao}\verb+mc()+} object, a
+pointer to an instance of the {\color{ao}\verb+MCSampleFormat+} class whose attributes are
+given in the table below.
+\verbdef{\expb}{const std::pair<MAint32,MAint32>& beamPDGID() const}
+\verbdef{\expc}{const std::pair<MAuint32,MAuint32>& beamPDFauthor() const}
+\verbdef{\expd}{const MAint32& weightMode() const}
+\verbdef{\expe}{const MAfloat64& xsection() const}
+\verbdef{\expf}{const MAfloat64& xsection_error() const}
+\verbdef{\expg}{const MAfloat64& sumweight_positive() const}
+\verbdef{\exph}{const MAfloat64& sumweight_negative() const}
+\verbdef{\expi}{const std::vector<ProcessFormat>& processes()}
+\verbdef{\expj}{const WeightDefinition& weight_definition()}
+\verbdef{\expk}{const std::pair<MAfloat64,MAfloat64>& beamE() const}
+\verbdef{\expl}{const std::pair<MAuint32,MAuint32>& beamPDFID() const}
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{l p{8.2cm}}
+\hline
+Method name and type & Description\\
+\hline
+\multicolumn{2}{l}{\color{ao}\expb}\\    &
+  PDG codes of the intial partons.\\
+\multicolumn{2}{l}{\color{ao}\expk}\\    &
+  Beam energy.\\
+\multicolumn{2}{l}{\color{ao}\expc}\\    &
+  Group associated with the used parton density set.\\
+\multicolumn{2}{l}{\color{ao}\expl}\\    &
+  Identifier of the used parton density set.\\
+\multicolumn{2}{l}{\color{ao}\expd}\\    &
+  Information on the event weights.\\
+\multicolumn{2}{l}{\color{ao}\expe}\\    &
+  Cross section associated with the sample.\\
+\multicolumn{2}{l}{\color{ao}\expf}\\    &
+  Uncertainty on the sample cross section.\\
+\multicolumn{2}{l}{\color{ao}\expg}\\    &
+  Sum of the weights of all positively-weighted events.\\
+\multicolumn{2}{l}{\color{ao}\exph}\\    &
+  Sum of the weights of all negatively-weighted events.\\
+\multicolumn{2}{l}{\color{ao}\expi}\\    &
+  List of all described processes (see below).\\
+\multicolumn{2}{l}{\color{ao}\expj}\\    &
+  Definitions of the different weights for events featuring multiple weights.\\
+\hline
+\end{tabular}
+\end{center}
+Those attributes rely on two classes, the {\color{ao}\verb+ProcessFormat+} one allowing
+for the description of a physical process and the {\color{ao}\verb+WeightDefinition+} one
+connected to the potential assignment of multiple weights to a given
+event\cite{Andersen:2014efa}. Whilst the
+following methods have been implemented for the former class,
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{l p{4.8cm}}
+\hline
+Method name and type & Description\\
+\hline
+\color{ao}\verb+const MAfloat64& xsection() const+ & Associated cross section.\\
+\color{ao}\verb+const MAfloat64& xsectionError() const+ & Error on the cross
+  section.\\
+\color{ao}\verb+const MAfloat64& weightMax() const+ & Maximum weight for an event.\\
+\color{ao}\verb+const MAuint32& processId() const+ & Process identification number.\\
+\hline
+\end{tabular}
+\end{center}
+the latter class only allows for listing the names of the set of weights
+associated with each event,
+{\color{ao}\begin{verbatim}
+ void Print() const
+\end{verbatim}}
+The {\color{ao}\verb+rec()+} method of the {\color{ao}\verb+MCSampleFormat+} class consists in an
+instance of the {\color{ao}\verb?RecSampleFormat?} class that does not come with any
+built-in method. This is left for future developments.
+
+\newpage
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{shaded}
+\section{\Large Data format for an event}
+\end{shaded}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+An event object possesses two attributes {\color{ao}\verb+mc()+} and {\color{ao}\verb+rec()+} that are
+this time instances of the {\color{ao}\verb+MCEventFormat+} and {\color{ao}\verb+RecEventFormat+}
+classes respectively. These two classes are respectively connected to Monte
+Carlo events (as simulated by a Monte Carlo event generator) and reconstructed
+events as obtained after gathering all final-state objects into reconstructed
+physical objects to be used for specific analyses. The {\color{ao}\verb+MCEventFormat+}
+class comes with the methods summarized in the following table.
+\verbdef{\expzza}{const MCParticleFormat& MET() const}
+\verbdef{\expzzb}{const MCParticleFormat& MHT() const}
+\verbdef{\expzzc}{MCParticleFormat& MET() const}
+\verbdef{\expzzd}{MCParticleFormat& MHT() const}
+\verbdef{\expzze}{const std::vector<MCParticleFormat>& particles() const}
+\verbdef{\expzzf}{const WeightCollection& multiweights() const}
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{l p{5.5cm}}
+\hline
+\multicolumn{2}{l}{\color{ao}\expzza}\\
+\multicolumn{2}{l}{\color{ao}\expzzc}\\    & Missing transverse energy\\
+\multicolumn{2}{l}{\color{ao}\expzzb}\\
+\multicolumn{2}{l}{\color{ao}\expzzd}\\    & Missing transverse hadronic energy. \\
+\color{ao}\verb+const MAfloat64& TET() const+ &
+   \multirow{2}{*}{Total (visible) transverse energy.}\\
+\color{ao}\verb+MAfloat64& TET() const+ &\\
+\color{ao}\verb+const MAfloat64& THT() const+ &
+  \multirow{2}{*}{Total hadronic transverse energy.}\\
+\color{ao}\verb+const MAfloat64& THT() const+ &\\
+\color{ao}\verb+const MAfloat64& Meff() const+ & \multirow{2}{*}{Effective mass
+  $\bigg(\sum_{\rm jets} p_T + \slashed{E}_T\bigg)$.}\\
+\color{ao}\verb+MAfloat64& Meff() const+ &\\
+\color{ao}\verb+const MAfloat64& alphaQED()  const+ & Used value for the electromagnetic
+  coupling.\\
+\color{ao}\verb+const MAfloat64& alphaQCD()  const+ & Used value for the strong
+  coupling.\\
+ \multicolumn{2}{l}{\color{ao}\expzzf}\\  & Container for all event weights.\\
+ \multicolumn{2}{l}{\color{ao}\expzze}\\  & All particles of the event.\\
+\color{ao}\verb+const MAuint32& processId() const+ & Identifier of the physical process
+  related to the event.\\
+\color{ao}\verb+const MAfloat64& scale() const+ & Factorization scale choice. \\
+\color{ao}\verb+const MAfloat64& weight() const+ & Event weight.\\
+\hline
+\end{tabular}
+\end{center}
+Weights (as returned by the {\color{ao}\verb+multiweights()+} method) are stored as an
+instance of the {\color{ao}\verb+WeightCollection+} class, which comes with the methods
+given in the table below.
+\verbdef{\expaaa}{const MAfloat64& Get(MAuint32 id) const}
+\verbdef{\expaab}{const std::map<MAuint32,MAfloat64>& GetWeights() const}
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{p{2.7cm} p{9.0cm}}
+\hline
+\multicolumn{2}{l}{\color{ao}\expaaa}\\    & Weight value corresponding to
+  the weight identifier {\color{ao}\verb+id+}.\\
+\multicolumn{2}{l}{\color{ao}\expaab}\\    &  The full list of weights as identifier-value
+  pairs.\\
+\hline
+\end{tabular}
+\end{center}
+As indicated above, the event particle content can be obtained via the method
+{\color{ao}\verb+particles()+} of the {\color{ao}\verb+MCEventFormat+} class. This returns a vector of
+{\color{ao}\verb+MCParticleFormat+} objects, each element corresponding to an
+initial-state, a final-state or an intermediate-state particle. This class
+inherits all methods available from the {\color{ao}\verb+ParticleBaseFormat+} class, that
+are collected in the table below.
+\verbdef{\expaac}{const MAfloat32 mt_met(const MALorentzVector& MET) const}
+\verbdef{\expaad}{const MALorentzVector& momentum() const}
+\verbdef{\expaae}{MALorentzVector& momentum()}
+\verbdef{\expaaf}{const MAfloat32 dphi_0_pi(const ParticleBaseFormat* p) const}
+\verbdef{\expaag}{const MAfloat32 dphi_0_pi(const ParticleBaseFormat& p) const}
+\verbdef{\expaah}{const MAfloat32 dphi_0_2pi(const ParticleBaseFormat* p) const}
+\verbdef{\expaai}{const MAfloat32 dphi_0_2pi(const ParticleBaseFormat& p) const}
+\verbdef{\expaaj}{const MAfloat32 dr(const ParticleBaseFormat& p) const}
+\verbdef{\expaak}{const MAfloat32 dr(const ParticleBaseFormat* p) const}
+\verbdef{\expaal}{const MAfloat32 angle(const ParticleBaseFormat& p) const}
+\verbdef{\expaam}{const MAfloat32 angle(const ParticleBaseFormat* p) const}
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{l p{6.3cm}}
+\hline
+\multicolumn{2}{l}{\color{ao}\expaae}\\
+\multicolumn{2}{l}{\color{ao}\expaad}\\ & {Four-momentum.}\\
+\color{ao}\verb+const MAfloat32 beta() const+ & Velocity (in $c$ units).\\
+\color{ao}\verb+const MAfloat32 e() const+    & Energy.\\
+\color{ao}\verb+const MAfloat32 et() const+   & Transverse energy.\\
+\color{ao}\verb+const MAfloat32 eta() const+  & Pseudorapidity.\\
+\color{ao}\verb+const MAfloat32 abseta() const+ & Pseudorapidity in absolute
+  value.\\
+\color{ao}\verb+const MAfloat32 gamma() const+ & Lorentz factor.\\
+\color{ao}\verb+const MAfloat32 m() const+   & Invariant mass.\\
+\color{ao}\verb+const MAfloat32 mt() const+  & Transverse mass.\\
+\color{ao}\verb+const MAfloat32 phi() const+ & Azimuthal angle.\\
+\color{ao}\verb+const MAfloat32 p() const+   & Magnitude of the momentum.\\
+\color{ao}\verb+const MAfloat32 pt() const+  & Transverse momentum.\\
+\color{ao}\verb+const MAfloat32 px() const+  & $x$-component of the momentum.\\
+\color{ao}\verb+const MAfloat32 py() const+  & $y$-component of the momentum.\\
+\color{ao}\verb+const MAfloat32 pz() const+  & $z$-component of the momentum.\\
+\color{ao}\verb+const MAfloat32 r() const+   & Position in the $\eta-\phi$ plane.\\
+\color{ao}\verb+const MAfloat32 theta() const+  & Polar angle.\\
+\color{ao}\verb+const MAfloat32 y() const+ & Rapidity.\\
+\hline
+\end{tabular}
+\end{center}
+The {\color{ao}\verb+ParticleBaseFormat+} class also includes a set of methods that
+involve the particle itself as well as another object. These are given in the
+following table.
+\renewcommand{\arraystretch}{1.1}%
+\begin{center}\begin{tabular}{p{2.7cm} p{9.0cm}}
+\hline
+\multicolumn{2}{l}{\color{ao}\expaal}\\
+\multicolumn{2}{l}{\color{ao}\expaam}\\ & Angular separation between the
+  particle momentum and the momentum of another particle \verb+p+.\\
+\multicolumn{2}{l}{\color{ao}\expaac}\\      & Transverse mass of the system made of
+    the particle and the missing momentum.\\
+\multicolumn{2}{l}{\color{ao}\expaaf}\\
+\multicolumn{2}{l}{\color{ao}\expaag}\\ & Azimuthal separation between the particle
+momentum and the momentum of another particle \verb+p+, normalized in $[0,\pi]$.
+\\
+\multicolumn{2}{l}{\color{ao}\expaah}\\
+\multicolumn{2}{l}{\color{ao}\expaai}\\ & Azimuthal separation between the particle
+  momentum and the momentum of another particle \verb+p+, normalized in $[0,
+  2\pi]$.\\
+\multicolumn{2}{l}{\color{ao}\expaaj}\\
+\multicolumn{2}{l}{\color{ao}\expaak}\\ & Angular distance, in the $\eta-\phi$ plane,
+  between the particle momentum and the momentum of another particle \verb+p+.\\
+\hline
+\end{tabular}
+\end{center}
+Moreover, the {\color{ao}\verb+MCParticleFormat+} class includes the extra methods
+listed below.
+\verbdef{\expbba}{const std::vector<MCParticleFormat*>& daughters() const}
+\verbdef{\expbbb}{const std::vector<MCParticleFormat*>& mothers() const}
+\verbdef{\expbbc}{const MALorentzVector& decay_vertex() const}
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{l p{6.1cm}}
+\hline
+\color{ao}\verb+const MAfloat64& ctau() const+ & Particle decay length.\\
+\color{ao}\verb+const MAbool& isPU()  const+ & Tests whether the particle belongs to the
+  pile-up event.\\
+\color{ao}\verb+const MAint32& pdgid()  const+ & PDG identifier of the particle.\\
+\color{ao}\verb+const MAfloat32& spin() const+ & Cosine of the angle between the particle
+  momentum and its spin vector, computed in the laboratory frame.\\
+\color{ao}\verb+const MAint16& statuscode() const+& Code indicating the particle initial-,
+intermediate- or final-state nature.\\
+\multicolumn{2}{l}{\color{ao}\expbba}\\ & Particles in which the current particle
+  decays into.\\
+\multicolumn{2}{l}{\color{ao}\expbbb}\\ & Particles from which the current
+  particle originates from.\\
+\multicolumn{2}{l}{\color{ao}\expbbc}\\ & Spacetime position of the particle decay.\\
+\hline
+\end{tabular}
+\end{center}
+
+A slightly different format is available for reconstructed events. An event is
+here provided as an instance of the {\color{ao}\verb+RecEventFormat+} class, which comes
+with the following methods.
+\verbdef{\expcca}{const std::vector<RecPhotonFormat>& photons() const}
+\verbdef{\expccb}{const std::vector<RecLeptonFormat>& electrons() const}
+\verbdef{\expccc}{const std::vector<RecLeptonFormat>& muons() const}
+\verbdef{\expccd}{const std::vector<RecTauFormat>& taus() const}
+\verbdef{\expcce}{const std::vector<RecJetFormat>& fatjets() const}
+\verbdef{\expccf}{const std::vector<RecJetFormat>& jets() const}
+\verbdef{\expccg}{const std::vector<RecJetFormat>& genjets() const}
+\verbdef{\expcch}{const std::vector<RecTrackFormat>& tracks() const}
+\verbdef{\expcci}{const std::vector<RecTowerFormat>& towers() const}
+\verbdef{\expccj}{const std::vector<RecTrackFormat>& EFlowTracks() const}
+\verbdef{\expcck}{const std::vector<RecParticleFormat>& EFlowPhotons() const}
+\verbdef{\expccl}{const std::vector<RecParticleFormat>& EFlowNeutralHadrons() const}
+\verbdef{\expccm}{const RecParticleFormat& MET() const}
+\verbdef{\expccn}{const RecParticleFormat& MHT() const}
+\verbdef{\expcco}{const MAfloat64& TET() const}
+\verbdef{\expccp}{const MAfloat64& THT() const}
+\verbdef{\expccq}{const MAfloat64& Meff() const}
+\verbdef{\expccr}{const std::vector<const MCParticleFormat*>& MCHadronicTaus() const}
+\verbdef{\expccs}{const std::vector<const MCParticleFormat*>& MCElectronicTaus() const}
+\verbdef{\expcct}{const std::vector<const MCParticleFormat*>& MCMuonicTaus() const}
+\verbdef{\expccu}{const std::vector<const MCParticleFormat*>& MCBquarks() const}
+\verbdef{\expccv}{const std::vector<const MCParticleFormat*>& MCCquarks() const}
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{p{2.7cm} p{9.0cm}}
+\hline
+\multicolumn{2}{l}{\color{ao}\expcca}\\  & Reconstructed photons.\\
+\multicolumn{2}{l}{\color{ao}\expccb}\\  & Reconstructed electrons.\\
+\multicolumn{2}{l}{\color{ao}\expccc}\\  & Reconstructed muons.\\
+\multicolumn{2}{l}{\color{ao}\expccd}\\  & Reconstructed hadronic taus.\\
+\multicolumn{2}{l}{\color{ao}\expcce}\\  & Reconstructed fat jets.\\
+\multicolumn{2}{l}{\color{ao}\expccf}\\  & Reconstructed jets.\\
+\multicolumn{2}{l}{\color{ao}\expccg}\\  & Parton-level jets.\\
+\multicolumn{2}{l}{\color{ao}\expcch}\\  & Tracks left in a detector.\\
+\multicolumn{2}{l}{\color{ao}\expcci}\\  & Calorimetric deposits left in a detector.\\
+\multicolumn{2}{l}{\color{ao}\expccj}\\  & Tracks left in a detector, reconstructed from
+  the particle flow information.\\
+\multicolumn{2}{l}{\color{ao}\expcck}\\  & Photons, reconstructed from the particle flow
+  information.\\
+\multicolumn{2}{l}{\color{ao}\expccl}\\  & Neutral hadrons, reconstructed from the
+  particle flow information.\\
+\multicolumn{2}{l}{\color{ao}\expccm}\\  & Missing transverse energy.\\
+\multicolumn{2}{l}{\color{ao}\expccn}\\  & Missing hadronic energy.\\
+\multicolumn{2}{l}{\color{ao}\expcco}\\  & Visible transverse energy.\\
+\hline
+\end{tabular}
+\end{center}
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{p{2.7cm} p{9.0cm}}
+\hline
+\multicolumn{2}{l}{\color{ao}\expccp}\\  & Hadronic transverse energy.\\
+\multicolumn{2}{l}{\color{ao}\expccq}\\  & Effective mass $\Big(\sum_{\rm jets} p_T +
+   \slashed{E}_T\Big)$.\\
+\multicolumn{2}{l}{\color{ao}\expccr}\\  & Parton-level taus that decayed hadronically.\\
+\multicolumn{2}{l}{\color{ao}\expccs}\\  & Parton-level taus that decayed into an electron
+  and missing energy. \\
+\multicolumn{2}{l}{\color{ao}\expcct}\\  & Parton-level taus that decayed into a muon and
+  missing energy. \\
+\multicolumn{2}{l}{\color{ao}\expccu}\\  & Parton-level $b$-quarks of the event.\\
+\multicolumn{2}{l}{\color{ao}\expccv}\\  & Parton-level $c$-quarks of the event.\\
+\hline
+\end{tabular}
+\end{center}
+The above methods introduce the data format implemented for all reconstructed
+objects. It relies on various types ({\color{ao}\verb+RecLeptonFormat+},
+{\color{ao}\verb+RecJetFormat+},
+{\color{ao}\verb+RecPhotonFormat+}, {\color{ao}\verb+RecTauFormat+}, {\color{ao}\verb+RecTrackFormat+} and
+{\color{ao}\verb+RecTowerFormat+)} that inherit from the {\color{ao}\verb+RecParticleFormat+} class
+based on the {\color{ao}\verb+BaseParticleFormat+} class (see above).
+All these new classes include the following set of methods.
+\verbdef{\expdda}{const MAfloat32& HEoverEE() const}
+\verbdef{\expddb}{const MAfloat32& EEoverHE() const}
+\verbdef{\expddc}{const MAuint16 ntracks() const}
+\verbdef{\expddd}{const int charge() const}
+\verbdef{\expdde}{MAbool isElectron() const}
+\verbdef{\expddf}{MAbool isMuon() const}
+\verbdef{\expddg}{MAfloat32 d0() const}
+\verbdef{\expddh}{MAfloat32 d0error() const}
+\verbdef{\expddi}{const MAbool& btag() const}
+\verbdef{\expddj}{const MAbool& ctag() const}
+\verbdef{\expddk}{const MAbool& true_btag() const}
+\verbdef{\expddl}{const MAbool& true_ctag() const}
+\verbdef{\expddm}{const std::vector<MAint32>& constituents() const}
+\verbdef{\expddn}{const MAint32 DecayMode() const}
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{p{2.7cm} p{9.0cm}}
+\hline
+\multicolumn{2}{l}{\color{ao}\expddb}\\  & Ratio of the electromagnetic to
+  hadronic calorimetric energy associated with the object.\\
+\multicolumn{2}{l}{\color{ao}\expdda}\\  & Ratio of the hadronic to
+  electromagnetic calorimetric energy associated with the object.\\
+\multicolumn{2}{l}{\color{ao}\expddn}\\  & Identifier of the decay mode of a
+  \verb+RecTauFormat+ object. The available choices are 1 ($\tau\to e \nu \nu$),
+  2 ($\tau \to \mu \nu \nu$),  3 ($\tau \to K \nu$), 4 ($\tau \to K^* \nu$),
+  5 ($\tau \to \rho (\to \pi \pi^0) \nu$), 6 ($\tau \to a_1 (\to \pi\pi^0\pi^0)
+  \nu$), 7 ($\tau \to a_1 (\to \pi\pi\pi) \nu$), 8 ($\tau \to \pi \nu$), 
+  9 ($\tau \to \pi\pi\pi \pi^0 \nu$) and 0 (any other decay mode).\\
+\multicolumn{2}{l}{\color{ao}\expddi}\\  & Indicates whether a {\color{ao}\verb+RecJetFormat+} object
+  has been $b$-tagged.\\
+\hline
+\end{tabular}
+\end{center}
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{p{2.7cm} p{9.0cm}}
+\hline
+\multicolumn{2}{l}{\color{ao}\expddj}\\  & Indicates whether a {\color{ao}\verb+RecJetFormat+} object
+  has been $c$-tagged.\\
+\multicolumn{2}{l}{\color{ao}\expddm}\\  & Returns the constituents of a
+  {\color{ao}\verb+RecJetFormat+} object.\\
+\multicolumn{2}{l}{\color{ao}\expddd}\\  & The electric charge of the object. This method
+  is available for the {\color{ao}\verb+RecLeptonFormat+}, {\color{ao}\verb+RecTauFormat+} and
+  {\color{ao}\verb+RecTrackFormat+} classes.\\
+\multicolumn{2}{l}{\color{ao}\expddg}\\ & Impact parameter of a {\color{ao}\verb+RecLeptonFormat+}
+  object. An extension to the other classes of reconstructed objects is
+  foreseen.\\
+\multicolumn{2}{l}{\color{ao}\expddh}\\ & Uncertainty on the impact parameter of a
+  {\color{ao}\verb+RecLeptonFormat+} object.\\
+\multicolumn{2}{l}{\color{ao}\expddc}\\ & Number of charged tracks associated with a
+  reconstructed object. This method is available for the {\color{ao}\verb+RecJetFormat+} and
+  {\color{ao}\verb+RecTauFormat+} classes.\\
+\multicolumn{2}{l}{\color{ao}\expdde}\\ & Indicates if a {\color{ao}\verb+RecLeptonFormat+} object is
+  an electron.\\
+\multicolumn{2}{l}{\color{ao}\expddf}\\ & Indicates if a {\color{ao}\verb+RecLeptonFormat+} object is
+  a muon.\\
+\multicolumn{2}{l}{\color{ao}\expddk}\\  & Indicates whether a {\color{ao}\verb+RecJetFormat+} object
+  is a true $b$-jet.\\
