cistematic/programs/parent.py

   1 ###########################################################################
   2 #                                                                         #
   3 # C O P Y R I G H T   N O T I C E                                         #
   4 #  Copyright (c) 2003-10 by:                                              #
   5 #    * California Institute of Technology                                 #
   6 #                                                                         #
   7 #    All Rights Reserved.                                                 #
   8 #                                                                         #
   9 # Permission is hereby granted, free of charge, to any person             #
  10 # obtaining a copy of this software and associated documentation files    #
  11 # (the "Software"), to deal in the Software without restriction,          #
  12 # including without limitation the rights to use, copy, modify, merge,    #
  13 # publish, distribute, sublicense, and/or sell copies of the Software,    #
  14 # and to permit persons to whom the Software is furnished to do so,       #
  15 # subject to the following conditions:                                    #
  16 #                                                                         #
  17 # The above copyright notice and this permission notice shall be          #
  18 # included in all copies or substantial portions of the Software.         #
  19 #                                                                         #
  20 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,         #
  21 # EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF      #
  22 # MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND                   #
  23 # NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS     #
  24 # BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN      #
  25 # ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN       #
  26 # CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE        #
  27 # SOFTWARE.                                                               #
  28 ###########################################################################
  29 #
  30 # parent.py - defines Parent class used by all children classes in cistematic.programs
  31 #
  32 class Parent:
  33     contents = ""
  34     tagID = ""
  35
  36
  37     def __init__(self, tagID="", inputFilePath="", outputFilePath=""):
  38         self.tagID = ""
  39         self.inputFilePath = inputFilePath
  40         self.outputFilePath = outputFilePath
  41
  42
  43     def setTagID(self, tid):
  44         self.tagID = tid
  45
  46
  47     def name(self):
  48         return self.__class__.__name__
  49
  50
  51     def inputFile(self, inputFilePath):
  52         self.inputFilePath = inputFilePath
  53
  54
  55     def outputFile(self, outputFilePath):
  56         self.outputFilePath = outputFilePath
  57
  58
  59     def setSeqLength(self, length):
  60         pass
  61
  62
  63     def run(self):
  64         pass
  65
  66
  67     def display(self):
  68         for line in self.contents:
  69             print line
  70
  71
  72     def load(self, inFilePath):
  73         inFile = open(inFilePath, "r")
  74         self.contents = inFile.readlines()
  75         inFile.close()
  76
  77
  78     def save(self):
  79         outFile = open(self.outputFilePath, "w")
  80         for line in self.contents:
  81             outFile.write(line)
  82
  83         outFile.close()