[問題] 我在書上遇到的問題???
package Restrictionmap;
use base ( "Restriction" );
#
# A class to find locations of restriction enzyme recognition sites in
# DNA sequence data, and to display them.
#
use strict;
use warnings;
use Carp;
# Class data and methods
{
# A list of all attributes with default values.
my %_attributes = (
# key = restriction enzyme name
# value = space-separated string of recognition sites => regular expressions
_rebase => { }, # A Rebase.pm object
_sequence => '', # DNA sequence data in raw format (only bases)
_enzyme => '', # space separated string of one or more enzyme names
_map => { }, # hash: enzyme names => arrays of locations
_graphictype => 'text', # one of 'text' or 'png' or some other
_graphic => '', # a graphic display of the restriction map
);
# Return a list of all attributes
sub _all_attributes {
keys %_attributes;
}
}
sub get_graphic {
my($self) = @_;
# If the graphic is not stored, calculate and store it
unless($self->{_graphic}) {
unless($self->{_graphictype}) {
croak 'Attribute graphictype not set (default is "text")';
}
# if graphictype is "xyz", method that makes the graphic is "_drawmap_xyz"
my $drawmapfunctionname = "_drawmap_" . $self->{_graphictype};
# Calculate and store the graphic
$self->{_graphic} = $self->$drawmapfunctionname;
}
# Return the stored graphic
return $self->{_graphic};
}
#
# Methods to output graphics in text format
#
sub _drawmap_text {
my($self) = @_;
my @annotation = ();
push(@annotation, _initialize_annotation_text($self->get_sequence));
foreach my $enzyme ($self->get_enzyme_names) {
_add_annotation_text(\@annotation, $enzyme, $self->get_enzyme_map($enzyme));
}
# Format the restriction map as sequence and annotation
my @output = _formatmaptext(50, $self->get_sequence, @annotation);
# Return output as a string, not an array of lines
return join('', @output);
}
# Make a blank string of the same length as the given sequence string
sub _initialize_annotation_text {
my($seq) = @_;
return ' ' x length($seq);
}
# Add annotation to an annotation string
sub _add_annotation_text {
my($array, $enz, @pos) = @_;
# $array is a reference to an array of annotations
# Put the labels for the enzyme name at the correct positions in the annotation
foreach my $location (@pos) {
# Loop through all the annotation strings as necessary
for( my $i = 0 ; $i < @$array ; ++$i ) {
# If the annotation contains only space characters at that position,
# insert the annotation
if(substr($$array[$i], $location-1, length($enz)) eq (' ' x length($enz))){
substr($$array[$i], $location-1, length($enz)) = $enz;
last;
# If the annotation collides, add it to the next annotation string on the
# next iteration of the "for" loop.
# But first, if there is not another annotation string, make one
}elsif($i == (@$array - 1)) {
push(@$array, _initialize_annotation_text($$array[0]));
}
}
}
}
# Sequence with annotation lines formatted for the page with line breaks
sub _formatmaptext {
my($line_length, $seq, @annotation) = @_;
my(@output) = ();
