--- a/TEisotools-1.1.a/commons/core/LoggerFactory.py	Thu Jul 21 07:36:44 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,139 +0,0 @@
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-
-## @mainpage Documentation of the REPET API
-#
-# Welcome to the API documentation!
-# This API is a set of packages and classes for pipeline(s) development.
-#
-# @par The "logger" package
-# 
-# Logging is managed via LoggerFactory. This class creates instances of logging.logging python class. It's strongly encouraged to use this factory each time you need to log something.
-#
-# @par The "checker" package
-#
-# This package is a set of classes designed to facilitate development of different kind of checks: filesystem  checks, environment checks, configuration file checks ...
-#
-# Classes should subclass checker::IChecker or if a logger is needed: checker::AbstractChecker.
-#
-# Methods should raise checker::CheckerException.
-#
-# Use checker::ConfigChecker and checker::ConfigException for configuration files checks.
-#
-# checker::CheckerUtils is a set of small static methods shared by other classes of checker package.
-#
-# @par The "coord" package
-#
-# This package is a set of classes dedicated to coordinates manipulations.
-# 
-# A coord::Range instance records a region on a given sequence (start, end and sequence name).
-#
-# A coord::Map instance is a coord::Range instance and record a named region on a given sequence (start, end, sequence name and name).
-#
-# A coord::Set instance is a coord::Map instance and record a named region on a given sequence with an identifier (start, end, sequence name, name and id).
-#
-# A coord::Align instance handle a match between two sequences, query and subject (pair of coordinates with E-value, score and identity).
-#
-# A coord::Path instance is a coord::Align instance and handle a match between two sequences, query and subject (pair of coordinates with E-value, score and identity) with an identifier.
-#
-# A coord::Match instance is a coord::Path instance and handle a chain of match(es) between two sequences, query and subject, with an identifier and the length of the input sequences.
-#
-# coord::Align, coord::Map, coord::Path and coord::Set come with utils classes: coord::AlignUtils, coord::MapUtils, coord::PathUtils and coord::SetUtils.        
-#
-# @par The "seq" package
-#
-# This package a set of classes dedicated to sequences manipulations.
-#
-# A seq::Bioseq instance records a sequence with its header. seq::Bioseq comes with an utils class: seq::BioseqUtils.
-#
-# A seq::BioseqDB instance handle a collection of a Bioseq (header-sequence).
-#
-# A seq::AlignedBioseqDB instance is a multiple sequence alignment representation.
-#
-# A seq::FastaUtils is a set of static methods for fasta file manipulation.
-#
-# @par The "sql" package
-#
-# This package is dedicated to persistance of coord package objects.   
-# All classes come with dedicated interfaces. Use these interfaces for class manipulation.
-# Class names patterns are ITable*Adaptator and Table*Adaptator.
-#
-# sql::ITablePathAdaptator, sql::TablePathAdaptator /
-# sql::ITableSetAdaptator, sql::TableSetAdaptator /
-# sql::ITableSeqAdaptator, sql::TableSeqAdaptator /
-# sql::ITableMapAdaptator, sql::TableMapAdaptator /
-# sql::ITableMatchAdaptator, sql::TableMatchAdaptator.
-#   
-
-import logging
-import sys
-
-DEFAULT_LEVEL = 1
-DEFAULT_FORMAT = "%(asctime)s - %(module)s - %(levelname)s - %(message)s"
-DATE_FORMAT = "%Y-%m-%d %H:%M:%S"
-
-## Use this class to create a instance of logging class.
-#
-class LoggerFactory(object):
-    
-    def createLogger(name, verbosity = DEFAULT_LEVEL, format = DEFAULT_FORMAT, out = sys.stdout):
-        log = logging.getLogger(name)
-        
-        hasStreamHandler = False
-        for handler in log.handlers: 
-            if handler.__class__ == logging.StreamHandler:
-                hasStreamHandler = True
-                break
-        if not hasStreamHandler:
-            formatter = logging.Formatter(format, DATE_FORMAT) 
-            handler = logging.StreamHandler(out)
-            handler.setFormatter(formatter)
-            log.addHandler(handler)
-        
-        LoggerFactory.setLevel(log, verbosity)
-        return log
-    
-    createLogger = staticmethod(createLogger)
-
-    def setLevel(log, verbosity):
-        log.disabled = False
-        if verbosity >= 4:
-            log.setLevel(logging.DEBUG)
-        elif verbosity == 3:
-            log.setLevel(logging.INFO)
-        elif verbosity == 2:
-            log.setLevel(logging.WARNING)
-        elif verbosity == 1:
-            log.setLevel(logging.ERROR)
-        elif verbosity == 0:
-            log.disabled = True
-            
-    setLevel = staticmethod(setLevel)