Package Bio :: Package AlignIO :: Module Interfaces :: Class SequentialAlignmentWriter

Class SequentialAlignmentWriter

     object --+    
              |    
AlignmentWriter --+
                  |
                 SequentialAlignmentWriter

Known Subclasses:

Base class for building MultipleSeqAlignment writers.

This assumes each alignment can be simply appended to the file.
You should write a write_alignment() method.
You may wish to redefine the __init__ method as well

Instance Methods

[hide private]

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

source code

write_alignment(self, alignment)
Use this to write a single alignment.

source code

write_file(self, alignments)
Use this to write an entire file containing the given alignments.

source code

write_footer(self)
Use this to write any footer.

source code

write_header(self)
Use this to write any header.

source code

Inherited from AlignmentWriter: clean

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

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, handle)
(Constructor)

source code

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

Overrides: object.__init__: (inherited documentation)

write_alignment(self, alignment)

source code

Use this to write a single alignment.

This method should be replaced by any derived class to do something
useful.

write_file(self, alignments)

source code

Use this to write an entire file containing the given alignments.

alignments - A list or iterator returning MultipleSeqAlignment objects

In general, this method can only be called once per file.

Overrides: AlignmentWriter.write_file

write_footer(self)

source code

Use this to write any footer.

This method should be replaced by any derived class to do something
useful.

write_header(self)

source code

Use this to write any header.

This method should be replaced by any derived class to do something
useful.

Class SequentialAlignmentWriter

__init__(self, handle) (Constructor)

write_alignment(self, alignment)

write_file(self, alignments)

write_footer(self)

write_header(self)

init(self, handle)
(Constructor)