--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/ParserChooser.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,128 @@
+#
+# 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 sys
+from commons.core.parsing.TranscriptListParser import TranscriptListParser
+from commons.core.parsing.MapperParser import MapperParser
+from commons.core.parsing.SequenceListParser import SequenceListParser
+from commons.core.parsing.BedParser import BedParser
+from commons.core.parsing.GffParser import GffParser
+from commons.core.parsing.MapperParser import MapperParser
+from commons.core.parsing.CoordsParser import CoordsParser
+from commons.core.parsing.SeqmapParser import SeqmapParser
+from commons.core.parsing.SoapParser import SoapParser
+from commons.core.parsing.Soap2Parser import Soap2Parser
+from commons.core.parsing.BlastParser import BlastParser
+from commons.core.parsing.PslParser import PslParser
+from commons.core.parsing.RmapParser import RmapParser
+from commons.core.parsing.ShrimpParser import ShrimpParser
+from commons.core.parsing.AxtParser import AxtParser
+from commons.core.parsing.ExoParser import ExoParser
+from commons.core.parsing.MaqParser import MaqParser
+from commons.core.parsing.SamParser import SamParser
+from commons.core.parsing.BamParser import BamParser
+from commons.core.parsing.BowtieParser import BowtieParser
+from commons.core.parsing.ElandParser import ElandParser
+from commons.core.parsing.GtfParser import GtfParser
+from commons.core.parsing.FastaParser import FastaParser
+from commons.core.parsing.FastqParser import FastqParser
+from commons.core.parsing.MapParser import MapParser
+from commons.core.parsing.NCListParser import NCListParser
+from commons.core.parsing.PklParser import PklParser
+
+#Attention!! Do not delete the imports!! They are used to know the type of file format!!!
+
+class ParserChooser(object):
+    """
+    A class that finds the correct parser
+    @ivar format: the format
+    @type format: string
+    @ivar type: transcript / mapping / sequence parser
+    @type type: string
+    @ivar parser: the parser
+    @type parser: object
+    @ivar verbosity: verbosity
+    @type verbosity: int        
+    """
+
+    def __init__(self, verbosity = 0):
+        """
+        Constructor
+        @param verbosity: verbosity
+        @type verbosity: int
+        """
+        self.type = None
+        self.parserClass = None
+        self.verbosity = verbosity
+    
+
+    def findFormat(self, format, type = None):
+        """
+        Find the correct parser
+        @ivar format: the format
+        @type format: string
+        @ivar type: transcript / mapping / sequence parser (None is all)
+        @type type: string
+        @return: a parser
+        """
+        classes = {}
+        if (type == "transcript"):
+            classes = {TranscriptListParser: "transcript"}
+        elif (type == "mapping"):
+            classes = {MapperParser: "mapping"}
+        elif (type == "sequence"):
+            classes = {SequenceListParser: "sequence"}
+        elif (type == None):
+            classes = {TranscriptListParser: "transcript", MapperParser: "mapping", SequenceListParser: "sequence"}
+        else:
+            raise Exception("Do not understand format type '%s'" % (type))
+
+        for classType in classes:
+            for parserClass in classType.__subclasses__():
+                if format in parserClass.getFileFormats():
+                    self.parserClass = parserClass
+                    self.type = classes[classType]
+                    return
+        raise Exception("Cannot get parser for format '%s'" % (format))
+
+
+    def getParser(self, fileName):
+        """
+        Get the parser previously found
+        @return: the parser
+        """
+        return self.parserClass(fileName, self.verbosity)
+
+
+    def getType(self):
+        """
+        Get the type of parser previously found
+        @return: the type of parser
+        """
+        return self.type