package SVG_image;

use strict;
use warnings;
use Bio::SeqIO;
use File::Basename qw<basename dirname>;
use GD::SVG;
use SVG;
use FindBin;
use lib "$FindBin::Bin/lib";
use Bio::TreeIO;
use Bio::Tree::NodeI;
use font_rotate;
use process;
use metrics;

use vars qw($image %hash_nif %color_hash %cluster_color_hash %cluster_color_hash_2 %direction_F_R %shift_distance_x $yellow $green $blue $black $red $white $gray $dgray $tree_width @array_image %cluster_GeneName_hash %tab_hash $width_tab_file @add_head);

#create a svg image 

sub create_image_SVG {

    my ($home_directory, $directory_part_TFT, $cluster_result, $strain_reorder_file, $phylogenetic_file, $show_tree_topology, $ref_hash_nif, $workplace, $ref_options) = @_;
    

    %hash_nif = %$ref_hash_nif;
    my %options = %$ref_options;

    #caculate the height size
    opendir DIR_PART_TFT, $directory_part_TFT or die $!;
    my  @dir_part_TFT_0 = readdir DIR_PART_TFT; 
    closedir DIR_PART_TFT;

    foreach (@dir_part_TFT_0){ 

            if (/~/) {

            system ("rm $directory_part_TFT/$_");
            
            }
    }

    opendir DIR_PART_TFT, $directory_part_TFT or die $!;  # reopen $directory_part_TFT to caculate the number of sub-TFT file
    my  @dir_part_TFT = readdir DIR_PART_TFT; 
    @dir_part_TFT =grep ($_!~/^\./ ,@dir_part_TFT);  #delete hidden file . ..
    closedir DIR_PART_TFT;

    my $image_height=$options{distance_between_two_genomes}*(scalar @dir_part_TFT)+$options{up_shift}+$options{down_shift};  # image_height 2019-06-20

    #subroutine to retrieve the lengthest width from FTL table files
    @array_image = process::figure_size_width ($home_directory, $directory_part_TFT, $options{font_family}, $options{font_style}, $options{strain_name_font_size});  
    %direction_F_R = %{$array_image[2]}; 
    %shift_distance_x = %{$array_image[3]};  
   
    if (defined $options{phylogenetic_file} && $options{show_tree_topology} eq "T") {
        $tree_width = tree_width($phylogenetic_file, $options{show_tree_branch}, $options{left_shift}, $options{x_step});# caclulate the width and height of the tree
    }else{

        $tree_width = $options{left_shift};
    }
    ### added by xiangyang on 20250206
    if (defined $options{expand_tab}){
        
        my %length_str;
        open (T, $options{expand_tab});
        my @exp_tab = <T>;
        my $add_head = shift @exp_tab;
        @add_head = split /\t/, $add_head;
        foreach(@exp_tab){
            chomp;
            my @tab = split /\t/, $_;
            #print "$tab[0]\t$tab[1]\n";
            my $expand_genome = shift @tab;
            
            my $ccnum=0;
            foreach (@tab){
                push @{$length_str{$ccnum}}, metrics::string_width_svg($_, "$options{font_family}:$options{font_style}", $options{Ename_font_size});

                $ccnum++;
            }

            $tab_hash{$expand_genome} = $_;
            #print "$expand_genome\t$tab_hash{$expand_genome}\n";
        }
        close T;
        
        my @length_str_max;
        foreach (sort keys %length_str){

            my @length_str_temp = @{$length_str{$_}};           

            @length_str_temp = sort{$a<=>$b} @length_str_temp;
            push @length_str_max, $length_str_temp[-1];
            #print "$_\t", $length_str_temp[-1], "\n";
        }           
        
        my $tab_width;
        foreach (@length_str_max){
            $tab_width += $_ + 5;
            #print "$_\n";
        }
        #$tab_width = $tab_width - 5;
        #print "$tab_width\n";
        foreach (keys %tab_hash){
            my @tt = split /\t/, $tab_hash{$_};
            my $expand_shown;
            my $cccnum=0;
            shift @tt; #the first element is the genome name
            foreach (@tt){
                my $substr_len = $length_str_max[$cccnum];
                my $substr_text = $tt[$cccnum];
                $expand_shown .= "$substr_text"."#"."$substr_len\t";
                #print "$expand_shown", length ($expand_shown), "\n";
                $cccnum++;
            }
            $expand_shown =~ s/\t$//g; # delete the last tab
            $tab_hash{$_} = $expand_shown;
            #print "$_\t$expand_shown\t1\t$tab_hash{$_}\n";
        }
        #$width_tab_file = &string_svg_width(\%tab_hash, $options{Ename_font_size}, $options{font_family}, $options{font_style});
        $width_tab_file = $tab_width+5;
    }else{
        $width_tab_file = 0;
    }
    ### add end