+\multicolumn{2}{l}{\color{ao}\expddl}\\  & Indicates whether a {\color{ao}\verb+RecJetFormat+} object
+  is a true $c$-jet.\\
+\hline
+\end{tabular}
+\end{center}
+
+\newpage
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{shaded}
+\section{\Large Lepton and photon isolation}
+\end{shaded}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+In the context of reconstructed events, lepton and photon isolation can be
+ensured by relying either on track information, on calorimetric information, on
+the combination of both or on a reconstruction based on the energy flow.
+Corresponding isolation methods are available, within the \MA\ data format,
+through the four classes,
+{\color{ao}\begin{verbatim}
+  PHYSICS->Isol->tracker           PHYSICS->Isol->calorimeter
+  PHYSICS->Isol->combined          PHYSICS->Isol->eflow
+\end{verbatim}}
+respectively connected to the four ways to enforce object isolation. All
+those classes come with two methods summarized in the table below.
+\verbdef{\expyya}{MAfloat64 relIsolation(const <x>& prt,const RecEventFormat* evt,}
+\verbdef{\expyyb}{       const double& DR, double PTmin=0.5) const}
+\verbdef{\expyyc}{MAfloat64 sumIsolation(const <x>& prt,const RecEventFormat* evt,}
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{p{2.7cm} p{9.0cm}}
+\hline
+\multicolumn{2}{l}{\color{ao}\expyya}\\
+\multicolumn{2}{l}{\color{ao}\expyyb}\\ & Sum of the transverse momenta of all objects
+  lying in a cone of radius \verb+DR+ centered on the considered object
+  {\color{ao}\verb+prt+}, and whose transverse momentum is larger than {\color{ao}\verb+PTmin+}. The sum
+  is evaluated relatively to the transverse momentum of the considered object
+  {\color{ao}\verb+prt+} that can be either a {\color{ao}\verb+RecLeptonFormat+} or a
+  {\color{ao}\verb+RecPhotonFormat+} object ({\it i.e.} the value of the {\color{ao}\verb+<x>+} type).\\
+\multicolumn{2}{l}{\color{ao}\expyyc}\\
+\multicolumn{2}{l}{\color{ao}\expyyb}\\ & Sum of the transverse momenta of all objects
+  lying in a cone of radius {\color{ao}\verb+DR+} centered on the considered object
+  {\color{ao}\verb+prt+}, and whose transverse momentum is larger than {\color{ao}\verb+PTmin+}. The
+  object {\color{ao}\verb+prt+} can be either a {\color{ao}\verb+RecLeptonFormat+} or a
+  {\color{ao}\verb+RecPhotonFormat+} object ({\it i.e.} the value of the {\color{ao}\verb+<x>+} type).\\
+\hline
+\end{tabular}
+\end{center}
+When isolation is imposed on the basis of the energy flow
+(\verb?PHYSICS->Isol->eflow?), those methods take an extra argument,
+{\color{ao}
+\begin{verbatim}
+MAfloat64 relIsolation(const <x>& prt, const RecEventFormat* evt,
+    const double& DR, double PTmin=0.5, ComponentType type) const
+
+MAfloat64 sumIsolation(const <x>& prt, const RecEventFormat* evt,
+    const double& DR, double PTmin=0.5, ComponentType type) const
+\end{verbatim}
+}
+where {\color{ao}\verb+type+} can take one of the four values,
+{\color{ao}\begin{verbatim}
+ TRACK_COMPONENT                    PHOTON_COMPONENT
+ NEUTRAL_COMPONENT                  ALL_COMPONENTS
+\end{verbatim}}
+In the first case, the activity around the considered object {\color{ao}\verb+prt+} is
+evaluated only from the charged track information, whilst in the
+second case, only the photon information is considered. In the
+third case, the neutral hadron activity is accounted for whilst the last option
+consists in the sum of the three previous cases.
+
+In addition, a series of {\color{ao}\verb+JetCleaning+} functions are provided in the aim of
+cleaning jet collections from objects present in a lepton collection or a photon
+collection.
+\verbdef{\expwwa}{std::vector<const RecJetFormat*> PHYSICS->Isol->JetCleaning(}
+\verbdef{\expwwb}{   const std::vector<const RecJetFormat*>& uncleaned,}
+\verbdef{\expwwc}{   const std::vector<const RecLeptonFormat*>& leptons,}
+\verbdef{\expwwd}{   double DeltaRmax = 0.1, double PTmin = 0.5) const}
+\verbdef{\expwwe}{   const std::vector<RecJetFormat>& uncleaned,}
+\verbdef{\expwwf}{   const std::vector<const RecPhotonFormat*>& photons,}
+\renewcommand{\arraystretch}{1.13}%
+\begin{center}\begin{tabular}{p{2.7cm} p{9.0cm}}
+\hline
+\multicolumn{2}{l}{\color{ao}\expwwa}\\
+\multicolumn{2}{l}{\color{ao}\expwwb}\\
+\multicolumn{2}{l}{\color{ao}\expwwc}\\
+\multicolumn{2}{l}{\color{ao}\expwwd}\\
+\multicolumn{2}{l}{\color{ao}\expwwa}\\
+\multicolumn{2}{l}{\color{ao}\expwwe}\\
+\multicolumn{2}{l}{\color{ao}\expwwc}\\
+\multicolumn{2}{l}{\color{ao}\expwwd}\\ & Removal from the \verb+uncleaned+ jet collection
+  of all leptons included in the \verb+leptons+ collection lying at an angular
+  distance of at most \verb+DeltaRmax+ of the jet, and whose transverse momentum
+  is of at least \verb+PTmin+.\\
+\multicolumn{2}{l}{\color{ao}\expwwa}\\
+\multicolumn{2}{l}{\color{ao}\expwwb}\\
+\multicolumn{2}{l}{\color{ao}\expwwf}\\
+\multicolumn{2}{l}{\color{ao}\expwwd}\\
+\multicolumn{2}{l}{\color{ao}\expwwa}\\
+\multicolumn{2}{l}{\color{ao}\expwwe}\\
+\multicolumn{2}{l}{\color{ao}\expwwf}\\
+\multicolumn{2}{l}{\color{ao}\expwwd}\\ & Removal from the {\color{ao}\verb+uncleaned+} jet collection
+  of all photons included in the {\color{ao}\verb+photons+} collection lying at an angular
+  distance of at most {\color{ao}\verb+DeltaRmax+} of the jet, and whose transverse momentum
+  is of at least {\color{ao}\verb+PTmin+}.\\
+\hline
+\end{tabular}
+\end{center}
+
+\vspace{2cm}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{shaded}
+\section{\Large Observables}
+\end{shaded}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\noindent The \spla\ data format contains various methods to compute observables
+connected to the entire event, which includes in particular a small set of
+common transverse variables and a set of methods related to object
+identification. They are available through a series of \verb+PHYSICS+ services,
+that first contain  the two general methods below.
+\verbdef{\expxxa}{MAint32 PHYSICS->GetTauDecayMode (const MCParticleFormat* part)}
+\verbdef{\expxxb}{double PHYSICS->SqrtS(const MCEventFormat* event) const}
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{p{2.7cm} p{9.0cm}}
+\hline
+\multicolumn{2}{l}{\color{ao}\expxxa}\\ & Returns the identifier of the decay mode of a
+  tau particle. The available values are 1 ($e \nu \nu$),
+  2 ($\mu \nu \nu$),  3 ($K \nu$), 4 ($K^* \nu$),
+  5 ($\rho (\to \pi \pi^0) \nu$), 6 ($a_1 (\to \pi\pi^0\pi^0)
+  \nu$), 7 ($a_1 (\to \pi\pi\pi) \nu$), 8 ($\pi \nu$),
+  9 ($\pi\pi\pi \pi^0 \nu$) and 0 (any other decay mode).\\
+\multicolumn{2}{l}{\color{ao}\expxxb}\\ & Returns the partonic center-of-mass energy.\\
+\hline
+\end{tabular}
+\end{center}
+Identification functions are collected as methods attached to the
+{\color{ao}\verb+PHYSICS->Id+} object. The list of available methods is given in the table
+below.
+\verbdef{\expxxc}{MAbool IsInitialState(const MCParticleFormat& part) const}
+\verbdef{\expxxd}{MAbool IsFinalState(const MCParticleFormat& part) const}
+\verbdef{\expxxe}{MAbool IsInterState(const MCParticleFormat& part) const}
+\verbdef{\expxxf}{MAbool IsInitialState(const MCParticleFormat* part) const}
+\verbdef{\expxxg}{MAbool IsFinalState(const MCParticleFormat* part) const}
+\verbdef{\expxxh}{MAbool IsInterState(const MCParticleFormat* part) const}
+\verbdef{\expxxj}{bool IsHadronic(const RecParticleFormat* part) const}
+\verbdef{\expxxk}{bool IsHadronic(const MCParticleFormat* part) const}
+\verbdef{\expxxl}{bool IsHadronic(MAint32 pdgid) const}
+\verbdef{\expxxm}{bool IsInvisible(const RecParticleFormat* part) const}
+\verbdef{\expxxn}{bool IsInvisible(const MCParticleFormat* part) const}
+\verbdef{\expxxo}{MAbool IsBHadron(MAint32 pdg)}
+\verbdef{\expxxp}{MAbool IsBHadron(const MCParticleFormat& part)}
+\verbdef{\expxxq}{MAbool IsBHadron(const MCParticleFormat* part)}
+\verbdef{\expxxs}{MAbool IsCHadron(MAint32 pdg)}
+\verbdef{\expxxt}{MAbool IsCHadron(const MCParticleFormat& part)}
+\verbdef{\expxxu}{MAbool IsCHadron(const MCParticleFormat* part)}
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{p{2.7cm} p{9.0cm}}
+\hline
+\multicolumn{2}{l}{\color{ao}\expxxc}\\
+\multicolumn{2}{l}{\color{ao}\expxxf}\\ & Tests the initial-state nature of an object.\\
+\multicolumn{2}{l}{\color{ao}\expxxh}\\
+\multicolumn{2}{l}{\color{ao}\expxxe}\\ & Tests the intermediate-state nature of an
+  object.\\
+\multicolumn{2}{l}{\color{ao}\expxxd}\\
+\multicolumn{2}{l}{\color{ao}\expxxg}\\ & Tests the final-state nature of an object.\\
+\multicolumn{2}{l}{\color{ao}\expxxj}\\
+\multicolumn{2}{l}{\color{ao}\expxxk}\\
+\multicolumn{2}{l}{\color{ao}\expxxl}\\ & Tests the hadronic nature of an object.\\
+\multicolumn{2}{l}{\color{ao}\expxxm}\\
+\multicolumn{2}{l}{\color{ao}\expxxn}\\ & Tests the invisible nature of an object.\\
+\multicolumn{2}{l}{\color{ao}\expxxo}\\
+\multicolumn{2}{l}{\color{ao}\expxxp}\\
+\multicolumn{2}{l}{\color{ao}\expxxq}\\ & Tests whether the object is a $B$-hadron.\\
+\multicolumn{2}{l}{\color{ao}\expxxs}\\
+\multicolumn{2}{l}{\color{ao}\expxxt}\\
+\multicolumn{2}{l}{\color{ao}\expxxu}\\ & Tests whether the object is a $C$-hadron.\\
+\hline
+\end{tabular}
+\end{center}
+Finally, a set of transverse variables can be evaluated by relying on the
+{\color{ao}\verb+PHYSICS->Transverse+} object. The following methods are available within
+the \spla\ data format.
+\verbdef{\expqqa}{double EventTET(const MCEventFormat* event) const}
+\verbdef{\expqqb}{double EventTET(const RecEventFormat* event) const}
+\verbdef{\expqqc}{double EventMET(const MCEventFormat* event) const}
+\verbdef{\expqqd}{double EventMET(const RecEventFormat* event) const}
+\verbdef{\expqqe}{double EventTHT(const MCEventFormat* event) const}
+\verbdef{\expqqf}{double EventTHT(const RecEventFormat* event) const}
+\verbdef{\expqqg}{double EventMEFF(const MCEventFormat* event) const}
+\verbdef{\expqqh}{double EventMEFF(const RecEventFormat* event) const}
+\verbdef{\expqqi}{double EventMHT(const MCEventFormat* event) const}
+\verbdef{\expqqj}{double EventMHT(const RecEventFormat* event) const}
+\verbdef{\expqqka}{double MT2(const MALorentzVector* p1, const MALorentzVector* p2,}
+\verbdef{\expqqkb}{   const MALorentzVector& met, const double &mass)}
+\verbdef{\expqqla}{double MT2W(std::vector<const RecJetFormat*> jets,}
+\verbdef{\expqqlb}{   const RecLeptonFormat* lep, const ParticleBaseFormat& met)}
+\verbdef{\expqqma}{double MT2W(std::vector<const MCParticleFormat*> jets}
+\verbdef{\expqqmb}{  const MCParticleFormat* lep,const ParticleBaseFormat& met)}
+\verbdef{\expqqn}{double AlphaT(const MCEventFormat*)}
+\verbdef{\expqqo}{double AlphaT(const RecEventFormat*)}
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{p{2.7cm} p{9.0cm}}
+\hline
+\multicolumn{2}{l}{\color{ao}\expqqn}\\
+\multicolumn{2}{l}{\color{ao}\expqqo}\\ & The $\alpha_T$ variable\cite{Randall:2008rw}.\\
+\multicolumn{2}{l}{\color{ao}\expqqg}\\
+\multicolumn{2}{l}{\color{ao}\expqqh}\\ & The effective mass of the event.\\
+\hline
+\end{tabular}
+\end{center}
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{p{2.7cm} p{9.0cm}}
+\hline
+\multicolumn{2}{l}{\color{ao}\expqqc}\\
+\multicolumn{2}{l}{\color{ao}\expqqd}\\ & The event missing transverse energy.\\
+\multicolumn{2}{l}{\color{ao}\expqqi}\\
+\multicolumn{2}{l}{\color{ao}\expqqj}\\ & The event missing transverse hadronic energy.\\
+\multicolumn{2}{l}{\color{ao}\expqqa}\\
+\multicolumn{2}{l}{\color{ao}\expqqb}\\ & The event total transverse energy.\\
+\multicolumn{2}{l}{\color{ao}\expqqe}\\
+\multicolumn{2}{l}{\color{ao}\expqqf}\\ & The event total transverse hadronic energy.\\
+\multicolumn{2}{l}{\color{ao}\expqqka}\\
+\multicolumn{2}{l}{\color{ao}\expqqkb}\\ & The event $m_{T2}$ variable computed from a system
+  of two visible objects \verb+p1+ and \verb+p2+, the event missing momentum
+  \verb+met+ and a test mass \verb+mass+\cite{Lester:1999tx,Cheng:2008hk}.\\
+\multicolumn{2}{l}{\color{ao}\expqqla}\\
+\multicolumn{2}{l}{\color{ao}\expqqlb}\\
+\multicolumn{2}{l}{\color{ao}\expqqma}\\
+\multicolumn{2}{l}{\color{ao}\expqqmb}\\ & The event $m_{T2}^W$ variable computed from a
+  system of jets \verb+jets+, a lepton \verb+lep+ and the missing
+  momentum \verb+met+~\cite{Bai:2012gs}.\\
+\hline
+\end{tabular}
+\end{center}
+
+\vspace{2cm}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{shaded}
+\section{\Large Signal regions, histograms and cuts}
+\end{shaded}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+The implementation of an analysis in \MA\ requires to deal with
+signal regions, selection cuts and histograms. Each analysis comes with an
+instance of the analysis manager class {\color{ao}\verb+RegionSelectionManager+}, named
+{\color{ao}\verb+Manager()+}, which allows the user to use the methods presented in the
+table below.
+\verbdef{\SRa}{void AddCut(const std::string&name, const std::string &RSname)}
+\verbdef{\SRba}{template<int NRS> void AddCut(const std::string&name,}
+\verbdef{\SRbb}{  std::string const(& RSnames)[NRS])}
+\verbdef{\SRbc}{void AddCut(const std::string &name)}
+\verbdef{\SRca}{void AddHisto(const std::string&name,unsigned int nb,}
+\verbdef{\SRcb}{  double xmin, double xmax)}
+\verbdef{\SRcd}{void AddHistoLogX(const std::string&name,unsigned int nb,}
+\verbdef{\SRce}{  double xmin, double xmax, const std::string &RSname)}
+\verbdef{\SRcf}{template <int NRS> void AddHisto(const std::string&name,}
+\verbdef{\SRcg}{  unsigned int nb, double xmin, double xmax,}
+\verbdef{\SRch}{template <int NRS> void AddHistoLogX(const std::string&name,}
+\verbdef{\SRd}{void AddRegionSelection(const std::string& name)}
+\verbdef{\SRe}{bool ApplyCut(bool cond, std::string const &name)}
+\verbdef{\SRf}{void FillHisto(std::string const&name, double val)}
+\verbdef{\SRg}{void InitializeForNewEvent(double EventWeight)}
+\verbdef{\SRh}{bool IsSurviving(const std::string &RSname)}
+\verbdef{\SRi}{void SetCurrentEventWeight(double weight)}
+\renewcommand{\arraystretch}{1.1}%
+\begin{center}\begin{tabular}{p{2.7cm} p{9.0cm}}
+\hline
+\multicolumn{2}{l}{\color{ao}\SRa}\\\multicolumn{2}{l}{\SRba}\\
+  \multicolumn{2}{l}{\color{ao}\SRbb}\\
+  \multicolumn{2}{l}{\color{ao}\SRbc}\\&
+  Declares a cut named \verb+name+ and associates it with one region (the second
+  argument is a string), with a set of regions (the second argument is an
+  array of strings) or with all regions (the second argument is omitted).\\
+\hline
+\end{tabular}
+\end{center}
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{p{2.7cm} p{9.0cm}}
+\hline
+\multicolumn{2}{l}{\color{ao}\SRca}\\ \multicolumn{2}{l}{\SRcb}\\
+  \multicolumn{2}{l}{\color{ao}\SRcd}\\ \multicolumn{2}{l}{\SRcb}\\&
+  Declares a histogram named \verb+name+ of \verb+nb+ bins ranging from
+  \verb+xmin+ to \verb+xmax+. The histogram is associated with all regions and
+  the $x$-axis can rely on a logarithmic scale (the second method).\\
+\multicolumn{2}{l}{\color{ao}\SRca}\\ \multicolumn{2}{l}{\SRce}\\
+  \multicolumn{2}{l}{\color{ao}\SRcd}\\ \multicolumn{2}{l}{\SRce}\\&
+  Same as above but the histogram is associated with a single region
+  \verb+RSname+.\\
+\multicolumn{2}{l}{\color{ao}\SRcf}\\ \multicolumn{2}{l}{\SRcg}\\
+  \multicolumn{2}{l}{\color{ao}\SRbb}\\
+  \multicolumn{2}{l}{\color{ao}\SRch}\\ \multicolumn{2}{l}{\SRcg}\\
+  \multicolumn{2}{l}{\color{ao}\SRbb}\\ &
+  Same as above but the histogram is associated with an array of regions.\\
+\multicolumn{2}{l}{\color{ao}\SRd}\\ &
+  Declares a new region named \verb+name+.\\
+\multicolumn{2}{l}{\color{ao}\SRe}\\ &
+  Applies the cut \verb+name+, an event passing this cut if the condition
+  \verb+cond+ is realized. The method returns \texttt{true} if at least one
+  region is passing all cuts applied so far, or \texttt{false} otherwise.\\
+\multicolumn{2}{l}{\color{ao}\SRf}\\ &
+  Fills the histogram named \verb+name+, the bin choice being driven by the
+  value \verb+value+.\\
+\multicolumn{2}{l}{\color{ao}\SRg}\\ &
+  To be called at the beginning of the analysis of an event in order to tag all
+  regions as surviving the cuts and initialize the event weight to the value
+  \verb+EventWeight+.\\
+\hline
+\end{tabular}
+\end{center}
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{p{2.7cm} p{9.0cm}}
+\hline
+\multicolumn{2}{l}{\color{ao}\SRh}\\ &
+  Verifies whether the region \verb+RSname+ survives all cut applied so far.\\
+\multicolumn{2}{l}{\color{ao}\SRi}\\ &
+  Modifies the weight of the current event to the value \verb+weight+.\\
+\hline
+\end{tabular}
+\end{center}
+
+\newpage
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{shaded}
+\section{\Large Message services}
+\end{shaded}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\noindent\spla\ handles four levels of streamers, that can be cast within any analysis
+code by typing one of the following lines,
+{\color{ao}
+\begin{verbatim}
+ INFO    << "..." << endmsg;
+ WARNING << "..." << endmsg;
+ ERROR   << "..." << endmsg;
+ DEBUG   << "..." << endmsg;
+\end{verbatim}}
+\noindent This allows the user to print informative, warning, error and debugging
+messages. Additionally, warning and error messages return information on the
+line number responsible for printing the message.
+The effect of a given message service can be modified by
+means of the methods presented in the table below.
+\verbdef{\ina}{void SetStream(std::ostream* stream)}
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{l p{8.3cm}}
+\hline
+\color{ao}\verb+void DisableColor()+ & Switches off the colored display of messages (that
+  is on by default).\\
+\color{ao}\verb+void EnableColor()+  & Switches on the colored display of messages.\\
+\color{ao}\verb+void SetMute()+      & Switches entirely off a given message service (that
+  is on by default).\\
+\multicolumn{2}{l}{\color{ao}\ina}\\ & Redirects the output of a given service to a file.
+  \\
+\color{ao}\verb+void SetUnMute()+   & Switches on a specific message service.\\
+\hline
+\end{tabular}
+\end{center}
+
+\vspace{2cm}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{shaded}
+\section{\Large Sorting particles and objects}
+\end{shaded}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\noindent It is usually important to order particle as a function of one of their
+properties, like their transverse momentum or their energy. For this reason,
+\spla\ contains a series of routines allowing to sort a set of objects, which
+can be called by implementing\\
+{\color{ao}
+\begin{verbatim}
+  SORTER->sort(objects, criterion)
+\end{verbatim}}
+\noindent where {\color{ao}\verb+objects+} is the vector of objects that needs to be sorted and
+\verb+criterion+ is the ordering variable. The latter can be {\color{ao}\verb+ETAordering+}
+(pseudorapidity), {\color{ao}\verb+ETordering+} (transverse energy), {\color{ao}\verb+Eordering+}
+(energy), {\color{ao}\verb+Pordering+} (the magnitude of the three-momentum),
+{\color{ao}\verb+PTordering+} (the transverse momentum), {\color{ao}\verb+PXordering+} (the
+$x$-component of the momentum), {\color{ao}\verb+PYordering+} (the $y$-component of the
+momentum) and {\color{ao}\verb+PZordering+} (the $z$-component of the momentum). As a
+result, the vector of objects is sorted by decreasing values of the ordering
+variable.
+
+\newpage
+
+\bibliographystyle{plain} % We choose the "plain" reference style
+\bibliography{main_expert}
+
+\end{document}

