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mg2c_2.1_web.pl
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mg2c_2.1_web.pl
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#!C:/Perl64/bin/perl
use strict;
use POSIX;
my ($svg_info2,$temp_info);
$svg_info2="Content-type:text/html"."\n\n";
$svg_info2.= "<HTML>"."\n";
$svg_info2.= "<HEAD>"."\n";
$svg_info2.= "<meta http-equiv=\"content-type\" content=\"text/html;charset=utf-8\">\n";
$svg_info2.="<TITLE>MapGene2Chrom</TITLE>"."\n";
$svg_info2.= "</HEAD>"."\n";
$svg_info2.= "<BODY>"."\n";
$svg_info2.="<div id=\"svgContainer\">";
my ($title_font_family,$title_font_size,$title_font_color);
my ($svg_width,$svg_height,$svg_color);
my ($svg_chrom_height,$svg_chrom_width,$svg_chrom_border_color,$svg_chrom_border_width,$svg_chrom_fill_color);
my ($chrom_init_len,$chrom_init_width);
my ($chrom_x,$chrom_y,$chrom_rx,$chrom_ry);
my ($chrom_fill_color,$chrom_border_color,$chrom_border_width);
my ($gene_display_type,$gene_line_type,$gene_line_color,$gene_line_width,$gene_name_font_color,$gene_name_font_family,$gene_name_font_size,$gene_name_margin);
my ($link_polyline_width,$link_polyline_color);
my ($geneName2chrom_margin);
my ($scale_len,$scale_chrom_margin_y,$scale_y,$scale_unit,$scale_unit_float,$scale_color);
my (@NameAndValuelists,$NameAndValue,$Name,$Value,$aatemp,@paras);
my ($gggene_info,$ccchrom_info);
my ($ruler_info,$ruler_width,$ruler_height,$seq_len,$ruler_KeDu_num,$ruler_x,$ruler_y,$ruler_color,$head_info);
#读取参数值，存入@paras数组中备用。
#my $QuerystringFromEnv=$ENV{QUERY_STRING};
my $QuerystringFromEnv;
if($ENV{"REQUEST_METHOD"} eq "GET"){
$QuerystringFromEnv=$ENV{"QUERY_STRING"};
}elsif($ENV{"REQUEST_METHOD"} eq "POST"){
#print "2222222222";
read(STDIN,$QuerystringFromEnv,$ENV{"CONTENT_LENGTH"});
}
@NameAndValuelists=split(/&/,$QuerystringFromEnv);
foreach $NameAndValue(@NameAndValuelists){
($Name,$Value)=split(/=/,$NameAndValue);
$Name=~tr/+//;
$Value=~s/%([\dA-Fa-f][\dA-Fa-f])/pack("c",hex($1))/eg;
$aatemp="$Name\=$Value";
push @paras,$aatemp;
if($Name eq "gene_info"){$gggene_info=$Value;}
if($Name eq "chrom_info"){$ccchrom_info=$Value;}
}
#获取各个参数的值
#$gggene_info=getParaValue("gene_info");
#$ccchrom_info=getParaValue("chrom_info");
$svg_width=getParaValue("svg_width");
$svg_height=getParaValue("svg_height");
$svg_color=getParaValue("svg_color");
$svg_chrom_height=getParaValue("svg_chrom_height");
$svg_chrom_width=getParaValue("svg_chrom_width");
$svg_chrom_border_color=getParaValue("svg_chrom_border_color");
$svg_chrom_border_width=getParaValue("svg_chrom_border_width");
$svg_chrom_fill_color=getParaValue("svg_chrom_fill_color");
$title_font_family=getParaValue("title_font_family");
$title_font_size=getParaValue("title_font_size");
$title_font_color=getParaValue("title_font_color");
$chrom_init_len=getParaValue("chrom_init_len");
$chrom_init_width=getParaValue("chrom_init_width");
$chrom_rx=getParaValue("chrom_rx");
$chrom_ry=getParaValue("chrom_ry");
$chrom_fill_color=getParaValue("chrom_fill_color");
$chrom_border_color=getParaValue("chrom_border_color");
$chrom_border_width=getParaValue("chrom_border_width");
$gene_display_type=getParaValue("gene_display_type");
$gene_line_type=getParaValue("gene_line_type");
$gene_line_color=getParaValue("gene_line_color");
$gene_line_width=getParaValue("gene_line_width");
$gene_name_font_color=$gene_line_color;
$gene_name_font_family=getParaValue("gene_name_font_family");
$gene_name_font_size=getParaValue("gene_name_font_size");
$gene_name_margin=$gene_name_font_size;
$geneName2chrom_margin=getParaValue("geneName2chrom_margin");
$link_polyline_color=$gene_line_color;
$link_polyline_width=getParaValue("link_polyline_width");
$ruler_width=getParaValue("ruler_width");
$ruler_KeDu_num=getParaValue("ruler_KeDu_num");;
$ruler_x=getParaValue("ruler_x");
$scale_unit_float=getParaValue("scale_unit_float");
$scale_unit=getParaValue("scale_unit");
$scale_color=getParaValue("scale_color");
my(@allGenes,%geneGroup,@group,$i,$rows,$columns,$chrom_num,$r,$c,$xn);
my ($svg_info,$j);
@allGenes=split(/\n/,$gggene_info);
@allGenes=cleanArray(@allGenes);
%geneGroup=splitGeneInfoByChrom(@allGenes);
my@aaa=keys %geneGroup;
my ($geneMaxNum,$diff_len);
$geneMaxNum=getMaxGeneNum();
if($gene_name_margin*$geneMaxNum/2>$chrom_init_len){
$diff_len=int(($gene_name_margin*$geneMaxNum/2)/10)*10-$chrom_init_len;
$chrom_init_len=int(($gene_name_margin*$geneMaxNum/2)/10)*10;
$svg_chrom_height=$svg_chrom_height+$diff_len;