    my $image_width = ($array_image[0]+$array_image[1])*$options{figure_Scale_up_multiple}/20+$options{right_shift}+$array_image[5]+$tree_width+$width_tab_file;  # image_height 2019-06-26

    print "\nStep 5(-SVG): Be going to create a size of ", $image_width, "x", "$image_height SVG image\n";

    print "\nStep 6(-SVG): SVG format was chosen to map\n";

       #create a width x height size image 
        $image=GD::SVG::Image->new($image_width, $image_height);
  

        $yellow = $image->colorAllocate(255,255,0);
        $green = $image->colorAllocate(0,100,0);  
        $blue = $image->colorAllocate(0,0,255);
        $black= $image->colorAllocate (0,0,0);
        $red = $image->colorAllocate(255,0,0);
        $white=$image->colorAllocate(255,255,255);
        $gray= $image->colorAllocate (212,212,212);
        $dgray= $image->colorAllocate (153,153,153);
        #$ddgray   = $image->colorAllocate(127,127,127);
        $image->setThickness($options{line_drawing_width}); #set the line drawing width
        $image->filledRectangle(0, 0, $image_width, $image_height, $white); #add a white background color in image

    %cluster_GeneName_hash = process::cluster_GeneName_hash($directory_part_TFT, $cluster_result);

    if ($options{gene_color_filled} eq  "T") {

        #subroutine to tranform a list of rgb color value into a color hash
        my $color_rgb_code = "$home_directory/color_configure/colors_configure_file";
        color_product($color_rgb_code);

        #subroutine to related color value with each set of homologous gene cluster
        my @ref_cluster_color_hash = process::cluster_color_hash($cluster_result, $color_rgb_code, \%color_hash, scalar @dir_part_TFT, $options{percent_strain_homologouscluster_color});
        %cluster_color_hash = %{$ref_cluster_color_hash[0]};
        %cluster_color_hash_2 = %{$ref_cluster_color_hash[1]};
        
    }

    print "\nStep 7(-SVG): SVG Figure will be generated, please wait!!!\n";
    # each tbl file is used as input file to generate map using draw_map subroutine 

    my $temp_strain_reorder_file;
    if (defined $options{phylogenetic_file}) {
        $temp_strain_reorder_file = TreeDraw($workplace, $phylogenetic_file, $options{show_tree_topology}, $options{show_tree_branch}, $options{show_tree_bootstrap}, $options{x_step}, $options{left_shift}, $options{up_shift}, $options{distance_between_two_genomes}, $options{font_family}, $options{strain_name_font_size});  # display the tree
    }

    my $eachfile=0;
    if (defined $options{strain_reorder_file} || defined $options{phylogenetic_file}) {
        my %strain_reorder_hash;
        if (defined $options{phylogenetic_file}) {open (STRAIN_REORDER, $temp_strain_reorder_file) or die "Must supply strain_reorder_file\n";} #$temp_strain_reorder_file
        if (defined $options{strain_reorder_file}) {open (STRAIN_REORDER, $strain_reorder_file) or die "Must supply strain_reorder_file\n";} #$strain_reorder_file

        while (<STRAIN_REORDER>){
 
            my @strain_reorder = split '\t', $_;
            $strain_reorder_hash{$strain_reorder[1]} = $strain_reorder[0];

        }

        foreach my $part_reorder (sort {$a<=>$b} keys %strain_reorder_hash){ 


            my $check_value = $strain_reorder_hash{$part_reorder};

            foreach my $tbl_part_file(sort @dir_part_TFT){ 
                my $tbl_part_file_new = $tbl_part_file;
                $tbl_part_file_new =~ s/.tbl_.*//g; #To voild some genomes having similar name, edited by Xiangyang Li on Aug 7, 2020
                if(($tbl_part_file_new eq $check_value) and ($tbl_part_file =~ /part$/)) { # delete temp file generated when part_TFT file were edited to modify the genename

