---
name: "Bio::Matrix::Mlagan"
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::Matrix::Mlagan"
---

# Bio::Matrix::Mlagan(3pm)

A generic matrix with mlagan fields

## NAME

Bio::Matrix::Mlagan - A generic matrix with mlagan fields

## SYNOPSIS

```
  # See L<Bio::Matrix::Generic> for most methods.
  # These are relevant for mlagan IO:
  $matrix->gap_open(-400);
  $matrix->gap_continue(-25);
```

## DESCRIPTION

This is based on Bio::Matrix::Generic, differing by storing gap\_open and gap\_continue data members to allow mlagan IO (see Bio::Matrix::IO::mlagan). (Those values are 'outside' the matrix.)

It also limits the structure to a 6x6 matrix with row & column names 'A', 'C', 'G', 'T', '.' and 'N'.

## FEEDBACK

### Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list.  Your participation is much appreciated.

```
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
```

### 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 of the bugs and their resolution. Bug reports can be submitted via the web:

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

## AUTHOR - Sendu Bala

Email bix@sendu.me.uk

## APPENDIX

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

### new

```
 Title   : new
 Usage   : my $obj = Bio::Matrix::Generic->new();
 Function: Builds a new Bio::Matrix::Generic object
 Returns : an instance of Bio::Matrix::Generic
 Args    : -values            => arrayref of arrayrefs of data initialization
           -matrix_id         => id of the matrix
           -matrix_name       => name of the matrix
           -matrix_init_value => default value to initialize empty cells
           -gap_open          => gap open penalty (int)
           -gap_continue      => gap continue penalty (int)
           NB: -rownames and -colnames should not be given here, since they are
           always being set to 'A', 'C', 'G', 'T', '.' and 'N'.
```

### gap\_open

```
 Title   : gap_open
 Usage   : $obj->gap_open(-400);
 Function: Get/set the gap open amount.
 Returns : int
 Args    : none to get, OR int to set
```

### gap\_continue

```
 Title   : gap_continue
 Usage   : $obj->gap_continue(-25);
 Function: Get/set the gap continue amount.
 Returns : int
 Args    : none to get, OR int to set
```

### add\_row

```
 Title   : add_row
 Usage   : Do not use
 Function: This generic method is not suitable for mlagan, where the number of
           rows is fixed.
 Returns : Warning
 Args    : none
```

### remove\_row

```
 Title   : remove_row
 Usage   : Do not use
 Function: This generic method is not suitable for mlagan, where the number of
           rows is fixed.
 Returns : Warning
 Args    : none
```

### add\_column

```
 Title   : add_column
 Usage   : Do not use
 Function: This generic method is not suitable for mlagan, where the number of
           columns is fixed.
 Returns : Warning
 Args    : none
```

### remove\_column

```
 Title   : remove_column
 Usage   : Do not use
 Function: This generic method is not suitable for mlagan, where the number of
           columns is fixed.
 Returns : Warning
 Args    : none
```