}
#读取染色体信息，包括染色体名称和长度ƍ
my @chroms=split(/\n/,$ccchrom_info);
@chroms=cleanArray(@chroms);
my $maxChromUnit=getMaxChromUnit();
$chrom_num=$#chroms+1; #计算显示的染色体个数
$columns=int(($svg_width-($ruler_x+$ruler_width))/$svg_chrom_width); #计算一行显示几条染色体？
$rows=ceil($chrom_num/$columns); #计算共显示几行染色体。
#print "$svg_width|$ruler_x|$ruler_width|$svg_chrom_width|$columns<br>";
#依据输入文件中有几个scaffold，智能调整svg整体尺寸的大小。
$svg_width=$ruler_x+$ruler_width+$columns*$svg_chrom_width;
$svg_height=$rows*$svg_chrom_height;
#输出SVG图形的开头部分
$temp_info="<?xml version=\"1.0\" standalone=\"no\"?>\n";
$temp_info.="<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.1//EN\" \"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd\">\n";
$svg_info="<svg width=\"$svg_width\" height=\"$svg_height\" color=\"$svg_color\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\">\n";
#r代表rows 第r行，从0开始计数；c代表columns 第c列，从0开始计数。
$r=0;$c=0;
for($i=0;$i<=$#chroms;$i++){
my ($ch_name,$ch_len)=split(/\s+/,$chroms[$i]);
$xn=$i+1;
@group=split(/\n/,$geneGroup{$ch_name});
@group=sortGenesAscByStart(@group);
my ($geneNameMax,$chrom_bps,$chrom_len,@temp,$chrom_rect_x,$chrom_rect_y);
my ($chrom_name_x,$chrom_name_y,$chrom_name);
$geneNameMax=getMaxlenGeneName(@group);
@temp=split(/\s+/,$group[0]);
$chrom_bps=$ch_len;
#if($temp[4] eq ""){
# $chrom_bps=$ch_len;
#}else{
# $chrom_bps=$temp[4];
#}
$chrom_name=$ch_name;
#if($temp[3] ne ""){
# $chrom_name=$temp[3];
#}else{
# $chrom_name=$ch_name;
#}
$chrom_len=($chrom_bps/$maxChromUnit)*10;
$chrom_len=ceil($chrom_len)/10;
$chrom_x=$ruler_x+$ruler_width+$svg_chrom_width/2-$chrom_init_width/2+$c*$svg_chrom_width;
$chrom_y=20+$title_font_size*2.5+$r*$svg_chrom_height;
if($c==0){
#$ruler_width=50;
my ($xxst,$xxse);
#$xxst=$r*$columns;
#$xxse=($r+1)*$columns-1;
$xxst=0;
$xxse=$#chroms;
$seq_len=getMaxChromLen($xxst,$xxse);
$ruler_height=ceil(($seq_len/$maxChromUnit)*10)/10;
#$ruler_KeDu_num=10;
#$ruler_x=10;
$ruler_y=$chrom_y;
$ruler_color=$scale_color;
$head_info="no";
$ruler_info="";
#问题出在这里，ruler的单位与染色体的单位不统一造成的。
$ruler_info=drawRuler($ruler_height,$seq_len,$ruler_KeDu_num,$ruler_x,$ruler_y,$ruler_color,$head_info,$maxChromUnit);
$svg_info.=$ruler_info."\n";
}
#计算染色体标题应该显示的位置。
$chrom_name_x=$ruler_x+$ruler_width+$svg_chrom_width/2+$c*$svg_chrom_width;
$chrom_name_y=$chrom_y-$title_font_size;
#绘制染色体边框的左上角坐标。
$chrom_rect_x=$ruler_x+$ruler_width+$c*$svg_chrom_width;
$chrom_rect_y=0+$r*$svg_chrom_height;
#输出染色体区域边框线
$svg_info.="<rect width=\"$svg_chrom_width\" height=\"$svg_chrom_height\" x=\"$chrom_rect_x\" y=\"$chrom_rect_y\" style=\"stroke-width:$svg_chrom_border_width;stroke:$svg_chrom_border_color; fill:$svg_chrom_fill_color;\"/>\n";
#输出染色体名称
$svg_info.="<text x=\"$chrom_name_x\" y=\"$chrom_name_y\" text-anchor=\"middle\" font-family=\"$title_font_family\" font-size=\"$title_font_size\" fill=\"$title_font_color\" >$chrom_name</text>\n";
#输出染色体
$svg_info.="<rect width=\"$chrom_init_width\" height=\"$chrom_len\" x=\"$chrom_x\" y=\"$chrom_y\" rx=\"$chrom_rx\" ry=\"$chrom_ry\" style=\"stroke-width:$chrom_border_width;stroke:$chrom_border_color;fill:$chrom_fill_color;\"/>\n";
#print "$title_font_size\n";
my ($text_x,$text_y);
my ($Rprev_y,$text_top_margin,$temp_y_margin);
my($poly_x1,$poly_x2,$poly_x3,$poly_x4);
my($poly_y1,$poly_y2,$poly_y3,$poly_y4);
#1. 在染色体的左右两边同时画；
if($gene_display_type==1){
#画将偶数基因画在染色体的左边
for($j=0;$j<=$#group;$j=$j+2){
my ($gname,$gstart,$gend,$chromID,$diy_color)=split(/\s+/,$group[$j],5);
my ($gene_x1,$gene_x2,$gene_y1,$gene_y2,$gene_x,$gene_y);
$gene_x1=$chrom_x;
$gene_x2=$chrom_x+$chrom_init_width;
$gene_y1=$chrom_y+$gstart/$maxChromUnit;
$gene_y2=$chrom_y+$gend/$maxChromUnit;
my $gene_height=($gend-$gstart)/$maxChromUnit;
$gene_y=($gene_y1+$gene_y2)/2;
$gene_y=sprintf("%.0f",$gene_y);
if($gene_line_type==1){
if($diy_color ne ""){$svg_info.="<line x1=\"$gene_x1\" y1=\"$gene_y\" x2=\"$gene_x2\" y2=\"$gene_y\" style=\"stroke:$diy_color;stroke-width:$gene_line_width\"/>\n";}
else{$svg_info.="<line x1=\"$gene_x1\" y1=\"$gene_y\" x2=\"$gene_x2\" y2=\"$gene_y\" style=\"stroke:$gene_line_color;stroke-width:$gene_line_width\"/>\n";}
}
if($gene_line_type==2){
if($diy_color ne ""){$svg_info.="<rect width=\"$chrom_init_width\" height=\"$gene_height\" x=\"$gene_x1\" y=\"$gene_y1\" style=\"stroke-width:$gene_line_width;stroke:$diy_color;fill:$diy_color;\"/>\n";}
else{$svg_info.="<line x1=\"$gene_x1\" y1=\"$gene_y\" x2=\"$gene_x2\" y2=\"$gene_y\" style=\"stroke:$gene_line_color;stroke-width:$gene_line_width\"/>\n";}
