Package csb :: Package bio :: Package io :: Module fasta :: Class OutputBuilder |
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# Class OutputBuilder

source code

    object --+
             |
            OutputBuilder

Known Subclasses:
  - A3MOutputBuilder
  - , FASTAOutputBuilder
  - , PIROutputBuilder

Base sequence/alignment string format builder.

Note: File builders are not guaranteed to check the correctness of the product. It is assumed that the client of the builder knows what it is doing.

Nested Classes
| __metaclass__ Metaclass for defining Abstract Base Classes (ABCs).

Instance Methods
__init__(self, output, headers=True) x.__init__(...) initializes x; see help(type(x)) for signature | source code
add_alignment(self, alignment) Format and append an alignment to the product. | source code
add_comment(self, text, comment=`'``#``'`, length=120) Append a comment line to the product. | source code
add_many(self, sequences) Format and append a collection of AbstractSequences to the product. | source code
add_separator(self, separator=`'````'`) Append a sequence separator to the product. | source code
add_sequence(self, sequence) Format and append a new sequence to the product. | source code
write(self, text) Write a chunk of `text` to the output stream. | source code
writeline(self, text) Write a chunk of `text`, followed by a newline terminator. | source code
Inherited from `object`: `__delattr__`, `__format__`, `__getattribute__`, `__hash__`, `__new__`, `__reduce__`, `__reduce_ex__`, `__repr__`, `__setattr__`, `__sizeof__`, `__str__`, `__subclasshook__`

Static Methods
OutputBuilder |
create(format, *a, **k) Create an output builder, which knows how to handle the specified sequence/alignment `format`. | source code
register(format, klass) Register a new output builder. | source code

Class Variables
| __abstractmethods__ = ``frozenset([``'``add_alignment``'``,` `'``add_sequenc``...``

Properties
bool | headers True if sequence headers will be written to the destination
stream | output Destination stream
Inherited from `object`: `__class__`

Method Details

### __init__(self, output, headers=True) (Constructor) | source code
x.__init__(...) initializes x; see help(type(x)) for signature Parameters: `output` (file) - destination stream, where the product is written. `headers` (bool) - if False, omit headers Overrides: object.__init__ (inherited documentation)

### add_alignment(self, alignment) | source code
Format and append an alignment to the product. Parameters: `alignment` (AbstractAlignment)

### add_comment(self, text, comment=`'``#``'`, length=120) | source code
Append a comment line to the product. Parameters: `text` (str) - comment text `comment` (str) - comment prefix `length` (int) - maximal comment length

### add_many(self, sequences) | source code
Format and append a collection of AbstractSequences to the product. Parameters: `sequences` (iterable of AbstractSequences)

### add_sequence(self, sequence) | source code
Format and append a new sequence to the product. Parameters: `sequence` (AbstractSequence)

### create(format, *a, **k) Static Method | source code
Create an output builder, which knows how to handle the specified sequence/alignment `format`. Additional arguments are passed to the builder's constructor. Parameters: `format` (EnumItem) - AlignmentFormats member Returns: OutputBuilder

### register(format, klass) Static Method | source code
Register a new output builder. Parameters: `format` (EnumItem) - AlignmentFormats member `klass` (type) - builder class (OutputBuilder sub-class)

Class Variable Details

  ### __abstractmethods__ Value:
      frozenset(['add_alignment', 'add_sequence'])

Property Details

### headers True if sequence headers will be written to the destination Get Method: unreachable.headers(self) - True if sequence headers will be written to the destination Type: bool

### output Destination stream Get Method: unreachable.output(self) - Destination stream Type: stream