--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/ncList/NCListHandler.py	Thu May 02 09:56:47 2013 -0400
@@ -0,0 +1,125 @@
+#! /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
+# "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 struct
+try:
+	import cPickle as pickle
+except:
+	import pickle
+from SMART.Java.Python.ncList.NCList import NCList
+from SMART.Java.Python.ncList.NCIndex import NCIndex
+from SMART.Java.Python.ncList.NCListFilePickle import NCListFileUnpickle
+
+LONG_SIZE = struct.calcsize('l')
+
+INFO_PER_NCLIST = 5
+H_FILE		    = 0
+L_FILE		    = 1
+G_FILE		    = 2
+FIRST_LIST_SIZE = 3
+INDEX		    = 4
+
+H = 0
+L = 1
+T = 2
+G = 3
+
+def pack(input):
+	return struct.pack("l", long(input))
+def unpack(input):
+	return struct.unpack("l", input)[0]
+
+
+class NCListHandler(object):
+
+	def __init__(self, verbosity):
+		self._verbosity = verbosity
+		self._index	    = False
+
+	def setFileName(self, fileName):
+		self._fileName = fileName
+		self._handle   = open(fileName, "rb")
+
+	def loadData(self):
+		self._chromosomes = pickle.load(self._handle)
+		self._nbElements = 0
+		self._nbElementsPerChromosome = {}
+		self._ncLists = {}
+		for chromosome in self._chromosomes:
+			self._nbElementsPerChromosome[chromosome] = unpack(self._handle.read(LONG_SIZE))
+			self._nbElements += self._nbElementsPerChromosome[chromosome]
+		self._headerPos = self._handle.tell()
+		for i, chromosome in enumerate(self._chromosomes):
+			ncList = NCList(self._verbosity)
+			ncList._hHandle = self._handle
+			ncList._lHandle = self._handle
+			ncList._parser  = NCListFileUnpickle(self._fileName)
+			self._handle.seek(self._headerPos + i * INFO_PER_NCLIST * LONG_SIZE + H_FILE * LONG_SIZE)
+			ncList.setOffset(H, unpack(self._handle.read(LONG_SIZE)))
+			self._handle.seek(self._headerPos + i * INFO_PER_NCLIST * LONG_SIZE + L_FILE * LONG_SIZE)
+			ncList.setOffset(L, unpack(self._handle.read(LONG_SIZE)))
+			self._handle.seek(self._headerPos + i * INFO_PER_NCLIST * LONG_SIZE + G_FILE * LONG_SIZE)
+			ncList.setOffset(G, unpack(self._handle.read(LONG_SIZE)))
+			self._handle.seek(self._headerPos + i * INFO_PER_NCLIST * LONG_SIZE + FIRST_LIST_SIZE * LONG_SIZE)
+			ncList._sizeFirstList = unpack(self._handle.read(LONG_SIZE))
+			self._handle.seek(self._headerPos + i * INFO_PER_NCLIST * LONG_SIZE + INDEX * LONG_SIZE)
+			indices = unpack(self._handle.read(LONG_SIZE))
+			if indices != -1:
+				self._handle.seek(indices)
+				data = pickle.load(self._handle)
+				index = NCIndex(self._verbosity)
+				index._indices = data
+				ncList._index = index
+			self._ncLists[chromosome] = ncList
+
+	def getChromosomes(self):
+		return self._chromosomes
+
+	def getNbElements(self):
+		return self._nbElements
+
+	def getNbElementsPerChromosome(self):
+		return self._nbElementsPerChromosome
+
+	def getNCLists(self):
+		return self._ncLists
+
+	def getParser(self, chromosome = None):
+		parser = NCListFileUnpickle(self._fileName)
+		if chromosome == None:
+			parser.setInitAddress(unpack(self._handle, self._headerPos + G_FILE * LONG_SIZE))
+			return parser
+		i = self._chromosomes.index(chromosome)
+		self._handle.seek(self._headerPos + i * INFO_PER_NCLIST * LONG_SIZE + G_FILE * LONG_SIZE)
+		pos = unpack(self._handle.read(LONG_SIZE))
+		parser.setInitAddress(pos)
+		parser.setChromosome(chromosome)
+		return parser