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 use strict;
  77
  78
  79 use base qw(Bio::Root::RootI);
  80
  81
  82 =head2 matrix_id
  83
  84  Title   : matrix_id
  85  Usage   : my $id = $matrix->matrix_id
  86  Function: Get the matrix ID
  87  Returns : string value
  88  Args    :
  89
  90
  91 =cut
  92
  93 sub matrix_id{
  94    my ($self) = @_;
  95    $self->throw_not_implemented();
  96 }
  97
  98 =head2 matrix_name
  99
 100  Title   : matrix_name
 101  Usage   : my $name = $matrix->matrix_name();
 102  Function: Get the matrix name
 103  Returns : string value
 104  Args    :
 105
 106
 107 =cut
 108
 109 sub matrix_name{
 110    my ($self) = @_;
 111
 112    $self->throw_not_implemented();
 113 }
 114
 115 =head2 get_entry
 116
 117  Title   : get_entry
 118  Usage   : my $entry = $matrix->get_entry($rowname,$columname)
 119  Function: Get the entry for a given row,column pair
 120  Returns : scalar
 121  Args    : $row name
 122            $column name
 123
 124
 125 =cut
 126
 127 sub get_entry{
 128    my ($self) = @_;
 129
 130     $self->throw_not_implemented();
 131 }
 132
 133
 134 =head2 get_column
 135
 136  Title   : get_column
 137  Usage   : my @row = $matrix->get_column('ALPHA');
 138  Function: Get a particular column
 139  Returns : Array (in array context) or arrayref (in scalar context)
 140            of values
 141  Args    : name of the column
 142
 143
 144 =cut
 145
 146 sub get_column{
 147    my ($self) = @_;
 148    $self->throw_not_implemented();
 149 }
 150
 151 =head2 get_row
 152
 153  Title   : get_row
 154  Usage   : my @row = $matrix->get_row('ALPHA');
 155  Function: Get a particular row
 156  Returns : Array (in array context) or arrayref (in scalar context)
 157            of values
 158  Args    : name of the row
 159
 160 =cut
 161
 162 sub get_row{
 163    my ($self) = @_;
 164    $self->throw_not_implemented();
 165 }
 166
 167
 168 =head2 get_diagonal
 169
 170  Title   : get_diagonal
 171  Usage   : my @diagonal = $matrix->get_diagonal;
 172  Function: Get the diagonal of the matrix
 173  Returns : Array (in array context) or arrayref (in scalar context)
 174  Args    : none
 175
 176
 177 =cut
 178
 179 sub get_diagonal{
 180    my ($self) = @_;
 181    $self->throw_not_implemented();
 182 }
 183
 184 =head2 column_num_for_name
 185
 186  Title   : column_num_for_name
 187  Usage   : my $num = $matrix->column_num_for_name($name)
 188  Function: Gets the column number for a particular column name
 189  Returns : integer
 190  Args    : string
 191
 192
 193 =cut
 194
 195 sub column_num_for_name{
 196    my ($self) = @_;
 197
 198     $self->throw_not_implemented();
 199 }
 200
 201 =head2 row_num_for_name
 202
 203  Title   : row_num_for_name
 204  Usage   : my $num = $matrix->row_num_for_name($name)
 205  Function: Gets the row number for a particular row name
 206  Returns : integer
 207  Args    : string
 208
 209
 210 =cut
 211
 212 sub row_num_for_name{
 213    my ($self) = @_;
 214    $self->throw_not_implemented();
 215 }
 216
 217 =head2 num_rows
 218
 219  Title   : num_rows
 220  Usage   : my $rowcount = $matrix->num_rows;
 221  Function: Get the number of rows
 222  Returns : integer
 223  Args    : none
 224
 225
 226 =cut
 227
 228 sub num_rows{
 229    my ($self) = @_;
 230    $self->throw_not_implemented();
 231 }
 232
 233
 234 =head2 num_columns
 235
 236  Title   : num_columns
 237  Usage   : my $colcount = $matrix->num_columns
 238  Function: Get the number of columns
 239  Returns : integer
 240  Args    : none
 241
 242
 243 =cut
 244
 245 sub num_columns{
 246    my ($self) = @_;
 247    $self->throw_not_implemented();
 248 }
 249
 250
 251 # inverse?
 252 =head2 reverse
 253
 254  Title   : reverse
 255  Usage   : my $matrix = $matrix->reverse
 256  Function: Get the reverse of a matrix
 257  Returns :
 258  Args    :
 259
 260
 261 =cut
 262
 263 sub reverse{
 264     my ($self) = @_;
 265     $self->throw_not_implemented();
 266 }
 267
 268 =head2 row_names
 269
 270  Title   : row_names
 271  Usage   : my @rows = $matrix->row_names
 272  Function: The names of all the rows
 273  Returns : array in array context, arrayref in scalar context
 274  Args    : none
 275
 276
 277 =cut
 278
 279 sub row_names{
 280    my ($self) = @_;
 281    $self->throw_not_implemented();
 282 }
 283
 284
 285 =head2 column_names
 286
 287  Title   : column_names
 288  Usage   : my @columns = $matrix->column_names
 289  Function: The names of all the columns
 290  Returns : array in array context, arrayref in scalar context
 291  Args    : none
 292
 293
 294 =cut
 295
 296 sub column_names{
 297    my ($self) = @_;
 298    $self->throw_not_implemented();
 299 }
 300
 301 1;