Package Bio :: Package Restriction :: Module PrintFormat :: Class PrintFormat
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Class PrintFormat

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object --+
         |
        PrintFormat

PrintFormat allow the printing of results of restriction analysis.

Instance Methods [hide private]
new PrintFormat Instance
__init__()
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
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print the results as specified
print_as(PF, what='list')
Valid format are : 'list' -> alphabetical order 'number' -> number of sites in the sequence 'map' -> a map representation of the sequence with the sites.
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print_that(self, dct, title='', s1='')
PF.print_that(dct, [title[, s1]]) -> Print dct nicely formatted.
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string
make_format(PF, cut, nc=[], title='', s=[])
Virtual method.
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string
_make_list(PF, ls, title, nc, s1)
return a string of form :
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string
_make_map(PF, ls, title, nc, s1)
return a string of form :
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string
_make_number(PF, ls, title, nc, s1)
title.
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string
_make_nocut(PF, ls, title, nc, s1)
return a formatted string of the non cutting enzymes.
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string
_make_nocut_only(PF, nc, s1)
return a formatted string of the non cutting enzymes.
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string
_make_list_only(PF, ls, title)
return a string of form :
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string
_make_number_only(PF, ls, title)
return a string of form :
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string
_make_map_only(PF, ls, title)
return a string of form :
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string
__next_section(FP, ls, into)
ls is a list of tuple (string, [int, int]).
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Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __str__

Class Variables [hide private]
  ConsoleWidth = 80
  NameWidth = 10
  MaxSize = 6
  Cmodulo = ConsoleWidth % NameWidth
  PrefWidth = ConsoleWidth-Cmodulo
  Indent = 4
  linesize = PrefWidth-NameWidth
Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__()
(Constructor)

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x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Returns: new PrintFormat Instance
Overrides: object.__init__

print_as(PF, what='list')

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Valid format are :
    'list'      -> alphabetical order
    'number'    -> number of sites in the sequence
    'map'       -> a map representation of the sequence with the sites.

If you want more flexibility over-ride the virtual method make_format.

Returns: print the results as specified

print_that(self, dct, title='', s1='')

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PF.print_that(dct, [title[, s1]]) -> Print dct nicely formatted.

dct is a dictionary as returned by a RestrictionBatch.search()

title is the title of the map. It must be a formated string, i.e. you must include the line break.

s1 is the title separating the list of enzymes that have sites from those without sites. s1 must be a formatted string as well.

The format of print_that is a list.

make_format(PF, cut, nc=[], title='', s=[])

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Virtual method. Here to be pointed to one of the _make_* methods. You can as well create a new method and point make_format to it.

Returns: string

_make_list(PF, ls, title, nc, s1)

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return a string of form :

title.

enzyme1 : position1, position2. enzyme2 : position1, position2, position3.

ls is a list of cutting enzymes. title is the title. nc is a list of non cutting enzymes. s1 is the sentence before the non cutting enzymes.

Returns: string

_make_map(PF, ls, title, nc, s1)

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return a string of form :

title.

    enzyme1, position
    |
AAAAAAAAAAAAAAAAAAAAA...
|||||||||||||||||||||
TTTTTTTTTTTTTTTTTTTTT...

ls is a list of cutting enzymes.
title is the title.
nc is a list of non cutting enzymes.
s1 is the sentence before the non cutting enzymes.

Returns: string

_make_number(PF, ls, title, nc, s1)

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title.

enzyme which cut 1 time :

enzyme1 : position1.

enzyme which cut 2 times :

enzyme2 : position1, position2. ...

ls is a list of cutting enzymes. title is the title. nc is a list of non cutting enzymes. s1 is the sentence before the non cutting enzymes.

Returns: string

_make_nocut(PF, ls, title, nc, s1)

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return a formatted string of the non cutting enzymes.

ls is a list of cutting enzymes -> will not be used. Here for compatibility with make_format.

title is the title. nc is a list of non cutting enzymes. s1 is the sentence before the non cutting enzymes.

Returns: string

_make_nocut_only(PF, nc, s1)

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return a formatted string of the non cutting enzymes.

nc is a list of non cutting enzymes. s1 is the sentence before the non cutting enzymes.

Returns: string

_make_list_only(PF, ls, title)

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return a string of form :

title.

enzyme1 : position1, position2. enzyme2 : position1, position2, position3. ...

ls is a list of results. title is a string. Non cutting enzymes are not included.

Returns: string

_make_number_only(PF, ls, title)

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return a string of form :

title.

enzyme which cut 1 time :

enzyme1 : position1.

enzyme which cut 2 times :

enzyme2 : position1, position2. ...

ls is a list of results. title is a string. Non cutting enzymes are not included.

Returns: string

_make_map_only(PF, ls, title)

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return a string of form :

title.

    enzyme1, position
    |
AAAAAAAAAAAAAAAAAAAAA...
|||||||||||||||||||||
TTTTTTTTTTTTTTTTTTTTT...

        
ls is a list of results.
title is a string.
Non cutting enzymes are not included.

Returns: string

__next_section(FP, ls, into)

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ls is a list of tuple (string, [int, int]). into is a string to which the formatted ls will be added.

Format ls as a string of lines : The form is :

enzyme1 : position1. enzyme2 : position2, position3.

then add the formatted ls to tot return tot.

Returns: string