=== added file 'doc/makedoc'
--- doc/makedoc	1970-01-01 00:00:00 +0000
+++ doc/makedoc	2019-02-13 11:05:44 +0000
@@ -0,0 +1,311 @@
+#!/usr/bin/env python
+
+################################################################################
+#  
+#  Copyright (C) 2012-2018 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/>
+#  
+################################################################################
+
+
+################################################################################
+# PYTHON VERSION CRITERION
+################################################################################
+
+"""This is the main executable, a simple frontend to set up the PYTHONPATH
+and call immediately the command line interface scripts"""
+
+# Checking if the correct release of Python is installed
+import sys
+if not sys.version_info[0] == 2 or sys.version_info[1] < 6:
+    sys.exit('Python release '+ sys.version + ' is detected.\n' + \
+    'MadAnalysis 5 works only with python 2.6 ' + \
+    'or later (but not python 3.X).\n' + \
+    'Please upgrade your version of python.')
+
+
+################################################################################
+# CLASS ARGUMENT
+################################################################################
+class Argument():
+   
+    @staticmethod
+    def PrintSyntax():
+        print "Syntax of the program: ./makedoc <arg>"
+        print "where <arg> can be:"
+        print "  help      ->  displying this message"
+        print "  clean     ->  removing temporary files (aux, bbl, log, ..."
+        print "  mrproper  ->  removing PDF files and temporary files"
+
+    @staticmethod
+    def Clean():
+        import glob
+        import os
+        todelete=glob.glob("*.aux")
+        todelete.extend(glob.glob("*.bbl"))
+        todelete.extend(glob.glob("*.bgl"))
+        todelete.extend(glob.glob("*.log"))
+        todelete.extend(glob.glob("*.out"))
+        todelete.extend(glob.glob("*.dvi"))
+        todelete.extend(glob.glob("*.blg"))
+        todelete.extend(glob.glob("*~"))
+        todelete.extend(glob.glob("*/*.aux"))
+        todelete.extend(glob.glob("*/*.bbl"))
+        todelete.extend(glob.glob("*/*.bgl"))
+        todelete.extend(glob.glob("*/*.log"))
+        todelete.extend(glob.glob("*/*.out"))
+        todelete.extend(glob.glob("*/*.dvi"))
+        todelete.extend(glob.glob("*/*.blg"))
+        todelete.extend(glob.glob("*/*~"))
+        for item in todelete:
+            os.remove(item)
+
+    @staticmethod
+    def Mrproper():
+        import glob
+        import os
+        Argument.Clean()
+        todelete=glob.glob("*.pdf")
+        todelete.extend(glob.glob("*/*.pdf"))
+        for item in todelete:
+            os.remove(item)
+
+
+################################################################################
+# CLASS MAKELATEX
+################################################################################
+class MakeLatex():
+   
+    def __init__(self, texfilename, bibfilename, outfilename, logfilename, workfolder):
+        self.texfilename = texfilename # latex file to compile
+        self.bibfilename = bibfilename # bib file associated to the latex file
+        self.outfilename = outfilename # pdf file to produce
+        self.logfilename = logfilename # log file to produce
+        self.workfolder  = workfolder  # folder where the temporary file
+                                       # (aux, bbl, log, ...) will be produced
+
+    @staticmethod
+    def ExecuteCommand(theCommands,workfolder='./',mute=True,show=False):
+        import subprocess
+
+        # Show
+        if show:
+             print '      command line: '+' '.join(theCommands)
+
+        # Launching the commands
+        try:
+            result=subprocess.Popen(theCommands,stdout=subprocess.PIPE, stderr=subprocess.STDOUT, cwd=workfolder)
+        except:
+            if not mute:
+                print '      ERROR: impossible to execute the commands: '+' '.join(theCommands)
+            return False, []
+
+        # Getting stdout
+        out, err = result.communicate()
+        if out==None:
+            return False, []
+
+        # Splitting the lines
+        msg = out.split('\n')
+
+        # Removing irrelevant component
+        msg2 = []
+        for item in msg:
+            if item=='':
+                continue
+            if len(msg2)!=0:
+                if msg2[-1]==item:
+                    continue
+            msg2.append(item)
+            
+        # Getting results
+        if result.returncode!=0:
+            if not mute:
+                print '      ERROR: command '+str(theCommands)+' is not found'
+            return False, msg2
+
+        # Return results
+        return True, msg2
+
+
+    @staticmethod  
+    def CheckPrograms():
+        ok = True
+
+        # Detection of pdflatex
+        test, result = MakeLatex.ExecuteCommand(['which','pdflatex'],mute=True)
+        ok = ok and test and (len(result)!=0)
+        if (not test) or len(result)==0:
+            print "  ERROR: pdflatex is not found"
+
+        # Detection of biblatex
+        result = MakeLatex.ExecuteCommand(['which','bibtex'],mute=True)
+        ok = ok and test and (len(result)!=0)
+        if (not test) or len(result)==0:
+            print "  ERROR: bibtex is not found"
+        return ok
+ 
+    def Execute(self):
+        log = file(self.logfilename,'w')
+        log.write('BUILDING THE LATEX FILE\n')
+        log.write(self.texfilename+'\n\n')
+
+        print '    - step 1/4: producing .aux file...'
+        log.write('\n')
+        log.write('*****************************************************\n')
+        log.write(' STEP 1/4\n') 
+        log.write('*****************************************************\n')
+        latex_cmd   = ['pdflatex','-interaction=nonstopmode', self.texfilename]
+        test, result = MakeLatex.ExecuteCommand(latex_cmd,  self.workfolder, show=True)
+        log.write('\n'.join(result)) 
+        if not test: 
+            return False
+        bibname = self.bibfilename
+        if self.bibfilename.endswith('.bib'):
+            bibname = bibname[:-4]
+        bibtex_cmd  = ['bibtex', bibname]
+
+        print '    - step 2/4: producing .bbl file with references...'
+        log.write('\n')
+        log.write('*****************************************************\n')
+        log.write(' STEP 2/4\n') 
+        log.write('*****************************************************\n')
+        test, result = MakeLatex.ExecuteCommand(bibtex_cmd, self.workfolder, show=True)
+        log.write('\n'.join(result)) 
+        if not test:
+            return False
+
+        print '    - step 3/4: creating the reference labels...'
+        log.write('\n')
+        log.write('*****************************************************\n')
+        log.write(' STEP 3/4 \n') 
+        log.write('*****************************************************\n')
+        test, result = MakeLatex.ExecuteCommand(latex_cmd,  self.workfolder, show=True)
+        log.write('\n'.join(result)) 
+        if not test:
+            return False
+
+        print '    - step 4/4: including the reference labels...'
+        log.write('\n')
+        log.write('*****************************************************\n')
+        log.write(' STEP 4/4 \n') 
+        log.write('*****************************************************\n')
+        test, result = MakeLatex.ExecuteCommand(latex_cmd,  self.workfolder, show=True)
+        log.write('\n'.join(result)) 
+        if not test:
+            return False
+
+        log.close()
+        print '    - finalizing the PDF file'
+        pdfname = self.texfilename[:-3]+'pdf'
+        if not os.path.isfile(pdfname):
+            print '      ERROR: PDF file is not found: '+pdfname
+            return False
+        os.rename(pdfname,self.outfilename)
+        return True
+
+
+################################################################################
+# MAIN PROGRAM
+################################################################################
+
+# Treating argument
+arguments=sys.argv[1:]
+if len(arguments)==1:
+    if arguments[0]=='clean':
+        Argument.Clean()
+        sys.exit()
+    elif arguments[0]=='mrproper':
+        Argument.Mrproper()
+        sys.exit()
+    elif arguments[0]=='help':
+        Argument.PrintSyntax()
+        sys.exit()
+    else:
+        print 'ERROR: wrong arguments'
+        Argument.PrintSyntax()
+        sys.exit()
+elif len(arguments)>=1:
+    print 'ERROR: wrong arguments'
+    PrintSyntax()
+    sys.exit()
+
+# Defining colors
+cyan   = '\x1b[36m'
+red    = '\x1b[31m'
+green  = '\x1b[32m'
+endmsg = '\x1b[0m'
+
+
+# The beginning
+print ""
+print cyan+"Welcome to MA5 reference-card maker!"+endmsg
+print ""
+
+# Finding the doc folder
+import os
+docpath = os.path.split(os.path.realpath( __file__ ))[0]
+if not os.path.isdir(docpath):
+    print red+'ERROR: '+endmsg+'the documentation folder is not here:\n'+docpath
+    print ""
+    sys.exit()
+print cyan+"- Documentation folder to process is here: "+endmsg+docpath
+
+# Detecting pdflatex and bibtex
+print cyan+"- Detecting of the presence of the Latex programs..."+endmsg
+if not MakeLatex.CheckPrograms():
+    print red+'Aborted'
+    print ""
+    sys.exit() 
+ok = True
+
+# Building normal-mode reference-card
+print cyan+"- Building reference card for the normal mode..."+endmsg
+maker=MakeLatex(docpath+'/normal_mode/main_normal.tex',\
+                docpath+'/normal_mode/main_normal.bib',\
+                docpath+'/normal_mode.pdf',\
+                docpath+'/normal_mode.log',\
+                docpath+'/normal_mode/')
+if not maker.Execute():
+    print red+"      ERROR:"+endmsg+" Impossible to build the reference card for the normal mode!" 
+    print "      see the log file: "+docpath+'/normal_mode.log'  
+    ok = False
+
+# Building expert-mode reference-card
+print cyan+"- Building reference card for the expert mode..."+endmsg
+maker=MakeLatex(docpath+'/expert_mode/main_expert.tex',\
+                docpath+'/expert_mode/main_expert.bib',\
+                docpath+'/expert_mode.pdf',\
+                docpath+'/expert_mode.log',\
+                docpath+'/expert_mode/')
+if not maker.Execute():
+    print red+"      ERROR:"+endmsg+" Impossible to build the reference card for the expert mode!" 
+    print "      see the log file: "+docpath+'/expert_mode.log'  
+    ok = False
+
+# It's the end of the word as we know it!
+if ok:
+    print green+"Success!"+endmsg
+    print ""
+    print cyan+"Goodbye! Have a good day!"+endmsg
+    print ""  
+else:
+    print red+"Aborted"+endmsg
+    print ""
+