}
if($j==0){$Rprev_y=$gene_y;}
$text_x=$gene_x1-$geneName2chrom_margin-1;
#计算基因连接线的坐标
$poly_x1=$gene_x1;
$poly_y1=$gene_y;
$poly_x2=$gene_x1-$geneName2chrom_margin*0.3;
$poly_y2=$gene_y;
$poly_x3=$gene_x1-$geneName2chrom_margin*0.7;
$poly_x4=$gene_x1-$geneName2chrom_margin*1.0;
my $g_num=$#group;
if($g_num*$gene_name_margin/2 >= $chrom_init_len*0.9){
$temp_y_margin=$gene_name_margin*0.5;
$text_y=$Rprev_y+$temp_y_margin+$gene_name_font_size*0.4;
$poly_y3=$Rprev_y+$temp_y_margin;
$poly_y4=$Rprev_y+$temp_y_margin;
}else{
if( $gene_y-$Rprev_y>=$gene_name_margin){
$text_y=$gene_y+$gene_name_font_size*0.4;
$poly_y3=$gene_y;
$poly_y4=$gene_y;
}else{
$temp_y_margin=$gene_name_margin*0.5;
$text_y=$Rprev_y+$temp_y_margin+$gene_name_font_size*0.4;
$poly_y3=$Rprev_y+$temp_y_margin;
$poly_y4=$Rprev_y+$temp_y_margin;
}
}
#输出基因线与基因名称的连接线；基因名称
if($diy_color ne ""){
#$svg_info.="<polyline points=\"$poly_x1,$poly_y1 $poly_x2,$poly_y2 $poly_x3,$poly_y3 $poly_x4,$poly_y4\" style=\"fill:none;stroke:$diy_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<polyline points=\"$poly_x1,$poly_y1 $poly_x4,$poly_y4\" style=\"fill:none;stroke:$diy_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<text x=\"$text_x\" y=\"$text_y\" text-anchor=\"end\" font-family=\"$gene_name_font_family\" font-size=\"$gene_name_font_size\" fill=\"$diy_color\">$gname</text>\n";
}else{
#$svg_info.="<polyline points=\"$poly_x1,$poly_y1 $poly_x2,$poly_y2 $poly_x3,$poly_y3 $poly_x4,$poly_y4\" style=\"fill:none;stroke:$link_polyline_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<polyline points=\"$poly_x1,$poly_y1 $poly_x4,$poly_y4\" style=\"fill:none;stroke:$link_polyline_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<text x=\"$text_x\" y=\"$text_y\" text-anchor=\"end\" font-family=\"$gene_name_font_family\" font-size=\"$gene_name_font_size\" fill=\"$gene_name_font_color\">$gname</text>\n";
}
$Rprev_y=$text_y;
}
#画将奇数基因画在染色体的右边
for($j=1;$j<=$#group;$j=$j+2){
my ($gname,$gstart,$gend,$chromID,$diy_color)=split(/\s+/,$group[$j],5);
my ($gene_x1,$gene_x2,$gene_y1,$gene_y2,$gene_x,$gene_y);
$gene_x1=$chrom_x;
$gene_x2=$chrom_x+$chrom_init_width;
$gene_y1=$chrom_y+$gstart/$maxChromUnit;
$gene_y2=$chrom_y+$gend/$maxChromUnit;
$gene_y=($gene_y1+$gene_y2)/2;
$gene_y=sprintf("%.0f",$gene_y);
my $gene_height=($gend-$gstart)/$maxChromUnit;
if($gene_line_type==1){
$svg_info.="<line x1=\"$gene_x1\" y1=\"$gene_y\" x2=\"$gene_x2\" y2=\"$gene_y\" style=\"stroke:$gene_line_color;stroke-width:$gene_line_width\"/>\n";
}
if($gene_line_type==2){
$svg_info.="<rect width=\"$chrom_init_width\" height=\"$gene_height\" x=\"$gene_x1\" y=\"$gene_y1\" style=\"stroke-width:$gene_line_width;stroke:$gene_line_color;fill:$gene_line_color;\"/>\n";
}
if($j==1){$Rprev_y=$gene_y;}
$text_x=$gene_x2+$geneName2chrom_margin+1;
#计算基因连接线的坐标
$poly_x1=$gene_x2;
$poly_y1=$gene_y;
$poly_x2=$gene_x2+$geneName2chrom_margin*0.3;
$poly_y2=$gene_y;
$poly_x3=$gene_x2+$geneName2chrom_margin*0.7;
$poly_x4=$gene_x2+$geneName2chrom_margin*1.0;
my $g_num=$#group;
if($g_num*$gene_name_margin/2 >= $chrom_init_len*0.9){
$temp_y_margin=$gene_name_margin*0.5;
$text_y=$Rprev_y+$temp_y_margin+$gene_name_font_size*0.4;
$poly_y3=$Rprev_y+$temp_y_margin;
$poly_y4=$Rprev_y+$temp_y_margin;
}else{
if( $gene_y-$Rprev_y>=$gene_name_margin){
$text_y=$gene_y+$gene_name_font_size*0.4;
$poly_y3=$gene_y;
$poly_y4=$gene_y;
}else{
$temp_y_margin=$gene_name_margin*0.5;
$text_y=$Rprev_y+$temp_y_margin+$gene_name_font_size*0.4;
$poly_y3=$Rprev_y+$temp_y_margin;
$poly_y4=$Rprev_y+$temp_y_margin;
}
}
#输出基因线与基因名称的连接线；基因名称
if($diy_color ne ""){
#$svg_info.="<polyline points=\"$poly_x1,$poly_y1 $poly_x2,$poly_y2 $poly_x3,$poly_y3 $poly_x4,$poly_y4\" style=\"fill:none;stroke:$diy_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<polyline points=\"$poly_x1,$poly_y1 $poly_x4,$poly_y4\" style=\"fill:none;stroke:$diy_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<text x=\"$text_x\" y=\"$text_y\" text-anchor=\"start\" font-family=\"$gene_name_font_family\" font-size=\"$gene_name_font_size\" fill=\"$diy_color\">$gname</text>\n";
}else{
#$svg_info.="<polyline points=\"$poly_x1,$poly_y1 $poly_x2,$poly_y2 $poly_x3,$poly_y3 $poly_x4,$poly_y4\" style=\"fill:none;stroke:$link_polyline_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<polyline points=\"$poly_x1,$poly_y1 $poly_x4,$poly_y4\" style=\"fill:none;stroke:$link_polyline_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<text x=\"$text_x\" y=\"$text_y\" text-anchor=\"start\" font-family=\"$gene_name_font_family\" font-size=\"$gene_name_font_size\" fill=\"$gene_name_font_color\">$gname</text>\n";
