--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/mySql/MySqlTranscriptTable.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,149 @@
+#
+# 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 random
+import sys
+from SMART.Java.Python.structure.TranscriptList import TranscriptList
+from SMART.Java.Python.mySql.MySqlExonTable import MySqlExonTable
+from SMART.Java.Python.mySql.MySqlTable import MySqlTable
+from SMART.Java.Python.structure.Transcript import Transcript
+from SMART.Java.Python.misc.Progress import Progress
+
+class MySqlTranscriptTable(MySqlTable):
+    """A table of transcripts in a mySQL database"""
+
+    def __init__(self, connection, name = None, chromosome = None, verbosity = 0):
+        if chromosome == None:
+            chromosome = ""
+        else:
+            chromosome = "_%s" % chromosome
+        if name == None:
+            name = "TmpTable_%d" % (random.randint(0, 100000))
+        name = "%s%s" % (name, chromosome)
+        super(MySqlTranscriptTable, self).__init__(connection, "%s_transcripts" % name, verbosity)
+
+
+    def createTranscriptTable(self):
+        self.create(Transcript.getSqlVariables(), Transcript.getSqlTypes(), Transcript.getSqlSizes())
+
+
+    def rename(self, name):
+        super(MySqlTranscriptTable, self).rename("%s_transcripts" % name)
+
+
+    def remove(self):
+        super(MySqlTranscriptTable, self).remove()
+        
+        
+    def clear(self):
+        super(MySqlTranscriptTable, self).clear()
+
+        
+    def copy(self, transcriptTable):
+        self.remove()
+        super(MySqlTranscriptTable, self).copy(transcriptTable)
+
+
+    def add(self, transcriptTable):
+        super(MySqlTranscriptTable, self).add(transcriptTable)
+
+
+    def addTranscript(self, transcript):
+        id = self.addLine(transcript.getSqlValues())
+        transcript.id = id
+            
+            
+    def addTranscriptList(self, transcriptList):
+        progress = Progress(transcriptList.getNbTranscript(), "Storing list to %s" % (self.name), self.verbosity)
+        for transcript in transcriptList.getIterator():
+            self.addTranscript(transcript)
+            progress.inc()
+        progress.done()
+
+            
+    def removeTranscript(self, transcript):
+        self.removeFromId(transcript.id)
+            
+            
+    def retrieveTranscriptFromId(self, id):
+        transcript = Transcript()
+        transcript.setSqlValues(self.retrieveFromId(id))
+        return transcript
+    
+    
+    def retrieveBulkTranscriptFromId(self, ids):
+        if not ids:
+            return []
+        transcripts = self.retrieveBulkFromId(ids)
+        idsToTranscripts = {}
+        for values in transcripts:
+            transcript = Transcript()
+            transcript.setSqlValues(values)
+            idsToTranscripts[values[0]] = transcript
+        return idsToTranscripts.values()
+    
+    
+    def selectTranscripts(self, command, simple = False):
+        MAXSIZE = 100000
+        found   = True
+        cpt     = 0
+        while found:
+            found = False
+            if simple:
+                thisCommand = command
+            else:
+                thisCommand = "%s LIMIT %d OFFSET %d" % (command, MAXSIZE, MAXSIZE * cpt)
+            query = self.mySqlConnection.executeQuery(thisCommand)
+            for line in query.getIterator():
+                found      = True
+                id         = int(line[0])
+                transcript = Transcript()
+                transcript.setSqlValues(line)
+                yield (id, transcript)
+            cpt += 1
+            if simple:
+                return
+
+    
+    def getIterator(self):
+        for id, transcript in self.selectTranscripts("SELECT * FROM '%s'" % (self.name)):
+            yield transcript
+
+
+    def retrieveTranscriptList(self):
+        transcriptList = TranscriptList()
+        for transcriptLine in self.getLines():
+            transcript = Transcript()
+            transcript.setSqlValues(transcriptLine)
+            transcriptList.addTranscript(transcript)
+        return transcriptList
+            
+
+    def setDefaultTagValue(self, name, value):
+        super(MySqlTranscriptTable, self).setDefaultTagValue(Transcript.getSqlVariables().index("tags")+1, name, value)