=== added directory 'doc/normal_mode'
=== added file 'doc/normal_mode/main_normal.bib'
--- doc/normal_mode/main_normal.bib	1970-01-01 00:00:00 +0000
+++ doc/normal_mode/main_normal.bib	2019-02-13 11:05:44 +0000
@@ -0,0 +1,1151 @@
+@article{Dumont:2014tja,
+      author         = "Dumont, B. and Fuks, B. and Kraml, S. and Bein, S. and
+                        Chalons, G. and Conte, E. and Kulkarni, S. and Sengupta,
+                        D. and Wymant, C.",
+      title          = "{Toward a public analysis database for LHC new physics
+                        searches using MADANALYSIS 5}",
+      journal        = "Eur. Phys. J.",
+      volume         = "C75",
+      year           = "2015",
+      number         = "2",
+      pages          = "56",
+      doi            = "10.1140/epjc/s10052-014-3242-3",
+      eprint         = "1407.3278",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "CERN-PH-TH-2014-109, LAPTH-048-14, LPSC14143",
+      SLACcitation   = "%%CITATION = ARXIV:1407.3278;%%"
+}
+
+@article{deFavereau:2013fsa,
+      author         = "de Favereau, J. and Delaere, C. and Demin, P. and
+                        Giammanco, A. and Lemaître, V. and Mertens, A. and
+                        Selvaggi, M.",
+      title          = "{DELPHES 3, A modular framework for fast simulation of a
+                        generic collider experiment}",
+      collaboration  = "DELPHES 3",
+      journal        = "JHEP",
+      volume         = "02",
+      year           = "2014",
+      pages          = "057",
+      doi            = "10.1007/JHEP02(2014)057",
+      eprint         = "1307.6346",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ex",
+      SLACcitation   = "%%CITATION = ARXIV:1307.6346;%%"
+}
+
+@article{Skands:2003cj,
+      author         = "Skands, Peter Z. and others",
+      title          = "{SUSY Les Houches accord: Interfacing SUSY spectrum
+                        calculators, decay packages, and event generators}",
+      journal        = "JHEP",
+      volume         = "07",
+      year           = "2004",
+      pages          = "036",
+      doi            = "10.1088/1126-6708/2004/07/036",
+      eprint         = "hep-ph/0311123",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "LU-TP-03-39, SHEP-03-24, CERN-TH-2003-204, ZU-TH-15-03,
+                        LMU-19-03, DCPT-03-108, IPPP-03-54, CTS-IISC-2003-07,
+                        DESY-03-166, MPP-2003-111",
+      SLACcitation   = "%%CITATION = HEP-PH/0311123;%%"
+}
+
+@article{Allanach:2008qq,
+      author         = "Allanach, B. C. and others",
+      title          = "{SUSY Les Houches Accord 2}",
+      journal        = "Comput. Phys. Commun.",
+      volume         = "180",
+      year           = "2009",
+      pages          = "8-25",
+      doi            = "10.1016/j.cpc.2008.08.004",
+      eprint         = "0801.0045",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "FERMILAB-PUB-07-036-T, SLAC-PUB-12765,
+                        CERN-PH-TH-2007-148, DAMTP-2007-76, EDINBURGH-2007-31,
+                        KEK-TH-1170, LAPTH-1204-07, LPT-ORSAY-07-81, SHEP-07-13",
+      SLACcitation   = "%%CITATION = ARXIV:0801.0045;%%"
+}
+
+@article{Degrande:2011ua,
+      author         = "Degrande, Celine and Duhr, Claude and Fuks, Benjamin and
+                        Grellscheid, David and Mattelaer, Olivier and Reiter,
+                        Thomas",
+      title          = "{UFO - The Universal FeynRules Output}",
+      journal        = "Comput. Phys. Commun.",
+      volume         = "183",
+      year           = "2012",
+      pages          = "1201-1214",
+      doi            = "10.1016/j.cpc.2012.01.022",
+      eprint         = "1108.2040",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "CP3-11-25, IPHC-PHENO-11-04, IPPP-11-39, DCPT-11-78,
+                        MPP-2011-68",
+      SLACcitation   = "%%CITATION = ARXIV:1108.2040;%%"
+}
+
+@article{Conte:2014zja,
+      author         = "Conte, Eric and Dumont, Béranger and Fuks, Benjamin and
+                        Wymant, Chris",
+      title          = "{Designing and recasting LHC analyses with MadAnalysis
+                        5}",
+      journal        = "Eur. Phys. J.",
+      volume         = "C74",
+      year           = "2014",
+      number         = "10",
+      pages          = "3103",
+      doi            = "10.1140/epjc/s10052-014-3103-0",
+      eprint         = "1405.3982",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "CERN-PH-TH-2014-088, LPSC-14-079, LAPTH-033-14,
+                        MCNET-14-11",
+      SLACcitation   = "%%CITATION = ARXIV:1405.3982;%%"
+}
+
+@article{Sirunyan:2017onm,
+      author         = "Sirunyan, Albert M and others",
+      title          = "{Search for dark matter and unparticles in events with a
+                        Z boson and missing transverse momentum in proton-proton
+                        collisions at $ \sqrt{s}=13 $ TeV}",
+      collaboration  = "CMS",
+      journal        = "JHEP",
+      volume         = "03",
+      year           = "2017",
+      pages          = "061",
+      doi            = "10.1007/JHEP09(2017)106, 10.1007/JHEP03(2017)061",
+      note           = "[Erratum: JHEP09,106(2017)]",
+      eprint         = "1701.02042",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ex",
+      reportNumber   = "CMS-EXO-16-010, CERN-EP-2016-309,
+                        FERMILAB-PUB-17-011-CMS",
+      SLACcitation   = "%%CITATION = ARXIV:1701.02042;%%"
+}
+
+@article{Abercrombie:2015wmb,
+      author         = "Abercrombie, Daniel and others",
+      editor         = "Boveia, Antonio and Doglioni, Caterina and Lowette,
+                        Steven and Malik, Sarah and Mrenna, Stephen",
+      title          = "{Dark Matter Benchmark Models for Early LHC Run-2
+                        Searches: Report of the ATLAS/CMS Dark Matter Forum     }",
+      year           = "2015",
+      eprint         = "1507.00966",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ex",
+      reportNumber   = "FERMILAB-PUB-15-282-CD",
+      SLACcitation   = "%%CITATION = ARXIV:1507.00966;%%"
+}
+
+@article{Georgi:2007ek,
+     author    = "Georgi, Howard",
+     title     = "{Unparticle Physics}",
+     journal   = "Phys. Rev. Lett.",
+     volume    = "98",
+     year      = "2007",
+     pages     = "221601",
+     eprint    = "hep-ph/0703260",
+     archivePrefix = "arXiv",
+     doi       = "10.1103/PhysRevLett.98.221601",
+     SLACcitation  = "%%CITATION = HEP-PH/0703260;%%"
+}
+
+@article{Georgi:2007si,
+     author    = "Georgi, Howard",
+     title     = "{Another Odd Thing About Unparticle Physics}",
+     journal   = "Phys. Lett.",
+     volume    = "B650",
+     year      = "2007",
+     pages     = "275-278",
+     eprint    = "0704.2457",
+     archivePrefix = "arXiv",
+     primaryClass  =  "hep-ph",
+     doi       = "10.1016/j.physletb.2007.05.037",
+     SLACcitation  = "%%CITATION = 0704.2457;%%"
+}
+
+@article{Alwall:2014hca,
+      author         = "Alwall, J. and Frederix, R. and Frixione, S. and Hirschi,
+                        V. and Maltoni, F. and Mattelaer, O. and Shao, H. -S. and
+                        Stelzer, T. and Torrielli, P. and Zaro, M.",
+      title          = "{The automated computation of tree-level and
+                        next-to-leading order differential cross sections, and
+                        their matching to parton shower simulations}",
+      journal        = "JHEP",
+      volume         = "07",
+      year           = "2014",
+      pages          = "079",
+      doi            = "10.1007/JHEP07(2014)079",
+      eprint         = "1405.0301",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "CERN-PH-TH-2014-064, CP3-14-18, LPN14-066, MCNET-14-09,
+                        ZU-TH-14-14",
+      SLACcitation   = "%%CITATION = ARXIV:1405.0301;%%"
+}
+
+@article{Sjostrand:2014zea,
+      author         = "Sjöstrand, Torbjörn and Ask, Stefan and Christiansen,
+                        Jesper R. and Corke, Richard and Desai, Nishita and Ilten,
+                        Philip and Mrenna, Stephen and Prestel, Stefan and
+                        Rasmussen, Christine O. and Skands, Peter Z.",
+      title          = "{An Introduction to PYTHIA 8.2}",
+      journal        = "Comput. Phys. Commun.",
+      volume         = "191",
+      year           = "2015",
+      pages          = "159-177",
+      doi            = "10.1016/j.cpc.2015.01.024",
+      eprint         = "1410.3012",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "LU-TP-14-36, MCNET-14-22, CERN-PH-TH-2014-190,
+                        FERMILAB-PUB-14-316-CD, DESY-14-178, SLAC-PUB-16122",
+      SLACcitation   = "%%CITATION = ARXIV:1410.3012;%%"
+}
+@article{Ball:2014uwa,
+      author         = "Ball, Richard D. and others",
+      title          = "{Parton distributions for the LHC Run II}",
+      collaboration  = "NNPDF",
+      journal        = "JHEP",
+      volume         = "04",
+      year           = "2015",
+      pages          = "040",
+      doi            = "10.1007/JHEP04(2015)040",
+      eprint         = "1410.8849",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "EDINBURGH-2014-15, IFUM-1034-FT, CERN-PH-TH-2013-253,
+                        OUTP-14-11P, CAVENDISH-HEP-14-11",
+      SLACcitation   = "%%CITATION = ARXIV:1410.8849;%%"
+}
+
+@article{Skands:2014pea,
+      author         = "Skands, Peter and Carrazza, Stefano and Rojo, Juan",
+      title          = "{Tuning PYTHIA 8.1: the Monash 2013 Tune}",
+      journal        = "Eur. Phys. J.",
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+      number         = "8",
+      pages          = "3024",
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+      eprint         = "1404.5630",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "CERN-PH-TH-2014-069, MCNET-14-08, OUTP-14-05P",
+      SLACcitation   = "%%CITATION = ARXIV:1404.5630;%%"
+}
+
+@article{Alwall:2014bza,
+      author         = "Alwall, Johan and Duhr, Claude and Fuks, Benjamin and
+                        Mattelaer, Olivier and Öztürk, Deniz Gizem and Shen,
+                        Chia-Hsien",
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+                        FeynRules  and MadGraph 5 _aMC@NLO}",
+      journal        = "Comput. Phys. Commun.",
+      volume         = "197",
+      year           = "2015",
+      pages          = "312-323",
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+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "CERN-PH-TH-2014-020, MCNET-14-03, IPPP-14-10, DCPT-14-20,
+                        CP3-14-11, CALT-68-2877, ZU-TH-02-14",
+      SLACcitation   = "%%CITATION = ARXIV:1402.1178;%%"
+}
+
+@article{Cacciari:2011ma,
+      author         = "Cacciari, Matteo and Salam, Gavin P. and Soyez, Gregory",
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+      primaryClass   = "hep-ph",
+      reportNumber   = "CERN-PH-TH-2011-297",
+      SLACcitation   = "%%CITATION = ARXIV:1111.6097;%%"
+}
+@article{Cacciari:2008gp,
+      author         = "Cacciari, Matteo and Salam, Gavin P. and Soyez, Gregory",
+      title          = "{The Anti-k(t) jet clustering algorithm}",
+      journal        = "JHEP",
+      volume         = "04",
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+      primaryClass   = "hep-ph",
+      reportNumber   = "LPTHE-07-03",
+      SLACcitation   = "%%CITATION = ARXIV:0802.1189;%%"
+}
+
+@article{CMS:2016kkf,
+      author         = "{CMS Collaboration}",
+      title          = "{Identification of b quark jets at the CMS Experiment in
+                        the LHC Run 2}",
+      year           = "2016",
+      journal  = "CMS-PAS-BTV-15-001",
+      SLACcitation   = "%%CITATION = CMS-PAS-BTV-15-001;%%",
+      url = "http://cds.cern.ch/record/2138504"
+}
+
+@article{inspire,
+      key            = "1618045",
+      author         = "Fuks, Benjamin",
+      title          = "{MadAnalysis5 implementation of the mono-Z analysis of
+                        CMS with 2.3 fb-1 of data (CMS-EXO-16-010)}",
+      doi            = "10.7484/INSPIREHEP.DATA.RK53.S39D",
+      year           = "2017",
+      SLACcitation   = "%%CITATION = INSPIRE-1618045;%%"
+}
+
+@article{Read:2002hq,
+      author         = "Read, Alexander L.",
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+      doi            = "10.1088/0954-3899/28/10/313",
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+}
+
+@article{Conte:2012fm,
+      author         = "Conte, Eric and Fuks, Benjamin and Serret, Guillaume",
+      title          = "{MadAnalysis 5, A User-Friendly Framework for Collider
+                        Phenomenology}",
+      journal        = "Comput. Phys. Commun.",
+      volume         = "184",
+      year           = "2013",
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+      doi            = "10.1016/j.cpc.2012.09.009",
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+      archivePrefix  = "arXiv",
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+      reportNumber   = "IPHC-PHENO-06",
+      SLACcitation   = "%%CITATION = ARXIV:1206.1599;%%"
+}
+
+@article{Arina:2016cqj,
+      author         = "Arina, Chiara and others",
+      title          = "{A comprehensive approach to dark matter studies:
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+      journal        = "JHEP",
+      volume         = "11",
+      year           = "2016",
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+      archivePrefix  = "arXiv",
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+}
+
+@article{Feng:2005gj,
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+      reportNumber   = "UCI-TR-2005-11",
+      SLACcitation   = "%%CITATION = HEP-PH/0503117;%%"
+}
+
+@article{Bai:2010hh,
+      author         = "Bai, Yang and Fox, Patrick J. and Harnik, Roni",
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+
+@article{Fox:2011fx,
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+                        Tsai, Yuhsin",
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+      SLACcitation   = "%%CITATION = ARXIV:1103.0240;%%"
+}
+
+@article{Bell:2012rg,
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+                        and Jacques, Thomas D. and Krauss, Lawrence M. and Weiler,
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+      SLACcitation   = "%%CITATION = ARXIV:1209.0231;%%"
+}
+@article{Petrov:2013nia,
+      author         = "Petrov, Alexey A. and Shepherd, William",
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+
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+}
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+
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+
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+      author         = "Aaboud, Morad and others",
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+
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+
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+      title          = "{A Practical Seedless Infrared-Safe Cone jet algorithm}",
+      journal        = "JHEP",
+      volume         = "05",
+      year           = "2007",
+      pages          = "086",
+      doi            = "10.1088/1126-6708/2007/05/086",
+      eprint         = "0704.0292",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      SLACcitation   = "%%CITATION = ARXIV:0704.0292;%%"
+}
+
+@article{Patrignani:2016xqp,
+      author         = "Patrignani, C. and others",
+      title          = "{Review of Particle Physics}",
+      collaboration  = "Particle Data Group",
+      journal        = "Chin. Phys.",
+      volume         = "C40",
+      year           = "2016",
+      number         = "10",
+      pages          = "100001",
+      doi            = "10.1088/1674-1137/40/10/100001",
+      SLACcitation   = "%%CITATION = CHPHD,C40,100001;%%"
+}
+
+
+@article{pgs,
+ journal = "{http://physics.ucdavis.edu/$\sim$conway/research/software/pgs/pgs4-general.htm}"
+}
+
+@article{Boucheneb:2014wza,
+      author         = "Boucheneb, Idir and Cacciapaglia, Giacomo and Deandrea,
+                        Aldo and Fuks, Benjamin",
+      title          = "{Revisiting monotop production at the LHC}",
+      journal        = "JHEP",
+      volume         = "01",
+      year           = "2015",
+      pages          = "017",
+      doi            = "10.1007/JHEP01(2015)017",
+      eprint         = "1407.7529",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "CERN-PH-TH-2014-140, LYCEN-2014-11",
+      SLACcitation   = "%%CITATION = ARXIV:1407.7529;%%"
+}
+
+@article{Agram:2013wda,
+      author         = "Agram, Jean-Laurent and Andrea, Jeremy and Buttignol,
+                        Michael and Conte, Eric and Fuks, Benjamin",
+      title          = "{Monotop phenomenology at the Large Hadron Collider}",
+      journal        = "Phys. Rev.",
+      volume         = "D89",
+      year           = "2014",
+      number         = "1",
+      pages          = "014028",
+      doi            = "10.1103/PhysRevD.89.014028",
+      eprint         = "1311.6478",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "CERN-PH-TH-2013-277",
+      SLACcitation   = "%%CITATION = ARXIV:1311.6478;%%"
+}
+
+@article{Andrea:2011ws,
+      author         = "Andrea, J. and Fuks, B. and Maltoni, F.",
+      title          = "{Monotops at the LHC}",
+      journal        = "Phys. Rev.",
+      volume         = "D84",
+      year           = "2011",
+      pages          = "074025",
+      doi            = "10.1103/PhysRevD.84.074025",
+      eprint         = "1106.6199",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "CP3-11-21, IPHC-PHENO-11-03",
+      SLACcitation   = "%%CITATION = ARXIV:1106.6199;%%"
+}
+
+@article{Davoudiasl:2011fj,
+      author         = "Davoudiasl, Hooman and Morrissey, David E. and Sigurdson,
+                        Kris and Tulin, Sean",
+      title          = "{Baryon Destruction by Asymmetric Dark Matter}",
+      journal        = "Phys. Rev.",
+      volume         = "D84",
+      year           = "2011",
+      pages          = "096008",
+      doi            = "10.1103/PhysRevD.84.096008",
+      eprint         = "1106.4320",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      SLACcitation   = "%%CITATION = ARXIV:1106.4320;%%"
+}
+
+@article{Kamenik:2011nb,
+      author         = "Kamenik, Jernej F. and Zupan, Jure",
+      title          = "{Discovering Dark Matter Through Flavor Violation at the
+                        LHC}",
+      journal        = "Phys. Rev.",
+      volume         = "D84",
+      year           = "2011",
+      pages          = "111502",
+      doi            = "10.1103/PhysRevD.84.111502",
+      eprint         = "1107.0623",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      SLACcitation   = "%%CITATION = ARXIV:1107.0623;%%"
+}
+
+@article{Alvarez:2013jqa,
+      author         = "Alvarez, Ezequiel and Coluccio Leskow, Estefania and
+                        Drobnak, Jure and Kamenik, Jernej F.",
+      title          = "{Leptonic Monotops at LHC}",
+      journal        = "Phys. Rev.",
+      volume         = "D89",
+      year           = "2014",
+      number         = "1",
+      pages          = "014016",
+      doi            = "10.1103/PhysRevD.89.014016",
+      eprint         = "1310.7600",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      SLACcitation   = "%%CITATION = ARXIV:1310.7600;%%"
+}
+
+@article{Aad:2014wza,
+      author         = "Aad, Georges and others",
+      title          = "{Search for invisible particles produced in association
+                        with single-top-quarks in proton-proton collisions at
+                        $\sqrt{s}$ = 8 TeV with the ATLAS detector}",
+      collaboration  = "ATLAS",
+      journal        = "Eur. Phys. J.",
+      volume         = "C75",
+      year           = "2015",
+      number         = "2",
+      pages          = "79",
+      doi            = "10.1140/epjc/s10052-014-3233-4",
+      eprint         = "1410.5404",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ex",
+      reportNumber   = "CERN-PH-EP-2014-231",
+      SLACcitation   = "%%CITATION = ARXIV:1410.5404;%%"
+}
+
+@article{CMS:2017gin,
+      author         = "{CMS Collaboration}",
+      title          = "{Search for dark matter in final states with a top quark
+                        and missing transverse momentum using new hadronic top
+                        quark tagging techniques}",
+      year           = "2017",
+      journal        = "CMS-PAS-EXO-16-051",
+      SLACcitation   = "%%CITATION = CMS-PAS-EXO-16-051;%%"
+}
+
+@article{Khachatryan:2014uma,
+      author         = "Khachatryan, Vardan and others",
+      title          = "{Search for Monotop Signatures in Proton-Proton
+                        Collisions at $\sqrt s =$ 8 TeV}",
+      collaboration  = "CMS",
+      journal        = "Phys. Rev. Lett.",
+      volume         = "114",
+      year           = "2015",
+      number         = "10",
+      pages          = "101801",
+      doi            = "10.1103/PhysRevLett.114.101801",
+      eprint         = "1410.1149",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ex",
+      reportNumber   = "CMS-B2G-12-022, CERN-PH-EP-2014-225",
+      SLACcitation   = "%%CITATION = ARXIV:1410.1149;%%"
+}
+
+@article{Artoisenet:2012st,
+      author         = "Artoisenet, Pierre and Frederix, Rikkert and Mattelaer,
+                        Olivier and Rietkerk, Robbert",
+      title          = "{Automatic spin-entangled decays of heavy resonances in
+                        Monte Carlo simulations}",
+      journal        = "JHEP",
+      volume         = "03",
+      year           = "2013",
+      pages          = "015",
+      doi            = "10.1007/JHEP03(2013)015",
+      eprint         = "1212.3460",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "NIKHEF-2012-021, CERN-PH-TH-2012-329",
+      SLACcitation   = "%%CITATION = ARXIV:1212.3460;%%"
+}
+
+@article{Chatrchyan:2012jua,
+      author         = "Chatrchyan, Serguei and others",
+      title          = "{Identification of b-quark jets with the CMS experiment}",
+      collaboration  = "CMS",
+      journal        = "JINST",
+      volume         = "8",
+      year           = "2013",
+      pages          = "P04013",
+      doi            = "10.1088/1748-0221/8/04/P04013",
+      eprint         = "1211.4462",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ex",
+      reportNumber   = "CMS-BTV-12-001, CERN-PH-EP-2012-262",
+      SLACcitation   = "%%CITATION = ARXIV:1211.4462;%%"
+}
+
+@article{Kraml:2013mwa,
+      author         = "Kraml, Sabine and Kulkarni, Suchita and Laa, Ursula and
+                        Lessa, Andre and Magerl, Wolfgang and
+                        Proschofsky-Spindler, Doris and Waltenberger, Wolfgang",
+      title          = "{SModelS: a tool for interpreting simplified-model
+                        results from the LHC and its application to
+                        supersymmetry}",
+      journal        = "Eur. Phys. J.",
+      volume         = "C74",
+      year           = "2014",
+      pages          = "2868",
+      doi            = "10.1140/epjc/s10052-014-2868-5",
+      eprint         = "1312.4175",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      SLACcitation   = "%%CITATION = ARXIV:1312.4175;%%"
+}
+
+@article{Papucci:2014rja,
+      author         = "Papucci, Michele and Sakurai, Kazuki and Weiler, Andreas
+                        and Zeune, Lisa",
+      title          = "{Fastlim: a fast LHC limit calculator}",
+      journal        = "Eur. Phys. J.",
+      volume         = "C74",
+      year           = "2014",
+      number         = "11",
+      pages          = "3163",
+      doi            = "10.1140/epjc/s10052-014-3163-1",
+      eprint         = "1402.0492",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "CERN-PH-TH-2014-019, DESY-14-010, KCL-PH-TH-2014-04,
+                        MCTP-14-03",
+      SLACcitation   = "%%CITATION = ARXIV:1402.0492;%%"
+}
+
+@article{Drees:2013wra,
+      author         = "Drees, Manuel and Dreiner, Herbi and Schmeier, Daniel and
+                        Tattersall, Jamie and Kim, Jong Soo",
+      title          = "{CheckMATE: Confronting your Favourite New Physics Model
+                        with LHC Data}",
+      journal        = "Comput. Phys. Commun.",
+      volume         = "187",
+      year           = "2015",
+      pages          = "227-265",
+      doi            = "10.1016/j.cpc.2014.10.018",
+      eprint         = "1312.2591",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "ADP-13-29-T849, IFT-UAM-CSIC-13-133,
+                        ADP-13-29-T849-IFT-UAM-CSIC-13-133",
+      SLACcitation   = "%%CITATION = ARXIV:1312.2591;%%"
+}
+
+@article{Buckley:2010ar,
+      author         = "Buckley, Andy and Butterworth, Jonathan and Lonnblad,
+                        Leif and Grellscheid, David and Hoeth, Hendrik and Monk,
+                        James and Schulz, Holger and Siegert, Frank",
+      title          = "{Rivet user manual}",
+      journal        = "Comput. Phys. Commun.",
+      volume         = "184",
+      year           = "2013",
+      pages          = "2803-2819",
+      doi            = "10.1016/j.cpc.2013.05.021",
+      eprint         = "1003.0694",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "MCNET-10-03",
+      SLACcitation   = "%%CITATION = ARXIV:1003.0694;%%"
+}
+
+@article{Balazs:2017moi,
+      author         = "Balázs, Csaba and others",
+      title          = "{ColliderBit: a GAMBIT module for the calculation of
+                        high-energy collider observables and likelihoods}",
+      collaboration  = "GAMBIT",
+      journal        = "Eur. Phys. J.",
+      volume         = "C77",
+      year           = "2017",
+      number         = "11",
+      pages          = "795",
+      doi            = "10.1140/epjc/s10052-017-5285-8",
+      eprint         = "1705.07919",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      SLACcitation   = "%%CITATION = ARXIV:1705.07919;%%"
+}
+
+@article{Andersen:2014efa,
+      author         = "Andersen, J. R. and others",
+      title          = "{Les Houches 2013: Physics at TeV Colliders: Standard
+                        Model Working Group Report}",
+      year           = "2014",
+      eprint         = "1405.1067",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      SLACcitation   = "%%CITATION = ARXIV:1405.1067;%%"
+}
+
+@article{Cheng:2008hk,
+      author         = "Cheng, Hsin-Chia and Han, Zhenyu",
+      title          = "{Minimal Kinematic Constraints and m(T2)}",
+      journal        = "JHEP",
+      volume         = "12",
+      year           = "2008",
+      pages          = "063",
+      doi            = "10.1088/1126-6708/2008/12/063",
+      eprint         = "0810.5178",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      SLACcitation   = "%%CITATION = ARXIV:0810.5178;%%"
+}
+@article{Lester:1999tx,
+      author         = "Lester, C. G. and Summers, D. J.",
+      title          = "{Measuring masses of semiinvisibly decaying particles
+                        pair produced at hadron colliders}",
+      journal        = "Phys. Lett.",
+      volume         = "B463",
+      year           = "1999",
+      pages          = "99-103",
+      doi            = "10.1016/S0370-2693(99)00945-4",
+      eprint         = "hep-ph/9906349",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "CAVENDISH-HEP-99-07",
+      SLACcitation   = "%%CITATION = HEP-PH/9906349;%%"
+}
+
+@article{Bai:2012gs,
+      author         = "Bai, Yang and Cheng, Hsin-Chia and Gallicchio, Jason and
+                        Gu, Jiayin",
+      title          = "{Stop the Top Background of the Stop Search}",
+      journal        = "JHEP",
+      volume         = "07",
+      year           = "2012",
+      pages          = "110",
+      doi            = "10.1007/JHEP07(2012)110",
+      eprint         = "1203.4813",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "SLAC-PUB-14897",
+      SLACcitation   = "%%CITATION = ARXIV:1203.4813;%%"
+}
+
+@article{Randall:2008rw,
+      author         = "Randall, Lisa and Tucker-Smith, David",
+      title          = "{Dijet Searches for Supersymmetry at the LHC}",
+      journal        = "Phys. Rev. Lett.",
+      volume         = "101",
+      year           = "2008",
+      pages          = "221803",
+      doi            = "10.1103/PhysRevLett.101.221803",
+      eprint         = "0806.1049",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      SLACcitation   = "%%CITATION = ARXIV:0806.1049;%%"
+}
+
+@article{Brun:1997pa,
+      author         = "Brun, R. and Rademakers, F.",
+      title          = "{ROOT: An object oriented data analysis framework}",
+      booktitle      = "{New computing techniques in physics research V.
+                        Proceedings, 5th International Workshop, AIHENP '96,
+                        Lausanne, Switzerland, September 2-6, 1996}",
+      journal        = "Nucl. Instrum. Meth.",
+      volume         = "A389",
+      year           = "1997",
+      pages          = "81-86",
+      doi            = "10.1016/S0168-9002(97)00048-X",
+      SLACcitation   = "%%CITATION = NUIMA,A389,81;%%"
+}
+
+@article{Ambrogi:2017neo,
+      author         = "Ambrogi, Federico and Kraml, Sabine and Kulkarni, Suchita
+                        and Laa, Ursula and Lessa, Andre and Magerl, Veronika and
+                        Sonneveld, Jory and Traub, Michael and Waltenberger,
+                        Wolfgang",
+      title          = "{SModelS v1.1 user manual: Improving simplified model
+                        constraints with efficiency maps}",
+      journal        = "Comput. Phys. Commun.",
+      volume         = "227",
+      year           = "2018",
+      pages          = "72-98",
+      doi            = "10.1016/j.cpc.2018.02.007",
+      eprint         = "1701.06586",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      reportNumber   = "LPSC17001, HEPHY-PUB-981-17",
+      SLACcitation   = "%%CITATION = ARXIV:1701.06586;%%"
+}
+
+@inproceedings{Fuks:2018yku,
+      author         = "Fuks, Benjamin and others",
+      title          = "{Proceedings of the first MadAnalysis 5 workshop on LHC
+                        recasting in Korea}",
+      pages = "35-39",
+      year           = "2018",
+      eprint         = "1806.02537",
+      archivePrefix  = "arXiv",
+      primaryClass   = "hep-ph",
+      SLACcitation   = "%%CITATION = ARXIV:1806.02537;%%"
+}

