"; //echo ""; // ********* //echo ""; echo "

Aminoacid matrix	"; echo "	"; /*** if( $Linux ) { $fmat = fopen( "../data/".$MATR.".matrix", "r" ); // ************ Linux } else { //$fmat = fopen( $wmFile, "r" ); $fmat = fopen( $MATR.".matrix", "r" ); } while( $buf = fgets( $fmat, 128 ) ) { echo $buf; } fclose( $fmat ); ***/ /*** if( $Linux ) { $fmat = "../../data/".$MATR.".matrix"; // ************ Linux *** 07.05.2001 } else { $fmat = $MATR.".matrix"; } readfile( $fmat ); echo "

"; ***/ /***** // -------------------------------------------------------- // List of the mouse sensitive msgs - maps' polygons, etc. // -------------------------------------------------------- $fmsg = fopen( $MAP_MSGS, "r" ); while( $buf = fgets( $fmsg, 128 ) ) { echo $buf; } fclose( $fmsg ); //echo ""; //echo ""; *****/ // -------------------------------------------------------- // Predicted annotation. // -------------------------------------------------------- function f_kwOut( $s, $xx, $KW_REF, &$aST ) { global $OUTPUT; //+$r = strpos( $s, " ", 5 ); //echo "r = ", $r, "
"; //+$kw = substr( $s, 5, $r - 5 ); $kw = rtrim(substr( $s, 5, 40 )); $r = strlen( $kw ) + 5; //echo $xx, " ", $kw, ""; if( $xx == "KW" ) echo $xx, " ", $kw, ""; else echo $xx, " ", $kw, ""; //echo substr( $s, $r, strlen( $s ) - $r - 1 ), " (stat)\n"; //$sd = strpos( $s, " SD", 41 ) - 6; // always found //echo substr( $s, $r, $sd - $r - 1 ), " "; //echo( substr( $s, $sd, 6 + 3 ) . "" . substr( $s, $sd + 6 + 3) ); $sd = strpos( $s, " SD", 41 ); // always found $prob = strpos( $s, " Prob", 41 ) + 1; // always found //echo substr( $s, $r, $prob - $r - 1 ), " "; // ***07.05.2001 echo( substr( $s, $r, $prob - $r - 1 ) . " " ); if( f_afind( $OUTPUT, "STAT" ) > -1 ) { echo( "" ); } echo( substr( $s , $prob , $sd - $prob ) ); if( f_afind( $OUTPUT, "STAT" ) > -1 ) echo( "" ); echo( substr( $s, $sd ) ); /**/ // KW Stats: $v = substr( $s, $sd, 6 ); settype( $v, "double" ); $tkw = $xx . ": " . $kw; if( isset($aST[ $tkw ]) ) { if( $aST[ $tkw ] < $v ) $aST[ $tkw ] = $v; } else $aST[ $tkw ] = $v; /**/ return $kw; } echo "

";

/**                                                      see at start
 //$F_PRE = "e:\vnickolaev\annot\\" . "44\\" . "44.pre";
 if( $Linux ) {
      $res_file = $outdir.$pid."-.ht0";    // *** 10.05.2001
      $F_PRE = $res_file.".pre";           // ************ Linux
      $F_M2M = $res_file.".m2m";           // ************ Linux
 } 
**/

 $fpre = fopen( $F_PRE, "r" );
 $iKW  = -1;
 $kwPrev = "";
 $kwLine = "*,";                           // *** 20.01.01
 $seqLen = 0;
 while( $buf = fgets( $fpre, 128 ) )    {
    $xx = substr($buf,0,2);
    if( $xx == "DE" || $xx == "KW" || $xx == "FT" ) {
      $kw = f_kwOut( $buf, $xx, $KW_REF, $aST );
      
      if( $iKW >= ($MN_KW - 1) ) continue; // <-------- too many keywords *** 02.02.01

      $tKw = $xx . ": " . $kw;
      if( $xx != "FT" ) {
        $iKW++; 
        //$aKW[$iKW] = $xx . ": " . $kw;
        $aKW[$iKW] = $tKw;
        $kwLine .= ( $tKw . "," );
      } else {
        if( $kw != $kwPrev ) {
          $iKW++;
          $kwPrev = $kw;               // Same FT keywords must be groupped together !
          //$aKW[$iKW] = $xx . ": " . $kw;
          $aKW[$iKW] = $tKw;
          $kwLine .= ( $tKw . "," );
        }
      }
    } else {

      // get seqLen:
      if( $xx == "ID" ) {
        echo( $buf );
        $pos = strpos( $buf, " AA." );
        if( $pos > 0 ) {
          $str = rtrim( substr( $buf, 0, $pos ) );
          $bla = strrpos( $str, " " );
          $seqLen = substr( $str, $bla+1 );
          settype( $seqLen, "integer" );
          //+echo "seqlen=" . $seqLen . "
";
        }

      // Set seq ref: 
      } else if( $xx == "SQ" ) {
        echo(  "" );
        echo( $buf );
        echo(  "" );

      } else
        echo $buf;
    }
 }
 fclose( $fpre );
 echo "

" . substr($s,0,strlen($s) - 2) . " [annotation]"); if( f_afind( $OUTPUT, "GRALI" ) > -1 ) echo( "[gr.alignment]" ); echo( "\n

";
   $fsta = fopen( $F_STA, "r" );
   $stat_on = FALSE;
   $i = 0;
   while( $buf = fgets( $fsta, 512 ) )    {
    if( ($pos = strpos( $buf,"_statist" )) > 4 ) {
      $i++; 
      //if( $i > 6 ) break;   // ------------>
      if( $i > 50 ) break;   // ------------>
      //if( $i > 15 ) break;   // ------------>

      //+$stat_on = TRUE;
      f_stOut( $buf, $pos );

      //+if( $i < 7 ) {   // 4
        $aBuf[0] = fgets( $fsta, 512 );
        $aBuf[1] = fgets( $fsta, 512 );
        $aBuf[2] = fgets( $fsta, 512 );
        $aBuf[3] = fgets( $fsta, 512 );
        $iw = 500; $ih = 250+10; // may be changed ?

/**
        if( $Linux ) {
          $sta_file = "../trash/".$pid. $F_IM3 . $i . $F_IMEXT; // ************ Linux ??
        } else {
          $sta_file = $F_IM3 . $i . $F_IMEXT; //"asta1_1.png";
        }
**/
        $sta_file = $F_IM3 . $i . $F_IMEXT; //"asta1_1.png";  // *** 20.08.2001

        f_staImage( $sta_file, $buf, $pos, $aBuf, $iw, $ih, $seqname, $MATR, $optline );
        echo( "
" );
        echo( "

" );

      //} else {
      //  if( $stat_on )
       
      //+}

      if( $test ) {
          echo $aBuf[0]; echo $aBuf[1];
          echo $aBuf[2]; echo $aBuf[3];
      }

      //}
    }
   } // end of while loop

   fclose( $fsta );
   echo "

";
 $fsta = fopen( "P10318.prn", "r" );
 while( $buf = fgets( $fsta, 256 ) )    {
    //if( ($pos = strpos( $buf,"_statist" )) > 4 ) {
    //  f_stOut( $buf, $pos );
    //} else {
      echo $buf;
    //}
 }
 fclose( $fsta );
 echo "