<?

function get_disp_option($attr,$types,$operation,$request,&$disp){
  if(preg_match("/disp/", $operation , $m)){
    while(preg_match("/^(.+?),(.+)$/",$types,$type)){
      $t = urlencode($type[1]);
      $fromFW = "disp-" . $attr ."-"  . $t;
      if(array_key_exists($fromFW, $request)){
        if($request[$fromFW] === 'off') {
          array_push ($disp, array($attr, $type[1]));
        }
      }
      $types = $type[2]; 
    }
    $t = urlencode($types);
    $fromFW = "disp-" . $attr ."-"  . $t;
    if(array_key_exists($fromFW, $request)){
      if($request[$fromFW] === 'off'){
        array_push ($disp, array($attr, $types));
      }
    }
  }
  return;
}

function get_color_option($attr,$types,$operation,$request,&$color,$count){
  if(preg_match("/color/",$operation,$m)){
    $usecolor =  $attr . "-color"  ;
    if ($usecolor == $request['usecolor'] || $count == 1){
       while(preg_match("/^(.+?),(.+)/",$types,$type)){
        $t = urlencode($type[1]);
        $fromFW = "color-" . $attr ."-"  . $t;
        if(preg_match("/\((\d+),(\d+),(\d+)\)/",$request[$fromFW],$col)){
          array_push ($color, array($attr, $type[1],$col[1],$col[2],$col[3]));
        }
        $types = $type[2]; 
      }
      $t = urlencode($types);
      $fromFW = "color-" . $attr ."-"  . $t;
      if(preg_match("/\((\d+),(\d+),(\d+)\)/",$request[$fromFW],$col)){
        array_push ($color, array($attr, $types,$col[1],$col[2],$col[3]));
      }
    }
  }
  return;
}

function get_select_option($attr,$types,$operation,$request, &$select){
  if(preg_match("/select/", $operation , $m)){
    $fromFW = 'select-' . $attr;
    if(array_key_exists($fromFW, $request)) {
      array_push ($select, array($attr, $request[$fromFW]));
    }
  }
  return;
}

function get_gradation_option($attr, $types, $operation, $request, &$gradation, $defColor, $count ) {
  if(preg_match("/gradation/",$operation,$m)){
    $usecolor = $attr . "-gradation";
     if ($usecolor == $request['usecolor'] || $count == 1){
      $fromFW_min = "gradation-" . $attr ."-min";
      $fromFW_max = "gradation-" . $attr ."-max";
      if(preg_match("/^(\S+),(\S+)/",$types,$type)){
        array_push ($gradation, $attr, $type[1], $defColor[0], $defColor[1], $defColor[2], $type[2], $defColor[0], $defColor[1], $defColor[2]);
        if (preg_match ("/\((\d+),(\d+),(\d+)\)/",$request[$fromFW_min],$col)){
          $gradation[2] = $col[1];
          $gradation[3] = $col[2];
          $gradation[4] = $col[3];
        }
        if (preg_match ("/\((\d+),(\d+),(\d+)\)/",$request[$fromFW_max],$col2)){
          $gradation[6] = $col2[1];
          $gradation[7] = $col2[2];
          $gradation[8] = $col2[3];
        }
      }
    }
  }
  return;
}

function get_ubound_option($attr, $operation, $request, &$ubound) {
  if(preg_match("/ubound/", $operation, $m)){
    $fromFW = 'ubound-' . $attr;
    if(array_key_exists($fromFW, $request)) {
      if (preg_match ("/^\d/",$request[$fromFW],$num)){
        array_push($ubound, array($attr, $request[$fromFW]));
      }
    }
  }
  return;
}

function get_lbound_option($attr, $operation, $request, &$lbound) {
  if(preg_match("/lbound/",$operation,$m)){
    $fromFW = 'lbound-' . $attr;
    if(array_key_exists($fromFW, $request)) {
      if (preg_match ("/^\d/",$request[$fromFW],$num)){
        array_push($lbound, array($attr, $request[$fromFW]));
      }
    }
  }
  return;
}


function get_disp_attr ($line, $disp){
  for ($i=0; $i<count($disp);$i++){
    $attr = $disp[$i][0];
    if(preg_match("/\b$attr=(\w+)\b/",  $line, $optline)){
      if ($optline[1] == $disp[$i][1]){
        return 0;
      }
    }
    if(preg_match("/$attr=\"(.+?)\"/",  $line, $optline)){
      if ($optline[1] == $disp[$i][1]){
        return 0;
      }
    }
  }
  return 1;
}    

function get_ubound_attr ($line, $ubound){
  for ($i=0; $i<count($ubound);$i++){
    $attr = $ubound[$i][0];
    $bound = $ubound[$i][1];
    if(preg_match("/\b$attr=(\S+)\b/",  $line, $optline)){
      if ($optline[1] > $bound){
        return 0;
      }
    }
  }
  return 1;
}

function get_lbound_attr ($line, $lbound){
  for ($i=0; $i<count($lbound);$i++){
    $attr = $lbound[$i][0];
    $bound = $lbound[$i][1];
    if(preg_match("/\b$attr=(\S+)\b/",  $line, $optline)){
      if ($optline[1] < $bound){
        return 0;
      }
    }
  }
  return 1;
}

/**
* $line（最初の行）からdefaultcolorを取得
* @access     public
* @param     string      $line    easyTrackの最初の行
*/
  function get_defaultcolor($line){
    $colorR = 0;
    $colorG = 0;
    $colorB = 0;
    if(preg_match("/\bcolor=(\d+),(\d+),(\d+)\b/",$line, $dcolor)){
      $colorR = $dcolor[1];
      $colorG = $dcolor[2];
      $colorB = $dcolor[3];
    }
    return array($colorR,$colorG,$colorB);
  }

function get_optional_attribute($first_line){
  if (preg_match("/\boptattr=\"(.+?)\"/",$first_line,$matches)){ #\"\"\b
      $optionalattrs = $matches[1];
      $optattrs = array();
      $i =0;
      while(preg_match("/(\w+)\/(\w+)\[(.+?)\]\((.+?)\)(.*)$/",$optionalattrs, $optionalattr)){ # \[\]\((\S+)\)[,\s] 
        $i++;
        array_push ($optattrs, array($optionalattr[1], $optionalattr[2], $optionalattr[3], $optionalattr[4]));
        if(preg_match("/^,(.+?)$/", $optionalattr[5], $remain)){
          $optionalattrs = $remain[1];
        }else {
          break;
        }
      }
  }
  return $optattrs;
}

  function get_genecolor_by_color($colordefault, $line, $attr, $coloroption){

    $color = $colordefault; 
    if(preg_match("/\b$attr=(\w+)\b/",  $line, $optline)){
      for($i=0;$i<count($coloroption);$i++){
        if($coloroption[$i][1] == $optline[1])
          $color = array($coloroption[$i][2], $coloroption[$i][3], $coloroption[$i][4] );
      }
    }
    if(preg_match("/$attr=\"(.+?)\"/",  $line, $optline)){
      for($i=0;$i<count($coloroption);$i++){
        if($coloroption[$i][1] == $optline[1])
          $color = array($coloroption[$i][2], $coloroption[$i][3], $coloroption[$i][4] );
      }
    }
    return $color;
  }    


  function get_genecolor_by_gradation($colordefault, $line, $attr, $coloroption){
    $color = $colordefault; 

     if(preg_match("/\b$attr=(\S+)\b/",  $line, $optline)){
        $ratio = ($optline[1] - $coloroption[1]) / ($coloroption[5] - $coloroption[1]);
        $colorR = $coloroption[2] + ($coloroption[6] - $coloroption[2]) * $ratio;
        $colorG = $coloroption[3] + ($coloroption[7] - $coloroption[3]) * $ratio;
        $colorB = $coloroption[4] + ($coloroption[8] - $coloroption[4]) * $ratio;
        $color = array($colorR , $colorG, $colorB); 

      }
    return $color;
  }

/**
* RGBの色配列から16進数表記変換する
* @access     public
* @param     array       $color     RGB10進数配列
*/
function getColorString($color){
	if($color[0] < 16){
		$r = '0'.dechex($color[0]);
	}else{
		$r = dechex($color[0]);
	}
	if($color[1] < 16){
		$g = '0'.dechex($color[1]);
	}else{
		$g = dechex($color[1]);
	}
	if($color[2] < 16){
		$b = '0'.dechex($color[2]);
	}else{
		$b = dechex($color[2]);
	}
	
	return '#'.$r.$g.$b;
}
  
function get_display_genes($file,$req){
  if($req['start'] < $req['end']){
    $start = $req['start'];
    $end = $req['end'];
  }else {
    $start = $req['end'];
    $end = $req['start'];
  }

  $genes = array();

  while (!feof ($file)) {
    $line = trim(fgets($file));
    if(strncmp($line, "gene", 4) != 0) continue;

    $target_line = substr(( strchr ($line, 'target=') ), 7);
    list($target, $remain) = split("[ \t]", $target_line);
    if(strcmp($target, $req['target']) != 0) continue;

    $range_line = substr(strchr ($line, 'range='), 6);
    list($range_start, $range_end, $remain) = split("[, \t]", $range_line);
    if($range_start > $range_end) {
      $tmp = $range_start;
      $range_start = $range_end;
      $range_end = $tmp;
    }
    if(($range_start > $end) || ($range_end < $start)) continue; 

