lib/CXGN/Transcript/DrawContigAlign/ContigAlign.pm

   1 =head1 NAME
   2
   3 CXGN::Transcript::DrawContigAlign::ContigAlign - stores alignment data for a strand in a unigene.
   4
   5 =head1 SYNOPSIS
   6
   7 Initialize it with all of the relevant values and use accessors to access the data.
   8
   9  $contigAlign = ContigAlign->new('Source ID', 'Sequence ID', '+', 10, 400, 20, 33, 1);
  10  $sourceID = $contigAlign->sourceID; #returns 'Source ID'
  11
  12 =head1 DESCRIPTION
  13
  14 ContigAlign stores alignment data for a strand in a unigene, primarily for use with CXGN::Transcript::DrawContigAlign, which uses it to store data that is being used to produce a graph.
  15
  16 =head1 AUTHORS
  17
  18 Rafael Lizarralde <xarbiogeek@gmail.com> (July 2009)
  19
  20 =head1 MEMBER FUNCTIONS
  21
  22 =head2 constructor C<new>
  23
  24 =over 10
  25
  26 =item Usage:
  27
  28 $contigAlign = CXGN::Transcript::DrawContigAlign::ContigAlign->new('Source ID', 'Sequence ID', '+', 10, 400, 20, 33, 1);
  29
  30 =item Ret:
  31
  32 a CXGN::Transcript::DrawContigAlign::ContigAlign object
  33
  34 =item Args:
  35
  36 =over 18
  37
  38 =item Str  $sourceID
  39
  40 the ID tag for the strand
  41
  42 =item Str  $sequenceID
  43
  44 the ID tag for the unigene
  45
  46 =item Str  $strand
  47
  48 identifier if the strand is complementary or not (if not, it should be '+')
  49
  50 =item Int  $startLoc
  51
  52 the base pair in the unigene's sequence at which this strand starts
  53
  54 =item Int  $endLoc
  55
  56 the base pair at which this strand ends
  57
  58 =item Int  $startTrim
  59
  60 the number of base pairs at the beginning that do not match
  61
  62 =item Int  $endTrim
  63
  64 the number of base pairs at the end that do not match
  65
  66 =item Bool $highlight
  67
  68 whether or not the strand should be highlighted on the graph
  69
  70 =back
  71
  72 =back
  73
  74 =head2 accessors:
  75
  76 =over 12
  77
  78 =item sourceID
  79
  80 returns a string with the ID tag for the strand
  81
  82 =item sequenceID
  83
  84 returns a string with the ID tag for the unigene
  85
  86 =item strand
  87
  88 returns a string with an identifier indicating whether the strand is complementary or not
  89
  90 =item  startLoc
  91
  92 returns an integer indicating the base pair at which this strand starts
  93
  94 =item endLoc
  95
  96 returns an integer indicating the base pair at which this strand ends
  97
  98 =item startTrim
  99
 100 returns an integer indicating the number of base pairs that do not match at the start
 101
 102 =item endTrim
 103
 104 returns an integer indicating the number of base pairs that do not match at the end
 105
 106 =item start
 107
 108 returns an integer indicating the first matching base pair (startLoc + startTrim)
 109
 110 =item end
 111
 112 returns an integer indicating the last matching base pair (endLoc - endTrim)
 113
 114 =item highlight
 115
 116 returns a boolean indicating whether this strand is highlighted
 117
 118 =back
 119
 120 =cut
 121
 122 package CXGN::Transcript::DrawContigAlign::ContigAlign;
 123
 124 use Moose;
 125 use MooseX::Method::Signatures;
 126
 127 has sourceID   => (is => 'ro', isa => 'Str');
 128 has sequenceID => (is => 'ro', isa => 'Str');
 129 has strand     => (is => 'ro', isa => 'Str');
 130 has startLoc   => (is => 'ro', isa => 'Int');
 131 has endLoc     => (is => 'ro', isa => 'Int');
 132 has startTrim  => (is => 'ro', isa => 'Int');
 133 has endTrim    => (is => 'ro', isa => 'Int');
 134 has start      => (is => 'ro', isa => 'Int');
 135 has end        => (is => 'ro', isa => 'Int');
 136 has highlight  => (is => 'ro', isa => 'Bool', default => undef);
 137
 138 sub BUILDARGS {
 139     my $class = shift;
 140     if(@_ == 8) {
 141         return { sourceID => $_[0], sequenceID => $_[1], strand => $_[2],
 142                  startLoc => $_[3], endLoc => $_[4], startTrim => $_[5], endTrim => $_[6],
 143                  start => $_[3] + $_[5], end => $_[4] - $_[6], highlight => $_[7],
 144         };
 145     } else { return $class->SUPER::BUILDARGS(@_); }
 146 }
 147
 148 =head2 accessor C<compare>
 149
 150 =over 10
 151
 152 =item Usage:
 153
 154 print "contig1 is less than contig2!" if($contig1->compare($contig2) < 0);
 155
 156 =item Ret:
 157
 158 a negative value if the instance from which the method is called is less than the argument, zero if they are equal, and a positive value if the argument is greater
 159
 160 =item Args:
 161
 162 $other    another ContigAlign object
 163
 164 =back
 165
 166 =cut
 167
 168 method compare (CXGN::Transcript::DrawContigAlign::ContigAlign $other!) {
 169     ($self->start - $other->start != 0) ?
 170         return $self->start - $other->start:
 171         return $self->end - $other->end;
 172 }
 173 no Moose;
 174 __PACKAGE__->meta->make_immutable;
 175 return 1;
 176
 177 =head1 SEE ALSO
 178
 179 This is primarily used by CXGN::Transcript::DrawContigAlign, which, in turn, is used by CXGN::Transcript::Unigene.
 180 DrawContigAlign also uses CXGN::Transcript::DrawContigAlign::DepthData and CXGN::Transcript::DrawContigAlign::Pane.
 181
 182 =cut