--- a/TEisotools-1.1.a/commons/core/coord/Map.py	Thu Jul 21 07:36:44 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,168 +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.
-
-
-from commons.core.coord.Range import Range
-
-
-## Record a named region on a given sequence
-#
-class Map( Range ):
-    
-    __slots__ = ("name")
-    
-    ## Constructor
-    #
-    # @param name the name of the region
-    # @param seqname the name of the sequence
-    # @param start the start coordinate
-    # @param end the end coordinate
-    # 
-    def __init__(self, name="", seqname="", start=-1, end=-1):
-        self.name = name
-        Range.__init__( self, seqname, start, end )
-        
-    ## Equal operator
-    #
-    # @param o a Map instance
-    #    
-    def __eq__(self, o):
-        if type(o) is type(self):
-            if self.name == o.name:
-                return Range.__eq__(self, o)
-        return False
-    
-    ## Not equal operator
-    #
-    def __ne__(self, o):
-        return not self.__eq__(o)
-    
-    ## Return name
-    #
-    def getName( self ):
-        return self.name
-    
-    ## Set attributes from tuple
-    #
-    # @param tuple: a tuple with (name,seqname,start,end)
-    # 
-    def setFromTuple(self, tuple):
-        self.name = tuple[0]
-        Range.setFromTuple(self, tuple[1:])
-    
-    ## Set attributes from string
-    #
-    # @param string a string formatted like name<sep>seqname<sep>start<sep>end
-    # @param sep field separator
-    #
-    def setFromString(self, string, sep="\t"):
-        string.strip()
-        self.setFromTuple(tuple(string.split(sep)))
-        
-    ## Reset
-    #
-    def reset(self):
-        self.setFromTuple(("", "", -1, -1))
-        
-    ## Read attributes from a Map file
-    # 
-    # @param fileHandler: file handler of the file being read
-    # @return: 1 on success, 0 at the end of the file
-    #
-    def read(self, fileHandler):
-        self.reset()
-        line = fileHandler.readline()
-        if line == "":
-            return 0
-        tokens = line.split("\t")
-        if len(tokens) < 4:
-            return 0
-        self.setFromTuple(tuple(tokens))
-        return 1
-    
-    ## Return the attributes as a formatted string
-    #
-    def toString(self):
-        string = "%s" % (self.name)
-        string += "\t%s" % (Range.toString(self))
-        return string
-    
-    ## Write attributes into a Map file
-    #
-    # @param fileHandler: file handler of the file being filled
-    #
-    def write(self, fileHandler):
-        fileHandler.write("%s\n" % (self.toString()))
-        
-    ## Save attributes into a Map file
-    #
-    # @param file: name of the file being filled
-    #
-    def save(self, file):
-        fileHandler = open( file, "a" )
-        self.write( fileHandler )
-        fileHandler.close()
-        
-    ## Return a Range instance with the attributes
-    #
-    def getRange(self):
-        return Range( self.seqname, self.start, self.end)
-    
-    ## Remove in the instance the region overlapping with another Map instance
-    #
-    # @param o a Map instance
-    # 
-    def diff(self, o):
-        iRange = Range.diff(self, o.getRange())
-        new = Map()
-        if not iRange.isEmpty():
-            new.name = self.name
-            new.seqname = self.seqname
-            new.start = iRange.start
-            new.end = iRange.end
-        return new
-    
-    ## Write attributes in a Path file, the name being the subject and the rest the Range query
-    #
-    # @param fileHandler: file handler of a Path file
-    #
-    def writeAsQueryOfPath(self, fileHandler):
-        string = "0"
-        string += "\t%s" % ( self.seqname )
-        string += "\t%i" % ( self.getMin() )
-        string += "\t%i" % ( self.getMax() )
-        string += "\t%s" % ( self.name )
-        string += "\t0"
-        string += "\t0"
-        string += "\t0.0"
-        string += "\t0"
-        string += "\t0"
-        fileHandler.write( "%s\n" % ( string ) )
-