annotate smart_toolShed/SMART/Java/Python/cleaning/CleanerChooser.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

#
# Copyright INRA-URGI 2009-2010
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# modify and/ or redistribute the software under the terms of the CeCILL
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import sys
from SMART.Java.Python.cleaning.TranscriptListCleaner import TranscriptListCleaner
from SMART.Java.Python.cleaning.GffCleaner import GffCleaner
from SMART.Java.Python.cleaning.GtfCleaner import GtfCleaner
from SMART.Java.Python.cleaning.DefaultCleaner import DefaultCleaner

#Attention!! Do not delete the imports!! They are used to know the type of file format!!!

class CleanerChooser(object):
	"""
	A class that finds the correct cleaner
	@ivar format: the format
	@type format: string
	@ivar cleaner: the parser
	@type cleaner: object
	@ivar cleanerClass: the class of the parser
	@type cleanerClass: class
	@ivar verbosity: verbosity
	@type verbosity: int		
	"""

	def __init__(self, verbosity = 0):
		"""
		Constructor
		@param verbosity: verbosity
		@type verbosity: int
		"""
		self.verbosity = verbosity
	

	def findFormat(self, format):
		"""
		Find the correct parser
		@ivar format: the format
		@type format: string
		@return: a cleaner
		"""
		for cleanerClass in TranscriptListCleaner.__subclasses__():
			if cleanerClass != None:
				if cleanerClass.getFileFormats() != None and format in cleanerClass.getFileFormats():
					self.cleanerClass = cleanerClass
					return
		self.cleanerClass = DefaultCleaner


	def getCleaner(self):
		"""
		Get the parser previously found
		@return: the parser
		"""
		return self.cleanerClass(self.verbosity)