# option指定を検索 ######

# option disp

    $disp = get_disp_attr($line, $req['disp']);
    if($disp == 0) continue;

# option real ubound

    $ubound = get_ubound_attr($line, $req['ubound']);
    if($ubound == 0) continue;

# option real lbound

    $lbound = get_lbound_attr($line, $req['lbound']);
    if($lbound == 0) continue;

    $genes[] = $line;
  }
  usort ($genes, "cmp_genes");
  return $genes;
}

function cmp_genes($a, $b){
    $range_line = substr(strchr ($a, 'range='), 6);
    list($start_a, $end_a, $remain) = split("[, \t]", $range_line);
    if($start_a > $end_a) {
      $start_a = $end_a;
    }

    $range_line = substr(strchr ($b, 'range='), 6);
    list($start_b, $end_b, $remain) = split("[, \t]", $range_line);
    if($start_b > $end_b) {
      $start_b = $end_b;
    }

    if ($start_a == $start_b) return 0;
    return ($start_a < $start_b) ? -1 : 1;
}

function cmp_genes_rev($a, $b){
    $range_line = substr(strchr ($a, 'range='), 6);
    list($start_a, $end_a, $remain) = split("[, \t]", $range_line);
    if($start_a > $end_a) {
      $end_a = $start_a;
    }

    $range_line = substr(strchr ($b, 'range='), 6);
    list($start_b, $end_b, $remain) = split("[, \t]", $range_line);
    if($start_b > $end_b) {
      $end_b = $start_b;
    }

    if ($end_a == $end_b) return 0;
    return ($end_a < $end_b) ? 1 : -1;
}

function get_style($select){
  for ($i=0; $i<count($select);$i++){
    $attr = $select[$i][0];
    if($attr == 'select'){
      return $select[$i][1];
    }
  }
  return 'full';
}

function draw_gene_style_dense($genes,$req,$colorD, $height){
  $num_genes = sizeof($genes);
  $basewidth = abs ($req['end'] - $req['start'] ) + 1;

  $h = floor($height / 2);
  $hgene = floor($height / 2); # 20

  $image = imagecreatetruecolor( $req['width'], $height );

  $white = imagecolorallocate( $image, 0xFF, 0xFF, 0xFF );
  $black = imagecolorallocate( $image, 0x00, 0x00, 0x00 );  

  imagefilledrectangle($image, 0, 0, $req['width']-1,$height-1, $white);

  for($num=0; $num < $num_genes; $num++){
    $line = $genes[$num];
    $range_line = substr(strchr ($line, 'range='), 6);
    list($range_start, $range_end, $remain) = split("[, \t]", $range_line);
    if($range_start > $range_end) {
      $tmp = $range_start;
      $range_start = $range_end;
      $range_end = $tmp;
    }

// 色の取得
    $colorRGB = $colorD;
   if(preg_match("/^(\w+)\-color$/",$req['usecolor'],$at)){
     $colorRGB = get_genecolor_by_color($colorD, $line, $at[1], $req['color']);
   }else if(preg_match("/^(\w+)\-gradation$/",$req['usecolor'],$at)){
     $colorRGB = get_genecolor_by_gradation($colorD, $line, $at[1], $req['gradation']);
   }

   $color = imagecolorallocate( $image, $colorRGB[0], $colorRGB[1], $colorRGB[2] );

    if($req['end'] >= $req['start']){
      $startpos = $req['width'] * ($range_start - $req['start'] ) / $basewidth;
      $endpos = $req['width'] * ($range_end - $req['start'] + 1) / $basewidth;
    } else {
      $startpos = $req['width'] * ($req['start'] - $range_end) / $basewidth;
      $endpos = $req['width'] * ($req['start'] - $range_start + 1) / $basewidth;
    }
    if($startpos < 0) $startpos = 0;
    if($endpos > $req['width']) $endpos = $req['width']-1;


    imageline($image, $startpos, $h, $endpos, $h, $color);

#    $strand = substr(strchr ($line, 'strand='), 7, 1);
#    if ( $strand == '+' xor $req['start'] >= $req['end']) {
#      for($i = $startpos; $i < $endpos-10; $i+=10){
# imageline($image, $i, $h-$hgene, $i+$hgene, $h, $color);
# imageline($image, $i, $h+$hgene, $i+$hgene, $h, $color);
#      }
#    }else if ( $strand == '-' xor $req['start'] >= $req['end']) {
#      for($i = $startpos; $i < $endpos -10; $i+=10){
# imageline($image, $i, $h, $i+$hgene, $h-$hgene, $color);
# imageline($image, $i, $h, $i+$hgene, $h+$hgene, $color);
#      }
#    }

    $exon_line = $line;
    for(;;){
      if(($exon = strchr ($exon_line, 'exon=')) == FALSE) break;
      $exon_line = substr($exon, 5);
      list($exon_start, $exon_end, $remain) = split("[, \t]", $exon_line);
      if($exon_start > $exon_end) {
        $tmp = $exon_start;
        $exon_start = $exon_end;
        $exon_end = $tmp;
      }


      if($req['end'] >= $req['start']){
        if ($exon_end < $req['start']) continue;
        if ($exon_start > $req['end']) continue;
        $startpos = $req['width'] * ($exon_start - $req['start'] ) / $basewidth;
        $endpos = $req['width'] * ($exon_end - $req['start'] + 1) / $basewidth;
      }else {
        if ($exon_end < $req['end']) continue;
        if ($exon_start > $req['start']) continue;
        $endpos = $req['width'] * ($req['start'] - $exon_start + 1) / $basewidth;
        $startpos = $req['width'] * ($req['start'] - $exon_end) / $basewidth;
      }

      if (($endpos < 0) || ($startpos >$req['width'] ))  continue;

      if($startpos < 0) $startpos = 0;
      if($endpos > $req['width']) $endpos = $req['width']-1;

      imagefilledrectangle($image, $startpos, $h-$hgene, $endpos, $h+$hgene, $color);

    }

  }

  header( 'Content-type: image/png' );
  imagepng( $image );

  imagedestroy( $image );

}

function draw_gene_style_full($genes, $req, $colorD, $h1, $hgene){

  $num_genes = sizeof($genes);
  $basewidth = abs ($req['end'] - $req['start'] ) + 1;

  $h2 = 0;

  $height = $num_genes * $h1 + $h2;
  if ($num_genes == 0) $height = 5;
  $image = imagecreatetruecolor( $req['width'], $height );
  $white = imagecolorallocate( $image, 0xFF, 0xFF, 0xFF );
  $black = imagecolorallocate( $image, 0x00, 0x00, 0x00 );  

// imagefill( $image, 0, 0, $white);
  imagefilledrectangle($image, 0, 0, $req['width']-1,$height-1, $white);

  draw_ruler($image, $req, $height);

  for($num=0; $num < $num_genes; $num++){
    $line = $genes[$num];
    $range_line = substr(strchr ($line, 'range='), 6);
    list($range_start, $range_end, $remain) = split("[, \t]", $range_line);
    if($range_start > $range_end) {
      $tmp = $range_start;
      $range_start = $range_end;
      $range_end = $tmp;
    }

// 色の取得
    $colorRGB = $colorD;
   if(preg_match("/^(\w+)\-color$/",$req['usecolor'],$at)){
     $colorRGB = get_genecolor_by_color($colorD, $line, $at[1], $req['color']);
   }else if(preg_match("/^(\w+)\-gradation$/",$req['usecolor'],$at)){
     $colorRGB = get_genecolor_by_gradation($colorD, $line, $at[1], $req['gradation']);
   }

   if (array_key_exists ('foundGene', $req) ){
     if(($name_pos = strpos($line, 'name=')) !== FALSE) {
       $name_line = substr($line, $name_pos + 5);
       list($name, $remain) = split("[ \t]", $name_line);
       if ($name == $req['foundGene']){
         $colorRGB = array(230,159,0);
       }
     }
   } 


   $color = imagecolorallocate( $image, $colorRGB[0], $colorRGB[1], $colorRGB[2] );

    $h = $h1 / 2 +  $h2 + $h1 * $num;
    if($req['end'] >= $req['start']){
      $startpos = $req['width'] * ($range_start - $req['start']) / $basewidth;
      $endpos = $req['width'] * ($range_end - $req['start'] + 1) / $basewidth;
    } else {
      $startpos = $req['width'] * ($req['start'] - $range_end) / $basewidth;
      $endpos = $req['width'] * ($req['start'] - $range_start + 1) / $basewidth;
    }
    if ($startpos < 0)  $startpos = 0;
    if ($endpos >$req['width'] )  $endpos = $req['width'];

    imageline($image, $startpos, $h, $endpos, $h, $color);

    $strand = substr(strchr ($line, 'strand='), 7, 1);
    if ( $strand == '+' xor $req['start'] >= $req['end']) {
      for($i = $startpos; $i < $endpos-10; $i+=10){
        imageline($image, $i, $h-$hgene, $i+$hgene, $h, $color);
        imageline($image, $i, $h+$hgene, $i+$hgene, $h, $color);
      }
    }else if ( $strand == '-' xor $req['start'] >= $req['end']) {
      for($i = $startpos; $i < $endpos -10; $i+=10){
        imageline($image, $i, $h, $i+$hgene, $h-$hgene, $color);
        imageline($image, $i, $h, $i+$hgene, $h+$hgene, $color);
      }
    }


    $exon_line = $line;
    for(;;){
      if(($exon = strchr ($exon_line, 'exon=')) == FALSE) break;
      $exon_line = substr($exon, 5);
      list($exon_start, $exon_end, $remain) = split("[, \t]", $exon_line);
      if($exon_start > $exon_end) {
        $tmp = $exon_start;
        $exon_start = $exon_end;
        $exon_end = $tmp;
      }
      if($req['end'] >= $req['start']){
        $startpos = $req['width'] * ($exon_start - $req['start']) / $basewidth;
        $endpos = $req['width'] * ($exon_end - $req['start'] + 1) / $basewidth;
      }else {
        $endpos = $req['width'] * ($req['start'] - $exon_start + 1) / $basewidth;
        $startpos = $req['width'] * ($req['start'] - $exon_end ) / $basewidth;
      }


      if (($endpos < 0) || ($startpos >$req['width'] ))  continue;

      if ($startpos < 0)  $startpos = 0;
      if ($endpos >$req['width'] )  $endpos = $req['width'];

      imagefilledrectangle($image, $startpos, $h-$hgene, $endpos, $h+$hgene, $color);
    }

  }

  // イメージの出力
  header( 'Content-type: image/png' );
  imagepng( $image );

  imagedestroy( $image );
}

function get_pack_height ($genes, $req, &$gene_height, $h1, $distance){
  $num_genes = sizeof($genes);
  $basewidth = abs ($req['end'] - $req['start'] + 1);
  if ($num_genes == 0) return 5;
  $base_end = array();
  for($num=0; $num < $num_genes; $num++){
    $line = $genes[$num];
    $range_line = substr(strchr ($line, 'range='), 6);
    list($range_start, $range_end, $remain) = split("[, \t]", $range_line);
    if($range_start > $range_end) {
      $tmp = $range_start;
      $range_start = $range_end;
      $range_end = $tmp;
    }

    if($req['end'] >= $req['start']){
      $startpos = $req['width'] * ($range_start - $req['start']) / $basewidth;
      $endpos = $req['width'] * ($range_end - $req['start']) / $basewidth;
    } else {
      $startpos = $req['width'] * ($req['start'] - $range_end) / $basewidth;
      $endpos = $req['width'] * ($req['start'] - $range_start) / $basewidth;
    }
   
    $height = sizeof ($base_end);
    $flag = 0;

    for($i=0; $i < $height; $i++){
      if($base_end[$i] <= ($startpos - $distance)){
        $base_end[$i] = $endpos;
        array_push ($gene_height, $i);
        $flag = 1; 
        break;
      }
    }
    if ($flag == 0){
      array_push ($base_end, $endpos);
      array_push ($gene_height, $height);
    }
  }

  return sizeof ($base_end) * $h1;
}

/**
* 各styleのgeneを描画する（ついでにXML(キャッシュ)ファイルも出力）
* @access     public
* @param     array      $genes    easyGeneTrackの内容
* @param     array      $req      GET/POST引数
* @param     array      $colorD   デフォルトカラー（エクソン）
* @param     int        $h1       一列の高さ
* @param     int        $hgene    エクソンの高さ
* @param     string     $style    描画スタイル（dense/full/pack/small）
* @param     string     $buffer   中間ファイルパス
* @param     string     $xml      XMLファイルパス
* @param     string     $cache_id キャッシュID
*/
function draw_gene_style($genes, $req, $colorD, $h1, $hgene, $style,$buffer,$xml,$cache_id){

	//easygenetrack文の解釈
	//gene数計数
	$num_genes = sizeof($genes);
	//縦の余白＝marginy
	$h2 = 0;
	//画像縦幅？
//	$height = $num_genes * $h1 + $h2;
	if ($num_genes == 0){
		$height = 5;
	}else{
		$height = 0;
	}
	
	//UTGDインスタンス作成
	$utgd = new UTGD4();
	//色指定
	$white = 'white';
	$black = 'black';
	
	//TTフォント設定
	$fontpath = '../../../lib/UTGD4/fonts/Abadi MT Condensed Light.ttf';
	$utgd->setFontFile($fontpath);
	//中間ファイル設定
    $utgd->openBufferFile($buffer);
	//カテゴリ宣言
	$utgd->insertCategory('GRAPH');

	//スケール描画
	if($style != 'dense'){
		$scale_col = '#A0A0A0';
		$utgd->drawScale('',$req['start'],$req['end'],0,100,1,500,$scale_col);
	}
		
	//test用文字追加
//	$utgd->drawStringTTF(1,'with LIB',4000,6,'black','RIGHT',0,0,NULL,NULL,NULL,FALSE);
  
	//easygenetrack読み込み
	$rownum = 0;
	foreach($genes as $line){
		//easygenetrackからデータ取得
		////EXONデータ取得
		$exon_array = array();
		$exon_line = $line;
		for(;;){
			// geneTrackデータからexon部分取得
			if(($exon = strchr ($exon_line, 'exon=')) == FALSE) break;
			$exon_line = substr($exon, 5);
			list($exon_start, $exon_end, $remain) = split("[, \t]", $exon_line);
			if($exon_start > $exon_end) {
				$tmp = $exon_start;
				$exon_start = $exon_end;
				$exon_end = $tmp;
			}
			// EXON開始、終了位置を格納
			array_push($exon_array,array($exon_start,$exon_end));
		}
		//// 色の取得
		$colorRGB = $colorD;	
		if(preg_match("/^(\w+)\-color$/",$req['usecolor'],$at)){
			$colorRGB = get_genecolor_by_color($colorD, $line, $at[1], $req['color']);
		}else if(preg_match("/^(\w+)\-gradation$/",$req['usecolor'],$at)){
			$colorRGB = get_genecolor_by_gradation($colorD, $line, $at[1], $req['gradation']);
		}
		//// gene name取得
		if(($name_pos = strpos($line, 'name=')) !== FALSE) {
			$name_line = substr($line, $name_pos + 5);
			list($name, $remain) = split("[ \t]", $name_line);
		}
		//// strand取得
	    $strand = substr(strchr ($line, 'strand='), 7, 1);
	    if($strand == '-'){
	    	$strand_s = -1;
	    }else{
	    	$strand_s = 1;
	    }
	    //// 操作XML用URL取得
	    if (preg_match("/url=\"(\S+)\"/",$line, $url)){
			$url[1] = preg_replace('/&/', "&amp;" , $url[1]);
			$operation = "mouse(link=$url[1])";
	    }else{
	    	$operation = "mouse(link=$url[1])";
	    }
		
		//styleによる描画オプションのヴァリエーション
		if($style == 'full'){
			$rownum++;//描画列加算
			$col_foundGene = array(230,159,0);//foundGeneの色指定
			$line_style = 4;//エクソン連結線スタイル（反復矢印）
			$name_draw = '';//遺伝子名描画文字列
			$gene_size = 2*$hgene; //エクソン縦幅
		}elseif($style == 'dense'){
			$utgd->insertCategory('FORCE');//描画列を強制的に決定
			$rownum = 1;//描画列は１に固定
			$col_foundGene = $colorD;//foundGeneの色指定
			$line_style = 1;//エクソン連結線スタイル（直線）
			$name_draw = '';//遺伝子名描画文字列
			$gene_size = $h1; //エクソン縦幅
		}elseif($style == 'small'){
			$rownum = 1;//描画列は自動計算
			$col_foundGene = array(230,159,0);//foundGeneの色指定
			$line_style = 1;//エクソン連結線スタイル（直線）
			$name_draw = '';//遺伝子名描画文字列
			$gene_size = 2*$hgene;  //エクソン縦幅
		}else{
			$rownum = 1;//描画列は自動計算
			$col_foundGene = array(230,159,0);//foundGeneの色指定
			$line_style = 4;//エクソン連結線スタイル（反復矢印）
			$name_draw = $name;//遺伝子名描画文字列
			$gene_size = 2*$hgene;  //エクソン縦幅
		}
    
		//直前処理
		////foundGeneチェック
		if (array_key_exists ('foundGene', $req) ){
				if ($name == $req['foundGene']){
					$colorRGB = $col_foundGene;
				}
		}
		////色再変換（二度手間）
		$colorDS = getColorString($colorD);
		$colorRGBS = getColorString($colorRGB);

		//gene描画
	    $utgd->drawGene($exon_array,$rownum,$gene_size,'',$colorRGBS,$name_draw,8,'LEFT',$colorRGBS,$line_style,$colorRGBS,1,'',$strand_s,1,$operation,'');

	}

    //中間ファイルクローズ
    $utgd->closeBufferFile();   
    
	//サイズの設定
	$utgd->setImageSize($req['width'],$height,1,$h1,$req['start'],$req['end'],0,$h2);
	//その他オプション設定
	$utgd->setImageOptions($white,$white,10);

	//中間ファイルのパース
	$utgd->parseBufferFile($buffer,'TILING');

	//画像枠の作成
	$utgd->createImage();
	//XMLファイルオープン
	$utgd->openXMLFile($xml);
	
	//図形の描画
	$utgd->drawImage();    
    //画像出力
	$utgd->outputImage();
	//XML出力
//	$utgd->outputXMLFile();
    //XMLキャッシュ出力
	$utgd->cacheXMLData($cache_id);

}

function draw_gene_style_pack($genes, $req, $colorD, $h1, $hgene){
  global $utgb_font_Abadi_file;