                    $tbl_part_file =~ s/(.tbl_.*)//g;
 
                    if ($tbl_part_file eq $check_value) {
                        $tbl_part_file .=$1; 

                        $eachfile++;
                        my $Y_parameter=$options{up_shift}+$options{distance_between_two_genomes}*$eachfile;    # strart Y 
                        my $tbl_part_infile = "$directory_part_TFT/$tbl_part_file" or die "Must supply input filename\n";
                 
                        draw_map_SVG ($tbl_part_infile, $Y_parameter, $tree_width, $options{arrow_relative_Length}, $options{arrow_relative_Height}, $options{strain_name_shift_Y},$options{gene_label_shift_Y}, $options{font_family}, $options{font_style}, $options{label_font_size}, $options{label_font_color}, $options{interested_gene_label_font_color}, $options{cds_color_border}, $options{pseudo_color_border}, $options{RNA_color_border}, $options{gene_no_color_filled}, $options{figure_Scale_up_multiple}, $options{rotate_gene_label}, $options{strain_name_font_size}, $options{strain_name_font_color}, $options{show_label}, $options{unification_label}, $eachfile, $options{Ename_font_size}, $options{Ename_font_color});

                    }

                 }
    
             }

        }

    }

    if (!defined $options{phylogenetic_file} && !defined $options{strain_reorder_file}) {

        foreach my $tbl_part_file(sort @dir_part_TFT){
            unless ($tbl_part_file =~ /.part$/){ next; }
            $eachfile++;
            my $Y_parameter=$options{up_shift}+$options{distance_between_two_genomes}*$eachfile;     # left_shift
        
            my $tbl_part_infile = "$directory_part_TFT/$tbl_part_file" or die "Must supply input filename\n";
                
            draw_map_SVG ($tbl_part_infile, $Y_parameter, $options{left_shift}, $options{arrow_relative_Length}, $options{arrow_relative_Height}, $options{strain_name_shift_Y},$options{gene_label_shift_Y}, $options{font_family}, $options{font_style}, $options{label_font_size}, $options{label_font_color}, $options{interested_gene_label_font_color}, $options{cds_color_border}, $options{pseudo_color_border}, $options{RNA_color_border}, $options{gene_no_color_filled}, $options{figure_Scale_up_multiple}, $options{rotate_gene_label}, $options{strain_name_font_size}, $options{strain_name_font_color}, $options{show_label}, $options{unification_label}, $eachfile, $options{Ename_font_size}, $options{Ename_font_color});
    
        }
    }

    open (SVG_MAP, ">$workplace/figure.svg") or die("Cannot open file for writing");

    binmode SVG_MAP;

    print SVG_MAP $image->svg();
        
}


##################################################################################################
###### Subrounting--color_product
###### Function:
###### translate color (rgb format) into hash 
##################################################################################################
sub color_product {

    my $color_rgb_code = shift;
    my $line=0;
    open (COLOR, $color_rgb_code) or die "Can't read file"; # limit the color number into 1488

    while(<COLOR>){
        chomp;
        if ($_ !~ /^#/) {
            $line++;
            my @color=split(" = ", $_);      
        
            my @gbR=split (",", $color[1]); 

            $color_hash{$line}=$image->colorAllocate($gbR[0],$gbR[1],$gbR[2]);# limit the color number into 1488
        }

    }

}


##################################################################################################
###### Subrounting--draw_map_SVG
###### Function:
###### main subrouting to draw gene cluster map
##################################################################################################
sub draw_map_SVG {
    my %given_color_hash = (
        'blue'                 => $blue, 
        'red'                  => $red,
        'black'                => $black,
        'white'                => $white,
        'gray'                 => $gray,
        'dgray'                => $dgray
       );

