erange 4.0a dev release with integrated cistematic

[erange.git] / cistematic / programs / parent.py

diff --git a/cistematic/programs/parent.py b/cistematic/programs/parent.py
new file mode 100644 (file)
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+++ b/cistematic/programs/parent.py
@@ -0,0 +1,83 @@
+###########################################################################
+#                                                                         #
+# 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