  $num_genes = sizeof($genes);

  if ($req['start'] > $req['end']){
    usort ($genes, "cmp_genes_rev");
  } 
  $basewidth = abs ($req['end'] - $req['start']) + 1;

  $size = 8;
  $fontfile = $utgb_font_Abadi_file;


#  $h1 = 10;
#  $hgene = 3; # 20
#  $h2 = 5;
#  $h2 = 1;
  $h2 = 0;

  $gene_height = array();
  $height = get_pack_height ($genes, $req, $gene_height, $h1, 100);

  $image = imagecreatetruecolor( $req['width'], $height );
  $white = imagecolorallocate( $image, 0xFF, 0xFF, 0xFF );
  $black = imagecolorallocate( $image, 0x00, 0x00, 0x00 );  

// imagefill( $image, 0, 0, $white);
  imagefilledrectangle($image, 0, 0, $req['width']-1,$height-1, $white);
  // イメージの作成

#  for($i=50; $i < $req['width']; $i = $i +50){
#    imageline($image, $i, 0, $i, $height, $black);
#  }

  draw_ruler($image, $req, $height);

  for($num=0; $num < $num_genes; $num++){
    $line = $genes[$num];
    $range_line = substr(strchr ($line, 'range='), 6);
    list($range_start, $range_end, $remain) = split("[, \t]", $range_line);
    if($range_start > $range_end) {
      $tmp = $range_start;
      $range_start = $range_end;
      $range_end = $tmp;
    }

// 色の取得
    $colorRGB = $colorD;
   if(preg_match("/^(\w+)\-color$/",$req['usecolor'],$at)){
     $colorRGB = get_genecolor_by_color($colorD, $line, $at[1], $req['color']);
   }else if(preg_match("/^(\w+)\-gradation$/",$req['usecolor'],$at)){
     $colorRGB = get_genecolor_by_gradation($colorD, $line, $at[1], $req['gradation']);
   }


   if (array_key_exists ('foundGene', $req) ){
     if(($name_pos = strpos($line, 'name=')) !== FALSE) {
       $name_line = substr($line, $name_pos + 5);
       list($name, $remain) = split("[ \t]", $name_line);
       if ($name == $req['foundGene']){
         $colorRGB = array(230,159,0);
       }  
     }
   } 

   $color = imagecolorallocate( $image, $colorRGB[0], $colorRGB[1], $colorRGB[2] );

    $h = $h1 / 2 +  $h2 + $h1 * $gene_height[$num];
    if($req['end'] >= $req['start']){
      $startpos = $req['width'] * ($range_start - $req['start']) / $basewidth;
      $endpos = $req['width'] * ($range_end - $req['start'] + 1) / $basewidth;
    } else {
      $startpos = $req['width'] * ($req['start'] - $range_end) / $basewidth;
      $endpos = $req['width'] * ($req['start'] - $range_start + 1) / $basewidth;
    }
    if($startpos < 0) $startpos = 0;
    if($endpos > $req['width']) $endpos = $req['width']-1;

    imageline($image, $startpos, $h, $endpos, $h, $color);

    $strand = substr(strchr ($line, 'strand='), 7, 1);
    if ( $strand == '+' xor $req['start'] >= $req['end']) {
      for($i = $startpos; $i < $endpos-10; $i+=10){
        imageline($image, $i, $h-$hgene, $i+$hgene, $h, $color);
        imageline($image, $i, $h+$hgene, $i+$hgene, $h, $color);
      }
    }else if ( $strand == '-' xor $req['start'] >= $req['end']) {
      for($i = $startpos; $i < $endpos -10; $i+=10){
        imageline($image, $i, $h, $i+$hgene, $h-$hgene, $color);
        imageline($image, $i, $h, $i+$hgene, $h+$hgene, $color);
      }
    }

    if($startpos > 100){
      if(($name_pos = strpos($line, 'name=')) !== FALSE) {
        $name_line = substr($line, $name_pos + 5);
        list($name, $remain) = split("[ \t]", $name_line);
      
        $strbox = imagettfbbox( $size, 0, $fontfile, $name );      
        imagettftext( $image, $size, 0, $startpos-$strbox[2]+$strbox[0]- 10, $h + (- $h2 + $strbox[3]-$strbox[5])/2, $color, $fontfile, $name);
      }
    }

    $exon_line = $line;
    for(;;){
      if(($exon = strchr ($exon_line, 'exon=')) == FALSE) break;
      $exon_line = substr($exon, 5);
      list($exon_start, $exon_end, $remain) = split("[, \t]", $exon_line);
      if($exon_start > $exon_end) {
        $tmp = $exon_start;
        $exon_start = $exon_end;
        $exon_end = $tmp;
      }
      if($req['end'] >= $req['start']){
        $startpos = $req['width'] * ($exon_start - $req['start']) / $basewidth;
        $endpos = $req['width'] * ($exon_end - $req['start'] + 1) / $basewidth;
      }else {
        $endpos = $req['width'] * ($req['start'] - $exon_start + 1) / $basewidth;
        $startpos = $req['width'] * ($req['start'] - $exon_end) / $basewidth;
      }
      if (($endpos < 0) || ($startpos >$req['width'] ))  continue;

      if($startpos < 0) $startpos = 0;
      if($endpos > $req['width']) $endpos = $req['width']-1;

      imagefilledrectangle($image, $startpos, $h-$hgene, $endpos, $h+$hgene, $color);
    }

  }

  // イメージの出力
  header( 'Content-type: image/png' );
  imagepng( $image );

  imagedestroy( $image );
}

function draw_gene_style_small($genes, $req, $colorD, $h1, $hgene){
  global $utgb_font_Abadi_file;

  $num_genes = sizeof($genes);

  if ($req['start'] > $req['end']){
    usort ($genes, "cmp_genes_rev");
  } 
  $basewidth = abs ($req['end'] - $req['start']) + 1;

  $size = 8;
  $fontfile = $utgb_font_Abadi_file;


#  $h1 = 10;
#  $hgene = 3; # 20
#  $h2 = 5;
#  $h2 = 1;
  $h2 = 0;

  $gene_height = array();
  $height = get_pack_height ($genes, $req, $gene_height, $h1,10);

  $image = imagecreatetruecolor( $req['width'], $height );
  $white = imagecolorallocate( $image, 0xFF, 0xFF, 0xFF );
  $black = imagecolorallocate( $image, 0x00, 0x00, 0x00 );  

// imagefill( $image, 0, 0, $white);
  imagefilledrectangle($image, 0, 0, $req['width']-1,$height-1, $white);
  // イメージの作成

#  for($i=50; $i < $req['width']; $i = $i +50){
#    imageline($image, $i, 0, $i, $height, $black);
#  }

  draw_ruler($image, $req, $height);

  for($num=0; $num < $num_genes; $num++){
    $line = $genes[$num];
    $range_line = substr(strchr ($line, 'range='), 6);
    list($range_start, $range_end, $remain) = split("[, \t]", $range_line);
    if($range_start > $range_end) {
      $tmp = $range_start;
      $range_start = $range_end;
      $range_end = $tmp;
    }

// 色の取得
    $colorRGB = $colorD;

   if(array_key_exists('usecolor', $req)) {
     if(preg_match("/^(\w+)\-color$/",$req['usecolor'],$at)){
       $colorRGB = get_genecolor_by_color($colorD, $line, $at[1], $req['color']);
     }else if(preg_match("/^(\w+)\-gradation$/",$req['usecolor'],$at)){
       $colorRGB = get_genecolor_by_gradation($colorD, $line, $at[1], $req['gradation']);
     }
   }

   if (array_key_exists ('foundGene', $req) ){
     if(($name_pos = strpos($line, 'name=')) !== FALSE) {
       $name_line = substr($line, $name_pos + 5);
       list($name, $remain) = split("[ \t]", $name_line);
       if ($name == $req['foundGene']){
         $colorRGB = array(230,159,0);
       }
     }
   } 

   $color = imagecolorallocate( $image, $colorRGB[0], $colorRGB[1], $colorRGB[2] );

    $h = $h1 / 2 +  $h2 + $h1 * $gene_height[$num];
    if($req['end'] >= $req['start']){
      $startpos = $req['width'] * ($range_start - $req['start']) / $basewidth;
      $endpos = $req['width'] * ($range_end - $req['start'] + 1) / $basewidth;
    } else {
      $startpos = $req['width'] * ($req['start'] - $range_end) / $basewidth;
      $endpos = $req['width'] * ($req['start'] - $range_start + 1) / $basewidth;
    }
    if($startpos < 0) $startpos = 0;
    if($endpos > $req['width']) $endpos = $req['width']-1;

    imageline($image, $startpos, $h, $endpos, $h, $color);

    $exon_line = $line;
    for(;;){
      if(($exon = strchr ($exon_line, 'exon=')) == FALSE) break;
      $exon_line = substr($exon, 5);
      list($exon_start, $exon_end, $remain) = split("[, \t]", $exon_line);
      if($exon_start > $exon_end) {
        $tmp = $exon_start;
        $exon_start = $exon_end;
        $exon_end = $tmp;
      }
      if($req['end'] >= $req['start']){
        $startpos = $req['width'] * ($exon_start - $req['start']) / $basewidth;
        $endpos = $req['width'] * ($exon_end - $req['start'] + 1) / $basewidth;
      }else {
        $endpos = $req['width'] * ($req['start'] - $exon_start + 1) / $basewidth;
        $startpos = $req['width'] * ($req['start'] - $exon_end) / $basewidth;
      }
      if (($endpos < 0) || ($startpos >$req['width'] ))  continue;

      if($startpos < 0) $startpos = 0;
      if($endpos > $req['width']) $endpos = $req['width']-1;

      imagefilledrectangle($image, $startpos, $h-$hgene, $endpos, $h+$hgene, $color);
    }