}
$Rprev_y=$text_y;
}
}
#2，仅在染色体左边画基因；
if($gene_display_type==2){
#画将偶数基因画在染色体的左边
for($j=0;$j<=$#group;$j=$j+1){
my ($gname,$gstart,$gend,$chromID,$diy_color)=split(/\s+/,$group[$j],5);
my ($gene_x1,$gene_x2,$gene_y1,$gene_y2,$gene_x,$gene_y);
$gene_x1=$chrom_x;
$gene_x2=$chrom_x+$chrom_init_width;
$gene_y1=$chrom_y+$gstart/$maxChromUnit;
$gene_y2=$chrom_y+$gend/$maxChromUnit;
my $gene_height=($gend-$gstart)/$maxChromUnit;
$gene_y=($gene_y1+$gene_y2)/2;
$gene_y=sprintf("%.0f",$gene_y);
if($gene_line_type==1){
if($diy_color ne ""){
$svg_info.="<line x1=\"$gene_x1\" y1=\"$gene_y\" x2=\"$gene_x2\" y2=\"$gene_y\" style=\"stroke:$diy_color;stroke-width:$gene_line_width\"/>\n";
}else{
$svg_info.="<line x1=\"$gene_x1\" y1=\"$gene_y\" x2=\"$gene_x2\" y2=\"$gene_y\" style=\"stroke:$gene_line_color;stroke-width:$gene_line_width\"/>\n";
}
}
if($gene_line_type==2){
if($diy_color ne ""){
$svg_info.="<rect width=\"$chrom_init_width\" height=\"$gene_height\" x=\"$gene_x1\" y=\"$gene_y1\" style=\"stroke-width:$gene_line_width;stroke:$diy_color;fill:$diy_color;\"/>\n";
}else{
$svg_info.="<rect width=\"$chrom_init_width\" height=\"$gene_height\" x=\"$gene_x1\" y=\"$gene_y1\" style=\"stroke-width:$gene_line_width;stroke:$gene_line_color;fill:$gene_line_color;\"/>\n";
}
}
if($j==0){$Rprev_y=$gene_y;}
$text_x=$gene_x1-$geneName2chrom_margin-1;
#计算基因连接线的坐标
$poly_x1=$gene_x1;
$poly_y1=$gene_y;
$poly_x2=$gene_x1-$geneName2chrom_margin*0.3;
$poly_y2=$gene_y;
$poly_x3=$gene_x1-$geneName2chrom_margin*0.7;
$poly_x4=$gene_x1-$geneName2chrom_margin*1.0;
my $g_num=$#group;
if($g_num*$gene_name_margin/2 >= $chrom_init_len*0.9){
$temp_y_margin=$gene_name_margin*0.5;
$text_y=$Rprev_y+$temp_y_margin+$gene_name_font_size*0.4;
$poly_y3=$Rprev_y+$temp_y_margin;
$poly_y4=$Rprev_y+$temp_y_margin;
}else{
if( $gene_y-$Rprev_y>=$gene_name_margin){
$text_y=$gene_y+$gene_name_font_size*0.4;
$poly_y3=$gene_y;
$poly_y4=$gene_y;
}else{
$temp_y_margin=$gene_name_margin*0.5;
$text_y=$Rprev_y+$temp_y_margin+$gene_name_font_size*0.4;
$poly_y3=$Rprev_y+$temp_y_margin;
$poly_y4=$Rprev_y+$temp_y_margin;
}
}
#输出基因线与基因名称的连接线；基因名称
if($diy_color ne ""){
#$svg_info.="<polyline points=\"$poly_x1,$poly_y1 $poly_x2,$poly_y2 $poly_x3,$poly_y3 $poly_x4,$poly_y4\" style=\"fill:none;stroke:$diy_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<polyline points=\"$poly_x1,$poly_y1 $poly_x4,$poly_y4\" style=\"fill:none;stroke:$diy_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<text x=\"$text_x\" y=\"$text_y\" text-anchor=\"end\" font-family=\"$gene_name_font_family\" font-size=\"$gene_name_font_size\" fill=\"$diy_color\">$gname</text>\n";
}else{
#$svg_info.="<polyline points=\"$poly_x1,$poly_y1 $poly_x2,$poly_y2 $poly_x3,$poly_y3 $poly_x4,$poly_y4\" style=\"fill:none;stroke:$link_polyline_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<polyline points=\"$poly_x1,$poly_y1 $poly_x4,$poly_y4\" style=\"fill:none;stroke:$link_polyline_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<text x=\"$text_x\" y=\"$text_y\" text-anchor=\"end\" font-family=\"$gene_name_font_family\" font-size=\"$gene_name_font_size\" fill=\"$gene_name_font_color\">$gname</text>\n";
}
$Rprev_y=$text_y;
}
}
#3，仅在染色体右边画基因；
if($gene_display_type==3){
#画将奇数基因画在染色体的右边
for($j=0;$j<=$#group;$j=$j+1){
my ($gname,$gstart,$gend,$chromID,$diy_color)=split(/\s+/,$group[$j],5);
my ($gene_x1,$gene_x2,$gene_y1,$gene_y2,$gene_x,$gene_y);
$gene_x1=$chrom_x;
$gene_x2=$chrom_x+$chrom_init_width;
$gene_y1=$chrom_y+$gstart/$maxChromUnit;
$gene_y2=$chrom_y+$gend/$maxChromUnit;
$gene_y=($gene_y1+$gene_y2)/2;
$gene_y=sprintf("%.0f",$gene_y);
my $gene_height=($gend-$gstart)/$maxChromUnit;
if($gene_line_type==1){
if($diy_color ne ""){
$svg_info.="<line x1=\"$gene_x1\" y1=\"$gene_y\" x2=\"$gene_x2\" y2=\"$gene_y\" style=\"stroke:$diy_color;stroke-width:$gene_line_width\"/>\n";
}else{
$svg_info.="<line x1=\"$gene_x1\" y1=\"$gene_y\" x2=\"$gene_x2\" y2=\"$gene_y\" style=\"stroke:$gene_line_color;stroke-width:$gene_line_width\"/>\n";
}
}
if($gene_line_type==2){
if($diy_color ne ""){
$svg_info.="<rect width=\"$chrom_init_width\" height=\"$gene_height\" x=\"$gene_x1\" y=\"$gene_y1\" style=\"stroke-width:$gene_line_width;stroke:$diy_color;fill:$diy_color;\"/>\n";
