Bio::Matrix MatrixI
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Summary
Bio::Matrix::MatrixI - An interface for describing a Matrix
Package variables
No package variables defined.
Inherit
Bio::Root::RootI
Synopsis
  # Get a Matrix object
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.
Methods
matrix_idDescriptionCode
matrix_nameDescriptionCode
get_entryDescriptionCode
get_columnDescriptionCode
get_rowDescriptionCode
get_diagonalDescriptionCode
column_num_for_nameDescriptionCode
row_num_for_nameDescriptionCode
num_rowsDescriptionCode
num_columnsDescriptionCode
reverseDescriptionCode
row_namesDescriptionCode
column_namesDescriptionCode
Methods description
matrix_idcode    nextTop
 Title   : matrix_id
Usage : my $id = $matrix->matrix_id
Function: Get the matrix ID
Returns : string value
Args :
matrix_namecodeprevnextTop
 Title   : matrix_name
Usage : my $name = $matrix->matrix_name();
Function: Get the matrix name
Returns : string value
Args :
get_entrycodeprevnextTop
 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_columncodeprevnextTop
 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_rowcodeprevnextTop
 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_diagonalcodeprevnextTop
 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_namecodeprevnextTop
 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_namecodeprevnextTop
 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_rowscodeprevnextTop
 Title   : num_rows
Usage : my $rowcount = $matrix->num_rows;
Function: Get the number of rows
Returns : integer
Args : none
num_columnscodeprevnextTop
 Title   : num_columns
Usage : my $colcount = $matrix->num_columns
Function: Get the number of columns
Returns : integer
Args : none
reversecodeprevnextTop
 Title   : reverse
Usage : my $matrix = $matrix->reverse
Function: Get the reverse of a matrix
Returns :
Args :
row_namescodeprevnextTop
 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_namescodeprevnextTop
 Title   : column_names
Usage : my @columns = $matrix->column_names
Function: The names of all the columns
Returns : array in array context, arrayref in scalar context
Args : none
Methods code
matrix_iddescriptionprevnextTop
sub matrix_id {
   my ($self) = @_;
   $self->throw_not_implemented();
}
matrix_namedescriptionprevnextTop
sub matrix_name {
   my ($self) = @_;

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

    $self->throw_not_implemented();
}
get_columndescriptionprevnextTop
sub get_column {
   my ($self) = @_;
   $self->throw_not_implemented();
}
get_rowdescriptionprevnextTop
sub get_row {
   my ($self) = @_;
   $self->throw_not_implemented();
}
get_diagonaldescriptionprevnextTop
sub get_diagonal {
   my ($self) = @_;
   $self->throw_not_implemented();
}
column_num_for_namedescriptionprevnextTop
sub column_num_for_name {
   my ($self) = @_;

    $self->throw_not_implemented();
}
row_num_for_namedescriptionprevnextTop
sub row_num_for_name {
   my ($self) = @_;
   $self->throw_not_implemented();
}
num_rowsdescriptionprevnextTop
sub num_rows {
   my ($self) = @_;
   $self->throw_not_implemented();
}
num_columnsdescriptionprevnextTop
sub num_columns {
   my ($self) = @_;
   $self->throw_not_implemented();
}


# inverse?
}
reversedescriptionprevnextTop
sub reverse {
    my ($self) = @_;
    $self->throw_not_implemented();
}
row_namesdescriptionprevnextTop
sub row_names {
   my ($self) = @_;
   $self->throw_not_implemented();
}
column_namesdescriptionprevnextTop
sub column_names {
   my ($self) = @_;
   $self->throw_not_implemented();
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 StajichTop
Email jason-at-bioperl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _