--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/Python/mySql/MySqlExonTable.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,97 @@
+#
+# 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
+from SMART.Java.Python.structure.Interval import Interval
+from SMART.Java.Python.mySql.MySqlTable import MySqlTable
+
+
+class MySqlExonTable(MySqlTable):
+    """A table of exon 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_exons" % (name, chromosome)
+        super(MySqlExonTable, self).__init__(connection, name, verbosity)
+
+
+    def createExonTable(self):
+        variables = Interval.getSqlVariables()
+        variables.append("transcriptId")
+        types = Interval.getSqlTypes()
+        types["transcriptId"] = "int"
+        sizes = Interval.getSqlSizes()
+        sizes["transcriptId"] = 11
+        self.create(variables, types, sizes)
+
+
+    def rename(self, name):
+        super(MySqlExonTable, self).rename("%s_exons" % name)
+    
+        
+    def addExon(self, exon, transcriptId):
+        values = exon.getSqlValues()
+        values["transcriptId"] = transcriptId
+        id = self.addLine(values)
+        exon.id = id
+
+
+    def retrieveExonsFromTranscriptId(self, transcriptId):
+        if not self.created:
+            return []
+        query = self.mySqlConnection.executeQuery("SELECT * FROM %s WHERE transcriptId = %d" % (self.name, transcriptId))
+        exons = []
+        for exonLine in query.getIterator():
+            exon = Interval()
+            exon.setSqlValues(exonLine)
+            exons.append(exon)
+        return exons
+            
+
+    def retrieveExonsFromBulkTranscriptIds(self, transcriptIds):
+        if not transcriptIds:
+            return {}
+        if not self.created:
+            return {}
+        exons = dict([(transcriptId, []) for transcriptId in transcriptIds])
+        query = self.mySqlConnection.executeQuery("SELECT * FROM %s WHERE transcriptId IN (%s)" % (self.name, ", ".join(["%s" % (transcriptId) for transcriptId in transcriptIds])))
+        for exonLine in query.getIterator():
+            exon = Interval()
+            exon.setSqlValues(exonLine)
+            exons[exonLine[-1]].append(exon)
+        return exons
+            
+
+    def removeFromTranscriptId(self, transcriptId):
+        self.mySqlConnection.executeQuery("DELETE FROM %s WHERE transcriptId = %d" % (self.name, transcriptId))