lib/Bio/Matrix/MatrixI.pm

   1 # $Id $
   2 #
   3 # BioPerl module for Bio::Matrix::MatrixI
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Jason Stajich <jason-at-bioperl.org>
   8 #
   9 # Copyright Jason Stajich
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::Matrix::MatrixI - An interface for describing a Matrix
  18
  19 =head1 SYNOPSIS
  20
  21   # Get a Matrix object
  22
  23 =head1 DESCRIPTION
  24
  25 This is an interface describing how one should be able to interact
  26 with a matrix.  One can have a lot of information I suppose and this
  27 outline won't really work for PWM or PSSMs.  We will have to derive a
  28 particular interface for those.
  29
  30 =head1 FEEDBACK
  31
  32 =head2 Mailing Lists
  33
  34 User feedback is an integral part of the evolution of this and other
  35 Bioperl modules. Send your comments and suggestions preferably to
  36 the Bioperl mailing list.  Your participation is much appreciated.
  37
  38   bioperl-l@bioperl.org                  - General discussion
  39   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  40
  41 =head2 Support
  42
  43 Please direct usage questions or support issues to the mailing list:
  44
  45 I<bioperl-l@bioperl.org>
  46
  47 rather than to the module maintainer directly. Many experienced and
  48 reponsive experts will be able look at the problem and quickly
  49 address it. Please include a thorough description of the problem
  50 with code and data examples if at all possible.
  51
  52 =head2 Reporting Bugs
  53
  54 Report bugs to the Bioperl bug tracking system to help us keep track
  55 of the bugs and their resolution. Bug reports can be submitted via
  56 email or the web:
  57
  58   https://github.com/bioperl/bioperl-live/issues
  59
  60 =head1 AUTHOR - Jason Stajich
  61
  62 Email jason-at-bioperl.org
  63
  64 =head1 APPENDIX
  65
  66 The rest of the documentation details each of the object methods.
  67 Internal methods are usually preceded with a _
  68
  69 =cut
  70
  71
  72 # Let the code begin...
  73
  74
  75 package Bio::Matrix::MatrixI;
  76
  77 use strict;
  78
  79
  80 use base qw(Bio::Root::RootI);
  81
  82
  83 =head2 matrix_id
  84
  85  Title   : matrix_id
  86  Usage   : my $id = $matrix->matrix_id
  87  Function: Get the matrix ID
  88  Returns : string value
  89  Args    :
  90
  91
  92 =cut
  93
  94 sub matrix_id{
  95    my ($self) = @_;
  96    $self->throw_not_implemented();
  97 }
  98
  99 =head2 matrix_name
 100
 101  Title   : matrix_name
 102  Usage   : my $name = $matrix->matrix_name();
 103  Function: Get the matrix name
 104  Returns : string value
 105  Args    :
 106
 107
 108 =cut
 109
 110 sub matrix_name{
 111    my ($self) = @_;
 112
 113    $self->throw_not_implemented();
 114 }
 115
 116 =head2 get_entry
 117
 118  Title   : get_entry
 119  Usage   : my $entry = $matrix->get_entry($rowname,$columname)
 120  Function: Get the entry for a given row,column pair
 121  Returns : scalar
 122  Args    : $row name
 123            $column name
 124
 125
 126 =cut
 127
 128 sub get_entry{
 129    my ($self) = @_;
 130
 131     $self->throw_not_implemented();
 132 }
 133
 134
 135 =head2 get_column
 136
 137  Title   : get_column
 138  Usage   : my @row = $matrix->get_column('ALPHA');
 139  Function: Get a particular column
 140  Returns : Array (in array context) or arrayref (in scalar context)
 141            of values
 142  Args    : name of the column
 143
 144
 145 =cut
 146
 147 sub get_column{
 148    my ($self) = @_;
 149    $self->throw_not_implemented();
 150 }
 151
 152 =head2 get_row
 153
 154  Title   : get_row
 155  Usage   : my @row = $matrix->get_row('ALPHA');
 156  Function: Get a particular row
 157  Returns : Array (in array context) or arrayref (in scalar context)
 158            of values
 159  Args    : name of the row
 160
 161 =cut
 162
 163 sub get_row{
 164    my ($self) = @_;
 165    $self->throw_not_implemented();
 166 }
 167
 168
 169 =head2 get_diagonal
 170
 171  Title   : get_diagonal
 172  Usage   : my @diagonal = $matrix->get_diagonal;
 173  Function: Get the diagonal of the matrix
 174  Returns : Array (in array context) or arrayref (in scalar context)
 175  Args    : none
 176
 177
 178 =cut
 179
 180 sub get_diagonal{
 181    my ($self) = @_;
 182    $self->throw_not_implemented();
 183 }
 184
 185 =head2 column_num_for_name
 186
 187  Title   : column_num_for_name
 188  Usage   : my $num = $matrix->column_num_for_name($name)
 189  Function: Gets the column number for a particular column name
 190  Returns : integer
 191  Args    : string
 192
 193
 194 =cut
 195
 196 sub column_num_for_name{
 197    my ($self) = @_;
 198
 199     $self->throw_not_implemented();
 200 }
 201
 202 =head2 row_num_for_name
 203
 204  Title   : row_num_for_name
 205  Usage   : my $num = $matrix->row_num_for_name($name)
 206  Function: Gets the row number for a particular row name
 207  Returns : integer
 208  Args    : string
 209
 210
 211 =cut
 212
 213 sub row_num_for_name{
 214    my ($self) = @_;
 215    $self->throw_not_implemented();
 216 }
 217
 218 =head2 num_rows
 219
 220  Title   : num_rows
 221  Usage   : my $rowcount = $matrix->num_rows;
 222  Function: Get the number of rows
 223  Returns : integer
 224  Args    : none
 225
 226
 227 =cut
 228
 229 sub num_rows{
 230    my ($self) = @_;
 231    $self->throw_not_implemented();
 232 }
 233
 234
 235 =head2 num_columns
 236
 237  Title   : num_columns
 238  Usage   : my $colcount = $matrix->num_columns
 239  Function: Get the number of columns
 240  Returns : integer
 241  Args    : none
 242
 243
 244 =cut
 245
 246 sub num_columns{
 247    my ($self) = @_;
 248    $self->throw_not_implemented();
 249 }
 250
 251
 252 # inverse?
 253 =head2 reverse
 254
 255  Title   : reverse
 256  Usage   : my $matrix = $matrix->reverse
 257  Function: Get the reverse of a matrix
 258  Returns :
 259  Args    :
 260
 261
 262 =cut
 263
 264 sub reverse{
 265     my ($self) = @_;
 266     $self->throw_not_implemented();
 267 }
 268
 269 =head2 row_names
 270
 271  Title   : row_names
 272  Usage   : my @rows = $matrix->row_names
 273  Function: The names of all the rows
 274  Returns : array in array context, arrayref in scalar context
 275  Args    : none
 276
 277
 278 =cut
 279
 280 sub row_names{
 281    my ($self) = @_;
 282    $self->throw_not_implemented();
 283 }
 284
 285
 286 =head2 column_names
 287
 288  Title   : column_names
 289  Usage   : my @columns = $matrix->column_names
 290  Function: The names of all the columns
 291  Returns : array in array context, arrayref in scalar context
 292  Args    : none
 293
 294
 295 =cut
 296
 297 sub column_names{
 298    my ($self) = @_;
 299    $self->throw_not_implemented();
 300 }
 301
 302 1;