  }

  // イメージの出力
  header( 'Content-type: image/png' );
  imagepng( $image );

  imagedestroy( $image );
}

/**
* geneTrackを描画する。
* @access     public
* @param     string      $file              geneファイルファイルポインタ
* @param     string      $first_line        geneファイル一行目
* @param     string      $buffer_tmp_dir    中間ファイル出力ディレクトリ
* @param     string      $xml_tmp_dir       XMLファイル出力ディレクトリ
*/
function draw_gene2($file,$first_line,$buffer_tmp_dir,$xml_tmp_dir){
  // 一行目の行頭9文字を削除（geneTrack）
  $first_line = trim (substr($first_line, 9));
  // 描画デフォルト色
  $colorD = get_defaultcolor($first_line);
  // Option Attribute
  $opattrs = get_optional_attribute($first_line);
  // $_REQUEST取得
  $req = get_request($_REQUEST, $opattrs, $colorD);
  // geneデータを配列に格納
  $genes = get_display_genes($file,$req);

  // styleの取得
  $style = $req['style'];
  
  // 中間ファイル、XMLファイル設定
  $buffer= $buffer_tmp_dir."/".$_REQUEST['sid']."_".$style.".txt";
  $xml= $xml_tmp_dir."/".$_REQUEST['sid']."_".$style.".xml";
  $cache_id = $_REQUEST['sid']."_".$style;
  
  // style毎の遺伝子描画
  if ($style == 'full'){
  	draw_gene_style($genes,$req,$colorD,9,3,$style,$buffer,$xml,$cache_id);
  }else if ($style == 'dense'){
  	draw_gene_style($genes,$req,$colorD,9,3,$style,$buffer,$xml,$cache_id);
  }else if ($style == 'pack'){
    draw_gene_style($genes,$req,$colorD,9,3,$style,$buffer,$xml,$cache_id);
  }else if ($style == 'small'){
  	draw_gene_style($genes,$req,$colorD,4,1,$style,$buffer,$xml,$cache_id);
  }
}

function draw_gene($file,$first_line){
  $first_line = trim (substr($first_line, 9));

  $colorD = get_defaultcolor($first_line);

  $opattrs = get_optional_attribute($first_line);

  $req = get_request($_REQUEST, $opattrs, $colorD);

  $genes = get_display_genes($file,$req);

  // styleの取得
  $style = $req['style'];
  
  // style毎の遺伝子描画
  if ($style == 'full'){
    draw_gene_style_full($genes,$req,$colorD,9,3);
  }else if ($style == 'dense'){
    draw_gene_style_dense($genes,$req,$colorD,9);
  }else if ($style == 'pack'){
    draw_gene_style_pack($genes,$req,$colorD, 9,3);
  }else if ($style == 'small'){
    draw_gene_style_small($genes,$req,$colorD, 4,1);
  }
}


function draw_gene_index_style($genes, $req, $colorD, $h1, $hgene, $style,$buffer,$buffer_track){
  global $utgb_font_Abadi_file;
  
	//easygenetrack文の解釈
	//gene数計数
	$num_genes = sizeof($genes);
	//縦の余白＝marginy
	$h2 = 0;
	//画像縦幅？
//	$height = $num_genes * $h1 + $h2;
	if ($num_genes == 0){
		$height = 5;
	}else{
		$height = 0;
	}
	
	//インデックス画像設定	
	$size = 8;
	$width = 100;

	//UTGDインスタンス作成
	$utgd = new UTGD4();
	//色指定
	$white = 'white';
	$black = 'black';
	
	//TTフォント設定
	$fontpath = '../../../lib/UTGD4/fonts/Abadi MT Condensed Light.ttf';
	$utgd->setFontFile($fontpath);
	//中間ファイル設定
	$buffer = $buffer;
    $utgd->openBufferFile($buffer);

	//カテゴリ宣言
	$utgd->insertCategory('INDEX');
	//easygenetrack読み込み
	$rownum = 0;
	foreach($genes as $line){
		//easygenetrackからデータ取得

		//// 色の取得
		$colorRGB = $colorD;	
		if(preg_match("/^(\w+)\-color$/",$req['usecolor'],$at)){
			$colorRGB = get_genecolor_by_color($colorD, $line, $at[1], $req['color']);
		}else if(preg_match("/^(\w+)\-gradation$/",$req['usecolor'],$at)){
			$colorRGB = get_genecolor_by_gradation($colorD, $line, $at[1], $req['gradation']);
		}
		//// gene name取得
		if(($name_pos = strpos($line, 'name=')) !== FALSE) {
			$name_line = substr($line, $name_pos + 5);
			list($name, $remain) = split("[ \t]", $name_line);
		}
		
		//styleによる描画オプションのヴァリエーション
		if($style == 'full'){
//			$rownum++;//描画列加算
			$col_foundGene = array(230,159,0);//foundGeneの色指定
		}elseif($style == 'dense'){
//			$utgd->insertCategory('FORCE');//描画列を強制的に決定
//			$rownum = 1;//描画列は１に固定
			$col_foundGene = $colorD;//foundGeneの色指定
//			$name_draw = '';//遺伝子名描画文字列
		}elseif($style == 'small'){
//			$rownum = 1;//描画列は自動計算
			$col_foundGene = array(230,159,0);//foundGeneの色指定
//			$name_draw = '';//遺伝子名描画文字列
			$size = 4;
		}else{
//			$rownum = 1;//描画列は自動計算
			$col_foundGene = array(230,159,0);//foundGeneの色指定
//			$line_style = 4;//エクソン連結線スタイル（反復矢印）
//			$name_draw = $name;//遺伝子名描画文字列
//			$gene_size = 2*$hgene;  //エクソン縦幅
		}
    
		//直前処理
		////foundGeneチェック
		if (array_key_exists ('foundGene', $req) ){
				if ($name == $req['foundGene']){
					$colorRGB = $col_foundGene;
				}
		}
		////色再変換（二度手間）
		$colorDS = getColorString($colorD);
		$colorRGBS = getColorString($colorRGB);

		//Index描画
		$utgd->drawIndex($name,1,$colorRGBS,$size,NULL,'CENTER','CENTER',0,0);

	}

    //中間ファイルクローズ
    $utgd->closeBufferFile();   
    
    //トラック画像サイズ取得
	//トラック画像サイズの設定
	$utgd->setImageSize($req['width'],$height,1,$h1,$req['start'],$req['end'],0,$h2);
	//その他オプション設定
	$utgd->setImageOptions($white,$white,10);
//	$utgd->setDebugOptions(TRUE,10);
	$utgd->openLogFile('./log.txt');
	//グラフ画像中間ファイルのパースシミュレート
	if(checkBufferFile($buffer_track)){
		list($rownum,$height) =  $utgd->parseBufferFile($buffer_track,'TILING',TRUE);
//		$utgd->addDebugMessage("$rownum,$height");
	}else{
		return FALSE;
	}
//print $rownum;
	//インデックス画像描画
	//インデックス画像サイズの設定
	$utgd->setImageSize($width,$height,$rownum,$h1,$req['start'],$req['end'],0,$h2);
	//その他オプション設定
	$utgd->setImageOptions($white,$white,0);
	//INDEX中間ファイルのパース
	$utgd->parseBufferFileIndex($buffer,'WITHIN',1,$rownum);
	
	//画像枠の作成
	$utgd->createImage();
	//図形の描画
	$utgd->drawImage();    
    //画像出力
	$utgd->outputImage();

}

/**
 * 中間ファイルがオープンできるかチェックする
 * @access     public
 * @param     string   $buffer    中間ファイルパス
 * @param     int      $limit     ファイル読み込み待ち最大時間（秒）
 * @param     int      $wait      再読み込み間隔（秒）
 * @return    boolean  TRUE/FALSE
 */
function checkBufferFile($buffer,$limit=120,$wait=10){
	if($limit<=0){
		$limit = 120;
	}
	if($wait<=0){
		$wait = 10;
	}
	for($i=0;$i<$limit;$i+=$wait){
		if($fp = fopen($buffer,'r')){
			//中間ファイルがオープンできた場合
			fclose($fp);
			return TRUE;
		}else{
			continue;
		}
	}
	
	//幾ら待っても中間ファイルが開かない
	return FALSE;
}

function draw_gene_index_style_full($genes,$req,$colorD, $h1, $hgene){
  global $utgb_font_Abadi_file;
  
  $num_genes = sizeof($genes);

  // イメージの生成
#  $h1 = 10;
#  $hgene = 5; # 20
  $h2 = 0;

  $size = 8;
  $fontfile = $utgb_font_Abadi_file;

  $height = $num_genes * $h1 + $h2;
  if ($num_genes == 0) $height = 5;
  $width = 100;
  $image = imagecreatetruecolor( $width, $height );
  $white = imagecolorallocate( $image, 0xFF, 0xFF, 0xFF );
  $black = imagecolorallocate( $image, 0x00, 0x00, 0x00 );  

