diff SMART/Java/Python/ncList/NCListParser.py @ 6:769e306b7933

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/ncList/NCListParser.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,74 @@
+#! /usr/bin/env python
+#
+# Copyright INRA-URGI 2009-2012
+# 
+# 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 random, os, time
+from optparse import OptionParser
+from commons.core.parsing.ParserChooser import ParserChooser
+from SMART.Java.Python.structure.Transcript import Transcript
+from SMART.Java.Python.structure.Interval import Interval
+from SMART.Java.Python.ncList.NCList import NCList
+from SMART.Java.Python.ncList.NCListCursor import NCListCursor
+try:
+   import cPickle as pickle
+except:
+   import pickle
+
+class NCListParser(object):
+    
+    def __init__(self, fileName, verbosity = 1):
+        self._fileName                = fileName
+        self._ncLists                 = {}
+        self._sortedFileNames         = {}
+        self._nbElements              = 0
+        self._nbElementsPerChromosome = {}
+        self._verbosity               = verbosity
+        
+    def parse(self):
+        handle                        = open(self._fileName)
+        self._sortedFileNames         = pickle.load(handle)
+        self._nbElements              = pickle.load(handle)
+        self._nbElementsPerChromosome = pickle.load(handle)
+        self._ncLists                 = pickle.load(handle)
+        for ncList in self._ncLists.values():
+            ncList._reopenFiles()
+        handle.close()
+
+    def getSortedFileNames(self):
+        return self._sortedFileNames
+
+    def getNbElements(self):
+        return self._nbElements
+
+    def getNbElementsPerChromosome(self):
+        return self._nbElementsPerChromosome
+
+    def getNCLists(self):
+        return self._ncLists