=== added file 'doc/normal_mode/main_normal.tex'
--- doc/normal_mode/main_normal.tex	1970-01-01 00:00:00 +0000
+++ doc/normal_mode/main_normal.tex	2019-02-13 11:05:44 +0000
@@ -0,0 +1,641 @@
+\documentclass[a4paper]{article}
+
+%% Language and font encodings
+\usepackage[english]{babel}
+\usepackage[utf8x]{inputenc}
+\usepackage[T1]{fontenc}
+\usepackage{url,slashed,multirow,cite,verbdef}
+\usepackage{hyperref}
+
+%% Sets page size and margins
+\usepackage[a4paper,top=3cm,bottom=2cm,left=3cm,right=3cm,marginparwidth=1.75cm]{geometry}
+
+%% Useful packages
+\usepackage{amsmath}
+\usepackage{graphicx}
+\usepackage{xcolor}
+\definecolor{ao}{rgb}{0.0, 0.0, 0.55}
+\usepackage{url}
+% faire des boites
+\usepackage{framed,color}
+\definecolor{shadecolor}{rgb}{0.4, 0.6, 0.8}
+
+% Tools
+\newcommand{\MG}{\textsc{MadGraph}~5\_aMC@NLO}
+\newcommand{\PY}{\textsc{Pythia}~8}
+\newcommand{\MA}{\textsc{MadAnalysis}~5}
+\newcommand{\MW}{\textsc{MadWidth}}
+\newcommand{\MS}{\textsc{MadSpin}}
+\newcommand{\MAnorm}{{MadAnalysis}~5}
+\newcommand{\FJ}{\textsc{FastJet}}
+\newcommand{\FJnorm}{{FastJet}}
+\newcommand{\DEL}{\textsc{Delphes}}
+\newcommand{\DELnorm}{{Delphes}}
+\newcommand{\ROOT}{\textsc{Root}}
+\newcommand{\lhe}{\textsc{Lhe}}
+\newcommand{\lhco}{\textsc{Lhco}}
+\newcommand{\hepmc}{\textsc{HepMC}}
+\newcommand{\stdhep}{\textsc{StdHep}}
+\newcommand{\INSP}{\textsc{Inspire}}
+\newcommand{\python}{\textsc{Python}}
+\newcommand{\spla}{\textsc{SampleAnalyzer}}
+%latin
+\newcommand{\eg}{\textit{e.g.}}
+\newcommand{\ie}{\textit{i.e.}}
+\newcommand{\etc}{\textit{etc.}}
+
+% environments
+\def\be{\begin{equation}}
+\def\ee{\end{equation}}
+\def\bsp#1\esp{\begin{split}#1\end{split}}
+
+
+
+
+
+
+\begin{document}
+\begin{center} 
+{\color{ao} \huge \textbf{\textsc{MadAnalysis} 5 v1.6}} \\ \vspace{0.25cm}
+{\color{ao} \huge \textbf{Normal-Mode reference card}} \\ \vspace{0.25cm}
+\vspace{0.1cm} \textsl{\today}\\
+\vspace{0.1cm} \textsl{website: \url{http://madanalysis.irmp.ucl.ac.be/}}\\
+\vspace{0.1cm} \textsl{references: \href{https://arxiv.org/abs/1206.1599}{arXiv:1206.1599[hep-ph]}, \href{https://arxiv.org/abs/1405.3982}{arXiv:1405.3982[hep-ph]}, \href{https://arxiv.org/abs/1407.3278}{arXiv:1407.3278[hep-ph]}}
+\end{center}
+
+\hspace{0.5cm}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{shaded}
+\section{\Large Starting the \MAnorm\ interpreter}
+\end{shaded}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\noindent The \MA\ command line interface can be started by typing in a shell\\
+{\color{ao}\begin{verbatim} bin/ma5 [options] [script] \end{verbatim}}
+\noindent where the potential options ({\color{ao}\verb+[options]+}) are given in the table below.
+\verbdef{\vv}{-v}
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{ p{2cm} p{2.5cm} p{8.1cm}}
+\hline
+Short & Full & Description\\
+\hline
+\color{ao}\verb?-P? & \color{ao}\verb?--partonlevel? & Parton-level mode.\\
+\color{ao}\verb?-H? & \color{ao}\verb?--hadronlevel? & Hadron-level mode.\\
+\color{ao}\verb?-R? & \color{ao}\verb?--recolevel?   & Reconstructed-level mode.\\
+\color{ao}\verb?-E? & \color{ao}\verb?--expert?      & Expert mode.\\
+\multirow{2}{*}{\color{ao}\vv} & \color{ao}\verb?--version?
+          & \multirow{2}{*}{Displays the current \MA\ version number.}\\
+          &  \color{ao}\verb?--release?    & \\
+\color{ao}\verb?-b? & \color{ao}\verb?--build?       & Builds of the \spla\ library.\\
+\color{ao}\verb?-f? & \color{ao}\verb?--forced?      & Skips \MA\ confirmation messages.\\
+\color{ao}\verb?-s? & \color{ao}\verb?--script?      & Executes a script containing all analysis
+    commands and exits the program. The file containing the script has to be
+    provided as {\color{ao}\verb+[script]+}. Removing the {\color{ao}\verb+-s+}
+    option prevents \MA\ from exiting.\\
+\color{ao}\verb?-h? & \color{ao}\verb?--help?        & Print all the available commands.\\
+\color{ao}\verb?-i? & \color{ao}\verb?--installcard? & Generates a file with information on the
+     \MA\ dependencies, \verb?installation_card.dat?, that is located in the
+     \verb+madanalysis/input+ folder.\\
+\color{ao}\verb?-d? & \color{ao}\verb?--debug?       & Debug mode.\\
+\hline
+\end{tabular}
+\end{center}
+In case of installation issues, the usage of the dependencies can be tuned by
+editing the file:\\
+{\centering \color{ao} \verb?madanalysis/input/installation_options.dat?}\\
+\noindent More information can be found in the original \MA\ manual~\cite{Conte:2012fm}.
+\newpage
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{shaded}
+\section{\Large Installation of optional packages}
+\end{shaded}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\noindent \MA\ is interfaced to several high-energy physics packages and can be linked to
+a variety of external plugins. Any of those can be installed by typing in the
+\MA\ interpreter,
+{\color{ao}\begin{verbatim} install [package]\end{verbatim}}
+where the different choices for \verb+[package]+ are given in the table below.
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{l p{9.2cm}}
+\hline
+Package & Description\\
+\hline
+\color{ao} \verb?PAD?            & The \MA\ Public Analysis Database of recasted LHC
+   analyses relying on \DEL~3 for the simulation of the detector effects.\\
+\color{ao}\verb?PADforMA5tune?  & The \MA\ Public Analysis Database of recasted LHC
+   analyses relying on the old tuned version of \DEL~3 for the simulation of the
+   detector effects.\\
+\color{ao}\verb?delphes?        & The current release of \DEL~3.\\
+\color{ao}\verb?delphesMA5tune? & The old tuned version of \DEL~3.\\
+\color{ao}\verb?fastjet?        & The \FJ\ and {\sc FastJetContrib} packages.\\
+\color{ao}\verb?samples?        & Some test Monte Carlo samples.\\
+\color{ao}\verb?zlib?           & The {\sc ZLib} library allowing to handle gzipped
+                        compressed files.\\
+\hline
+\end{tabular}
+\end{center}
+\vspace{2cm}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{shaded}
+\section{\Large Commands available from the \MAnorm\ interpreter}
+\end{shaded}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\noindent A small set of commands, to be typed from the \MA\ interpreter, are related to
+console actions.\\
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{l p{8.8cm}}
+\hline
+Command & Description\\
+\hline
+\color{ao} \verb?quit?           & \multirow{2}{*}{Exits \MA.}\\
+\color{ao} \verb?EOF?            & \\
+\color{ao} \verb?help?           & Displays the list of available commands.\\
+\color{ao} \verb?help [command]? & Displays details about a specific command.\\
+\color{ao} \verb?history?        & Displays the history of all commands that have been
+                        typed by the user.\\
+\color{ao} \verb?reset?          & Clears the \MA\ memory as when the program is started.\\
+\color{ao} \verb?restart?        & Restarts \MA.\\
+\color{ao} \verb?shell [command]?& \multirow{2}{*}{Executes a {\sc Unix} command from the
+   interpreter.}\\
+\color{ao} \verb?![command]?     & \\
+\color{ao} \verb?#[text]?        & Indicates a comment.\\
+\hline
+\end{tabular}
+\end{center}
+\verbdef{\verbtexta}{define [(multi)particle label] = [ID1] [ID2] ...}
+\verbdef{\verbtextb}{define_region [label1] [label2] ...}
+\verbdef{\verbtextc}|plot [obs]([part1] [part2] ...) nbins min max [ [opts] ] { [regs] }|
+\verbdef{\verbtextda}{reject ([part]) [criterion]}
+\verbdef{\verbtextdb}{select ([part]) [criterion]}
+\verbdef{\verbtexte}{[criterion]}
+\verbdef{\verbtextf}{swap main.selection[n1] main.selection[n2]}
+In order to design an analysis in the \MA\ framework, the user can rely on the
+following commands.
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{p{3.40cm} p{8.75cm}}
+\hline
+Command & Description\\
+\hline
+\multicolumn{2}{l}{\color{ao} \verbtexta}\\
+   & Creates a new (multi)particle label attached to the provided PDG codes
+      \verb+[ID1]+, \verb+[ID2]+, $\ldots$\\
+\multicolumn{2}{l}{\color{ao} \verbtextb}\\
+   & Creates one or more signal regions named \verb+[label1]+, \verb+[label2]+,
+   ...\\
+\color{ao} \verb?import [label]?        & Imports a sample or a UFO model.\\
+\color{ao} \verb?open [folder]?         & Opens a report from the folder \verb?[folder]?.
+   If the folder is unspecified, the last created report is open.\\
+\multicolumn{2}{l}{\color{ao} \verbtextc}\\
+   & Defines a histogram with the distribution in the observable \verb?[obs]?.
+    Its computation may require to combine the momenta of several objects
+    \verb?[part1]?, \verb+[part2]+, $\ldots$ Any other parameter is optional.
+    The \verb?nbins?,
+    \verb?min? and \verb?max? quantities respectively correspond to the number
+    of bins, and the upper and lower bound of the $x$-axis of the histogram. The
+    options \verb?[opts]? (see below) allow the user to tune the
+    display of the histogram, and \verb+[regs]+ indicates to which signal region
+    one needs to attach this histogram.\\
+\color{ao} \verb?reject [criterion]?
+\color{ao} \verb?select [criterion]? & Defines a selection cut that leads
+  to the rejection (or selection) of an event if the \verbtexte condition is
+  satisfied.\\
+\multicolumn{2}{l}{\color{ao} \verbtextda}\\
+\multicolumn{2}{l}{\color{ao} \verbtextdb}\\
+  & Defines a selection cut that leads to the rejection (or selection) of an
+    object candidate if the \verb?[criterion]? condition is satisfied.\\
+\color{ao} \verb?remove [object]? & Deletes an object (a (multi)particle label, a region, a
+ histogram or a cut).\\
+\color{ao} \verb?resubmit? & Adjusts the last generated C++ code relatively to the commands
+  issued after the last \verb?submit? command, and executes it.\\
+\color{ao} \verb?set [obj] = [val]? & Sets an attribute of a specific object to a given
+  value.\\
+\color{ao} \verb?submit [folder]? & Generates, compiles and executes the C++ code
+  corresponding to the current analysis either in a folder named
+  \verb?[folder]?, if specified, or in an arbitrary folder otherwise.\\
+\multicolumn{2}{l}{\color{ao} \verbtextf}\\ & Swaps the analysis steps
+   number \verb?[n1]? and \verb?[n2]?.\\
+\hline
+\end{tabular}
+\end{center}
+Throughout the analysis, information can be printed to the screen by means of
+the following commands.
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{p{4.00cm} p{7.70cm}}
+\hline
+Command & Description\\
+\hline
+\color{ao} \verb+display [object]+       & Displays the properties of a specific object.\\
+\color{ao} \verb+display_datasets+       & Displays the list of all defined datasets.\\
+\color{ao} \verb+display_multiparticles+ &
+   Displays the list of all defined multiparticle labels.\\
+\color{ao} \verb+display_particles+      &
+   Displays the list of all defined particle labels.\\
+\color{ao} \verb+display_regions+        &
+   Displays the list of all defined signal regions.\\
+\hline
+\end{tabular}
+\end{center}
+\newpage
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{shaded}
+\section{\Large Properties of the main object}
+\end{shaded}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+The \verb+main+ object of \MA\ allows to setup varied options (see the table
+below) to impact the code on run time. They can be modified and
+displayed by using the \verb+set+ and \verb+display+ commands introduced above.\\
+
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{l p{7.50cm}}
+\hline
+Command & Description\\
+\hline
+\color{ao} \verb?main.currentdir?     & Folder containing \MA.\\
+\color{ao} \verb?main.fastsim.package?& The package used for the fast-simulation of the
+  detector response. The available choices are \verb?fastjet?, \verb?delphes?,
+  \verb?delphesMA5tune? and \verb?none?.\\
+\color{ao} \verb?main.fom.formula?    & Formula to be used to calculate the figure of merit
+  in the cutflow charts. Denoting by $S$ and $B$ the number of signal and
+  background events, the available choices are 1 ($S/B$), 2 ($S/\sqrt{B}$), 3
+  ($S/\sqrt{B}$), 4 ($S/\sqrt{S+B}$) and 5 ($S/\sqrt{S+B+x_B^2}$). For this last
+  formula, the $x_B$ parameter is specified via \verb?main.fom.x?.\\
+\color{ao} \verb?main.graphic_render? & Package to use for figure generation. The
+  available choices are \verb?root?, \verb?matplotlib? and \verb?none?.\\
+\color{ao} \verb?main.isolation.algorithm? & Algorithm to be used for particle isolation.
+  The available choices are \verb?cone? (no activity in a cone of radius
+  specified by \verb+main.isolation.radius+) and \verb+sumpt+ (the scalar sum of
+  the transverse momenta of all particles lying in a given cone around the
+  candidate must be smaller than \verb?main.isolation.sumPT? and the ratio of
+  the transverse energy of all particles in this cone to the transverse momentum
+  of the candidate must be smaller than
+  \verb?main.isolation.ET_PT?).\\
+\end{tabular}
+\begin{tabular}{l p{8.4cm}}
+\color{ao} \verb?main.lumi? & Integrated luminosity, in $\textrm{fb}^{-1}$, to use for
+  histogram and cutflow normalization.\\
+\color{ao} \verb?main.normalize? & Way in which histograms have to be normalized. The
+  available choices are \verb?none? (each event counts for 1), \verb?lumi?
+  (normalization to the integrated luminosity without taking into account the
+  event weights), \verb?lumi_weight? (as \verb?lumi? but with the
+  event weights).\\
+\color{ao} \verb?main.outputfile? & Name of the output file to write events onto.\\
+\color{ao} \verb?main.recast? & Switching the recasting mode \verb?on? and \verb?off?.\\
+\color{ao} \verb?main.stacking_method? & Way in which the contributions of the different
+  datasets to a histogram are displayed. The available choices are
+  \verb?normalize2one? (the integral of each contribution equals 1),
+  \verb?stack? (each contribution is stacked) and \verb?superimpose? (each
+  contribution is superimposed).\\
+\hline
+\end{tabular}
+\end{center}
+\newpage 
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{shaded}
+\section{\Large Observables to be used for histograms and cuts}
+\end{shaded}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+As shown in the tables above, the definition of a histogram or of a cut
+condition necessitates to provide an observable that could depend on the momentum
+of one or more particles or objects. We list in the tables below all observables
+supported by \MA, and begin with those that do not depend on the momenta of any
+object. They are therefore called without any argument.\\
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{l p{10.2cm}}
+\hline
+Symbol& Description\\
+\hline
+\color{ao} \verb?ALPHA_QCD? & Value of the QCD coupling constant.\\
+\color{ao} \verb?ALPHA_QED? & Value of the electromagnetic coupling constant.\\
+\color{ao} \verb?ALPHA_T?   & The $\alpha_T$ variable\cite{Randall:2008rw}.\\
