--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/coord/Map.py	Tue Apr 30 15:02:29 2013 -0400
@@ -0,0 +1,161 @@
+# 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 ):
+    
+    ## 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 self.name == o.name:
+            return Range.__eq__(self, o)
+        return False
+    
+    ## 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"):
+        if string[-1] == "\n":
+            string = string[:-1]
+        self.setFromTuple( 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) < len(self.__dict__.keys()):
+            return 0
+        self.setFromTuple(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 ) )
+