    my $inputfile = shift;
    my $Y_centre = shift;       # position in Y axis
    my $left_shift = shift;
    my $arrow_length = shift;    # arrow length
    my $arrow_high = shift;       # arrow width
    my $strain_name_shift_Y = shift;
    my $gene_label_shift_Y = shift;
    my $font_family = shift;
    my $font_style = shift;
    my $label_font_size = shift;
    my $label_font_color = shift;
    my $interested_gene_label_font_color = shift;
    my $cds_color_border = shift;
    my $pseudo_color_border = shift;
    my $RNA_color_border = shift;
    my $gene_no_color_filled = shift;
    my $figure_Scale_up_multiple = shift;  # figure size Scale up multiple
    my $rotate_gene_label = shift;
    my $strain_name_font_size = shift;
    my $strain_name_font_color = shift;
    my $show_label = shift;    
    my $unification_label = shift;
    my $eachfile = shift;
    my $filename = basename $inputfile;
    my $filename_shift = basename $inputfile;
    my $Ename_font_size = shift;
    my $Ename_font_color = shift;
    $filename =~ s/.tbl(.*)//g;
    #$filename =~ s/_/ /g;
    my $strain_name_height = metrics::string_height_svg("$font_family:$font_style", $strain_name_font_size);
    $image->stringrotate($left_shift+10, $Y_centre+$strain_name_height/4-$strain_name_shift_Y, $font_family, $font_style, $strain_name_font_size, $filename, $given_color_hash{$strain_name_font_color}, 0); # genomic names
    
    ### added by xiangyang on 20250206
    if (defined $tab_hash{$filename}){

        my @tab_text = split /\t/, $tab_hash{$filename};
	#my @add_head;
	#@add_head = ("Serotype") if scalar @tab_text ==1;
	#@add_head = ("Serotype", "ST") if scalar @tab_text ==2;
	#@add_head = ("Serotype", "ST", "cgST") if scalar @tab_text ==3;
        my $extand_rigth_distance = 0;
        my $ccccnum = 1;
        foreach (@tab_text){
            my ($text, $max_width) = split /\#/, $_;
            $image->stringrotate($tree_width+10+$array_image[5]+5+$extand_rigth_distance, $Y_centre+$strain_name_height/4-$strain_name_shift_Y, $font_family, $font_style, $Ename_font_size, $text, $given_color_hash{$Ename_font_color}, 0); # if defined $tab_hash{$filename}; # tab names
            $image->stringrotate($tree_width+10+$array_image[5]+5+$extand_rigth_distance+$max_width/6, $Y_centre-$arrow_high-$gene_label_shift_Y, $font_family, $font_style, $Ename_font_size, $add_head[$ccccnum], $given_color_hash{"red"}, -$rotate_gene_label) if $eachfile == 1; # Serotype, ST and cgST
            $extand_rigth_distance += $max_width+5;
            $ccccnum++;
        }
    }
    ### added end
    open (ABL, $inputfile);

    my @min=();

    while (<ABL>){
        my @arr= split "\t", $_;
        $arr[0]=~ s/[><]//g;
        $arr[1]=~ s/[><]//g;
        push (@min,@arr[0,1]);
    }
    @min = sort{$a<=>$b} @min;

    seek (ABL,0,0);
    #my $highlight_gene;
    while (<ABL>){
        my @cds= split "\t", $_;
        $cds[0]=~ s/[><]//g;
        $cds[1]=~ s/[><]//g;

        my %geneName_change_hash;
        my $tag;
        if ($cds[3] =~ /;/) {
            my @geneName_array = split ";", $cds[3];
            $geneName_change_hash{$geneName_array[1]} = $geneName_array[0];
            $geneName_change_hash{$geneName_array[1]} = $cluster_GeneName_hash{$geneName_array[1]} if ( (defined $cluster_GeneName_hash{$geneName_array[1]}) && ($unification_label eq "T") ); #uniform gene name for homologs
            #$geneName_change_hash{$geneName_array[1]} = $geneName_array[0] if (!defined $cluster_GeneName_hash{$geneName_array[1]});
            $tag = $geneName_array[1]; 
        }else {
            $geneName_change_hash{$cds[3]} = $cds[3];
            $geneName_change_hash{$cds[3]} = $cluster_GeneName_hash{$cds[3]} if ( (defined $cluster_GeneName_hash{$cds[3]}) && ($unification_label eq "T") ); #uniform gene name for homologs            
            #$geneName_change_hash{$cds[3]} = $cds[3] if (!defined $cluster_GeneName_hash{$cds[3]});
            $tag = $cds[3];
        }
	
        my ($strart, $end);
        #print "$array_image[5]\n";
        if ($direction_F_R{$filename_shift} ge 1) {
 
