Processing your request...
\n" ); //$PROG = "e:\kvi\projects\alig\debug\aligra.exe"; $PROG = "e:\kvi\projects\alig\debug\alig.exe"; $PARSER = "perl.exe e:\vnickolaev\parser\bsp.pl"; // Linux File names: } else { $TMP = tempnam("../tmp", "alig"); # unique filename prefix $IMAGE_PREF = tempnam( "../../trash/", "alig" ); $PROG = "./aligra"; $PARSER = "perl /usr/local/apache/cgi-bin/bsp.pl"; } if( $Linux ) { #........add to database......... //require("/www/db/connect.php"); $TaskID=7; $SenderMail=$email; $emailaddress; //insert_message_to_db($TaskID, $SenderMail); #............................... } $PROTOCOL = $TMP.".txt"; $PARMFILE = $TMP.".opt"; $ALIGNFILE = $TMP.".ali"; $ERRFILE = $TMP.".err"; // Parser files $PARSERIN = $TMP.".in"; $PARSEROUT = $TMP.".out"; // Basic/advanced ? if( isset( $WIDTH ) ) { //if( isset( $adv_opt ) ) { $Advanced = TRUE; //echo "Advanced mode
\n"; } else { $Advanced = FALSE; //echo "Basic mode
\n"; // ----------------------- // Set default parameters for Basic mode // ----------------------- $WIDTH = 800; $HEIGHT = "AUTO"; //480; $FILLING = "7"; $SPLIT = "NONE"; $GROUPTYPE = "0"; // AUTO } // Default picture if( !isset($PICTURE[0]) ) $PICTURE[0] = "ALLGROUPS"; // Default matrix *** 07.09.2001 if( !isset($MATR) ) $MATR = "blosum62"; if( $test ) { echo 'Win=', $Windows, ', Linux=', $Linux, "
"; } include "aligfun.inc"; if( $test ) { echo " Base of /some/two/base.matr = ", f_fileBase( "/some/two/base.matr" ), "
"; } # -------------------------------------------------------- # Check some conditions. # -------------------------------------------------------- if( !isset($ALIGN) || $ALIGN == "" ) { echo "
I guess, you forgot to enter/paste your favorite alignment.
I can't read that guy out of your mind so far. Sorry.
"; exit; } // -------------------------------- split seq //echo "SEQ = " , $seq, "
"; echo '
'; if( $test ) { echo "
ALIGN = " , $align, "

"; } # -------------------------------------------------------- # Creats lock-file for input file # -------------------------------------------------------- $T = 0; //++$T = 5*( count( $P_BANKS ) + count( $N_BANKS ) ); if( $T == 0 ) $T = 3; //5; echo "Estimated time before completing your request is approximately $T minutes...

"; flush(); #_____________________________________ Parser: include "bspfun.inc"; $ALIGN_SOU = $ALIGN; // save to print $ALIGN = f_getParserAlign( $ALIGN, $PARSER, $PARSERIN, $PARSEROUT ); //+$ALIGN_SOU = $ALIGN; f_setAlignOpt ( $ALIGN, $ALGO, $PARMFILE, $HEIGHT, $IMAGE_PREF ); //+f_exeAlignProg( $ALIGN, $PROG, $PARMFILE, $ALIGNFILE, $PROTOCOL ); $fp = fopen( $ALIGNFILE, "w" ); // fputs( $fp, $ALIGN ); fclose( $fp ); #________________________________________________C++ CALL $prog = "$PROG $PARMFILE $ALIGNFILE > $PROTOCOL"; //+echo $prog . "
\n"; system( $prog ); # ----------------------------------------------------------- # Output results. # ----------------------------------------------------------- #_________________________ Banner echo "

"; echo ""; echo "

ALiGraf - GeneBee Graphical Image of Alignment

"; //if( $TITLE != "" ) echo "

",$TITLE,"

"; if( $TITLE != "" ) echo "

" . $TITLE . "

"; // __________________________References: //-echo "

References:

"; #_________________________ Content //echo "

"; //+echo "
"; //echo "
"; echo ""; echo ""; echo "
"; //+echo "

Contents:

    "; echo "

    Contents:



"; #_________________________ Parameters. echo "

Parameters

"; echo '

'; echo " "; echo " "; if( $TITLE != "" ) { printPar("Title","",$TITLE); } if( $EMAIL != "" ) { printPar("User Email Address","",$EMAIL); } if( $ALGO != "" ) { printPar("Short name","",$ALGO); } f_outAlignSpecOpt(); echo "
Name Value
"; #___________________________________ molType & other errors function f_outErrors( $f ) { //echo "

\n"; echo ""; echo "

WARNING

"; echo "
";
   readfile ( $f );
   echo "
\n"; echo ""; } if( file_exists( $ERRFILE ) ) { f_outErrors( $ERRFILE ); if( $Windows ) { unlink( $ERRFILE ); } } #_________________________ Alignment. echo "

Source Alignment

"; echo "
";
 echo $ALIGN_SOU . "
\n"; //++#_________________________ Groups. //++echo "

Letter Groups

"; ?> 
      1. _______A G _______________ 

      2. _______C _________________ 

      3. _______D E N Q B Z _______ 

      4. _______I L M V ___________ 

      5. _______F W Y _____________

      6. _______H _________________ 

      7. _______K R _______________ 

      8. _______P _________________ 

      9. _______S T _______________

     10. _______Others ____________
*****/ ?>

Graphical Alignment

"; /***** #_________________________ Loop on Matrices. for( $i = 0; $i < $numMatr; $i++ ) { $wm_ = strToUpper( f_fileBase( $wmList[$i] ) ); $wmFile = $wmList[$i]; echo "

Weight Matrix of $wm_

"; echo "

"; *****/ f_outAlignImages( "pic_", "gali_im", $IMAGE_PREF ); // args: images prefs $section = "BOTTOM"; include "aligmli.h"; #_____________________________ Delete all temporary files. if( $Linux ) { system( "rm $ALIGNFILE" ); system( "rm $PROTOCOL" ); system( "rm $PARMFILE" ); // ? + images system( "rm $PARSERIN" ); system( "rm $PARSEROUT" ); system( "rm $ERRFILE" ); //for( $i = 0; $i < $numMatr; $i++ ) { //system( "rm ".$IMAGE_PREF.$i.".png" ); //} } ?>
Designed by Valeri Kazatchenko. Last updated: September 7, 2001.
Comments and bug-reports send to Vladimir Nikolaev
Created: .