Bio/Matrix/Scoring.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Matrix::Scoring
   4 #
   5 # Cared for by Jason Stajich <jason-at-bioperl-dot-org>
   6 #
   7 # Copyright Jason Stajich
   8 #
   9 # You may distribute this module under the same terms as perl itself
  10
  11 # POD documentation - main docs before the code
  12
  13 =head1 NAME
  14
  15 Bio::Matrix::Scoring - Object which can hold scoring matrix information
  16
  17 =head1 SYNOPSIS
  18
  19   use Bio::Matrix::Scoring;
  20
  21 =head1 DESCRIPTION
  22
  23 An object which can handle AA or NT scoring matrix information.  Some
  24 transformation properties are available too.
  25
  26 =head1 FEEDBACK
  27
  28 =head2 Mailing Lists
  29
  30 User feedback is an integral part of the evolution of this and other
  31 Bioperl modules. Send your comments and suggestions preferably to
  32 the Bioperl mailing list.  Your participation is much appreciated.
  33
  34   bioperl-l@bioperl.org                  - General discussion
  35   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  36
  37 =head2 Reporting Bugs
  38
  39 Report bugs to the Bioperl bug tracking system to help us keep track
  40 of the bugs and their resolution. Bug reports can be submitted via
  41 the web:
  42
  43   http://bugzilla.open-bio.org/
  44
  45 =head1 AUTHOR - Jason Stajich
  46
  47 Email jason-at-bioperl-dot-org
  48
  49 =head1 APPENDIX
  50
  51 The rest of the documentation details each of the object methods.
  52 Internal methods are usually preceded with a _
  53
  54 =cut
  55
  56
  57 # Let the code begin...
  58
  59
  60 package Bio::Matrix::Scoring;
  61 use strict;
  62
  63
  64 use base qw(Bio::Matrix::Generic);
  65
  66 =head2 new
  67
  68  Title   : new
  69  Usage   : my $obj = Bio::Matrix::Scoring->new();
  70  Function: Builds a new Bio::Matrix::Scoring object
  71  Returns : an instance of Bio::Matrix::Scoring
  72  Args    :
  73
  74
  75 =cut
  76
  77
  78 sub new {
  79     my ($class, @args) = @_;
  80     my $self = $class->SUPER::new(@args);
  81
  82     my ($entropy,$expected,$scale,$scaleval,$database,
  83                   $lowestscore,$highestscore,$lambda,$H) =
  84                          $self->_rearrange([qw(
  85         ENTROPY EXPECTED SCALE SCALE_VALUE DATABASE
  86                   LOWEST_SCORE HIGHEST_SCORE LAMBDA H)], @args);
  87
  88     $self->entropy  ($entropy);
  89     $self->expected_score($expected);
  90     $self->scale    ($scale);
  91     $self->scale_value($scaleval);
  92     $self->database ($database);
  93     $self->lowest_score($lowestscore);
  94     $self->highest_score($highestscore);
  95     $self->lambda($lambda);
  96     $self->H($H);
  97
  98     return $self;
  99 }
 100
 101 =head2 entropy
 102
 103  Title   : entropy
 104  Usage   : $obj->entropy($newval)
 105  Function:
 106  Example :
 107  Returns : value of entropy (a scalar)
 108  Args    : on set, new value (a scalar or undef, optional)
 109
 110
 111 =cut
 112
 113 sub entropy{
 114     my $self = shift;
 115
 116     return $self->{'entropy'} = shift if @_;
 117     return $self->{'entropy'};
 118 }
 119
 120 =head2 expected_score
 121
 122  Title   : expected_score
 123  Usage   : $obj->expected_score($newval)
 124  Function:
 125  Example :
 126  Returns : value of expected (a scalar)
 127  Args    : on set, new value (a scalar or undef, optional)
 128
 129
 130 =cut
 131