+\color{ao} \verb?MEFF?      & Effective mass being defined as the sum of the transverse
+                   momentum of all final-state objects and the missing
+                   transverse energy.\\
+\color{ao} \verb?MET?       & Missing transverse energy.\\
+\color{ao} \verb?MHT?       & Missing transverse energy defined from the jet activity
+                   only.\\
+\color{ao} \verb?NPID?      & Particle content (PDG code distribution).\\
+\color{ao} \verb?NAPID?     & Particle content (PDG code distribution in
+                   absolute value).\\
+\color{ao} \verb?SQRTS?     & Partonic center-of-mass energy.\\
+\color{ao} \verb?SCALE?     & Energy scale of the event.\\
+\color{ao} \verb?TET?       & Scalar sum of the transverse energy of all final-state
+                   objects.\\
+\color{ao} \verb?THT?       & Scalar sum of the transverse energy of all final-state
+                   jets.\\
+\color{ao} \verb?WEIGHTS?   & Event weights.\\
+\hline
+\end{tabular}
+\end{center}
+The set of observables provided in the following table can be used to study the
+properties of a given object or particle, and thus requires to provide one
+four-momentum or one combination of four-momenta as an argument of the
+observable function.
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{l p{10.2cm}}
+\hline
+Symbol& Description\\
+\hline
+\color{ao} \verb?ABSETA? & Absolute value of the pseudorapidity.\\
+\color{ao} \verb?BETA?   & Velocity $\beta=v/c$ (relatively to the speed of light).\\
+\color{ao} \verb?E?      & Energy.\\
+\color{ao} \verb?EE_HE?  & Ratio of the electromagnetic energy to the hadronic energy (for
+   a jet).\\
+\color{ao} \verb?ET?     & Transverse energy.\\
+\color{ao} \verb?ETA?    & Pseudorapidity.\\
+\color{ao} \verb?GAMMA?  & Lorentz-factor.\\
+\color{ao} \verb?HE_EE?  & Ratio of the hadronic energy to the electromagnetic energy (for
+   a jet).\\
+\color{ao} \verb?M?      & Invariant mass.\\
+\color{ao} \verb?MT?     & Transverse mass.\\
+\color{ao} \verb?MT_MET? & Transverse mass of the system comprised of the object and the
+   missing momentum.\\
+\color{ao} \verb?NTRACKS?& Number of tracks (inside a jet).\\
+\color{ao} \verb?P?      & Magnitude of the three-momentum.\\
+\color{ao} \verb?PHI?    & Azimuthal angle.\\
+\color{ao} \verb?PT?     & Transverse momentum.\\
+\color{ao} \verb?PX?     & $x$-component of the momentum.\\
+\color{ao} \verb?PY?     & $y$-component of the momentum.\\
+\color{ao} \verb?PZ?     & $z$-component of the momentum.\\
+\color{ao} \verb?R?      & Position in the $(\eta, \phi)$ plane.\\
+\color{ao} \verb?Y?      & Rapidity.\\
+\hline
+\end{tabular}
+\end{center}
+\noindent Three additional observables involving two objects are also available, the
+methods given in the table below taking thus two arguments separated by a comma.
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{l p{10.0cm}}
+\hline
+Symbol& Description\\
+\hline
+\color{ao} \verb?DELTAR?     & Angular distance, in the transverse plane, between the
+  objects.\\
+\color{ao} \verb?DPHI_0_PI?  & Angular distance in azimuth between the objects. The
+  bounds for the angle are $[0,\pi]$.\\
+\color{ao} \verb?DPHI_0_2PI? & Angular distance in azimuth between the objects. The
+  bounds for the angle are $[0,2\pi]$.\\
+\hline
+\end{tabular}
+\end{center}
+\noindent For all arguments of any of the above observable, any sequence of momenta
+separated with spaces will lead to a sum of these momenta before computing the
+observable. For instance,
+{\color{ao} \begin{verbatim}
+  plot M(e+ e-)
+\end{verbatim}}
+\noindent allows for the computation of the invariant of an electron-positron system.
+\newpage
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{shaded}
+\section{\Large Options for histograms}
+\end{shaded}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\noindent The command \verb+plot+ accept varied options \verb+[opts]+,
+{\color{ao} \begin{verbatim}
+plot [obs]([part1] [part2] ...) nbins min max [ [opts] ] { [regs] }
+\end{verbatim}}
+to be provided between squared brackets. The list of all available choices is
+given in the table below.
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{l p{9.4cm}}
+\hline
+Symbol& Description\\
+\hline
+\color{ao} \verb?Eordering?     & Sorts the objects in increasing energy.\\
+\color{ao} \verb?ETordering?    & Sorts the objects in increasing transverse energy.\\
+\color{ao} \verb?ETAordering?   & Sorts the objects in increasing pseudorapidity.\\
+\color{ao} \verb?Pordering?     & Sorts the objects in increasing three-momentum magnitude.
+  \\
+\color{ao} \verb?PTordering?    & Sorts the objects in increasing transverse momentum.\\
+\color{ao} \verb?PXordering?    & Sorts the objects in increasing momentum $x$-component.\\
+\color{ao} \verb?PYordering?    & Sorts the objects in increasing momentum $y$-component.\\
+\color{ao} \verb?PZordering?    & Sorts the objects in increasing momentum $z$-component.\\
+\color{ao} \verb?allstate?      & Considers all (initial-state, final-state and
+  intermediate-state) objects in the events.\\
+\color{ao} \verb?finalstate?    & Considers only final-state objects (default).\\
+\color{ao} \verb?initialstate?  & Considers only initial-state objects.\\
+\color{ao} \verb?interstate?    & Considers only objects that are neither initial-state nor
+  final-state objects.\\
+\color{ao} \verb?logX?          & Logarithmic scale for the $x$-axis.\\
+\color{ao} \verb?logY?          & Logarithmic scale for the $y$-axis.\\
+\color{ao} \verb?normalize2one? & Normalizes the histogram to 1.\\
+\color{ao} \verb?stack?         & Stacks the contributions of different datasets in the
+  histogram.\\
+\color{ao} \verb?superimpose?   & Superimposes the contributions of different datasets in
+  the histogram.\\
+\hline
+\end{tabular}
+\end{center}
+
+\vspace{2cm}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{shaded}
+\section{\Large Options for datasets}
+\end{shaded}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\noindent Once one or more samples have been imported as a dataset, properties that will
+impact the display of the subsequent contribution in histograms can be modified
+by using the \verb+set+ command. For instance, a dataset named \verb?defaultset?
+can be imported as
+{\color{ao} \begin{verbatim}
+  import <path-to-sample> as defaultset
+\end{verbatim}}
+\noindent and its properties can be modified by typing in
+{\color{ao} \begin{verbatim}
+  set defaulset.<property> = <value>
+\end{verbatim}}
+\noindent The list of available properties is given in the table below, together with the
+allowed values.
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{l p{9.1cm}}
+\hline
+Symbol& Description\\
+\hline
+\color{ao} \verb?backcolor? & Background color in a histogram. The available colors are
+   \verb?auto?, \verb?black?, \verb?blue?, \verb?cyan?, \verb?green?,
+   \verb?grey?, \verb?none? (transparent), \verb?orange?, \verb?purple?,
+   \verb?red?, \verb?white? and \verb?yellow?. The color can be made lighter or
+    darker by adding an explicit $\pm 1$, $\pm 2$ or $\pm 3$.\\
+\color{ao} \verb?backstyle? & Background texture in a histogram. The available values are
+   \verb?dline? (diagonal-lines), \verb?dotted? (dots), \verb?hline? (horizontal
+   lines), \verb?solid? (uniform color) and \verb?vline? (vertical lines).\\
+\color{ao} \verb?linecolor? & Color of the histogram lines. The available colors are the
+   same as for the \verb?backcolor? attribute.\\
+\color{ao} \verb?linestyle? & Style of the histogram lines. The available values are
+   \verb?dash-dotted?, \verb?dashed?, \verb?dotted? and \verb?solid?.\\
+\color{ao} \verb?linewidth? & Width of the histogram lines, given as an integer smaller
+   than 10.\\
+\color{ao} \verb?title?     & Name of the dataset (for histogram legends).\\
+\color{ao} \verb?type?      & \verb?background? or \verb?signal? nature of a given sample
+  (for figure-of-merit calculations).\\
+\color{ao} \verb?weight?    & Reweights each histogram entry with a constant factor. The
+  value has to be a floating-point number.\\
+\color{ao} \verb?weighted_events? & Allows \MA\ to ignore the weights of the events
+  (property to be set to \verb?true? or \verb?false?).\\
+\color{ao} \verb?xsection?  & This overwrites the event sample cross section. The value has
+  to be given in pb.\\
+\hline
+\end{tabular}
+\end{center}
+
+\vspace{2cm}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{shaded}
+\section{\Large Using \FJnorm\ through \MAnorm}
+\end{shaded}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\noindent In order to activate the usage of \FJ\ through \MA, the program has to be
+started in the reconstructed mode and the first command to be typed in the
+interpreter has to be
+{\color{ao} \begin{verbatim}
+  set main.fastsim.package = fastjet
+\end{verbatim}}
+\noindent This allows for various option of the \verb+main.fastsim+ object, tuning the
+properties of the jet algorithm that has to be employed. Those options are set
+by typing in
+{\color{ao} \begin{verbatim}
+  set main.fastsim.<property> = <value>
+\end{verbatim}}
+\noindent the list of all available properties being presented, together with the allowed
+values, in the following table.
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{l p{9.4cm}}
+\hline
+Symbol& Description\\
+\hline
+\color{ao} \verb?algorithm? & Sets up the jet algorithm to use. The allowed
+  values are \verb?antikt?\cite{Cacciari:2008gp}, \verb?Cambridge?\cite{%
+   Dokshitzer:1997in,Wobisch:1998wt}, \verb?cdfjetclu?\cite{Abe:1991ui},
+   \verb?cdfmidpoint?\cite{Blazey:2000qt}, \verb?genkt?\cite{Cacciari:2011ma},
+   \verb?gridjet?\cite{Cacciari:2011ma}, \verb?kt?\cite{Catani:1993hr,%
+   Ellis:1993tq}, \verb?none? and \verb?siscone?\cite{Salam:2007xv}.\\
+\color{ao} \verb?areafraction? & Controls the size of the cones in the CDF midpoint
+  algorithm.\\
+\color{ao} \verb?exclusive_id? & Exclusive mode for jet reconstruction. If set
+  to \verb+false+, electrons muons and photons issued from hadron decays are
+  included into the electron, muon and photon collections respectively.\\
+\color{ao} \verb?input_ptmin? & Soft protojet threshold in the siscone
+  algorithm.\\
+\color{ao} \verb?iratch? & Switching on ratcheting for the CDF jet clustering algorithm.\\
+\color{ao} \verb?npassmax? & Number of iterations in the siscone algorithm.\\
+\color{ao} \verb?overlap? & Fraction of overlapping momentum used to combine
+  protojets in the siscone and CDF reconstruction algorithms.\\
+\color{ao} \verb?p? & $p$ parameter of the generalized $k_T$ algorithm.\\
+\color{ao} \verb?ptmin? & Threshold for the transverse momentum of the
+  reconstructed jets.\\
+\color{ao} \verb?radius? & Radius parameter relevant for most jet
+  clustering algorithms.\\
+\color{ao} \verb?seed? & Threshold parameter used in the constituent merging
+  procedure of the CDF reconstruction algorithms.\\
+\color{ao} \verb?spacing? & Grid spacing in the grid jet algorithm.\\
+\color{ao} \verb?ymax? & Maximum rapidity value in the grid jet algorithm.\\
+\hline
+\end{tabular}
+\end{center}
+\vspace{0.1cm}
+\noindent In addition, basic detector simulation effects can be mimicked through setting
+up the parameters included in the table below.
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{l p{8.4cm}}
+\hline
+Symbol& Description\\
+\hline
+\color{ao} \verb?bjet_id.efficiency? & $b$-tagging efficiency, as a float.\\
+\color{ao} \verb?bjet_id.exclusive? & Allows several $b$-jets to be issued from a single
+  $B$-hadron.\\
+\color{ao} \verb?bjet_id.matching_dr? & Angular distance parameter matching a $b$-jet
+  with a $B$-hadron.\\
+\color{ao} \verb?bjet_id.misid_cjet? & Mistagging rate of a $c$-jet as a $b$-jet, as
+  a float.\\
+\color{ao} \verb?bjet_id.misid_ljet? & Mistagging rate of a light jet as a $b$-jet,
+  as a float.\\
+\color{ao} \verb?tau_id.efficiency? & Tau-tagging efficiency, as a float.\\
+\color{ao} \verb?tau_id.misid_ljet? &  Mistagging rate of a light jet as a hadronic tau,
+   as a float.\\
+\hline
+\end{tabular}
+\end{center}
+
+\vspace{2cm}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{shaded}
+\section{\Large Using \DELnorm\ through \MAnorm}
+\end{shaded}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+\noindent In order to activate the usage of \DEL\ through \MA, the program has to be
+started in the reconstructed mode and the first command to be typed in the
+interpreter has to be
+{\color{ao}\begin{verbatim}
+  set main.fastsim.package = delphes
+\end{verbatim}}
+\noindent The properties of the simulation of the detector can then be adjusted through
+{\color{ao} \begin{verbatim}  set main.fastsim.<property> = <value>
+\end{verbatim}}
+the allowed choices being given in the table below.
+\renewcommand{\arraystretch}{1.2}%
+\begin{center}\begin{tabular}{l p{8.4cm}}
+\hline
+Symbol& Description\\
+\hline
+\color{ao} \verb?detector? & Determines which detector card to use. The card can be further
+  modified on run time).\\
+\color{ao} \verb?output?   & Saves the output \ROOT\ file (\verb+true+ or \verb+false+).\\
+\color{ao} \verb?rootfile? & Name of the output file.\\
+\color{ao} \verb?pileup? & Specifies the path to the input pile-up event file.\\
+\color{ao} \verb?skim_genparticles? & If set to \verb?true?, the generator-level
+  particles are not stored in the output file.\\
+\color{ao} \verb?skim_tracks? & If set to \verb?true?, the track collection is not stored
+  in the output file.\\
+\color{ao} \verb?skim_towers? & If set to \verb?true?, the collection of calorimetric
+  towers is not stored in the output file.\\
+\color{ao} \verb?skim_eflow? & If set to \verb?true?, the collection of particle-flow
+  towers is not stored in the output file.\\
+\hline
+\end{tabular}
+\end{center}
+
+\vspace{2cm}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{shaded}
+\section{\Large Multipartonic matrix element merging}
+\end{shaded}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\noindent \MA\ can be used to double check the merging procedure of event samples related
+to a given hard process but with matrix elements featuring a different
+final-state jet multiplicity. \MA\ has to be started in the hadronic mode, and
+the check is then performed by typing in
+{\color{ao}\begin{verbatim}
+ set main.merging.check = true
+\end{verbatim}}
+\noindent Two extra options are available,
+{\color{ao}\begin{verbatim}
+  set main.merging.ma5_mode = <true or false>
+  set main.merging.njets = <integer>
+\end{verbatim}}
+\noindent the first one indicating to extract the number of extra hard jets from the
+process identifier, and the second one setting up the maximum number of extra
+jets to consider.
+
+\newpage
+\bibliographystyle{plain} 
+\bibliography{main_normal}
+
+\end{document}