            $strart=($cds[0]-$min[0]+$shift_distance_x{$filename_shift})*$figure_Scale_up_multiple/20+$left_shift+$array_image[5]+5+$width_tab_file;
            $end=($cds[1]-$min[0]+$shift_distance_x{$filename_shift})*$figure_Scale_up_multiple/20+$left_shift+$array_image[5]+5+$width_tab_file;

        }

        else {

            $strart=(abs($cds[0]-$min[$#min])+$shift_distance_x{$filename_shift})*$figure_Scale_up_multiple/20+$left_shift+$array_image[5]+5+$width_tab_file; 
            $end=(abs($cds[1]-$min[$#min])+$shift_distance_x{$filename_shift})*$figure_Scale_up_multiple/20+$left_shift+$array_image[5]+5+$width_tab_file; 

        }

       # my $left=($end+$strart)/2;          
       # my $right=$Y_centre-1.25*$arrow_high;
        #my $tag=$cds[3];

        ### gene_label mark
        if ($show_label eq "T") {

        if (defined ($hash_nif{$tag})) {

            #$highlight_gene = $hash_nif{$tag};

            $image->stringrotate(($end+$strart)/2, $Y_centre-$arrow_high-$gene_label_shift_Y, $font_family, $font_style, $label_font_size, $geneName_change_hash{$tag}, $given_color_hash{$interested_gene_label_font_color}, -$rotate_gene_label); # highligth interested gene
        }
        elsif (!(defined ($hash_nif{$tag}))){           
           #$tag =~ s/;.*//g; #delete locus_Tag
            $image->stringrotate(($end+$strart)/2, $Y_centre-$arrow_high-$gene_label_shift_Y, $font_family, $font_style, $label_font_size, $geneName_change_hash{$tag}, $given_color_hash{$label_font_color}, -$rotate_gene_label); # Default color is dgray for gene label of the other genes

        }

        }

        # CDS: forward direction
        if ($end>$strart){                                            

            if(exists $cluster_color_hash_2{$tag}){      

                $image->filledPolygon(rec_arrow_F($strart, $end, $arrow_length, $arrow_high, $Y_centre), $cluster_color_hash{$tag});
                $image->polygon(rec_arrow_F($strart, $end, $arrow_length, $arrow_high, $Y_centre), $given_color_hash{$cds_color_border}); #border
            }
            else{ 
                
                $image->filledPolygon(rec_arrow_F($strart,$end,$arrow_length,$arrow_high, $Y_centre), $given_color_hash{$gene_no_color_filled});
                $image->polygon(rec_arrow_F($strart, $end, $arrow_length, $arrow_high, $Y_centre), $given_color_hash{$cds_color_border}) if $cds[2] eq "CDS"; #set color of border for CDS genes
                $image->polygon(rec_arrow_F($strart, $end, $arrow_length, $arrow_high, $Y_centre), $given_color_hash{$pseudo_color_border}) if scalar @cds > 5; #set color of border for Pseudo genes
                $image->polygon(rec_arrow_F($strart, $end, $arrow_length, $arrow_high, $Y_centre), $given_color_hash{$RNA_color_border}) if $cds[2] =~ /^rRNA|^tRNA/; #set color of border for RNA genes
 
            }                 # map
        }

        # CDS: reverse direction
        elsif ($end<$strart){                           
    
            if(exists $cluster_color_hash_2{$tag}){ 
           
                $image->filledPolygon(rec_arrow_R($strart,$end,$arrow_length,$arrow_high, $Y_centre), $cluster_color_hash{$tag});
                $image->polygon(rec_arrow_R($strart, $end, $arrow_length, $arrow_high, $Y_centre), $given_color_hash{$cds_color_border}); #border

