view SMART/Java/Python/ncList/ @ 6:769e306b7933

Change the repository level.
author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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#! /usr/bin/env python
# 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
# "".
# 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 cPickle as pickle
	 import pickle
from SMART.Java.Python.structure.Transcript import Transcript

class NCListFilePickle(object):
	def __init__(self, fileName, verbosity = 1):
		self.fileName  = fileName
		self.handle	= open(fileName, "wb")
		self.verbosity = verbosity

	def __del__(self):
		if self.handle != None:
	def addTranscript(self, transcript):
		pickle.dump(transcript, self.handle, -1)

	def write(self):

	def close(self):

class NCListFileUnpickle(object):
	def __init__(self, fileName, verbosity = 1):
		self.handle		   = open(fileName, "rb")
		self.verbosity	   = verbosity
		self.initAddress   = 0
		self.address	   = self.initAddress
		self.nbTranscripts = None
		self.fileName	   = fileName
		self.over		   = False
		self.chromosome    = None

	def __del__(self):
		if self.handle != None:

	def reset(self):
		self.initAddress = 0

	def setChromosome(self, chromosome):
		self.chromosome = chromosome
	def getNbTranscripts(self):
		if self.nbTranscripts != None:
			return self._nbTranscripts
		self.nbTranscripts = 0
		for transcript in self.getIterator():
			self_nbTranscripts += 1
		return self.nbTranscripts

	def gotoAddress(self, address):
		self.address = address

	def getNextTranscript(self):
		self.address = self.handle.tell()
			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):
		while True:
			transcript = self.getNextTranscript()
			if not transcript:
				self.over = True
			yield transcript

	def setInitAddress(self, address):
		self.initAddress = address

	def getCurrentTranscriptAddress(self):
		return self.address

	def isOver(self):
		return self.over