=== modified file 'madanalysis/IOinterface/job_writer.py'
--- madanalysis/IOinterface/job_writer.py	2018-05-29 21:42:05 +0000
+++ madanalysis/IOinterface/job_writer.py	2019-02-13 11:05:44 +0000
@@ -382,6 +382,20 @@
         return
 
     def CreateMainFct(self,file,analysisName,outputName):
+
+        # Info function
+        file.write('// -----------------------------------------------------------------------\n')
+        file.write('// Info function\n')
+        file.write('// -----------------------------------------------------------------------\n')
+        file.write('int Info(SampleAnalyzer& manager)\n')
+        file.write('{\n')
+        file.write('  INFO << "BEGIN " << __FILE__ << endmsg;\n')
+        file.write('  manager.AnalyzerList().Print();\n')
+        file.write('  INFO << "END " << __FILE__ << endmsg;\n')
+        file.write('  return 0;\n')
+        file.write('}\n')
+
+        # Main program
         file.write('// -----------------------------------------------------------------------\n')
         file.write('// main program\n')
         file.write('// -----------------------------------------------------------------------\n')
@@ -392,6 +406,15 @@
         file.write('  BuildUserTable(manager.AnalyzerList());\n')
         file.write('\n')
 
+        # Info about the job
+        file.write('  // Identifying --info argument\n')
+        file.write('  if (argc==2)\n')
+        file.write('  {\n')
+        file.write('    std::string arg=argv[1];\n')
+        file.write('    if (arg=="--info") return Info(manager);\n')
+        file.write('  }\n')
+        file.write('\n')
+
         # Initializing
         file.write('  // ---------------------------------------------------\n')
         file.write('  //                    INITIALIZATION\n')

=== modified file 'madanalysis/UpdateNotes.txt'
--- madanalysis/UpdateNotes.txt	2018-05-29 21:42:05 +0000
+++ madanalysis/UpdateNotes.txt	2019-02-13 11:05:44 +0000
@@ -1,7 +1,55 @@
 Update notes for MadAnalysis 5 (in reverse time order)
 
+<<<<<<< TREE
 123           (2018/05/29) fuks:    updating copyrights 
 
+=======
+156           (2019/02/07) fuks:    Adding the jet mass information to the delphes reader 
+
+155           (2019/01/23) fuks:    Fixing a typo in install_pad 
+
+154           (2019/01/17) fuks:    Fixing the linecolor bug #1807107 (connected to matplotlib) 
+
+153           (2019/01/17) fuks:    Reorganisation of the delphes(MA5tune) installation and activation 
+                                   modules 
+
+152           (2019/01/15) fuks:    Many improvements: PAD and PADForMA5tune are again both available; 
+                                   delphes installation, delphes ma5tune installation; delphes 
+                                   detection, compatiblitily of delphsma5tun with root6, etc. 
+
+149           (2018/11/24) fuks:    Updating delphesMA5tune installer 
+
+147           (2018/11/23) fuks:    Externalizing the PAD 
+
+139           (2018/11/20) fuks:    cleaning the code (syntax improvements) 
+
+138           (2018/10/14) fuks:    Bug fixing in LHE event reader 
+
+137           (2018/09/17) fuks:    Bug when reading the first event of an LHE file 
+
+136           (2018/09/11) fuks:    pad update 
+
+135           (2018/09/04) fuks:    Updating the PAD 
+
+134           (2018/08/28) fuks:    Adding analyses to the PAD 
+
+133           (2018/07/24) fuks:    Fixing a problem with the arguments 
+
+132           (2018/07/24) fuks:    Updating the PAD 
+
+129           (2018/07/10) fuks:    Bug fix #1780945 
+
+128           (2018/07/10) fuks:    fixing merging plot bug; first steps with tagging 
+
+127           (2018/06/26) fuks:    Adding some methods to the RecJetFormat class 
+
+126           (2018/06/06) fuks:    Updating the PAD 
+
+125           (2018/05/29) fuks:    Updating the copyrights 
+
+124           (2018/05/13) fuks:    Bug fix for deltaR used with combinations 
+
+>>>>>>> MERGE-SOURCE
 
 196  1.6   (2018/05/04) ma5team:    - Finalization of the interface with mg5
                                     - Two jet collections are now allowed in the expert mode

=== modified file 'madanalysis/configuration/fastsim_configuration.py'
--- madanalysis/configuration/fastsim_configuration.py	2018-05-29 21:42:05 +0000
+++ madanalysis/configuration/fastsim_configuration.py	2019-02-13 11:05:44 +0000
@@ -78,7 +78,7 @@
             return {}
 
 
-    def user_SetParameter(self,parameter,value,datasets,level,fastjet,delphes,delphesMA5tune):
+    def user_SetParameter(self,parameter,value,datasets,level,archi_info):
 
         # algorithm
         if parameter=="package":
@@ -112,17 +112,17 @@
                     return
                 
                 # Fastjet ?
-                if value=='fastjet' and not fastjet:
+                if value=='fastjet' and not archi_info.has_fastjet:
                     logging.getLogger('MA5').error("fastjet library is not installed. Clustering algorithms are not available.")
                     return
 
                 # Delphes ?
-                if value=='delphes' and not delphes:
+                if value=='delphes' and not archi_info.has_delphes:
                     logging.getLogger('MA5').error("delphes library is not installed. This fast-simulation package is not available.")
                     return
 
                 # DelphesMA5tune ?
-                if value=='delphesMA5tune' and not delphesMA5tune:
+                if value=='delphesMA5tune' and not archi_info.has_delphesMA5tune:
                     logging.getLogger('MA5').error("delphesMA5tune library is not installed. This fast-simulation package is not available.")
                     return
 

=== modified file 'madanalysis/configuration/fom_configuration.py'
--- madanalysis/configuration/fom_configuration.py	2018-05-29 21:42:05 +0000
+++ madanalysis/configuration/fom_configuration.py	2019-02-13 11:05:44 +0000
@@ -25,15 +25,17 @@
 import logging
 class FomConfiguration:
 
-    userVariables = { "formula" : ['1','2','3','4','5'] }
+    userVariables = { "formula" : ['1','2','3','4','5','6'] }
 
     # 1: S/B
     # 2: S/sqrt(B)
     # 3: S/(S+B)
     # 4: S/sqrt(S+B)
     # 5: S/sqrt(S+B+(xB)**2)
+    # 6: sqrt(2)*sqrt((S+B)log(1+S/B)-S)
 
-    allformula = [ 'S/B', 'S/sqrt(B)', 'S/(S+B)', 'S/sqrt(S+B)', 'S/sqrt(S+B+(xB)**2)' ]
+    allformula = [ 'S/B', 'S/sqrt(B)', 'S/(S+B)', 'S/sqrt(S+B)', 'S/sqrt(S+B+(xB)**2)',\
+                   'sqrt(2)*sqrt((S+B)log(1+S/B)-S)']
 
 
     def __init__(self):

=== modified file 'madanalysis/configuration/recast_configuration.py'
--- madanalysis/configuration/recast_configuration.py	2018-05-29 21:42:05 +0000
+++ madanalysis/configuration/recast_configuration.py	2019-02-13 11:05:44 +0000
@@ -47,60 +47,24 @@
         self.pad        = False
         self.padtune    = False
         self.store_root = False
-        self.DelphesDic = {
-          "delphes_card_cms_standard.tcl"         : ["cms_sus_14_001_monojet", "cms_sus_13_016", "cms_sus_13_012", "cms_sus_13_011"],
-          "delphes_card_cms_sus14004.tcl"         : ["cms_sus_14_001_TopTag"],
-          "delphes_card_atlas_sus_2013_05.tcl"    : ["atlas_susy_2013_21", "atlas_sus_13_05"],
-          "delphes_card_atlas_sus_2013_05_pad.tcl": ["ATLAS_EXOT_2014_06"],
-          "delphes_card_atlas_sus_2013_11.tcl"    : ["atlas_higg_2013_03", "atlas_susy_2013_11", "atlas_1405_7875"],
-          "delphes_card_atlas_sus_2014_10.tcl"    : ["atlas_susy_2014_10"] ,
-          "delphes_card_atlas_sus_2013_04.tcl"    : ["atlas_susy_2013_04"] ,
-          "delphes_card_cms_b2g_12_012.tcl"       : ["CMS_B2G_12_012", "cms_exo_12_047", "cms_exo_12_048"],
-          "delphes_card_cms_b2g_14_004.tcl"       : ["cms_b2g_12_022", "cms_b2g_14_004"],
-          "delphes_card_ATLAS_1604_07773.tcl"     : ["ATLAS_1604_07773", "atlas_1605_03814"],
-          "delphes_card_ATLAS_1711_03301.tcl"     : ["ATLAS_1711_03301"],
-          "delphes_card_ATLAS_CONF_2016_086.tcl"  : ["ATLAS_CONF_2016_086"],
-          "delphes_card_cms_exo_16_010.tcl"       : ["cms_exo_16_010", "cms_sus_17_001"],
-          "delphes_card_cms_top_17_009.tcl"       : ["cms_top_17_009"],
-          "delphes_card_cms_exo_16_012.tcl"       : ["CMS_EXO_16_012_2gamma"],
-          "delphes_card_cms_SUS_16_052.tcl"       : ["CMS_SUS_16_052"],
-          "delphes_card_atlas_2016_32.tcl"        : ["ATLAS_EXOT_2016_32"],
-          "delphes_card_atlas_2016_25.tcl"        : ["ATLAS_EXOT_2016_25"],
-          "delphes_card_cms_sus_16_041.tcl"       : ["cms_sus_16_039"]
-        }
-
-        self.description = {
-          "ATLAS_1604_07773"       : "ATLAS - 13 TeV - Monojet (3.2 fb-1)",
-          "ATLAS_1711_03301"       : "ATLAS - 13 TeV - Monojet (36.1 fb-1)",
-          "ATLAS_EXOT_2016_25"     : "ATLAS - 13 TeV - Mono-Higgs in the bbar channel (36.1 fb-1)",
-          "ATLAS_EXOT_2016_32"     : "ATLAS - 13 TeV - Monophoton (36.1 fb-1)",
-          "atlas_1605_03814"       : "ATLAS - 13 TeV - Multijet (2-6 jets) + met",
-          "ATLAS_CONF_2016_086"    : "ATLAS - 13 TeV - Dark matter in the b+bar+met channel",
-          "cms_exo_16_010"         : "CMS   - 13 TeV - Mono-Z",
-          "CMS_EXO_16_012_2gamma"  : "CMS   - 13 TeV - Mono-Higgs in the diphoton channel (2.3 fb-1)",
-          "cms_sus_16_039"         : "CMS   - 13 TeV - SUSY multileptons (36 fb-1)",
-          "CMS_SUS_16_052"         : "CMS   - 13 TeV - SUSY 1 lepton + jets (36 fb-1)",
-          "cms_sus_17_001"         : "CMS   - 13 TeV - stops in the OS dilepton + jets channel (35.9 fb-1)",
-          "cms_top_17_009"         : "CMS   - 13 TeV - 4 top analysis in the SS2L and multilepton channel (35.9 fb-1)",
-          "atlas_susy_2013_04"     : "ATLAS - 8 TeV - multijet + met", 
-          "atlas_sus_13_05"        : "ATLAS - 8 TeV - stop/sbottom - 0 lepton + 2 bjets + met",
-          "atlas_susy_2013_11"     : "ATLAS - 8 TeV - ewkinos - 2 leptons + met",
-          "atlas_susy_2013_21"     : "ATLAS - 8 TeV - monojet",
-          "atlas_susy_2014_10"     : "ATLAS - 8 TeV - squark-gluino - 2 leptons + jets + met",
-          "atlas_1405_7875"        : "ATLAS - 8 TeV - squark-gluino - 0 leptons + 2-6 jets + met",
-          "atlas_higg_2013_03"     : "ATLAS - 8 TeV - ZH to invisible + 2 leptons",
-          "ATLAS_EXOT_2014_06"     : "ATLAS - 8 TeV - monophoton",
-          "cms_sus_13_012"         : "CMS   - 8 TeV - squark-gluino - MET/MHT",
-          "cms_sus_13_016"         : "CMS   - 8 TeV - gluinos - 2 leptons + bjets + met",
-          "cms_sus_14_001_monojet" : "CMS   - 8 TeV - stop - the monojet channel",
-          "cms_sus_14_001_TopTag"  : "CMS   - 8 TeV - stop - the top tagging channel",
-          "cms_sus_13_011"         : "CMS   - 8 TeV - stop - 1 lepton + bjets + met",
-          "cms_exo_12_047"         : "CMS   - 8 TeV - monophoton",
-          "cms_exo_12_048"         : "CMS   - 8 TeV - monojet",
-          "CMS_B2G_12_012"         : "CMS   - 8 TeV - T5/3 partners in the SSDL channel",
-          "cms_b2g_12_022"         : "CMS   - 8 TeV - Monotop search",
-          "cms_b2g_14_004"         : "CMS   - 8 TeV - Dark matter production with a ttbar pair"
-        }
+        self.DelphesDic = { }
+        self.description = { }
+        self.ma5dir = os.path.abspath(os.path.join(os.path.dirname(os.path.realpath( __file__ )),os.pardir,os.pardir))
+        for mypad in ['PAD', 'PADForMa5tune']:
+            if os.path.isfile(os.path.join(self.ma5dir,'tools',mypad,'Input','recast_config.dat')):
+                dico_file = open(os.path.join(self.ma5dir,'tools',mypad,'Input','recast_config.dat'), 'r')
+                for line in dico_file:
+                    if line.strip().startswith('#'):
+                        continue
+                    self.DelphesDic[line.split('|')[0].strip()] = line.split('|')[1].split()
+                dico_file.close()
+            if os.path.isfile(os.path.join(self.ma5dir,'tools',mypad,'Input','analysis_description.dat')):
+                dico_file = open(os.path.join(self.ma5dir,'tools',mypad,'Input','analysis_description.dat'), 'r')
+                for line in dico_file:
+                    if line.strip().startswith('#'):
+                        continue
+                    self.description[line.split('|')[0].strip()] = line.split('|')[1][:-1]
+                dico_file.close()
 
         self.CLs_numofexps= 100000
         self.card_path= ""
@@ -156,7 +120,7 @@
             return
         return
 
-    def user_SetParameter(self,parameter,value,level,hasroot,hasdelphes,hasMA5tune,datasets, hasPAD, hasPADtune):
+    def user_SetParameter(self,parameter,value,level,archi_info,session_info,datasets):
         # algorithm
         if parameter=="status":
             # Switch on the clustering
@@ -168,28 +132,28 @@
                     return
 
                 # Only if ROOT is install
-                if not hasroot:
+                if not archi_info.has_root:
                     self.logger.error("recasting is only available if ROOT is installed")
                     return
 
                 canrecast=False
                 # Delphes and the PAD?
-                if hasdelphes:
+                if archi_info.has_delphes:
                     self.delphes=True
-                if hasPAD:
+                if session_info.has_pad:
                     self.pad=True
-                if not hasPAD or not hasdelphes:
+                if not archi_info.has_delphes or not session_info.has_pad:
                     self.logger.warning("Delphes and/or the PAD are not installed (or deactivated): " + \
                         "the corresponding analyses will be unavailable")
                 else:
                     canrecast=True
 
