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# $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
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=head1 NAME
Bio::Matrix::MatrixI - An interface for describing a Matrix 
=head1 SYNOPSIS
  # Get a Matrix object
=head1 DESCRIPTION
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.
=head1 FEEDBACK
=head2 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
=head2 Support 
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Jason Stajich
Email jason-at-bioperl.org
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Matrix::MatrixI;
$Bio::Matrix::MatrixI::VERSION = '1.7.8';
use strict;
use base qw(Bio::Root::RootI);
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=head2 matrix_id
 Title   : matrix_id
 Usage   : my $id = $matrix->matrix_id
 Function: Get the matrix ID
 Returns : string value
 Args    : 
=cut
sub matrix_id{
   my ($self) = @_;
   $self->throw_not_implemented();
}
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=head2 matrix_name
 Title   : matrix_name
 Usage   : my $name = $matrix->matrix_name();
 Function: Get the matrix name
 Returns : string value
 Args    :
=cut
sub matrix_name{
   my ($self) = @_;
   $self->throw_not_implemented();
}
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=head2 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
           $column name 
=cut
sub get_entry{
   my ($self) = @_;
    $self->throw_not_implemented();
}
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=head2 get_column
 Title   : get_column
 Usage   : my @row = $matrix->get_column('ALPHA');
 Function: Get a particular column
 Returns : Array (in array context) or arrayref (in scalar context)
           of values
 Args    : name of the column
=cut
sub get_column{
   my ($self) = @_;
   $self->throw_not_implemented();
}
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=head2 get_row
 Title   : get_row
 Usage   : my @row = $matrix->get_row('ALPHA');
 Function: Get a particular row
 Returns : Array (in array context) or arrayref (in scalar context)
           of values
 Args    : name of the row
=cut
sub get_row{
   my ($self) = @_;
   $self->throw_not_implemented();
}
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=head2 get_diagonal
 Title   : get_diagonal
 Usage   : my @diagonal = $matrix->get_diagonal; 
 Function: Get the diagonal of the matrix
 Returns : Array (in array context) or arrayref (in scalar context)
 Args    : none
=cut
sub get_diagonal{
   my ($self) = @_;
   $self->throw_not_implemented();
}
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=head2 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
=cut
sub column_num_for_name{
   my ($self) = @_;
    $self->throw_not_implemented();
}
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=head2 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
=cut
sub row_num_for_name{
   my ($self) = @_;
   $self->throw_not_implemented();
}
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=head2 num_rows
 Title   : num_rows
 Usage   : my $rowcount = $matrix->num_rows;
 Function: Get the number of rows
 Returns : integer
 Args    : none
=cut
sub num_rows{
   my ($self) = @_;
   $self->throw_not_implemented();
}
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=head2 num_columns
 Title   : num_columns
 Usage   : my $colcount = $matrix->num_columns
 Function: Get the number of columns
 Returns : integer
 Args    : none
=cut
sub num_columns{
   my ($self) = @_;
   $self->throw_not_implemented();
}
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# inverse?
=head2 reverse
 Title   : reverse
 Usage   : my $matrix = $matrix->reverse
 Function: Get the reverse of a matrix
 Returns : 
 Args    :
=cut
sub reverse{
    my ($self) = @_;
    $self->throw_not_implemented();
}
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=head2 row_names
 Title   : row_names
 Usage   : my @rows = $matrix->row_names
 Function: The names of all the rows
 Returns : array in array context, arrayref in scalar context
 Args    : none
=cut
sub row_names{
   my ($self) = @_;
   $self->throw_not_implemented();
}
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=head2 column_names
 Title   : column_names
 Usage   : my @columns = $matrix->column_names
 Function: The names of all the columns
 Returns : array in array context, arrayref in scalar context
 Args    : none
=cut
sub column_names{
   my ($self) = @_;
   $self->throw_not_implemented();
}
1;