--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/PklParser.py	Tue Apr 30 15:02:29 2013 -0400
@@ -0,0 +1,112 @@
+#
+# Copyright INRA-URGI 2009-2010
+# 
+# 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.
+#
+import re
+import sys
+try:
+	 import cPickle as pickle
+except:
+	 import pickle
+from SMART.Java.Python.structure.Interval import Interval
+from commons.core.parsing.TranscriptListParser import TranscriptListParser
+from SMART.Java.Python.structure.Transcript import Transcript
+
+
+class PklParser(TranscriptListParser):
+	"""A class that parses the intern PKL file and create a transcript list"""
+		
+	def __init__(self, fileName, verbosity = 1):
+		self.title = None
+		super(PklParser, self).__init__(fileName, verbosity)
+		self.handle		   = open(fileName, "rb")
+		self.verbosity	   = verbosity
+		self.initAddress   = 0
+		self.address	   = self.initAddress
+		self.over		   = False
+		self.chromosome	= None
+
+	def __del__(self):
+		super(PklParser, self).__del__()
+
+	def getFileFormats():
+		return ["pkl"]
+	getFileFormats = staticmethod(getFileFormats)
+
+
+	def skipFirstLines(self):
+		return
+
+
+	def reset(self):
+		self.handle.seek(0)
+		self.initAddress = 0
+
+
+	def setChromosome(self, chromosome):
+		self.chromosome = chromosome
+	
+
+	def gotoAddress(self, address):
+		self.handle.seek(address)
+		self.address = address
+
+
+	def getNextTranscript(self):
+		self.address = self.handle.tell()
+		try:
+			transcript = pickle.load(self.handle)
+			if self.chromosome != None and transcript.getChromosome() != self.chromosome:
+				self.over = True
+				return False
+			return transcript
+		except EOFError:
+			self.over = True
+			return False
+
+
+	def getIterator(self):
+		self.gotoAddress(self.initAddress)
+		while True:
+			transcript = self.getNextTranscript()
+			if not transcript:
+				self.over = True
+				return
+			yield transcript
+
+
+	def setInitAddress(self, address):
+		self.initAddress = address
+
+
+	def getCurrentTranscriptAddress(self):
+		return self.address
+
+
+	def isOver(self):
+		return self.over