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1 #
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2 # Copyright INRA-URGI 2009-2010
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3 #
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4 # This software is governed by the CeCILL license under French law and
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5 # abiding by the rules of distribution of free software. You can use,
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6 # modify and/ or redistribute the software under the terms of the CeCILL
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7 # license as circulated by CEA, CNRS and INRIA at the following URL
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8 # "http://www.cecill.info".
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9 #
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10 # As a counterpart to the access to the source code and rights to copy,
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11 # modify and redistribute granted by the license, users are provided only
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12 # with a limited warranty and the software's author, the holder of the
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13 # economic rights, and the successive licensors have only limited
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14 # liability.
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15 #
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16 # In this respect, the user's attention is drawn to the risks associated
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17 # with loading, using, modifying and/or developing or reproducing the
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18 # software by the user in light of its specific status of free software,
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19 # that may mean that it is complicated to manipulate, and that also
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20 # therefore means that it is reserved for developers and experienced
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21 # professionals having in-depth computer knowledge. Users are therefore
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22 # encouraged to load and test the software's suitability as regards their
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23 # requirements in conditions enabling the security of their systems and/or
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24 # data to be ensured and, more generally, to use and operate it in the
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25 # same conditions as regards security.
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26 #
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27 # The fact that you are presently reading this means that you have had
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28 # knowledge of the CeCILL license and that you accept its terms.
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29 #
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30
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31 class SequenceListWriter(object):
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32 """
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33 An interface that writes a list of sequences into a file
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34 @ivar fileName: name of the file
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35 @type fileName: string
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36 @ivar handle: handle to the file
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37 @type handle: file handle
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38 @ivar header: first lines of the file
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39 @type header: string
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40 """
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41
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42
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43 def __init__(self, fileName, verbosity = 0):
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44 """
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45 Constructor
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46 @param fileName: name of the file
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47 @type fileName: string
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48 @param verbosity: verbosity
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49 @type verbosity: int
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50 """
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51 self.fileName = fileName
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52 self.verbosity = verbosity
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53 self.handle = open(self.fileName, "w")
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54
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55
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56 def __del__(self):
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57 """
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58 Destructor
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59 """
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60 self.close()
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61
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62
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63 def write(self):
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64 """
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65 No-op
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66 """
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67 pass
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68
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69
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70 def close(self):
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71 """
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72 Close writer
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73 """
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74 if self.handle != None:
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75 self.handle.close()
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76
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77
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78 def addSequence(self, sequence):
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79 """
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80 Add a sequence to the list of sequence to be written
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81 @param sequence: sequence to be written
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82 @type sequence: class L{Sequence<Sequence>}
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83 """
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84 self.handle.write(self.getLine(sequence))
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85
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86
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87 def addElement(self, element):
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88 """
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89 Same as "addSequence"
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90 @param element: sequence to be written
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91 @type element: class L{Sequence<Sequence>}
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92 """
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93 self.addSequence(element)
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94
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