}else{
$svg_info.="<rect width=\"$chrom_init_width\" height=\"$gene_height\" x=\"$gene_x1\" y=\"$gene_y1\" style=\"stroke-width:$gene_line_width;stroke:$gene_line_color;fill:$gene_line_color;\"/>\n";
}
}
if($j==1){$Rprev_y=$gene_y;}
$text_x=$gene_x2+$geneName2chrom_margin+1;
#计算基因连接线的坐标
$poly_x1=$gene_x2;
$poly_y1=$gene_y;
$poly_x2=$gene_x2+$geneName2chrom_margin*0.3;
$poly_y2=$gene_y;
$poly_x3=$gene_x2+$geneName2chrom_margin*0.7;
$poly_x4=$gene_x2+$geneName2chrom_margin*1.0;
my $g_num=$#group;
if($g_num*$gene_name_margin/2 >= $chrom_init_len*0.9){
$temp_y_margin=$gene_name_margin*0.5;
$text_y=$Rprev_y+$temp_y_margin+$gene_name_font_size*0.4;
$poly_y3=$Rprev_y+$temp_y_margin;
$poly_y4=$Rprev_y+$temp_y_margin;
}else{
if( $gene_y-$Rprev_y>=$gene_name_margin){
$text_y=$gene_y+$gene_name_font_size*0.4;
$poly_y3=$gene_y;
$poly_y4=$gene_y;
}else{
$temp_y_margin=$gene_name_margin*0.5;
$text_y=$Rprev_y+$temp_y_margin+$gene_name_font_size*0.4;
$poly_y3=$Rprev_y+$temp_y_margin;
$poly_y4=$Rprev_y+$temp_y_margin;
}
}
#输出基因线与基因名称的连接线；基因名称
if($diy_color ne ""){
#$svg_info.="<polyline points=\"$poly_x1,$poly_y1 $poly_x2,$poly_y2 $poly_x3,$poly_y3 $poly_x4,$poly_y4\" style=\"fill:none;stroke:$diy_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<polyline points=\"$poly_x1,$poly_y1 $poly_x4,$poly_y4\" style=\"fill:none;stroke:$diy_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<text x=\"$text_x\" y=\"$text_y\" text-anchor=\"start\" font-family=\"$gene_name_font_family\" font-size=\"$gene_name_font_size\" fill=\"$diy_color\">$gname</text>\n";
}else{
#$svg_info.="<polyline points=\"$poly_x1,$poly_y1 $poly_x2,$poly_y2 $poly_x3,$poly_y3 $poly_x4,$poly_y4\" style=\"fill:none;stroke:$link_polyline_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<polyline points=\"$poly_x1,$poly_y1 $poly_x4,$poly_y4\" style=\"fill:none;stroke:$link_polyline_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<text x=\"$text_x\" y=\"$text_y\" text-anchor=\"start\" font-family=\"$gene_name_font_family\" font-size=\"$gene_name_font_size\" fill=\"$gene_name_font_color\">$gname</text>\n";
}
$Rprev_y=$text_y;
}
}
#4，在染色体左边画基因，同时在右边标注位置；
if($gene_display_type==4){
#画将偶数基因画在染色体的左边
for($j=0;$j<=$#group;$j=$j+1){
my ($gname,$gstart,$gend,$chromID,$diy_color)=split(/\s+/,$group[$j],5);
my ($gene_x1,$gene_x2,$gene_y1,$gene_y2,$gene_x,$gene_y);
$gene_x1=$chrom_x;
$gene_x2=$chrom_x+$chrom_init_width;
$gene_y1=$chrom_y+$gstart/$maxChromUnit;
$gene_y2=$chrom_y+$gend/$maxChromUnit;
my $gene_height=($gend-$gstart)/$maxChromUnit;
$gene_y=($gene_y1+$gene_y2)/2;
$gene_y=sprintf("%.0f",$gene_y);
if($gene_line_type==1){
if($diy_color ne ""){
$svg_info.="<line x1=\"$gene_x1\" y1=\"$gene_y\" x2=\"$gene_x2\" y2=\"$gene_y\" style=\"stroke:$diy_color;stroke-width:$gene_line_width\"/>\n";
}else{
$svg_info.="<line x1=\"$gene_x1\" y1=\"$gene_y\" x2=\"$gene_x2\" y2=\"$gene_y\" style=\"stroke:$gene_line_color;stroke-width:$gene_line_width\"/>\n";
}
}
if($gene_line_type==2){
if($diy_color ne ""){
$svg_info.="<rect width=\"$chrom_init_width\" height=\"$gene_height\" x=\"$gene_x1\" y=\"$gene_y1\" style=\"stroke-width:$gene_line_width;stroke:$diy_color;fill:$diy_color;\"/>\n";
}else{
$svg_info.="<rect width=\"$chrom_init_width\" height=\"$gene_height\" x=\"$gene_x1\" y=\"$gene_y1\" style=\"stroke-width:$gene_line_width;stroke:$gene_line_color;fill:$gene_line_color;\"/>\n";
}
}
if($j==0){$Rprev_y=$gene_y;}
$text_x=$gene_x1-$geneName2chrom_margin-1;
#计算基因连接线的坐标
$poly_x1=$gene_x1;
$poly_y1=$gene_y;
$poly_x2=$gene_x1-$geneName2chrom_margin*0.3;
$poly_y2=$gene_y;
$poly_x3=$gene_x1-$geneName2chrom_margin*0.7;
$poly_x4=$gene_x1-$geneName2chrom_margin*1.0;
my $g_num=$#group;
if($g_num*$gene_name_margin/2 >= $chrom_init_len*0.9){
$temp_y_margin=$gene_name_margin*0.5;
$text_y=$Rprev_y+$temp_y_margin+$gene_name_font_size*0.4;
$poly_y3=$Rprev_y+$temp_y_margin;
$poly_y4=$Rprev_y+$temp_y_margin;
}else{
if( $gene_y-$Rprev_y>=$gene_name_margin){
$text_y=$gene_y+$gene_name_font_size*0.4;
$poly_y3=$gene_y;
$poly_y4=$gene_y;
}else{
$temp_y_margin=$gene_name_margin*0.5;
$text_y=$Rprev_y+$temp_y_margin+$gene_name_font_size*0.4;
$poly_y3=$Rprev_y+$temp_y_margin;
$poly_y4=$Rprev_y+$temp_y_margin;
}
}
#输出基因线与基因名称的连接线；基因名称
if($diy_color ne ""){
