--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/commons/core/writer/WriterChooser.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,127 @@
+#
+# 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.writer.TranscriptListWriter import TranscriptListWriter
+from commons.core.writer.SequenceListWriter import SequenceListWriter
+from commons.core.writer.BedWriter import BedWriter
+from commons.core.writer.CsvWriter import CsvWriter
+from commons.core.writer.EmblWriter import EmblWriter
+from commons.core.writer.FastaWriter import FastaWriter
+from commons.core.writer.FastqWriter import FastqWriter
+from commons.core.writer.GbWriter import GbWriter
+from commons.core.writer.Gff2Writer import Gff2Writer
+from commons.core.writer.SamWriter import SamWriter
+from commons.core.writer.UcscWriter import UcscWriter
+from commons.core.writer.WigWriter import WigWriter
+from commons.core.writer.Gff3Writer import Gff3Writer
+from commons.core.writer.GtfWriter import GtfWriter
+from commons.core.writer.MapWriter import  MapWriter
+
+ 
+class WriterChooser(object):
+    """
+    A class that finds the correct writer
+    @ivar type: transcript / sequence writer
+    @type type: string
+    @ivar format: the format of the writer
+    @type format: string
+    @ivar writerClass: the class of the writer
+    @type writerClass: string
+    @ivar extension: default extension of the file
+    @type extension: string
+    @ivar verbosity: verbosity
+    @type verbosity: int        
+    """
+
+    def __init__(self, verbosity = 0):
+        """
+        Constructor
+        @param verbosity: verbosity
+        @type    verbosity: int
+        """
+        self.type = None
+        self.format = None
+        self.writerClass = None
+        self.extension = None
+        self.verbosity = verbosity
+    
+
+    def findFormat(self, format, type = None):
+        """
+        Find the correct parser
+        @ivar format: the format
+        @type format: string
+        @ivar type: transcript sequence parser (None is all)
+        @type type: string
+        @return: a parser
+        """
+        classes = {}
+        if (type == "transcript"):
+            classes = {TranscriptListWriter: "transcript"}
+        elif (type == "sequence"):
+            classes = {SequenceListWriter: "sequence"}
+        elif (type == None):
+            classes = {TranscriptListWriter: "transcript", SequenceListWriter: "sequence"}
+        else:
+            sys.exit("Do not understand format type '%s'" % (type))
+
+        for classType in classes:
+            for writerClass in classType.__subclasses__():
+                if format in writerClass.getFileFormats():
+                    self.writerClass = writerClass
+                    self.extension = writerClass.getExtension()
+                    self.type = classes[classType]
+                    return
+        sys.exit("Cannot get writer for format '%s'" % (format))
+
+
+    def getWriter(self, fileName):
+        """
+        Get the writer previously found
+        @return: the writer
+        """
+        return self.writerClass(fileName, self.verbosity)
+
+
+    def getType(self):
+        """
+        Get the type of writer previously found
+        @return: the type of writer
+        """
+        return self.type
+
+
+    def getExtension(self):
+        """
+        Get the default extension of writer previously found
+        @return: the extension
+        """
+        return self.extension
+