# Split strings into lines of $line_length
for ( my $pos = 0 ; $pos < length($seq) ; $pos += $line_length ) {
# Print annotation on top of sequence, using reverse
foreach my $string ( reverse ($seq, @annotation) ) {
# Discard blank lines?
# if ( substr($string, $pos, $line_length) !~ /[^ \n]/ ) {
# next;
# }
# Add line to output
push(@output, substr($string, $pos, $line_length) . "\n");
}
# separate the lines
push(@output,"\n");
}
# Return the merged annotation and sequence
return @output;
}
#
# Method to output graphics in PNG format
#
sub _drawmap_png {
my($self) = @_;
# Get text version of graphic
my @maptext = split( /\n+/, $self->_drawmap_text);
# Now make a PNG graphic from the text version
use GD;
#
# Layout information: fonts, margins, image size
#
# Use built-in GD fixed-width font 'gdMediumBoldFont' (could use TrueType fonts)
#
# Font character size in pixels
my ($fontwidth, $fontheight) = (gdMediumBoldFont->width, gdMediumBoldFont->height);
# Margins top, bottom, right, left, and between lines
my ($tmarg, $bmarg, $rmarg, $lmarg, $linemarg) = (10, 10, 10, 10, 5);
# Image width is length of line times width of a character, plus margins
my ($imagewidth) = (length($maptext[0]) * $fontwidth) + $lmarg + $rmarg;
# Image height is height of font plus margin times number of lines, plus margins
my ($imageheight) =
(($fontheight + $linemarg) * (scalar @maptext)) + $tmarg + $bmarg;
my $image = new GD::Image($imagewidth, $imageheight);
# First one becomes background color
my $white = $image->colorAllocate(255, 255, 255);
my $black = $image->colorAllocate(0, 0, 0);
my $red = $image->colorAllocate(255, 0, 0);
# Origin at upper left hand corner
my ($x, $y) = ($lmarg, $tmarg);
#
# Draw the lines on the image
#
foreach my $line (@maptext) {
chomp $line;
# Draw annotation in red
if($line =~ / /) { #annotation has spaces
$image->string(gdMediumBoldFont, $x, $y, $line, $red);
# Draw sequence in black
}else{ #sequence
$image->string(gdMediumBoldFont, $x, $y, $line, $black);
}
$y += ($fontheight + $linemarg);
}
return $image->png;
}
#
# Method to output graphics in JPEG format
#
sub _drawmap_jpg {
my($self) = @_;
# Get text version of graphic
my @maptext = split( /\n+/, $self->_drawmap_text);
# Now make a JPEG graphic from the text version
use GD;
#
# Layout information: fonts, margins, image size
#
# Use built-in GD fixed-width font 'gdMediumBoldFont' (could use TrueType fonts)
#
# Font character size in pixels
my ($fontwidth, $fontheight) = (gdMediumBoldFont->width, gdMediumBoldFont->height);
# Margins top, bottom, right, left, and between lines
my ($tmarg, $bmarg, $rmarg, $lmarg, $linemarg) = (10, 10, 10, 10, 5);
# Image width is length of line times width of a character, plus margins
my ($imagewidth) = (length($maptext[0]) * $fontwidth) + $lmarg + $rmarg;
# Image height is height of font plus margin times number of lines, plus margins
my ($imageheight) =
(($fontheight + $linemarg) * (scalar @maptext)) + $tmarg + $bmarg;
my $image = new GD::Image($imagewidth, $imageheight);
# First one becomes background color
my $white = $image->colorAllocate(255, 255, 255);
my $black = $image->colorAllocate(0, 0, 0);
my $red = $image->colorAllocate(255, 0, 0);
# Origin at upper left hand corner
my ($x, $y) = ($lmarg, $tmarg);
#
# Draw the lines on the image
#
foreach my $line (@maptext) {
chomp $line;
# Draw annotation in red
if($line =~ / /) { #annotation has spaces
$image->string(gdMediumBoldFont, $x, $y, $line, $red);
# Draw sequence in black
}else{ #sequence
$image->string(gdMediumBoldFont, $x, $y, $line, $black);
}
$y += ($fontheight + $linemarg);
}
return $image->jpeg;
}
=head1 Restrictionmap
Restrictionmap: Given a Rebase object, sequence, and list of restriction enzyme
names, return the locations of the recognition sites in the sequence
=head1 Synopsis
use Restrictionmap;
use Rebase;
use strict;
use warnings;
my $rebase = Rebase->new(
dbmfile => 'BIONET',
bionetfile => 'bionet.212'
);
my $restrict = Restrictionmap->new(
rebase => $rebase,
enzyme => 'EcoRI HindIII',
sequence => 'ACGAATTCCGGAATTCG',
graphictype => 'text',
);
print "Locations are ", join ' ', $restrict->get_enzyme_map('EcoRI'), "\n";
print $restrict->get_graphic;
=head1 AUTHOR
James Tisdall
=head1 COPYRIGHT
Copyright (c) 2003, James Tisdall
=cut
1;
以上是一個模組，
我的問題是要怎麼讓跑出來的結果，
酵素名子認到正確的位置，而且酵素名子的下一行可以加上一條線
且也是跟酵素認一樣的位置，
請問要怎麼修改模組中的程式才可以達到我要的目的
請大家幫幫我這個Perl新手
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