diff SMART/Java/Python/structure/SequenceList.py @ 6:769e306b7933

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/structure/SequenceList.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,72 @@
+#
+# 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 math
+
+class SequenceList(object):
+    """A class that codes for a list of sequences"""
+
+    def __init__(self, verbosity = 0):
+        self.sequences = []
+        self.verbosity = verbosity
+
+
+    def nbSequences(self):
+        return len(self.sequences)
+
+
+    def getSequence(self, index):
+        return self.sequences[index]
+        
+
+    def addSequence(self, sequence):
+        self.sequences.append(sequence)
+        
+
+    def split(self, number):
+        sequenceLists = []
+        size          = math.ceil(self.nbSequences() / number)
+
+        sequenceList = SequenceList()
+        for i in range(0, self.nbSequences()):
+            sequenceList.addSequence(self.getSequence(i))
+            if (sequenceList.nbSequences() == size):
+                sequenceLists.append(sequenceList)
+                sequenceList = SequenceList()
+        if (sequenceList.nbSequences() != 0):
+            sequenceLists.append(sequenceList)
+        return sequenceLists
+
+
+    def printFasta(self):
+        string = ""
+        for sequence in self.sequences:
+            string += sequence.printFasta()
+        return string
+