--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/ncList/NCListMerger.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,126 @@
+#! /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, os, shutil
+try:
+	import cPickle as pickle
+except:
+	import pickle
+
+LONG_SIZE = struct.calcsize('l')
+
+INFO_PER_NCLIST = 5
+H_FILE		    = 0
+L_FILE		    = 1
+G_FILE		    = 2
+FIRST_LIST_SIZE = 3
+INDEX		    = 4
+
+def pack(input):
+	return struct.pack("l", long(input))
+def unpack(input):
+	return struct.unpack("l", input)[0]
+
+
+class NCListMerger(object):
+
+	def __init__(self, verbosity):
+		self._verbosity = verbosity
+		self._index	 = False
+
+	def setFileName(self, fileName):
+		self._handle = open(fileName, "wb")
+
+	def setNCLists(self, ncLists):
+		self._ncLists = ncLists
+		self._chromosomes = sorted(self._ncLists.keys())
+
+	def addIndex(self, boolean):
+		self._index = boolean
+
+	def merge(self):
+		self._writeHeader()
+		self._addNCLists()
+		self._handle.close()
+		self._removeInputFiles()
+
+	def _writeHeader(self):
+		pickle.dump(self._chromosomes, self._handle, -1)
+		for chromosome in self._chromosomes:
+			self._handle.write(pack(self._ncLists[chromosome]._nbLines))
+		self._headerPos = self._handle.tell()
+		for chromosome in self._chromosomes:
+			for i in range(INFO_PER_NCLIST):
+				self._handle.write(pack(-1))
+
+	def _addInHeader(self, i, info, value = None):
+		currentPos = self._handle.tell()
+		if value == None:
+			value = currentPos
+		self._handle.seek(self._headerPos + i * INFO_PER_NCLIST * LONG_SIZE + info * LONG_SIZE)
+		self._handle.write(pack(value))
+		self._handle.seek(currentPos)
+
+	def _addNCLists(self):
+		self._inputFileNames = []
+		for i, chromosome in enumerate(self._chromosomes):
+			ncList = self._ncLists[chromosome]
+			self._addInHeader(i, H_FILE)
+			hFile = open(ncList._hFileName)
+			shutil.copyfileobj(hFile, self._handle)
+			hFile.close()
+			self._inputFileNames.append(ncList._hFileName)
+		for i, chromosome in enumerate(self._chromosomes):
+			ncList = self._ncLists[chromosome]
+			self._addInHeader(i, L_FILE)
+			lFile = open(ncList._lFileName)
+			shutil.copyfileobj(lFile, self._handle)
+			lFile.close()
+			self._inputFileNames.append(ncList._lFileName)
+		for i, chromosome in enumerate(self._chromosomes):
+			ncList = self._ncLists[chromosome]
+			self._addInHeader(i, FIRST_LIST_SIZE, ncList.getSizeFirstList())
+		if self._index:
+			for i, chromosome in enumerate(self._chromosomes):
+				ncList = self._ncLists[chromosome]
+				self._addInHeader(i, INDEX)
+				pickle.dump(ncList.getIndex()._indices, self._handle, -1)
+		for i, chromosome in enumerate(self._chromosomes):
+			ncList = self._ncLists[chromosome]
+			self._addInHeader(i, G_FILE)
+			tFile = open(ncList._transcriptFileName)
+			shutil.copyfileobj(tFile, self._handle)
+			tFile.close()
+			self._inputFileNames.append(ncList._transcriptFileName)
+
+	def _removeInputFiles(self):
+		for fileName in self._inputFileNames:
+			os.remove(fileName)