#$svg_info.="<polyline points=\"$poly_x1,$poly_y1 $poly_x2,$poly_y2 $poly_x3,$poly_y3 $poly_x4,$poly_y4\" style=\"fill:none;stroke:$diy_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<polyline points=\"$poly_x1,$poly_y1 $poly_x4,$poly_y4\" style=\"fill:none;stroke:$diy_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<text x=\"$text_x\" y=\"$text_y\" text-anchor=\"end\" font-family=\"$gene_name_font_family\" font-size=\"$gene_name_font_size\" fill=\"$diy_color\">$gname</text>\n";
}else{
#$svg_info.="<polyline points=\"$poly_x1,$poly_y1 $poly_x2,$poly_y2 $poly_x3,$poly_y3 $poly_x4,$poly_y4\" style=\"fill:none;stroke:$link_polyline_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<polyline points=\"$poly_x1,$poly_y1 $poly_x4,$poly_y4\" style=\"fill:none;stroke:$link_polyline_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<text x=\"$text_x\" y=\"$text_y\" text-anchor=\"end\" font-family=\"$gene_name_font_family\" font-size=\"$gene_name_font_size\" fill=\"$gene_name_font_color\">$gname</text>\n";
}
#输出基因线与基因位置的连接线；基因位置
my($nx1,$nx2,$nx3,$nx4,$na,$txx);
$na=$poly_x1+0.5*$chrom_init_width;
$nx1=2*$na-$poly_x1;
$nx2=2*$na-$poly_x2;
$nx3=2*$na-$poly_x3;
$nx4=2*$na-$poly_x4;
$txx=2*$na-$text_x;
if($diy_color ne ""){
#$svg_info.="<polyline points=\"$nx1,$poly_y1 $nx2,$poly_y2 $nx3,$poly_y3 $nx4,$poly_y4\" style=\"fill:none;stroke:$diy_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<polyline points=\"$nx1,$poly_y1 $nx4,$poly_y4\" style=\"fill:none;stroke:$diy_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<text x=\"$txx\" y=\"$text_y\" text-anchor=\"start\" font-family=\"$gene_name_font_family\" font-size=\"$gene_name_font_size\" fill=\"$diy_color\">$gstart</text>\n";
}else{
#$svg_info.="<polyline points=\"$nx1,$poly_y1 $nx2,$poly_y2 $nx3,$poly_y3 $nx4,$poly_y4\" style=\"fill:none;stroke:$link_polyline_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<polyline points=\"$nx1,$poly_y1 $nx4,$poly_y4\" style=\"fill:none;stroke:$link_polyline_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<text x=\"$txx\" y=\"$text_y\" text-anchor=\"start\" font-family=\"$gene_name_font_family\" font-size=\"$gene_name_font_size\" fill=\"$gene_name_font_color\">$gstart</text>\n";
}
$Rprev_y=$text_y;
}
}
#5，在染色体右边画基因，同时在左边标注位置；
if($gene_display_type==5){
#画将奇数基因画在染色体的右边
for($j=0;$j<=$#group;$j=$j+1){
my ($gname,$gstart,$gend,$chromID,$diy_color)=split(/\s+/,$group[$j],5);
my ($gene_x1,$gene_x2,$gene_y1,$gene_y2,$gene_x,$gene_y);
$gene_x1=$chrom_x;
$gene_x2=$chrom_x+$chrom_init_width;
$gene_y1=$chrom_y+$gstart/$maxChromUnit;
$gene_y2=$chrom_y+$gend/$maxChromUnit;
$gene_y=($gene_y1+$gene_y2)/2;
$gene_y=sprintf("%.0f",$gene_y);
my $gene_height=($gend-$gstart)/$maxChromUnit;
if($gene_line_type==1){
if($diy_color ne ""){
$svg_info.="<line x1=\"$gene_x1\" y1=\"$gene_y\" x2=\"$gene_x2\" y2=\"$gene_y\" style=\"stroke:$diy_color;stroke-width:$gene_line_width\"/>\n";
}else{
$svg_info.="<line x1=\"$gene_x1\" y1=\"$gene_y\" x2=\"$gene_x2\" y2=\"$gene_y\" style=\"stroke:$gene_line_color;stroke-width:$gene_line_width\"/>\n";
}
}
if($gene_line_type==2){
if($diy_color ne ""){
$svg_info.="<rect width=\"$chrom_init_width\" height=\"$gene_height\" x=\"$gene_x1\" y=\"$gene_y1\" style=\"stroke-width:$gene_line_width;stroke:$diy_color;fill:$diy_color;\"/>\n";
}else{
$svg_info.="<rect width=\"$chrom_init_width\" height=\"$gene_height\" x=\"$gene_x1\" y=\"$gene_y1\" style=\"stroke-width:$gene_line_width;stroke:$gene_line_color;fill:$gene_line_color;\"/>\n";
}
}
if($j==1){$Rprev_y=$gene_y;}
$text_x=$gene_x2+$geneName2chrom_margin+1;
#计算基因连接线的坐标
$poly_x1=$gene_x2;
$poly_y1=$gene_y;
$poly_x2=$gene_x2+$geneName2chrom_margin*0.3;
$poly_y2=$gene_y;
$poly_x3=$gene_x2+$geneName2chrom_margin*0.7;
$poly_x4=$gene_x2+$geneName2chrom_margin*1.0;
my $g_num=$#group;
if($g_num*$gene_name_margin/2 >= $chrom_init_len*0.9){
$temp_y_margin=$gene_name_margin*0.5;
$text_y=$Rprev_y+$temp_y_margin+$gene_name_font_size*0.4;
$poly_y3=$Rprev_y+$temp_y_margin;
$poly_y4=$Rprev_y+$temp_y_margin;
}else{
if( $gene_y-$Rprev_y>=$gene_name_margin){
$text_y=$gene_y+$gene_name_font_size*0.4;
$poly_y3=$gene_y;
$poly_y4=$gene_y;
}else{
$temp_y_margin=$gene_name_margin*0.5;
$text_y=$Rprev_y+$temp_y_margin+$gene_name_font_size*0.4;
$poly_y3=$Rprev_y+$temp_y_margin;
$poly_y4=$Rprev_y+$temp_y_margin;
}
}
#输出基因线与基因名称的连接线；基因名称
if($diy_color ne ""){
#$svg_info.="<polyline points=\"$poly_x1,$poly_y1 $poly_x2,$poly_y2 $poly_x3,$poly_y3 $poly_x4,$poly_y4\" style=\"fill:none;stroke:$diy_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<polyline points=\"$poly_x1,$poly_y1 $poly_x4,$poly_y4\" style=\"fill:none;stroke:$diy_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<text x=\"$text_x\" y=\"$text_y\" text-anchor=\"start\" font-family=\"$gene_name_font_family\" font-size=\"$gene_name_font_size\" fill=\"$diy_color\">$gname</text>\n";
