Bio::Matrix::MatrixI - An interface for describing a Matrix

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::Matrix::MatrixI - An interface for describing a Matrix

SYNOPSIS

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  # Get a Matrix object

DESCRIPTION

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This is an interface describing how one should be able to interact with a matrix. One can have a lot of information I suppose and this outline won't really work for PWM or PSSMs. We will have to derive a particular interface for those.

FEEDBACK

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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 email or the web:

  https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich

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Email jason-at-bioperl.org

APPENDIX

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

matrix_id

 Title   : matrix_id
 Usage   : my $id = $matrix->matrix_id
 Function: Get the matrix ID
 Returns : string value
 Args    :

matrix_name

 Title   : matrix_name
 Usage   : my $name = $matrix->matrix_name();
 Function: Get the matrix name
 Returns : string value
 Args    :

get_entry

 Title   : get_entry
 Usage   : my $entry = $matrix->get_entry($rowname,$columname)
 Function: Get the entry for a given row,column pair
 Returns : scalar
 Args    : $row name
           $column name

get_column

 Title   : get_column
 Usage   : my @row = $matrix->get_column('ALPHA');
 Function: Get a particular column
 Returns : Array (in array context) or arrayref (in scalar context)
           of values
 Args    : name of the column

get_row

 Title   : get_row
 Usage   : my @row = $matrix->get_row('ALPHA');
 Function: Get a particular row
 Returns : Array (in array context) or arrayref (in scalar context)
           of values
 Args    : name of the row

get_diagonal

 Title   : get_diagonal
 Usage   : my @diagonal = $matrix->get_diagonal; 
 Function: Get the diagonal of the matrix
 Returns : Array (in array context) or arrayref (in scalar context)
 Args    : none

column_num_for_name

 Title   : column_num_for_name
 Usage   : my $num = $matrix->column_num_for_name($name)
 Function: Gets the column number for a particular column name
 Returns : integer
 Args    : string

row_num_for_name

 Title   : row_num_for_name
 Usage   : my $num = $matrix->row_num_for_name($name)
 Function: Gets the row number for a particular row name
 Returns : integer
 Args    : string

num_rows

 Title   : num_rows
 Usage   : my $rowcount = $matrix->num_rows;
 Function: Get the number of rows
 Returns : integer
 Args    : none

num_columns

 Title   : num_columns
 Usage   : my $colcount = $matrix->num_columns
 Function: Get the number of columns
 Returns : integer
 Args    : none

reverse

 Title   : reverse
 Usage   : my $matrix = $matrix->reverse
 Function: Get the reverse of a matrix
 Returns : 
 Args    :

row_names

 Title   : row_names
 Usage   : my @rows = $matrix->row_names
 Function: The names of all the rows
 Returns : array in array context, arrayref in scalar context
 Args    : none

column_names

 Title   : column_names
 Usage   : my @columns = $matrix->column_names
 Function: The names of all the columns
 Returns : array in array context, arrayref in scalar context
 Args    : none
BioPerl documentation Contained in the BioPerl distribution. 
# $Id $
#
# BioPerl module for Bio::Matrix::MatrixI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Jason Stajich <jason-at-bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code



# Let the code begin...


package Bio::Matrix::MatrixI;
use strict;


use base qw(Bio::Root::RootI);



sub matrix_id{
   my ($self) = @_;
   $self->throw_not_implemented();
}


sub matrix_name{
   my ($self) = @_;

   $self->throw_not_implemented();
}


sub get_entry{
   my ($self) = @_;

    $self->throw_not_implemented();
}



sub get_column{
   my ($self) = @_;
   $self->throw_not_implemented();
}


sub get_row{
   my ($self) = @_;
   $self->throw_not_implemented();
}



sub get_diagonal{
   my ($self) = @_;
   $self->throw_not_implemented();
}


sub column_num_for_name{
   my ($self) = @_;

    $self->throw_not_implemented();
}


sub row_num_for_name{
   my ($self) = @_;
   $self->throw_not_implemented();
}


sub num_rows{
   my ($self) = @_;
   $self->throw_not_implemented();
}



sub num_columns{
   my ($self) = @_;
   $self->throw_not_implemented();
}


# inverse?

sub reverse{
    my ($self) = @_;
    $self->throw_not_implemented();
}


sub row_names{
   my ($self) = @_;
   $self->throw_not_implemented();
}



sub column_names{
   my ($self) = @_;
   $self->throw_not_implemented();
}

1;