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

source code

object --+
         |
        PrintFormat
Known Subclasses:

PrintFormat allow the printing of results of restriction analysis.

Instance Methods [hide private]
new PrintFormat Instance

__init__() source code
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.
source code
 
print_that(self, dct, title='', s1='')
PF.print_that(dct, [title[, s1]]) -> Print dct nicely formatted.
source code
string

make_format(PF, cut, nc=[], title='', s=[])
Virtual method.
source code
string

_make_list(PF, ls, title, nc, s1)
return a string of form:
source code
string

_make_map(PF, ls, title, nc, s1)
return a string of form:
source code
string

_make_number(PF, ls, title, nc, s1)
title.
source code
string

_make_nocut(PF, ls, title, nc, s1)
return a formatted string of the non cutting enzymes.
source code
string

_make_nocut_only(PF, nc, s1)
return a formatted string of the non cutting enzymes.
source code
string

_make_list_only(PF, ls, title)
return a string of form:
source code
string

_make_number_only(PF, ls, title)
return a string of form:
source code
string

_make_map_only(PF, ls, title)
return a string of form:
source code
string

__next_section(FP, ls, into)
ls is a list of tuple (string, [int, int]).
source code

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables [hide private]
  ConsoleWidth = 80
  NameWidth = 10
  MaxSize = 6
  Cmodulo = 0
  PrefWidth = 80
  Indent = 4
  linesize = 70
Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__()
(Constructor)

source code 


Returns:
new PrintFormat Instance

Overrides: object.__init__

print_as(PF, what='list')

source code 
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='')

source code 
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 formatted 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=[])

source code 
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)

source code 
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)

source code 
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)

source code 
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)

source code 
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)

source code 
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)

source code 
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)

source code 
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)

source code 
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)

source code 
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