                 # DelphesMA5tune and the PADFor MA5TUne?
-                if hasMA5tune:
+                if archi_info.has_delphesMA5tune:
                     self.ma5tune=True
-                if hasPADtune:
+                if session_info.has_padma5:
                     self.padtune=True
-                if not hasPADtune or not hasMA5tune:
+                if not archi_info.has_delphesMA5tune or not session_info.has_padma5:
                     self.logger.warning("DelphesMA5tune and/or the PADForMA5tune are not installed " + \
                         "(or deactivated): the corresponding analyses will be unavailable")
                 else:
@@ -304,12 +268,11 @@
         ToLoopOver=[]
         padlist=[]
         tunelist=[]
-        ma5dir = os.path.abspath(os.path.join(os.path.dirname(os.path.realpath( __file__ )),os.pardir,os.pardir))
         if self.pad:
-            padfile  = open(os.path.normpath(os.path.join(ma5dir,"PAD/Build/Main/main.cpp")), 'r')
+            padfile  = open(os.path.normpath(os.path.join(self.ma5dir,"tools/PAD/Build/Main/main.cpp")), 'r')
             ToLoopOver.append([padfile, padlist])
         if self.padtune:
-            tunefile = open(os.path.normpath(os.path.join(ma5dir,"PADForMA5tune/Build/Main/main.cpp")), 'r')
+            tunefile = open(os.path.normpath(os.path.join(self.ma5dir,"tools/PADForMA5tune/Build/Main/main.cpp")), 'r')
             ToLoopOver.append([tunefile, tunelist])
         for myfile,mylist in ToLoopOver:
             for line in myfile:
@@ -340,14 +303,14 @@
                 if myver!="v1.2":
                     self.logger.error("Recasting card: invalid analysis (not present in the PAD): " + myana)
                     return False
-                if not os.path.isfile(os.path.normpath(os.path.join(ma5dir,'PAD/Input/Cards',mydelphes))):
+                if not os.path.isfile(os.path.normpath(os.path.join(self.ma5dir,'tools/PAD/Input/Cards',mydelphes))):
                     self.logger.error("Recasting card: PAD analysis linked to an invalid delphes card: " + myana + " - " + mydelphes)
                     return False
             elif myana in  [x[0] for x in tunelist]:
                 if myver!="v1.1":
                     self.logger.error("Recasting card: invalid analysis (not present in the PADForMA5tune): " + myana)
                     return False
-                if not os.path.isfile(os.path.normpath(os.path.join(ma5dir,'PADForMA5tune/Input/Cards',mydelphes))):
+                if not os.path.isfile(os.path.normpath(os.path.join(self.ma5dir,'tools/PADForMA5tune/Input/Cards',mydelphes))):
                     self.logger.error("Recasting card: PADForMA5tune analysis linked to an invalid delphes card: " + myana + " - " + mydelphes)
                     return False
             else:
@@ -370,8 +333,7 @@
 
 
     def CreateMyCard(self,dirname,padtype,write=True):
-        ma5dir = os.path.abspath(os.path.join(os.path.dirname(os.path.realpath( __file__ )),os.pardir,os.pardir))
-        mainfile  = open(os.path.normpath(os.path.join(ma5dir,padtype,"Build/Main/main.cpp")), 'r')
+        mainfile  = open(os.path.normpath(os.path.join(self.ma5dir,'tools',padtype,"Build/Main/main.cpp")), 'r')
         thecard=[]
         if write:
             exist=os.path.isfile(dirname+'/Input/recasting_card.dat')
@@ -399,10 +361,11 @@
                 thecard.append(analysis.ljust(30,' ') + mytype.ljust(12,' ') + 'on    ' + mydelphes.ljust(50, ' ')+\
                       ' # '+descr)
         mainfile.close()
-        thecard.append('')
+        thecard.sort()
         if write:
             card = open(dirname+'/Input/recasting_card.dat','a')
             card.write('\n'.join(thecard))
+            card.write('#\n')
             card.close()
         else:
             return thecard

=== modified file 'madanalysis/core/launcher.py'
--- madanalysis/core/launcher.py	2018-05-29 21:42:05 +0000
+++ madanalysis/core/launcher.py	2019-02-13 11:05:44 +0000
@@ -89,6 +89,14 @@
     output.write('# fastjet_veto     = 0 # 0=No, 1=Yes\n')
     output.write('# fastjet_bin_path = /home/fastjet/build/bin/\n')
     output.write('\n')
+    output.write('# -----PAD-----\n')
+    output.write('# pad_veto = 0 # 0=No, 1=Yes\n')
+    output.write('# pad_build_path = /home/PAD/build/\n')
+    output.write('\n')
+    output.write('# -----PADForMA5Tune-----\n')
+    output.write('# padma5_veto = 0 # 0=No, 1=Yes\n')
+    output.write('# padma5_build_path = /home/PADForMA5tune/build/\n')
+    output.write('\n')
     output.write('# -----PDFLATEX-----\n')
     output.write('# pdflatex_veto = 0 # 0=No, 1=Yes\n')
     output.write('\n')
@@ -256,6 +264,10 @@
     if not main.BuildLibrary(forced=mode.build):
         sys.exit()
 
+    # Checking the present configuration
+    if not main.CheckConfig2(debug=mode.debug):
+        sys.exit()
+
     logging.getLogger('MA5').info("*************************************************************")
 
 

=== modified file 'madanalysis/core/main.py'
--- madanalysis/core/main.py	2018-05-29 21:42:05 +0000
+++ madanalysis/core/main.py	2019-02-13 11:05:44 +0000
@@ -27,6 +27,7 @@
 from madanalysis.selection.selection                    import Selection
 from madanalysis.interpreter.cmd_base                   import CmdBase
 from madanalysis.region.region_collection               import RegionCollection
+from madanalysis.tagging.tagger                         import Tagger
 from madanalysis.system.session_info                    import SessionInfo
 from madanalysis.system.architecture_info               import ArchitectureInfo
 from madanalysis.core.library_builder                   import LibraryBuilder
@@ -86,6 +87,7 @@
         self.madgraph       = MadGraphInterface()
         self.logger         = logging.getLogger('MA5')
         self.redirectSAlogger = False
+        self.tagger         = Tagger()
 
 
     def ResetParameters(self):
@@ -432,13 +434,23 @@
             return False
         if not checkup.CheckOptionalProcessingPackages():
             return False
+        if not checkup.SetFolder():
+            return False
+        return True
+
+
+    def CheckConfig2(self,debug=False):
+        checkup = CheckUp(self.archi_info, self.session_info, debug, self.script)
+        # Reinterpretation packages
+        if not checkup.CheckOptionalReinterpretationPackages():
+            return False
+
+        # Graphical packages
         if not checkup.CheckOptionalGraphicalPackages():
             return False
         self.AutoSetGraphicalRenderer()
-#        if not checkup.CheckGraphicalPackages():
-#            return False
-        if not checkup.SetFolder():
-            return False
+
+        # Ok
         return True
 
 

=== modified file 'madanalysis/dataset/dataset.py'
--- madanalysis/dataset/dataset.py	2018-05-29 21:42:05 +0000
+++ madanalysis/dataset/dataset.py	2019-02-13 11:05:44 +0000
@@ -59,7 +59,7 @@
         self.weighted_events   = True
         self.measured_global   = SampleInfo() 
         self.measured_detail   = []
-        
+
     def __len__(self):
         return len(self.filenames)
 
@@ -237,7 +237,7 @@
                 return
 
         #weight
-        elif variable == "weight" or variable == "xsection":
+        elif variable in ["weight", "xsection"]:
             try:
                 tmp = float(value)
             except:
@@ -304,7 +304,7 @@
 
     def user_DisplayParameter(self,parameter):
         if parameter=="weight":
-            logging.getLogger('MA5').info("   User-imposed weight of the set = "+str(self.weight))
+            logging.getLogger('MA5').info("   User-imposed weight value for the set = "+str(self.weight))
         elif parameter=="xsection":
             logging.getLogger('MA5').info("   User-imposed cross section = "+str(self.xsection))
         elif parameter=="type":

=== modified file 'madanalysis/dataset/sample_info.py'
--- madanalysis/dataset/sample_info.py	2018-05-29 21:42:05 +0000
+++ madanalysis/dataset/sample_info.py	2019-02-13 11:05:44 +0000
@@ -29,5 +29,3 @@
         self.nevents  = 0L
         self.sumw_positive = 0.
         self.sumw_negative = 0.
-        
-        

=== modified file 'madanalysis/input/installation_options.dat'
--- madanalysis/input/installation_options.dat	2017-08-22 00:44:45 +0000
+++ madanalysis/input/installation_options.dat	2019-02-13 11:05:44 +0000
@@ -33,6 +33,14 @@
 # fastjet_veto     = 0 # 0=No, 1=Yes
 # fastjet_bin_path = /home/fastjet/build/bin/
 
+# -----PAD-----
+# pad_veto = 0 # 0=No, 1=Yes
+# pad_build_path = /home/PAD/build/
+
+# -----PADForMA5Tune-----
+# padma5_veto = 0 # 0=No, 1=Yes
+# padma5_build_path = /home/PADForMA5tune/build/
+
 # -----PDFLATEX-----
 # pdflatex_veto = 0 # 0=No, 1=Yes
 
@@ -41,3 +49,4 @@
 
 # -----SCIPY-----
 # scipy_veto = 0 # 0=No, 1=Yes
+

=== modified file 'madanalysis/install/detector_manager.py'
--- madanalysis/install/detector_manager.py	2018-05-29 21:42:05 +0000
+++ madanalysis/install/detector_manager.py	2019-02-13 11:05:44 +0000
@@ -32,6 +32,7 @@
     def manage(self, detector):
         # initialization
         # Getting the 'already installed' flags
+        import logging
         if detector == 'delphes':
             installed     = self.main.archi_info.has_delphes
             uninstalled   = self.main.archi_info.has_delphesMA5tune

=== modified file 'madanalysis/install/install_delphes.py'
--- madanalysis/install/install_delphes.py	2018-05-29 21:42:05 +0000
+++ madanalysis/install/install_delphes.py	2019-02-13 11:05:44 +0000
@@ -29,7 +29,6 @@
 from madanalysis.IOinterface.folder_writer  import FolderWriter
 from madanalysis.system.checkup             import CheckUp
 from shell_command import ShellCommand
-from string_tools  import StringTools
 import os
 import sys
 import logging
@@ -38,20 +37,22 @@
 
 class InstallDelphes:
 
-    def __init__(self,main):
+    def __init__(self,main,package):
         self.main        = main
-        self.toolsdir    = os.path.normpath(self.main.archi_info.ma5dir+'/tools')
-        self.installdir  = os.path.normpath(self.toolsdir+'/delphes')
+        self.package     = 'delphes'
+        if package == 'delphesma5tune':
+            self.package = 'delphesMA5tune'
+        self.toolsdir    = os.path.join(self.main.archi_info.ma5dir,'tools')
+        self.installdir  = os.path.join(self.toolsdir,self.package)
         self.tmpdir      = self.main.session_info.tmpdir
         self.downloaddir = self.main.session_info.downloaddir
-        self.untardir    = os.path.normpath(self.tmpdir + '/MA5_delphes/')
+        self.untardir    = os.path.join(self.tmpdir, 'MA5_'+self.package)
         self.ncores      = 1
 #        self.files = {"delphes.tar.gz" : "http://cp3.irmp.ucl.ac.be/downloads/Delphes-3.1.1.tar.gz"}
 #        self.files = {"delphes.tar.gz" : "http://cp3.irmp.ucl.ac.be/downloads/Delphes-3.3.0.tar.gz"}
 #        self.files = {"delphes.tar.gz" : "http://cp3.irmp.ucl.ac.be/downloads/Delphes-3.3.1.tar.gz"}
 #        self.files = {"delphes.tar.gz" : "http://cp3.irmp.ucl.ac.be/downloads/Delphes-3.3.3.tar.gz"}
-        self.files = {"delphes.tar.gz" : "http://cp3.irmp.ucl.ac.be/downloads/Delphes-3.4.1.tar.gz"}
-#https://madanalysis.irmp.ucl.ac.be/attachment/wiki/WikiStart/Delphes-3.4.1.tar.gz
+        self.files = {package+".tar.gz" : "http://cp3.irmp.ucl.ac.be/downloads/Delphes-3.4.1.tar.gz"}
         self.logger = logging.getLogger('MA5')
 
 
@@ -78,7 +79,7 @@
     def CreatePackageFolder(self):
         if not InstallService.create_tools_folder(self.toolsdir):
             return False
-        if not InstallService.create_package_folder(self.toolsdir,'delphes'):
+        if not InstallService.create_package_folder(self.toolsdir,self.package):
             return False
         return True
 
@@ -105,14 +106,48 @@
     def Unpack(self):
         # Logname
         logname = os.path.normpath(self.installdir+'/unpack.log')
+
         # Unpacking the tarball
-        ok, packagedir = InstallService.untar(logname, self.downloaddir,self.tmpdir,'delphes.tar.gz')
+        ok, packagedir = InstallService.untar(logname, self.downloaddir,self.tmpdir,
+          self.package.lower()+'.tar.gz')
         if not ok:
             return False
+
+        # Patching delphesMA5tune
+        if self.package == 'delphesMA5tune':
+            # Copying the patch
+            self.logger.debug('Copying the patch ...')
+            input=self.toolsdir+'/SampleAnalyzer/Interfaces/delphesMA5tune/patch_delphesMA5tune.tgz'
+            output=packagedir+'/patch_delphesMA5tune.tgz'
+            try:
+                shutil.copy(input,output)
+            except:
+                self.logger.error('impossible to copy the patch '+input+' to '+output)
+                return False
+
+            # Unpacking the folder
+            logname = os.path.normpath(self.installdir+'/unpack_patch.log')
+            theCommands=['tar','xzf','patch_delphesMA5tune.tgz']
+            self.logger.debug('shell command: '+' '.join(theCommands))
+            ok, out= ShellCommand.ExecuteWithLog(theCommands,logname,packagedir,silent=False)
+            if not ok:
+                self.logger.error('impossible to untar the patch '+output)
+                return False
+
+            # Applying the patch
+            logname = os.path.normpath(self.installdir+'/patch.log')
+            theCommands=[sys.executable,'patch.py']
+            self.logger.debug('shell command: '+' '.join(theCommands))
+            ok, out= ShellCommand.ExecuteWithLog(theCommands,logname,packagedir,silent=False)
+            if not ok:
+                self.logger.error('impossible to apply the patch '+output)
+                return False
+
         # Getting the list of files
         self.logger.debug('Getting the list of files ...')
         myfiles=glob.glob(packagedir+'/*')
         self.logger.debug('=> '+str(myfiles))
+
         # Moving files from packagedir to installdir
         self.logger.debug('Moving files from '+packagedir+' to '+self.installdir+' ...')
         for myfile in myfiles:
@@ -130,55 +165,53 @@
                     self.logger.error('impossible to move the file/folder '+myfile+' from '+packagedir+' to '+self.installdir)
                     return False
 
-        # Updating Makefile
-        filename = self.installdir+'/Makefile'
-        self.logger.debug('Updating files '+filename+ ': no CMSSW\n')
-        self.SwitchOffCMSSW(filename)
-        
+        if self.package=='delphes':
+            # Updating DelphesFormula
+            filename = self.installdir+'/classes/DelphesFormula.cc'
+            self.logger.debug('Updating files '+filename+ ': adding d0\n')
+            self.AddD0(filename)
+
         # Updating Makefile
         filename = self.installdir+'/doc/genMakefile.tcl'
         self.logger.debug('Updating files '+filename+ ': no CMSSW\n')
         self.SwitchOffCMSSW(filename)
 
-        # Updating DelphesFormula
-        filename = self.installdir+'/classes/DelphesFormula.cc'
-        self.logger.debug('Updating files '+filename+ ': adding d0\n')
-        self.AddD0(filename)
-
         # Updating ExRootTask
         filename = self.installdir+'/external/ExRootAnalysis/ExRootTask.cc'
         self.logger.debug('Updating files: commenting out lines in: '+filename+' ...')
         self.CommentLines(filename,[64,65,66],'//')
-        
+
         # Updating ExRootTask
         filename = self.installdir+'/external/ExRootAnalysis/ExRootConfReader.cc'
         self.logger.debug('Updating files: commenting out lines in: '+filename+' ...')
         self.CommentLines(filename,[177,178,179,180],'//')
 
         # Adding files
-        filesToAdd = ["MA5GenParticleFilter","MA5EfficiencyD0"]
+        if self.package=='delphes':
+            filesToAdd = ["MA5GenParticleFilter","MA5EfficiencyD0"]
+        elif self.package=='delphesMA5tune':
+            filesToAdd = ["MA5GenParticleFilter"]
         if not self.CopyFiles(filesToAdd):
             return False
         if not self.UpdateDictionnary(filesToAdd):
             return False
-        
+
         # Ok
         return True
 
 
     def Configure(self):
-
-        # KNOWn DELPHES ISsues: GENERATE ISSUES BECAuse IT USES TCSLSH COMMAND
-        
+        # Known delphes issues: generate issues because it uses tcslsh command
         # Input
         theCommands=['./configure']
         logname=os.path.normpath(self.installdir+'/configuration.log')
         # Execute
         self.logger.debug('shell command: '+' '.join(theCommands))
-        ok, out= ShellCommand.ExecuteWithLog(theCommands,\
-                                             logname,\
-                                             self.installdir,\
-                                             silent=False)
+        ok, out= ShellCommand.ExecuteWithLog(theCommands,logname,self.installdir,silent=False)
+
+        # Updating the Makefile
+        self.logger.debug('Updating the Makefiles: no CMSSW\n')
+        self.SwitchOffCMSSW(os.path.join(self.installdir, 'Makefile'))
 
         # return result
         if not ok:
@@ -186,94 +219,15 @@
             self.logger.error(logname)
         return ok
 
-        
-    def BuildOld(self):
-
-        # Input
-        theCommands=['make','ClassesDict_rdict.pcm','ExRootAnalysisDict_rdict.pcm', 'ModulesDict_rdict.pcm', 'FastJetDict_rdict.pcm']
-        logname=os.path.normpath(self.installdir+'/compilation_Dict.log')
-        # Execute
-        self.logger.debug('shell command: '+' '.join(theCommands))
-        ok, out= ShellCommand.ExecuteWithLog(theCommands,\
-                                             logname,\
-                                             self.installdir,\
-                                             silent=False)
-        # return result
-        if not ok:
-            pass # only for ROOT6
-
-        # Input
-        theCommands=['make','-j'+str(self.ncores),'libDelphes.so']
-        logname=os.path.normpath(self.installdir+'/compilation_libDelphes.log')
-        # Execute
-        self.logger.debug('shell command: '+' '.join(theCommands))
-        ok, out= ShellCommand.ExecuteWithLog(theCommands,\
-                                             logname,\
-                                             self.installdir,\
-                                             silent=False)
-        # return result
-        if not ok:
-            self.logger.error('impossible to build the project. For more details, see the log file:')
-            self.logger.error(logname)
-            return ok
-
-        # Input
-        theCommands=['make','DelphesSTDHEP']
-        logname=os.path.normpath(self.installdir+'/compilation_STDHEP.log')
-        # Execute
-        self.logger.debug('shell command: '+' '.join(theCommands))
-        ok, out= ShellCommand.ExecuteWithLog(theCommands,\
-                                             logname,\
-                                             self.installdir,\
-                                             silent=False)
-        # return result
-        if not ok:
-            self.logger.error('impossible to build the project. For more details, see the log file:')
-            self.logger.error(logname)
-            return ok
-
-        # Input
-        theCommands=['make','DelphesLHEF']
-        logname=os.path.normpath(self.installdir+'/compilation_LHEF.log')
-        # Execute
-        self.logger.debug('shell command: '+' '.join(theCommands))
-        ok, out= ShellCommand.ExecuteWithLog(theCommands,\
-                                             logname,\
-                                             self.installdir,\
-                                             silent=False)
-        # return result
-        if not ok:
-            self.logger.error('impossible to build the project. For more details, see the log file:')
-            self.logger.error(logname)
-            return ok
-
-        # Input
-        theCommands=['make','DelphesHepMC']
-        logname=os.path.normpath(self.installdir+'/compilation_HepMC.log')
-        # Execute
-        self.logger.debug('shell command: '+' '.join(theCommands))
-        ok, out= ShellCommand.ExecuteWithLog(theCommands,\
-                                             logname,\
-                                             self.installdir,\
-                                             silent=False)
-        # return result
-        if not ok:
-            self.logger.error('impossible to build the project. For more details, see the log file:')
-            self.logger.error(logname)
-        return ok
-
 
     def Build(self):
 
         # Input
-        theCommands=['make']
+        theCommands=['make', '-j'+str(self.ncores)]
         logname=os.path.normpath(self.installdir+'/compilation.log')
         # Execute
         self.logger.debug('shell command: '+' '.join(theCommands))
-        ok, out= ShellCommand.ExecuteWithLog(theCommands,\
-                                             logname,\