+###########################################################################
+# #
+# C O P Y R I G H T N O T I C E #
+# Copyright (c) 2003-10 by: #
+# * California Institute of Technology #
+# #
+# All Rights Reserved. #
+# #
+# Permission is hereby granted, free of charge, to any person #
+# obtaining a copy of this software and associated documentation files #
+# (the "Software"), to deal in the Software without restriction, #
+# including without limitation the rights to use, copy, modify, merge, #
+# publish, distribute, sublicense, and/or sell copies of the Software, #
+# and to permit persons to whom the Software is furnished to do so, #
+# subject to the following conditions: #
+# #
+# The above copyright notice and this permission notice shall be #
+# included in all copies or substantial portions of the Software. #
+# #
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, #
+# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF #
+# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND #
+# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS #
+# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN #
+# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN #
+# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE #
+# SOFTWARE. #
+###########################################################################
+#
+# parent.py - defines Parent class used by all children classes in cistematic.programs
+#
+class Parent:
+ contents = ""
+ tagID = ""
+
+
+ def __init__(self, tagID="", inputFilePath="", outputFilePath=""):
+ self.tagID = ""
+ self.inputFilePath = inputFilePath
+ self.outputFilePath = outputFilePath
+
+
+ def setTagID(self, tid):
+ self.tagID = tid
+
+
+ def name(self):
+ return self.__class__.__name__
+
+
+ def inputFile(self, inputFilePath):
+ self.inputFilePath = inputFilePath
+
+
+ def outputFile(self, outputFilePath):
+ self.outputFilePath = outputFilePath
+
+
+ def setSeqLength(self, length):
+ pass
+
+
+ def run(self):
+ pass
+
+
+ def display(self):
+ for line in self.contents:
+ print line
+
+
+ def load(self, inFilePath):
+ inFile = open(inFilePath, "r")
+ self.contents = inFile.readlines()
+ inFile.close()
+
+
+ def save(self):
+ outFile = open(self.outputFilePath, "w")
+ for line in self.contents:
+ outFile.write(line)
+
+ outFile.close()
\ No newline at end of file