            }
            else{ 

                $image->filledPolygon(rec_arrow_R($strart,$end,$arrow_length,$arrow_high, $Y_centre), $given_color_hash{$gene_no_color_filled});
                $image->polygon(rec_arrow_R($strart, $end, $arrow_length, $arrow_high, $Y_centre), $given_color_hash{$cds_color_border}) if $cds[2] eq "CDS"; #set color of border for CDS genes
                $image->polygon(rec_arrow_R($strart, $end, $arrow_length, $arrow_high, $Y_centre), $given_color_hash{$pseudo_color_border}) if scalar @cds > 5; #set color of border for Pseudo genes
                $image->polygon(rec_arrow_R($strart, $end, $arrow_length, $arrow_high, $Y_centre), $given_color_hash{$RNA_color_border}) if $cds[2] =~ /^rRNA|^tRNA/; #set color of border for RNA genes

            }                     # map
        }

    }

 return $image;

} 


##################################################################################################
###### Subrounting--rec_arrow_F
###### Function:
###### generate senven points to draw polygon (CDS: forward direction) 
##################################################################################################
sub rec_arrow_F {
    my $s=shift;
    my $e=shift;
    my $a_l=shift;
    my $w_h=shift;
    $w_h = $w_h*2;
    my $Y_c=shift;
    my $rec_arrow=GD::Polygon-> new();
    $rec_arrow->addPt($e, $Y_c);                  # piont1
    $rec_arrow->addPt($e-$a_l, $Y_c-$w_h);        # piont2
    $rec_arrow->addPt($e-$a_l, $Y_c-$w_h/2);      # piont3
    $rec_arrow->addPt($s, $Y_c-$w_h/2);           # piont4
    $rec_arrow->addPt($s, $Y_c+$w_h/2);           # piont5
    $rec_arrow->addPt($e-$a_l, $Y_c+$w_h/2);      # piont6
    $rec_arrow->addPt($e-$a_l, $Y_c+$w_h);        # piont7

return $rec_arrow;              

}


##################################################################################################
###### Subrounting--rec_arrow_R
###### Function:
###### generate senven points to draw polygon (CDS: reverse direction) 
##################################################################################################
sub rec_arrow_R {
    my $s=shift;
    my $e=shift;
    my $a_l=shift;
    my $w_h=shift;
    $w_h = $w_h*2;
    my $Y_c=shift;
    my $rec_arrow=GD::Polygon-> new();
    $rec_arrow->addPt($e, $Y_c);                  # piont1
    $rec_arrow->addPt($e+$a_l, $Y_c-$w_h);        # piont2
    $rec_arrow->addPt($e+$a_l, $Y_c-$w_h/2);      # piont3
    $rec_arrow->addPt($s, $Y_c-$w_h/2);           # piont4
    $rec_arrow->addPt($s, $Y_c+$w_h/2);           # piont5
    $rec_arrow->addPt($e+$a_l, $Y_c+$w_h/2);      # piont6
    $rec_arrow->addPt($e+$a_l, $Y_c+$w_h);        # piont7

return $rec_arrow; 

}


sub TreeDraw {

my ($workplace, $phylogenetic_file, $show_tree_topology, $use_branch, $bootstrap, $xstep, $left_shift, $up_shift, $ystep, $font, $font_size) = @_;

my $temp_strain_reorder_file = "$workplace/temp_strain_reorder_file-svg.txt";

my %xx;            # horizontal coordinate for each node
my %yy;            # vertical coordinate for each node
my $tree_object;   # first Bio::Tree::Tree object
#$xstep = 10;         # branch length in drawing      
my $tip = 5; # extra space between tip and label

##########################################################################################################
    my $treeio = Bio::TreeIO->new(-format => 'newick',
                                  -file   => $phylogenetic_file); 
    $tree_object = $treeio->next_tree;  
    my @taxa1 = $tree_object->get_leaf_nodes;
    my $root1 = $tree_object->get_root_node;

    open (STRAIN_REORDER_FILE, ">$temp_strain_reorder_file");
    my $count_number=0;
    my @strain_order = reverse $tree_object->get_nodes(-order => 'depth', sortby => 'height');
    pop @strain_order; # skip root

    my $y = $up_shift+$ystep;
    for my $node_leaf (@strain_order) {
        #print $node_leaf->id;
        if ($node_leaf->is_Leaf){
            $count_number++;
            print STRAIN_REORDER_FILE $node_leaf->id, "\t", "$count_number", "\n";