// imagefill( $image, 0, 0, $white);
  imagefilledrectangle($image, 0, 0, $width-1,$height-1, $white);
  // イメージの作成

  for($num=0; $num < $num_genes; $num++){
    $line = $genes[$num];
// 色の取得
    $colorRGB = $colorD;
    if(preg_match("/^(\w+)\-color$/",$req['usecolor'],$at)){
      $colorRGB = get_genecolor_by_color($colorD, $line, $at[1], $req['color']);
    }else if(preg_match("/^(\w+)\-gradation$/",$req['usecolor'],$at)){
      $colorRGB = get_genecolor_by_gradation($colorD, $line, $at[1], $req['gradation']);
    }


    if (array_key_exists ('foundGene', $req) ){
      if(($name_pos = strpos($line, 'name=')) !== FALSE) {
        $name_line = substr($line, $name_pos + 5);
        list($name, $remain) = split("[ \t]", $name_line);
        if ($name == $req['foundGene']){
          $colorRGB = array(230,159,0);
        }
      }
    } 

    $color = imagecolorallocate( $image, $colorRGB[0], $colorRGB[1], $colorRGB[2] );

    $h = $h1 * $num;

    if(($name_pos = strpos($line, 'name=')) !== FALSE) {
      $name_line = substr($line, $name_pos + 5);
      list($name, $remain) = split("[ \t]", $name_line);

      $strbox = imagettfbbox( $size, 0, $fontfile, $name );      
      imagettftext( $image, $size, 0, ($width-$strbox[2]+$strbox[0])/2, $h + ($h1 + $h2 + $strbox[3]-$strbox[5])/2, $color, $fontfile, $name);
    }
  }

  // イメージの出力
  
( 'Content-type: image/png' );
  imagepng( $image );

  imagedestroy( $image );
}


function draw_gene_index_style_dense($genes,$req,$colorD,$height){
  $num_genes = sizeof($genes);

  $width = 100;
  $image = imagecreatetruecolor( $width, $height );
  $white = imagecolorallocate( $image, 0xFF, 0xFF, 0xFF );
  $black = imagecolorallocate( $image, 0x00, 0x00, 0x00 );  

  imagefilledrectangle($image, 0, 0, $width-1,$height-1, $white);

  // イメージの出力
  header( 'Content-type: image/png' );
  imagepng( $image );

  imagedestroy( $image );
}

function  draw_gene_index_style_pack($genes,$req,$colorD, $h1,$hgene){
  global $utgb_font_Abadi_file;
  
  $num_genes = sizeof($genes);
  if ($req['start'] > $req['end']){
    usort ($genes, "cmp_genes_rev");
  } 
  $basewidth = abs ($req['end'] - $req['start'] + 1);
  // イメージの生成
  $h2 = 0;

  $size = 8;
  $fontfile = $utgb_font_Abadi_file;


  $gene_height = array();
  $height = get_pack_height ($genes, $req, $gene_height, $h1, 100);

  $width = 100;
  $image = imagecreatetruecolor( $width, $height );
  $white = imagecolorallocate( $image, 0xFF, 0xFF, 0xFF );
  $black = imagecolorallocate( $image, 0x00, 0x00, 0x00 );  

// imagefill( $image, 0, 0, $white);
  imagefilledrectangle($image, 0, 0, $width-1,$height-1, $white);
  // イメージの作成

  for($num=0; $num < $num_genes; $num++){
    $line = $genes[$num];
    $range_line = substr(strchr ($line, 'range='), 6);
    list($range_start, $range_end, $remain) = split("[, \t]", $range_line);
    if($range_start > $range_end) {
      $tmp = $range_start;
      $range_start = $range_end;
      $range_end = $tmp;
    }

// 色の取得
    $colorRGB = $colorD;
   if(preg_match("/^(\w+)\-color$/",$req['usecolor'],$at)){
     $colorRGB = get_genecolor_by_color($colorD, $line, $at[1], $req['color']);
   }else if(preg_match("/^(\w+)\-gradation$/",$req['usecolor'],$at)){
     $colorRGB = get_genecolor_by_gradation($colorD, $line, $at[1], $req['gradation']);
   }


   if (array_key_exists ('foundGene', $req) ){
     if(($name_pos = strpos($line, 'name=')) !== FALSE) {
       $name_line = substr($line, $name_pos + 5);
       list($name, $remain) = split("[ \t]", $name_line);
       if ($name == $req['foundGene']){
         $colorRGB = array(230,159,0);
       }
     }
   } 

   $color = imagecolorallocate( $image, $colorRGB[0], $colorRGB[1], $colorRGB[2] );

    $h = $h1 * $gene_height[$num];
    if($req['end'] >= $req['start']){
      $startpos = $req['width'] * ($range_start - $req['start']) / $basewidth;
      $endpos = $req['width'] * ($range_end - $req['start']) / $basewidth;
    } else {
      $startpos = $req['width'] * ($req['start'] - $range_end) / $basewidth;
      $endpos = $req['width'] * ($req['start'] - $range_start) / $basewidth;
    }

    if($startpos <= 100){

    if(($name_pos = strpos($line, 'name=')) !== FALSE) {
      $name_line = substr($line, $name_pos + 5);
      list($name, $remain) = split("[ \t]", $name_line);
      #imagestring($image, 1, 10, $h-20, $name, $black);
      // Replace path by your own font path

      $strbox = imagettfbbox( $size, 0, $fontfile, $name );      
      imagettftext( $image, $size, 0, ($width-$strbox[2]+$strbox[0])/2, $h + ($h1 + $h2 + $strbox[3]-$strbox[5])/2, $color, $fontfile, $name);
    }
    }
  }

  // イメージの出力
  header( 'Content-type: image/png' );
  imagepng( $image );

  imagedestroy( $image );
}

function  draw_gene_index_style_small($genes,$req,$colorD,$h1,$hgene){
  global $utgb_font_Abadi_file;

  $num_genes = sizeof($genes);
  if ($req['start'] > $req['end']){
    usort ($genes, "cmp_genes_rev");
  } 
  $basewidth = abs ($req['end'] - $req['start'] + 1);
  // イメージの生成
  $h2 = 0;

  $size = 8;
  $fontfile = $utgb_font_Abadi_file;


  $gene_height = array();
  $height = get_pack_height ($genes, $req, $gene_height, $h1, 10);
  $width = 100;
  $image = imagecreatetruecolor( $width, $height );
  $white = imagecolorallocate( $image, 0xFF, 0xFF, 0xFF );
  $black = imagecolorallocate( $image, 0x00, 0x00, 0x00 );  

// imagefill( $image, 0, 0, $white);
  imagefilledrectangle($image, 0, 0, $width-1,$height-1, $white);
  // イメージの出力
  header( 'Content-type: image/png' );
  imagepng( $image );

  imagedestroy( $image );

}

/**
* eastyGeneTrackのindex画像を描画する
* @access     public
* @param     string      $file              geneファイルファイルポインタ
* @param     string      $first_line        geneファイル一行目
* @param     string      $buffer_tmp_dir    中間ファイル出力ディレクトリ
*/
function draw_gene_index2($file, $first_line,$buffer_tmp_dir){
  // 一行目の行頭9文字を削除（geneTrack）
  $first_line = trim (substr($first_line, 9));

  // 描画デフォルト色
  $colorD = get_defaultcolor($first_line);

  // Option Attribute
  $opattrs = get_optional_attribute($first_line);

  // $_REQUEST取得
  $req = get_request($_REQUEST, $opattrs, $colorD);

  // geneデータを配列に格納
  $genes = get_display_genes($file,$req);

  // styleの取得
  $style = $req['style'];
  
  // インデックス中間ファイル、トラック画像中間ファイル設定
  $buffer = $buffer_tmp_dir."/".$_REQUEST['sid']."_".$style."_index.txt";
  $buffer_track = $buffer_tmp_dir."/".$_REQUEST['sid']."_".$style.".txt";

  // style の検索
  $style = $req['style'];
  if ($style == 'full'){
    draw_gene_index_style($genes,$req,$colorD,9,3,$style,$buffer,$buffer_track);
  }else if ($style == 'dense'){
    draw_gene_index_style($genes,$req,$colorD,9,3,$style,$buffer,$buffer_track);
  }else if ($style == 'pack'){
    draw_gene_index_style($genes,$req,$colorD,9,3,$style,$buffer,$buffer_track);
  }else if ($style == 'small'){
    draw_gene_index_style($genes,$req,$colorD,4,1,$style,$buffer,$buffer_track);
  }
}

function draw_gene_index($file, $first_line){
  $first_line = trim (substr($first_line, 9));

  $colorD = get_defaultcolor($first_line);

  $opattrs = get_optional_attribute($first_line);

  $req = get_request($_REQUEST, $opattrs, $colorD);

  $genes = get_display_genes($file,$req);

  // style の検索
  $style = $req['style'];
  if ($style == 'full'){
    draw_gene_index_style_full($genes,$req,$colorD,9,3);
  }else if ($style == 'dense'){
    draw_gene_index_style_dense($genes,$req,$colorD,9);
  }else if ($style == 'pack'){
    draw_gene_index_style_pack($genes,$req,$colorD,9,3);
  }else if ($style == 'small'){
    draw_gene_index_style_small($genes,$req,$colorD,4,1);
  }
}

function def_gene_operation_style_full($genes,$req,$h1,$hgene){
  $num_genes = sizeof($genes);
  $basewidth = abs ($req['end'] - $req['start']) + 1;

