diff TEisotools-1.1.a/commons/core/coord/Set.py @ 16:836ce3d9d47a draft default tip

Uploaded

--- a/TEisotools-1.1.a/commons/core/coord/Set.py	Thu Jul 21 07:36:44 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,132 +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.Map import Map
-
-
-## Record a named region on a given sequence with an identifier
-#  
-class Set( Map ):
-    
-    __slots__ = ("id")
-    
-    ## Constructor
-    #
-    # @param id identifier
-    # @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, id=-1, name="", seqname="", start=-1, end=-1):
-        Map.__init__( self, name, seqname, start, end )
-        self.id = id
-        
-    ## Equal operator
-    #    
-    def __eq__(self, o):
-        if type(o) is not type(self) or self.id != o.id:
-            return False
-        else:
-            return Map.__eq__(self, o)
-        
-    ## Not equal operator
-    #
-    def __ne__(self, o):
-        return not self.__eq__(o)
-    
-    def getId(self):
-        return self.id
-        
-    ## Reset
-    #
-    def reset(self):
-        self.setFromTuple([-1, "", "", -1, -1 ])
-            
-    ## Set attributes from tuple
-    #
-    # @param tuple: a tuple with (id, name, seqname, start, end)
-    # 
-    def setFromTuple(self, tuple):
-        self.id = int(tuple[0])
-        Map.setFromTuple(self, tuple[1:])
-        
-    ## Return the attributes as a formatted string
-    #
-    def toString(self):
-        string = "%i" % (self.id)
-        string += "\t%s" % (Map.toString(self))
-        return string
-    
-    ## Merge the instance with another Set instance
-    #
-    # @param o a Set instance
-    #
-    def merge(self, o):
-        if self.seqname == o.seqname:
-            Map.merge(self, o)
-            self.id = min(self.id, o.id)
-    
-    ## Return a Map instance with the attributes
-    #
-    def getMap(self):
-        return Map(self.name, self.seqname, self.start, self.end)
-    
-    ## Remove in the instance the region overlapping with another Set instance
-    #
-    # @param o a Set instance
-    #  
-    def diff(self, o):
-        iMap = Map.diff(self, o.getMap())
-        new = Set()
-        if not iMap.isEmpty():
-            new.id = self.id
-            new.name = self.name
-            new.seqname = self.seqname
-            new.start = iMap.start
-            new.end = iMap.end
-        return new
-    
-    ## Return a Map instance with the identifier in the name
-    #
-    def set2map(self):
-        return Map(self.name+"::"+str(self.id),self.seqname,self.start,self.end)
-    
-    
-    def getMapInstance( self ):
-        iMap = Map()
-        lAttributes = []
-        lAttributes.append( self.name )
-        lAttributes.append( self.seqname )
-        lAttributes.append( self.start )
-        lAttributes.append( self.end )
-        iMap.setFromTuple( lAttributes )
-        return iMap