}else{
#$svg_info.="<polyline points=\"$poly_x1,$poly_y1 $poly_x2,$poly_y2 $poly_x3,$poly_y3 $poly_x4,$poly_y4\" style=\"fill:none;stroke:$link_polyline_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<polyline points=\"$poly_x1,$poly_y1 $poly_x4,$poly_y4\" style=\"fill:none;stroke:$link_polyline_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<text x=\"$text_x\" y=\"$text_y\" text-anchor=\"start\" font-family=\"$gene_name_font_family\" font-size=\"$gene_name_font_size\" fill=\"$gene_name_font_color\">$gname</text>\n";
}
#输出基因线与基因位置的连接线；基因位置
my($nx1,$nx2,$nx3,$nx4,$na,$txx);
$na=$poly_x1-0.5*$chrom_init_width;
$nx1=2*$na-$poly_x1;
$nx2=2*$na-$poly_x2;
$nx3=2*$na-$poly_x3;
$nx4=2*$na-$poly_x4;
$txx=2*$na-$text_x;
if($diy_color ne ""){
#$svg_info.="<polyline points=\"$nx1,$poly_y1 $nx2,$poly_y2 $nx3,$poly_y3 $nx4,$poly_y4\" style=\"fill:none;stroke:$diy_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<polyline points=\"$nx1,$poly_y1 $nx4,$poly_y4\" style=\"fill:none;stroke:$diy_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<text x=\"$txx\" y=\"$text_y\" text-anchor=\"end\" font-family=\"$gene_name_font_family\" font-size=\"$gene_name_font_size\" fill=\"$diy_color\">$gstart</text>\n";
}else{
#$svg_info.="<polyline points=\"$nx1,$poly_y1 $nx2,$poly_y2 $nx3,$poly_y3 $nx4,$poly_y4\" style=\"fill:none;stroke:$link_polyline_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<polyline points=\"$nx1,$poly_y1 $nx4,$poly_y4\" style=\"fill:none;stroke:$link_polyline_color;stroke-width:$link_polyline_width\"/>\n";
$svg_info.="<text x=\"$txx\" y=\"$text_y\" text-anchor=\"end\" font-family=\"$gene_name_font_family\" font-size=\"$gene_name_font_size\" fill=\"$gene_name_font_color\">$gstart</text>\n";
}
$Rprev_y=$text_y;
}
}
if(($i+1)%$columns==0){$r++;$c=0;}
else{$c++;}
}
$svg_info.='</svg>';
$svg_info=$temp_info.$svg_info;
my $hdir1="mg2c_v2.1";
my $hdir2="temp";
my $file=time()."_".int(rand(1000)).".svg";
my $output="$hdir1/$hdir2/$file";
my $output1="$hdir2/$file";
print "Chrome, FireFox or IE9+ support SVG files better.<br>";
print "Success! download <a color='#FF0000' href='$output1' style='text-decoration:none;'>SVG file</a> by right click and save file to your PC.<br>";
print "<br>".$svg_info2."\n".$svg_info."</div><br>";
print '<button onclick="svg2jpg()">download JPG1</button> ';
print '<button onclick="svg2png()">download PNG1</button> ';
print '<button onclick="svg2tiff()">download TIFF1</button> ';
print '<br><a href="'.$output1.'" download="'.$output1.'">download SVG file by right-click and save it as local file.</a>';
open(OUT,">$output");
print OUT $svg_info;
close OUT;
#print "Success! Save <a color='#FF0000' href='$output1' style='text-decoration:none;'>SVG file</a> by right click and save file to your PC.<br>";
print "</BODY>"."\n";
print '<script src="js/svg2img.js"></script>';
print '<script src="js/svg3.js"></script>';
print "</HTML>"."\n";
#绘制染色体标尺
sub drawRuler{
my ($ruler_height,$seq_len,$ruler_KeDu_num,$ruler_x,$ruler_y,$ruler_color,$maxChromUnit)=@_;
my ($line_x,$line_y,$line_len,$arrow_height,$arrow_width,$line_color,$line_width);
my ($x1,$y1,$x2,$y2);
my ($arrow_info,$svg_width,$svg_height);
$line_x=$ruler_x;
$line_y=$ruler_y;
$arrow_height=6;
$arrow_width=3;
$line_width=2;
$line_len=$ruler_height+$arrow_height*2;
$line_color=$ruler_color;
#my $seq_len=1000*1000*1000;
my $ruler_unit=$seq_len/$ruler_KeDu_num;
my $ruler_unit_str;
my $ruler_step;
if($scale_unit eq "bp"){
if($ruler_unit/(1000*1000)>=1){
$ruler_unit_str=" Mb";
#$ruler_step=sprintf("%0.".$scale_unit_float."f",$ruler_unit/(1000*1000));
$ruler_step=sprintf("%0.".$scale_unit_float."f",$ruler_unit/(1000*1000));
}elsif($ruler_unit/(1000)>=1){
$ruler_unit_str=" Kb";
$ruler_step=sprintf("%0.".$scale_unit_float."f",$ruler_unit/1000);
}else{
$ruler_unit_str=" bp";
$ruler_step=sprintf("%0.".$scale_unit_float."f",$ruler_unit);
}
}elsif($scale_unit eq "cM"){
$ruler_unit_str=" cM";
$ruler_step=sprintf("%0.".$scale_unit_float."f",$ruler_unit);
}
$x1=$line_x-$line_width/2;
$y1=$line_y;
$x2=$line_x+$arrow_width*1.5;
$y2=$line_y;
$arrow_info.="<line x1=\"$x1\" y1=\"$y1\" x2=\"$x2\" y2=\"$y2\" style=\"stroke:$line_color;stroke-width:$line_width\"/>";
my $i=0;
