---
name: "Bio::AlignIO::xmfa"
section: "3pm"
platform: "linux"
package: "libbio-perl-perl"
version: "1.7.8-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::AlignIO::xmfa"
---

# Bio::AlignIO::xmfa(3pm)

XMFA MSA Sequence input/output stream

## NAME

Bio::AlignIO::xmfa - XMFA MSA Sequence input/output stream

## SYNOPSIS

Do not use this module directly.  Use it via the Bio::AlignIO class.

## DESCRIPTION

This object can transform Bio::SimpleAlign objects from XMFA flat file databases.  For more information, see:

```
  http://asap.ahabs.wisc.edu/mauve-aligner/mauve-user-guide/mauve-output-file-formats.html
```

This module is based on the AlignIO::fasta parser written by Peter Schattner

## TODO

Finish **write\_aln()**, clean up code, allow LargeLocatableSeq (e.g. for very large sequences from Mauve).

## FEEDBACK

### Support

Please direct usage questions or support issues to the mailing list:

*bioperl-l@bioperl.org*

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

### Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution.  Bug reports can be submitted via the web:

```
  https://github.com/bioperl/bioperl-live/issues
```

## AUTHORS

Chris Fields

## APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a \_

### next\_aln

```
 Title   : next_aln
 Usage   : $aln = $stream->next_aln
 Function: returns the next alignment in the stream.
 Returns : Bio::Align::AlignI object - returns 0 on end of file
            or on error
 Args    : -width => optional argument to specify the width sequence
           will be written (60 chars by default)
```

See Bio::Align::AlignI

### write\_aln

```
 Title   : write_aln
 Usage   : $stream->write_aln(@aln)
 Function: writes the $aln object into the stream in xmfa format
 Returns : 1 for success and 0 for error
 Args    : L<Bio::Align::AlignI> object
```

See Bio::Align::AlignI

### \_get\_len

```
 Title   : _get_len
 Usage   :
 Function: determine number of alphabetic chars
 Returns : integer
 Args    : sequence string
```

### width

```
 Title   : width
 Usage   : $obj->width($newwidth)
           $width = $obj->width;
 Function: Get/set width of alignment
 Returns : integer value of width
 Args    : on set, new value (a scalar or undef, optional)
```