// 共通パラメータ
  $h2 = 0;

  $height = $num_genes * $h1 + $h2;
  if ($num_genes == 0) $height = 5;

// xml出力
  header('Content-Type: text/xml');

  print"<?xml version=\"1.0\" ?>\n";
  print "<operation_layer>\n";
  for($num=0; $num < $num_genes; $num++){
    $line = $genes[$num];
    $range_line = substr(strchr ($line, 'range='), 6);
    list($range_start, $range_end, $remain) = split("[, \t]", $range_line);
    if($range_start > $range_end) {
      $tmp = $range_start;
      $range_start = $range_end;
      $range_end = $tmp;
    }

    if($req['end'] >= $req['start']){
      $startpos = $req['width'] * ($range_start - $req['start']) / $basewidth;
      $endpos = $req['width'] * ($range_end - $req['start'] + 1) / $basewidth;
    } else {
      $startpos = $req['width'] * ($req['start'] - $range_end) / $basewidth;
      $endpos = $req['width'] * ($req['start'] - $range_start + 1) / $basewidth;
    }

    $h = $h1 / 2 +  $h2 + $h1 * $num;

    $y1 = $h-$hgene;
    $y2 = $h+$hgene+1;
    if ($startpos < 0) {
      $x1 = 0;
    }else {
      $x1 = floor ($startpos); // 0;
    }
    if ($endpos >= $req['width']) {
      $x2 = $req['width']-1;
    }else {
      $x2 = ceil($endpos) ; // $req['width']-1;
    }
    // URLの取得
    if (preg_match("/url=\"(\S+)\"/",$line, $url)){
    $url[1] = preg_replace('/&/', "&amp;" , $url[1]);
    print "  <rect_area rect=\"($x1,$y1,$x2,$y2)\">\n" ;
    print "    <mouseclick_event>\n";

    print "      <link_operation url=\"$url[1]\" />\n";

    print "    </mouseclick_event>\n" ;
    print "  </rect_area>\n" ;
    }else if (preg_match("/url=(\S+)/",$line, $url)){
    $url[1] = preg_replace('/&/', "&amp;" , $url[1]);
    print "  <rect_area rect=\"($x1,$y1,$x2,$y2)\">\n" ;
    print "    <mouseclick_event>\n";

    print "      <link_operation url=\"$url[1]\" />\n";

    print "    </mouseclick_event>\n" ;
    print "  </rect_area>\n" ;
    }

  }
  print "</operation_layer>";
}

function def_gene_operation_style_dense($genes,$req,$h1){
// xml出力
  header('Content-Type: text/xml');

  print "<?xml version=\"1.0\" ?>\n";
  print "<operation_layer>\n";
  
  print "</operation_layer>";
}

function def_gene_operation_style_pack($genes, $req,$h1,$hgene){
  global $utgb_font_Abadi_file;

  $num_genes = sizeof($genes);
  if ($req['start'] > $req['end']){
    usort ($genes, "cmp_genes_rev");
  } 

  $basewidth = abs ($req['end'] - $req['start'] + 1);

  $size = 8;
  $fontfile = $utgb_font_Abadi_file;

#  $h2 = 5;
  $h2 = 0;

  $gene_height = array();
  $height = get_pack_height ($genes, $req, $gene_height, $h1, 100);

// xml出力
//  header('Content-Type: text/xml');

  print "<?xml version=\"1.0\" ?>\n";
  print "<operation_layer>\n";
  for($num=0; $num < $num_genes; $num++){
    $line = $genes[$num];
    $range_line = substr(strchr ($line, 'range='), 6);
    list($range_start, $range_end, $remain) = split("[, \t]", $range_line);
    if($range_start > $range_end) {
      $tmp = $range_start;
      $range_start = $range_end;
      $range_end = $tmp;
    }

    $h = $h1 / 2 +  $h2 + $h1 * $gene_height[$num];
    if($req['end'] >= $req['start']){
      $startpos = $req['width'] * ($range_start - $req['start']) / $basewidth;
      $endpos = $req['width'] * ($range_end - $req['start'] + 1) / $basewidth;
    } else {
      $startpos = $req['width'] * ($req['start'] - $range_end) / $basewidth;
      $endpos = $req['width'] * ($req['start'] - $range_start + 1) / $basewidth;
    }

    if($startpos > 100){
      if(($name_pos = strpos($line, 'name=')) !== FALSE) {
        $name_line = substr($line, $name_pos + 5);
        list($name, $remain) = split("[ \t]", $name_line);
        $strbox = imagettfbbox( $size, 0, $fontfile, $name );
        $startpos = $startpos - $strbox[2] + $strbox[0] - 10;
      }
    }

    $y1 = $h-$hgene;
    $y2 = $h+$hgene+1;
    if ($startpos < 0) {
      $x1 = 0;
    }else {
      $x1 = floor ($startpos); // 0;
    }
    if ($endpos >= $req['width']) {
      $x2 = $req['width']-1;
    }else {
      $x2 = ceil($endpos) ; // $req['width']-1;
    }
    // URLの取得
    if (preg_match("/url=\"(\S+)\"/",$line, $url)){
    $url[1] = preg_replace('/&/', "&amp;" , $url[1]);
    print "  <rect_area rect=\"($x1,$y1,$x2,$y2)\">\n" ;
    print "    <mouseclick_event>\n";

    print "      <link_operation url=\"$url[1]\" />\n";

    print "    </mouseclick_event>\n" ;
    print "  </rect_area>\n" ;
    }else if (preg_match("/url=(\S+)/",$line, $url)){
    $url[1] = preg_replace('/&/', "&amp;" , $url[1]);
    print "  <rect_area rect=\"($x1,$y1,$x2,$y2)\">\n" ;
    print "    <mouseclick_event>\n";

    print "      <link_operation url=\"$url[1]\" />\n";

    print "    </mouseclick_event>\n" ;
    print "  </rect_area>\n" ;
    }
  }
  print "</operation_layer>";

}

function def_gene_operation_style_small($genes, $req,$h1,$hgene){
  global $utgb_font_Abadi_file;
  $num_genes = sizeof($genes);
  if ($req['start'] > $req['end']){
    usort ($genes, "cmp_genes_rev");
  } 

  $basewidth = abs ($req['end'] - $req['start'] + 1);

  $size = 8;
  $fontfile = $utgb_font_Abadi_file;


#  $h2 = 5;
  $h2 = 0;

  $gene_height = array();
  $height = get_pack_height ($genes, $req, $gene_height, $h1, 10);

// xml出力
//  header('Content-Type: text/xml');

  print "<?xml version=\"1.0\" ?>\n";
  print "<operation_layer>\n";
  for($num=0; $num < $num_genes; $num++){
    $line = $genes[$num];
    $range_line = substr(strchr ($line, 'range='), 6);
    list($range_start, $range_end, $remain) = split("[, \t]", $range_line);
    if($range_start > $range_end) {
      $tmp = $range_start;
      $range_start = $range_end;
      $range_end = $tmp;
    }

    $h = $h1 / 2 +  $h2 + $h1 * $gene_height[$num];
    if($req['end'] >= $req['start']){
      $startpos = $req['width'] * ($range_start - $req['start']) / $basewidth;
      $endpos = $req['width'] * ($range_end - $req['start'] + 1) / $basewidth;
    } else {
      $startpos = $req['width'] * ($req['start'] - $range_end) / $basewidth;
      $endpos = $req['width'] * ($req['start'] - $range_start + 1) / $basewidth;
    }

#    if($startpos > 100){
#      if(($name_pos = strpos($line, 'name=')) !== FALSE) {
# $name_line = substr($line, $name_pos + 5);
# list($name, $remain) = split("[ \t]", $name_line);
# $strbox = imagettfbbox( $size, 0, $fontfile, $name );
# $startpos = $startpos - $strbox[2] + $strbox[0] - 10;
#      }
#    }

    $y1 = $h-$hgene;
    $y2 = $h+$hgene+1;
    if ($startpos < 0) {
      $x1 = 0;
    }else {
      $x1 = floor ($startpos); // 0;
    }
    if ($endpos >= $req['width']) {
      $x2 = $req['width']-1;
    }else {
      $x2 = ceil($endpos) ; // $req['width']-1;
    }
    // URLの取得
    if (preg_match("/url=\"(\S+)\"/",$line, $url)){
    $url[1] = preg_replace('/&/', "&amp;" , $url[1]);
    print "  <rect_area rect=\"($x1,$y1,$x2,$y2)\">\n" ;
    print "    <mouseclick_event>\n";

    print "      <link_operation url=\"$url[1]\" />\n";

    print "    </mouseclick_event>\n" ;
    print "  </rect_area>\n" ;
    }else if (preg_match("/url=(\S+)/",$line, $url)){
    $url[1] = preg_replace('/&/', "&amp;" , $url[1]);
    print "  <rect_area rect=\"($x1,$y1,$x2,$y2)\">\n" ;
    print "    <mouseclick_event>\n";

    print "      <link_operation url=\"$url[1]\" />\n";

    print "    </mouseclick_event>\n" ;
    print "  </rect_area>\n" ;
    }
  }
  print "</operation_layer>";