 132 sub expected_score{
 133     my $self = shift;
 134
 135     return $self->{'expected'} = shift if @_;
 136     return $self->{'expected'};
 137 }
 138
 139 =head2 scale
 140
 141  Title   : scale
 142  Usage   : $obj->scale($newval)
 143  Function:
 144  Example :
 145  Returns : value of scale (a scalar)
 146  Args    : on set, new value (a scalar or undef, optional)
 147
 148
 149 =cut
 150
 151 sub scale{
 152     my $self = shift;
 153
 154     return $self->{'scale'} = shift if @_;
 155     return $self->{'scale'};
 156 }
 157
 158 =head2 scale_value
 159
 160  Title   : scale_value
 161  Usage   : $obj->scale_value($newval)
 162  Function:
 163  Example :
 164  Returns : value of scale_value (a scalar)
 165  Args    : on set, new value (a scalar or undef, optional)
 166
 167
 168 =cut
 169
 170 sub scale_value{
 171     my $self = shift;
 172
 173     return $self->{'scale_value'} = shift if @_;
 174     return $self->{'scale_value'};
 175 }
 176
 177 =head2 description
 178
 179  Title   : description
 180  Usage   : $obj->description($newval)
 181  Function:
 182  Example :
 183  Returns : value of description (a scalar)
 184  Args    : on set, new value (a scalar or undef, optional)
 185
 186
 187 =cut
 188
 189 sub description{
 190     my $self = shift;
 191
 192     return $self->{'description'} = shift if @_;
 193     return $self->{'description'};
 194 }
 195
 196 =head2 database
 197
 198  Title   : database
 199  Usage   : $obj->database($newval)
 200  Function:
 201  Example :
 202  Returns : value of database (a scalar)
 203  Args    : on set, new value (a scalar or undef, optional)
 204
 205
 206 =cut
 207
 208 sub database{
 209     my $self = shift;
 210
 211     return $self->{'database'} = shift if @_;
 212     return $self->{'database'};
 213 }
 214
 215 =head2 lowest_score
 216
 217  Title   : lowest_score
 218  Usage   : $obj->lowest_score($newval)
 219  Function:
 220  Example :
 221  Returns : value of lowest_score (a scalar)
 222  Args    : on set, new value (a scalar or undef, optional)
 223
 224
 225 =cut
 226
 227 sub lowest_score{
 228     my $self = shift;
 229
 230     return $self->{'lowest_score'} = shift if @_;
 231     return $self->{'lowest_score'};
 232 }
 233
 234 =head2 highest_score
 235
 236  Title   : highest_score
 237  Usage   : $obj->highest_score($newval)
 238  Function:
 239  Example :
 240  Returns : value of highest_score (a scalar)
 241  Args    : on set, new value (a scalar or undef, optional)
 242
 243
 244 =cut
 245
 246 sub highest_score{
 247     my $self = shift;
 248
 249     return $self->{'highest_score'} = shift if @_;
 250     return $self->{'highest_score'};
 251 }
 252
 253 =head2 lambda
 254
 255  Title   : lambda
 256  Usage   : $obj->lambda($newval)
 257  Function:
 258  Example :
 259  Returns : value of lambda (a scalar)
 260  Args    : on set, new value (a scalar or undef, optional)
 261
 262
 263 =cut
 264
 265 sub lambda{
 266     my $self = shift;
 267
 268     return $self->{'lambda'} = shift if @_;
 269     return $self->{'lambda'};
 270 }
 271
 272 =head2 H
 273
 274  Title   : H
 275  Usage   : $obj->H($newval)
 276  Function:
 277  Example :
 278  Returns : value of H (a scalar)
 279  Args    : on set, new value (a scalar or undef, optional)
 280
 281
 282 =cut
 283
 284 sub H{
 285     my $self = shift;
 286     return $self->{'H'} = shift if @_;
 287     return $self->{'H'};
 288 }
 289
 290 1;