            #print "test:   ", $node_leaf->id, "\n";
            $xx{$node_leaf} = 0;                 # a temp value
            $yy{$node_leaf} = $y;                # leaf y-value
            $y += $ystep;
        }
    }
    close STRAIN_REORDER_FILE;

if($show_tree_topology eq "T") {

########################################################################################################## 
#set width of the image###################################################################################

    my @stack;
    my @queue; # postorder traversal
    push @stack, $tree_object->get_root_node;
    while (@stack) {
        my $node = pop @stack;
        push @queue, $node;
        foreach my $child ($node->each_Descendent(-sortby => 'internal_id')) {
            push @stack, $child;
        }
     }

    
########################################################################################################## 

    if ($use_branch eq "F") { # ragged right, ignoring branch lengths

    @queue = reverse @queue;
    my @floor;
    for my $node (@queue) {
        if (!$node->is_Leaf) {
            my @children = $node->each_Descendent;
            my $child = shift @children;
            my $xmin = $xx{$child};    # a temp value
            foreach $child (@children) {
	        $xmin = $xx{$child} if $xx{$child} < $xmin;
            }
            $xx{$node} = $xmin - $xstep;
            push @floor,  $xx{$node};
        }
        
    }

        @floor = sort {$a<=>$b} @floor;
        my $floor_tree = ($floor[$#floor] - $floor[0])/$xstep; 
        my $x = $left_shift + $xstep * ($floor_tree+1) + $tip;

        for my $taxon (reverse @taxa1) { 
            $xx{$taxon} = $x - $tip;
        }        

        for my $node (@queue) {
            if (!$node->is_Leaf) {

                my @children = $node->each_Descendent;
                my $child = shift @children;
                my $xmin = $xx{$child};
                my $ymin = my $ymax = $yy{$child};
                    foreach $child (@children) {
	                $xmin = $xx{$child} if $xx{$child} < $xmin;
	                $ymax = $yy{$child} if $yy{$child} > $ymax;
	                $ymin = $yy{$child} if $yy{$child} < $ymin;
                    }

                $xx{$node} = $xmin - $xstep;

                $yy{$node} = ($ymin + $ymax)/2;    # no-leaf y-value
            }
        
        }

        my @preorder = $tree_object->get_nodes(-order => 'depth', sortby => 'height');

        my $root_strain = shift @preorder; # skip root

        for my $node (@preorder) {

              $xx{$node} = $xx{$node->ancestor} + $xstep;    # determinate the all nodes values in x-axis

        }


    } else { # set to aspect ratio and use branch lengths if available
        
        @queue = reverse @queue;
        for my $node (@queue) {
            if (!$node->is_Leaf) {
                my @children = $node->each_Descendent;
                my $child = shift @children;
                my $ymin = my $ymax = $yy{$child};

                foreach $child (@children) {
	            $ymax = $yy{$child} if $yy{$child} > $ymax;
	            $ymin = $yy{$child} if $yy{$child} < $ymin;
                }

                $yy{$node} = ($ymin + $ymax)/2;

            }
        
        }

        my @length_x;
        for ( $root1->get_all_Descendents ) {
            $xx{$_} = $left_shift + depth1($_)*2000;   # determinate the all nodes values in x-axis
        }        

    }

    my @strain_tree = reverse $tree_object->get_nodes(-order => 'depth', sortby => 'height');
    pop @strain_tree; # skip root

    for my $taxon (@strain_tree) {
        #print $node_leaf->id;
        if ($taxon->is_Leaf){
            #$image->stringrotate($xx{$taxon} + $tip, $yy{$taxon}+$font_size / 3, $font, "bold", $font_size/1.5, $taxon->id, $red, 0); # draw strain
            dottedline (5+$tree_width,$yy{$taxon},$xx{$taxon},$yy{$taxon}, $dgray);  #align right strain name using dotted line 
            
        }
    }

##############################################################################################################
##############################################################################################################
    for my $node ($tree_object->get_nodes) {

        if ($node->ancestor) {
        
            if (defined $xx{$node->ancestor}) {

                $image->line($xx{$node},$yy{$node},$xx{$node->ancestor},$yy{$node},$black);


                $image->line($xx{$node->ancestor},$yy{$node},$xx{$node->ancestor},$yy{$node->ancestor},$black);
            } else {

