--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/cleaning/TranscriptListCleaner.py	Tue Apr 30 15:02:29 2013 -0400
@@ -0,0 +1,63 @@
+#
+# 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 sys
+from SMART.Java.Python.structure.TranscriptList import TranscriptList
+from SMART.Java.Python.misc.Progress import Progress
+from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
+
+class TranscriptListCleaner(object):
+	"""A (quite generic) class that cleans a file containing transcripts"""
+
+	def __init__(self, verbosity = 0):
+		self.verbosity = verbosity
+
+	def setInputFileName(self, fileName):
+		try:
+			self.inputHandle = open(fileName)
+		except IOError:
+			raise Exception("Error! Transcript file '%s' does not exist! Exiting..." % (self.fileName))
+
+	def setOutputFileName(self, fileName):
+		try:
+			self.outputHandle = open(fileName, "w")
+		except IOError:
+			raise Exception("Error! Transcript file '%s' does not exist! Exiting..." % (self.fileName))
+
+	def getFileFormats():
+		pass
+	getFileFormats = staticmethod(getFileFormats)
+
+	def close(self):
+		self.inputHandle.close()
+		self.outputHandle.close()
+
+	def clean(self):
+		self._clean()
+		self.close()