#
# 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.
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# 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
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# same conditions as regards security.
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# The fact that you are presently reading this means that you have had
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#
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()