                $image->line($xx{$node},$yy{$node},$left_shift,$yy{$node},$black);
                $image->line($left_shift,$yy{$node},$left_shift,$yy{$node->ancestor},$black);
            }

                if ( $bootstrap eq "T" ) {               
                    if (defined $node->ancestor->id) {
                        my $bootstrap_value =  int (($node->ancestor->id)*100);
 
                        $image->stringrotate($xx{$node->ancestor}+ $font_size/10, $yy{$node->ancestor}+ ($font_size / 3), $font, 'normal', $font_size*0.8, $bootstrap_value, $black, 0); # draw bootstrap value
                    } 

                }

        }

    }
########################################################################################################## 
#set root value of the image##############################################################################
    my $ymin = $yy{$root1};
    my $ymax = $yy{$root1};
    foreach my $child ($root1->each_Descendent) {
        $ymax = $yy{$child} if $yy{$child} > $ymax;
        $ymin = $yy{$child} if $yy{$child} < $ymin;
    }

    my $zz = ($ymin + $ymax)/2;

    if (!defined  $xx{$root1}) {
        $xx{$root1} = $left_shift;
 
    }
 
    $image->line($xx{$root1},$zz,$xx{$root1}- $xstep, $zz,$black);   


    #return $image;
}
    return $temp_strain_reorder_file;
}

sub dottedline {   # output dotted line

    my ($x1, $y1, $x2, $y2, $color) = @_;

    my $dotted_step = 2;

    for (my $change_x=0; $change_x<=$x1-$x2-$dotted_step; $change_x++) {
        $change_x += $dotted_step;
        $image->line($x2 + $dotted_step+$change_x, $y1, $x2+$change_x, $y2, $color);
        $change_x += $dotted_step;
    }

    return $image;

}


sub depth1 {
   
   my $depth = 0;
   my $node = shift;
   while( defined $node->ancestor ) { 

       my $branch_length_node;
       if (defined $node->branch_length) {
           $branch_length_node = $node->branch_length;
       }else{  
           $branch_length_node = 0;  #the length of some branches length may lose
       } 
      
       $depth += $branch_length_node;
       $node = $node->ancestor;

   }
   return $depth;
}


sub tree_width {

my ($phylogenetic_file, $use_branch, $left_shift, $xstep) = @_;
my %xx;        # horizontal coordinate for each node
my $width;     # total drawing width

    my $treeio = Bio::TreeIO->new(-format => 'newick',
                                  -file   => $phylogenetic_file); 
    my $tree_obj = $treeio->next_tree;  # first Bio::Tree::Tree object
    my @taxa = $tree_obj->get_leaf_nodes;
    my $root = $tree_obj->get_root_node;

    for my $taxon (reverse @taxa) {     #strain_name in Y-aixs    xiangyang Li 2019-07-17
        $xx{$taxon} = 0;  # a temp value

    }

    #$xstep = 10;  # branch length in drawing

    my @stack;
    my @queue; # postorder traversal
    push @stack, $root;
    while (@stack) {
        my $node = pop @stack;
        push @queue, $node;
        foreach my $child ($node->each_Descendent(-sortby => 'internal_id')) {
            push @stack, $child;
        }
     }

    if ($use_branch eq "F") { # ignoring branch lengths

    @queue = reverse @queue;
    my @floor;
    for my $node (@queue) {
        if (!$node->is_Leaf) {
            my @children = $node->each_Descendent;
            my $child = shift @children;
            my $xmin = $xx{$child};    # a temp value
            foreach $child (@children) {
	        $xmin = $xx{$child} if $xx{$child} < $xmin;
            }
            $xx{$node} = $xmin - $xstep;
            push @floor,  $xx{$node};
        }
        
    }

        @floor = sort {$a<=>$b} @floor;
        my $floor_tree = ($floor[$#floor] - $floor[0])/$xstep;
 
        $width = $left_shift + $xstep * ($floor_tree+1) ; # set the width of the treemap 

    } else { # set to aspect ratio and use branch lengths if available

        my @length_x;
        for ( $root->get_all_Descendents ) {
            push @length_x, depth1($_);           
            $xx{$_} = $left_shift + depth1($_)*2000;  
 
        }        
        @length_x = sort {$a<=>$b} @length_x;
        $width = $left_shift + $length_x[$#length_x]*2000; # set the width of the treemap 

    }

    return $width;

}


1;

__END__