my $ruler_lable_font_family=$gene_name_font_color;
my $ruler_lable_font_size=$gene_name_font_size;
my $ruler_lable_font_color=$ruler_color;
my $ruler_lable=$ruler_step*$i.$ruler_unit_str;
my $ruler_lable_x=$line_x+$line_width/2+$arrow_width*2;
my $ruler_lable_y=$line_y+$i*($line_len-$arrow_height*2)/$ruler_KeDu_num+$ruler_lable_font_size/2;
$arrow_info.="<text x=\"$ruler_lable_x\" y=\"$ruler_lable_y\" text-anchor=\"left\" font-family=\"$ruler_lable_font_family\" font-size=\"$ruler_lable_font_size\" fill=\"$ruler_lable_font_color\" >$ruler_lable</text>\n";
for($i=1;$i<=$ruler_KeDu_num;$i++){
my $llw;
if($i%5==0){
$x1=$line_x-$line_width/2;
$y1=$line_y+$i*($line_len-$arrow_height*2)/$ruler_KeDu_num;
$x2=$line_x+$line_width/2+$arrow_width*1.5;
$y2=$line_y+$i*($line_len-$arrow_height*2)/$ruler_KeDu_num;
$llw=$line_width;
}else{
$x1=$line_x-$line_width/2;
$y1=$line_y+$i*($line_len-$arrow_height*2)/$ruler_KeDu_num;
$x2=$line_x+$line_width/2+$arrow_width*0.75;
$y2=$line_y+$i*($line_len-$arrow_height*2)/$ruler_KeDu_num;
$llw=$line_width;
}
$ruler_lable=$ruler_step*$i.$ruler_unit_str;
$ruler_lable_x=$line_x+$line_width/2+$arrow_width*2;
$ruler_lable_y=$line_y+$i*($line_len-$arrow_height*2)/$ruler_KeDu_num+$ruler_lable_font_size/2;
$arrow_info.="<line x1=\"$x1\" y1=\"$y1\" x2=\"$x2\" y2=\"$y2\" style=\"stroke:$line_color;stroke-width:$llw\"/>";
$arrow_info.="<text x=\"$ruler_lable_x\" y=\"$ruler_lable_y\" text-anchor=\"left\" font-family=\"$ruler_lable_font_family\" font-size=\"$ruler_lable_font_size\" fill=\"$ruler_lable_font_color\" >$ruler_lable</text>\n";
}
$x1=$line_x;
$y1=$line_y;
$x2=$line_x;
$y2=$line_y+$line_len;
$arrow_info.="<line x1=\"$x1\" y1=\"$y1\" x2=\"$x2\" y2=\"$y2\" style=\"stroke:$line_color;stroke-width:$line_width\"/>";
$x1=$line_x;
$y1=$line_y+$line_len;
$x2=$line_x-$arrow_width/2;
$y2=$line_y+$line_len-$arrow_height;
$arrow_info.="<line x1=\"$x1\" y1=\"$y1\" x2=\"$x2\" y2=\"$y2\" style=\"stroke:$line_color;stroke-width:$line_width\"/>";
$x1=$line_x;
$y1=$line_y+$line_len;
$x2=$line_x+$arrow_width/2;
$y2=$line_y+$line_len-$arrow_height;
$arrow_info.="<line x1=\"$x1\" y1=\"$y1\" x2=\"$x2\" y2=\"$y2\" style=\"stroke:$line_color;stroke-width:$line_width\"/>";
my $ruler_info=$arrow_info;
$ruler_info;
}
#获取指定染色体名称的序列长度
sub getChromLen{
my ($chrom)=@_;
my $chrom_len;
$chrom_len=0;
foreach my $line(@chroms){
$line=~s/\n//g;
my ($cname,$clen)=split(/\s+/,$line);
if($chrom eq $cname){
$chrom_len=int($clen);
}
}
$chrom_len;
}
#获取染色体长度的最大值
sub getMaxChromLen{
my ($st,$se)=@_;
my ($maxChromLen,$chromLen);
$maxChromLen=0;
if($se>=$#chroms){
$se=$#chroms;
}
my $i;
for($i=$st;$i<=$se;$i++){
my $line=$chroms[$i];
$line=~s/\n//g;
my ($cname,$clen)=split(/\s+/,$line);
$chromLen=$clen;
if($chromLen<1){
#print "$line chromLen must be more than 1<br>";
}else{
if($maxChromLen<=$chromLen){
$maxChromLen=$chromLen;
}
}
#print "$maxChromLen\t$chromLen<br>";
#print "$line ----$chromLen===$maxChromLen<br>";
}
#$maxChromLen=$maxChromLen;
$maxChromLen;
}
#将基因信息，按其开始位置升序排列
sub sortGenesAscByStart{
my @array=@_;
my($i,$j,$itemp,$jtemp,%genes,$key);
my ($gname,$gstart,$gend,$chromID,$chromLen);
for($i=0;$i<=$#array;$i++){
($gname,$gstart,$gend,$chromID,$chromLen)=split(/\s+/,$array[$i],5);
$genes{$gstart}=$array[$i];
}
my @nArray;
foreach $key(sort {$a <=> $b} keys %genes){
push @nArray,$genes{$key};
}
#print "array=$#array; nArray=$#nArray<br>";
@nArray;
}
#获取基因名称最长的字符数。
sub getMaxlenGeneName{
my @array=@_;
my ($gname,$gstart,$gend,$chromID,$chromLen);
my ($i);
my $maxLenGeneName=0;
for($i=0;$i<$#array;$i++){
($gname,$gstart,$gend,$chromID,$chromLen)=split(/\s+/,$array[$i],5);
if(length($gname)>$maxLenGeneName){
$maxLenGeneName=length($gname);
}
}
$maxLenGeneName;
}
#获取单个染色体含有基因数量的最大值
sub getMaxGeneNum{
my ($line);
my ($maxGeneNum,$num);
$maxGeneNum=0;
foreach $line(keys %geneGroup){
@group=split(/\n/,$geneGroup{$line});
$num=$#group+1;
if($maxGeneNum<$num){
$maxGeneNum=$num;
}
}
$maxGeneNum;
}
#获取染色体单位长度的最大值
sub getMaxChromUnit{
my ($maxChromUnit,$unit,$line,$chromLen);
$maxChromUnit=0;
foreach $line(keys %geneGroup){
$chromLen=getChromLen($line);
if($chromLen<1){
#print "$line chromLen must be more than 1<br>";
}else{
#染色体长度，除以染色体初始尺寸。
$unit=$chromLen/$chrom_init_len;
$unit=sprintf("%.$scale_unit_float"."f",$unit);
#print "$line=$unit 2222<br>";
}
if($scale_unit eq "bp"){
if($unit>=1000){
$unit=(ceil($unit/1000))*1000;
}
}elsif($scale_unit eq "cM"){
$unit=sprintf("%.$scale_unit_float"."f",$unit);
}else{