Bio-Align-Graphics
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lib/Bio/Align/Graphics.pm view on Meta::CPAN
##Produces: An image file##Revision History:#09/01/2006 - WDM - Introduction of "wrap" flag, allowing alignment to be# wrapped at a set base and stacked vertically# Addition of internal members y_num and y_size for tracking# of number of vertical panels and size of panels,# respectively##09/06/2006 - WDM - Introduction of "p_legend" flag, for printing of an optional# colored legend when protein coloring is selected##09/24/2008 - WDM - Test file created for the module##03/01/2009 - YH - Introduction of "show_nonsynonymous" flag which enables# highlighting of nonsynonymous mutations in nucleotide# alignments. Addition of internal members codon_table and# missense_pos for translating codons -> amino acids and for# keeping track of missense mutation positions respectively.##03/05/2009 - YH - Swapped names of subroutines x_label and y_label to match
lib/Bio/Align/Graphics.pm view on Meta::CPAN
font=>defined($options{font}) ?$FONT_TABLE{$options{font}} :$FONT_TABLE{2},x_label=>defined($options{x_label}) ?$options{x_label} : 1,y_label=>defined($options{y_label}) ?$options{y_label} : 1,#Colorsbg_color=>$options{bg_color} ||'white',fg_color=>$options{font_color} ||'black',x_label_color=>$options{x_label_color} ||'blue',y_label_color=>$options{y_label_color} ||'red',p_color=>$options{p_color} ||undef,p_legend=>$options{p_legend} ||undef,p_color_table=>undef,#Sequence Defaultsreference=>$options{reference} ||undef,reference_id=>$options{reference_id} ||undef,match_char=>$options{match_char} ||".",block_size=>defined($options{block_size}) ?$options{block_size} : 10,block_space=>defined($options{block_space}) ? ($options{block_space} * ($options{font} ?$FONT_TABLE{$options{font}}->width :$FONT_TABLE{2}->width)) : ( ($options{font} ? ($FONT_TABLE{$options{font}}->width * 2 ) : ($FONT_TABLE{2}->width * 2)) )...wrap=>$options{wrap} || 80,show_nonsynonymous=>$options{show_nonsynonymous} ||undef,# If turned on, will highlight nonsynonymous (missense) mutations. Valid only for nucleotide alignments
lib/Bio/Align/Graphics.pm view on Meta::CPAN
$self->{seq_start_y} = ($self->{pad_top} +length($self->{seq_length_aa}) +$self->{y_label_space}) *$self->{y_char_size};$self->{width} =$self->{seq_start_x} + ((($self->{wrap} /$self->{block_size}) + 1) *$self->{block_space}) + ( ($self->{wrap} +$self->{pad_right}) * ($self->{x_char_size} + 1.2) ) + ( ($self->{seq_length} / 3) * 2);# Needed to add this for widt...}else{$self->{seq_start_y} = ($self->{pad_top} +length($self->{seq_length}) +$self->{y_label_space}) *$self->{y_char_size};$self->{width} =$self->{seq_start_x} + ((($self->{wrap} /$self->{block_size}) + 1) *$self->{block_space}) + ($self->{wrap} +$self->{pad_right}) *$self->{x_char_size};}$self->{footer_start} =$self->{seq_start_y} +$self->{y_size} *$self->{y_num};if(defined($self->{p_color}) &&defined($self->{p_legend}) &&$self->{p_legend}){$self->{height} =$self->{seq_start_y} +$self->{footer_size} +$self->{y_size} *$self->{y_num};}else{$self->{height} =$self->{seq_start_y} +$self->{y_size} *$self->{y_num};}$self->{image} = GD::Simple->new($self->{width},$self->{height});$self->{image}->alphaBlending(1);$self->{image}->saveAlpha(1);$self->{image}->bgcolor($self->{bg_color});$self->{image}->fgcolor($self->{fg_color});$self->{image}->rectangle(0,0,$self->{width}-1,$self->{height} - 1);
lib/Bio/Align/Graphics.pm view on Meta::CPAN
}elsif(defined($self->{show_nonsynonymous}) ){$self->{codon_table} = Bio::Tools::CodonTable->new();$self->{missense_pos} = {};# print STDERR "You are using option show_nonsynonymous. Option works best if wrap value is a multiple of 4.\n"}if(defined($self->{p_color}) &&$self->{seq_format} eq"protein"){$self->_draw_colored_sequences();if(defined($self->{p_legend}) &&$self->{p_legend}){$self->_draw_legend();}}elsif(defined($self->{p_color}) && ($self->{seq_format} ne"protein")){die"draw:Option p_color only works with Protein alignments!\n";}else{$self->_draw_sequences();}if(defined($self->{dm_label_start}))
lib/Bio/Align/Graphics.pm view on Meta::CPAN
}$block_total+=$block_num;}$block_total= 0;}}}sub_draw_legend{my$self=shift;my$title_font=$FONT_TABLE{3};my@l_order= ("Negatively Charged","Positively Charged","Hydrophobic","Aromatic","Found in Loops","Large Polar Acids");my%legend= ("Negatively Charged"=> ["D","E"] ,"Positively Charged"=> ["K","R"] ,"Hydrophobic"=> ["A","F","I","L","M","V","W","Y"] ,"Aromatic"=> ["F","H","W","Y"] ,"Found in Loops"=> ["D","G","P","S","T"] ,"Large Polar Acids"=> ["H","K","N","Q","R"]);my$x1= 2;my$x2= 42;my$colors=$self->{p_color_table};my$y_start=$self->{footer_start};my$label="Protein Color Legend";$self->{image}->bgcolor($self->{bg_color});
lib/Bio/Align/Graphics.pm view on Meta::CPAN
foreachmy$c_label(@l_order){if( ($count% 2) == 0){$self->{image}->moveTo($x2*$self->{x_char_size},$y_start+ ( ($count- 1) *$self->{y_char_size}));$self->{image}->font($self->{font});$self->{image}->string($c_label);my$i= 0;foreachmy$chars(@{$legend{$c_label}}){$self->{image}->bgcolor($$colors{$chars});$self->{image}->fgcolor($$colors{$chars});$self->{image}->rectangle( ($x2+ 20 +$i) *$self->{x_char_size},$y_start+ ( ($count- 2) *$self->{y_char_size}), ($x2+ 20 +$i+ 1) *$self->{x_char_size},$y_start+ ( ($count-1) *$self->{y_char_size}));$self->{image}->bgcolor($self->{bg_color});$self->{image}->fgcolor($self->{fg_color});$i++;}}else{$self->{image}->moveTo($x1*$self->{x_char_size} ,$y_start+ ($count*$self->{y_char_size}));$self->{image}->font($self->{font});$self->{image}->string($c_label);my$i= 0;foreachmy$chars(@{$legend{$c_label}}){$self->{image}->bgcolor($$colors{$chars});$self->{image}->fgcolor($$colors{$chars});$self->{image}->rectangle( ($x1+ 20 +$i) *$self->{x_char_size},$y_start+ ( ($count- 1) *$self->{y_char_size}), ($x1+ 20 +$i+ 1) *$self->{x_char_size},$y_start+ ( ($count) *$self->{y_char_size}));$self->{image}->bgcolor($self->{bg_color});$self->{image}->fgcolor($self->{fg_color});$i++;}}
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