}

/**
* geneTrackの操作XMLを標準出力する。（ソースとしてXMLキャッシュファイル使用）
* @access     public
* @param     string      $xml_tmp_dir       XMLファイル出力ディレクトリ
* @param     string      $cache_id          キャッシュID
* @param     string      $style             描画スタイル
*/
function def_gene_operation2($xml_dir_path,$cache_id,$style){
	//UTGDインスタンス作成
	$utgd = new UTGD4();
	//XMLファイルパス取得
	$xml_file_path = $xml_dir_path."/".$_REQUEST['sid']."_".$style.".xml";
//print $xml_file_path;
//print $cache_id;
	//キャッシュID
	if(!($cache_id)){
		return FALSE;
	}

	//キャッシュを使う場合
	//XMLファイル指定（XMLファイルパス、新規作成フラグ）
	$utgd->openXMLFile($xml_file_path,FALSE);
	//XMLデータ標準出力
	$utgd->outputCachedXMLData($cache_id);

}

/**
* geneTrackの操作XMLを標準出力する。（ソースとしてXMLファイル使用）
* @access     public
* @param     string      $xml_file_path     XMLファイル出力ディレクトリ
* @param     string      $style             描画スタイル
*/
function def_gene_operation4($xml_dir_path,$style){
	//UTGDインスタンス作成
	$utgd = new UTGD4();
	//XMLファイルパス取得
	$xml_file_path = $xml_dir_path."/".$_REQUEST['sid']."_".$style.".xml";
//print $xml_file_path;
//print $cache_id;

	//XMLファイルを使う場合
	//XMLファイル指定（XMLファイルパス、新規作成フラグ）
	$utgd->openXMLFile($xml_file_path,FALSE);
	//XMLデータ標準出力
	$utgd->outputXMLDataStandardFromFile();

}

/**
* geneTrackの操作XMLを標準出力する。（中間ファイルからgeneTrackの描画位置の再計算を行う）
* @access     public
* @param     array       $req       POST/GET引数配列
* @param     string      $style     描画スタイル
* @param     string      $buffer    中間ファイルパス
* @param     string      $xml       XMLファイル出力ディレクトリ（形式的に必要）
*/
function def_gene_operation3($req,$style,$buffer,$xml){
		//styleによる描画オプションのヴァリエーション
		if($style == 'full'){
			$h1 = 9;
		}elseif($style == 'dense'){
			$h1 = 9;
		}elseif($style == 'small'){
			$h1 = 4;
		}else{
			$h1 = 9;
		}

	//縦の余白＝marginy
	$h2 = 0;
	//画像縦幅
	$height = 0;//自動なので
	
	//UTGDインスタンス作成
	$utgd = new UTGD4();
	//色指定
	$white = 'white';
	$black = 'black';
	
	//TTフォント設定
	$fontpath = '../../../lib/UTGD4/fonts/Abadi MT Condensed Light.ttf';
	$utgd->setFontFile($fontpath);

	//サイズの設定
	$utgd->setImageSize($req['width'],$height,1,$h1,$req['start'],$req['end'],0,$h2);
	//その他オプション設定
	$utgd->setImageOptions($white,$white,10);

	//中間ファイルのパース
	$utgd->parseBufferFile($buffer,'TILING');

	//画像枠の作成
	$utgd->createImage();
	//XMLファイルオープン
	$utgd->openXMLFile($xml);
	
	//図形の描画
	$utgd->drawImage();    
//    //画像出力
//	$utgd->outputImage();
	//XML出力
//	$utgd->outputXMLFile();
//    //XMLキャッシュ出力
//	$utgd->cacheXMLData($cache_id);
	//XML標準出力
	$utgd->outputXMLDataStandard();

}


function def_gene_operation($file, $first_line){
// イメージサイズの取得
  $first_line = trim (substr($first_line, 9));

  $opattrs = get_optional_attribute($first_line);

  $req = get_request($_REQUEST, $opattrs, $colorD);

  $genes = get_display_genes($file,$req);

  // style の検索
  $style = $req['style'];

  if ($style == 'full'){
    def_gene_operation_style_full($genes,$req,9,3);
  }else if ($style == 'dense'){
    def_gene_operation_style_dense($genes,$req,9);
  }else if ($style == 'pack'){
    def_gene_operation_style_pack($genes,$req,9,3);
  }else if ($style == 'small'){
    def_gene_operation_style_small($genes,$req,4,1);
  }
}

function def_gene_index_operation_style_full($genes,$req,$h1, $hgene){
  $num_genes = sizeof($genes);

// 共通パラメータ
  $h2 = 0;

  $height = $num_genes * $h1 + $h2;
  if($num_genes == 0) $height = 5;
  $width = 100;

// xml出力
  header('Content-Type: text/xml');

  print "<?xml version=\"1.0\" ?>\n"; 
  print "<operation_layer>\n";
  for($num=0; $num < $num_genes; $num++){
    $line = $genes[$num];

    $h = $h1 / 2 +  $h2 + $h1 * $num;

    $y1 = $h-$hgene;
    $y2 = $h+$hgene+1;

    $x1 = 0;
    $x2 = $width-1;

    // URLの取得
    if (preg_match("/url=\"(\S+)\"/",$line, $url)){
    $url[1] = preg_replace('/&/', "&amp;" , $url[1]);
    print "  <rect_area rect=\"($x1,$y1,$x2,$y2)\">\n" ;
    print "    <mouseclick_event>\n";

    print "      <link_operation url=\"$url[1]\" />\n";

    print "    </mouseclick_event>\n" ;
    print "  </rect_area>\n" ;
    }else if (preg_match("/url=(\S+)/",$line, $url)){
    $url[1] = preg_replace('/&/', "&amp;" , $url[1]);
    print "  <rect_area rect=\"($x1,$y1,$x2,$y2)\">\n" ;
    print "    <mouseclick_event>\n";

    print "      <link_operation url=\"$url[1]\" />\n";

    print "    </mouseclick_event>\n" ;
    print "  </rect_area>\n" ;
    }

  }
  print "</operation_layer>";
}

function def_gene_index_operation_style_dense($genes,$req,$height){
// xml出力
  header('Content-Type: text/xml');

  print "<?xml version=\"1.0\" ?>\n";
  print "<operation_layer>\n";
  
  print "</operation_layer>";
}

function def_gene_index_operation_style_pack($genes, $req,$h1,$hgene){

print_r($genes);
  $num_genes = sizeof($genes);
  if ($req['start'] > $req['end']){
    usort ($genes, "cmp_genes_rev");
  } 
  $basewidth = abs ($req['end'] - $req['start'] + 1);

#  $h2 = 5;
  $h2 = 0;

  $gene_height = array();
  $height = get_pack_height ($genes, $req, $gene_height, $h1, 100);
  $width = 100;

// xml出力
  header('Content-Type: text/xml');

  print "<?xml version=\"1.0\" ?>\n";
  print "<operation_layer>\n";
  for($num=0; $num < $num_genes; $num++){
    $line = $genes[$num];
    $range_line = substr(strchr ($line, 'range='), 6);
    list($range_start, $range_end, $remain) = split("[, \t]", $range_line);
    if($range_start > $range_end) {
      $tmp = $range_start;
      $range_start = $range_end;
      $range_end = $tmp;
    }

    $h = $h1 / 2 +  $h2 + $h1 * $gene_height[$num];
    if($req['end'] >= $req['start']){
      $startpos = $req['width'] * ($range_start - $req['start']) / $basewidth;
      $endpos = $req['width'] * ($range_end - $req['start']) / $basewidth;
    } else {
      $startpos = $req['width'] * ($req['start'] - $range_end) / $basewidth;
      $endpos = $req['width'] * ($req['start'] - $range_start) / $basewidth;
    }

    if($startpos <= 100){

    $y1 = $h-$hgene;
    $y2 = $h+$hgene+1;

    $x1 = 0;
    $x2 = $width-1;

    // URLの取得
    if (preg_match("/url=\"(\S+)\"/",$line, $url)){
    $url[1] = preg_replace('/&/', "&amp;" , $url[1]);
    print "  <rect_area rect=\"($x1,$y1,$x2,$y2)\">\n" ;
    print "    <mouseclick_event>\n";

    print "      <link_operation url=\"$url[1]\" />\n";

    print "    </mouseclick_event>\n" ;
    print "  </rect_area>\n" ;
    }else if (preg_match("/url=(\S+)/",$line, $url)){
    $url[1] = preg_replace('/&/', "&amp;" , $url[1]);
    print "  <rect_area rect=\"($x1,$y1,$x2,$y2)\">\n" ;
    print "    <mouseclick_event>\n";

    print "      <link_operation url=\"$url[1]\" />\n";

    print "    </mouseclick_event>\n" ;
    print "  </rect_area>\n" ;
    }


    }
  }
  print "</operation_layer>";

}


function def_gene_index_operation($file, $first_line){
  $first_line = trim (substr($first_line, 9));

  $opattrs = get_optional_attribute($first_line);

  $req = get_request($_REQUEST, $opattrs, $colorD);

  $genes = get_display_genes($file,$req);

  // style の検索
  $style = $req['style'];
  if ($style == 'full'){
    def_gene_index_operation_style_full($genes,$req,9,3);
  }else if ($style == 'dense'){
    def_gene_index_operation_style_dense($genes,$req,10);
  }else if ($style == 'pack'){
    def_gene_index_operation_style_pack($genes,$req,9,3);
  }else if ($style == 'small'){
    def_gene_index_operation_style_dense($genes,$req,10);
  }
}
?>