'; echo " "; echo " "; if( $TITLE != "" ) { printPar("Title","",$TITLE); } if( $EMAIL != "" ) { printPar("User Email Address","",$EMAIL); } if( $ALGO1 != "" ) { printPar("Short name of the 1st alignment","",$ALGO1); } if( $ALGO2 != "" ) { printPar("Short name of the 2nd alignment","",$ALGO2); } if( $CWIDTH == $cwid ) { printPar( "Comparison picture width" , "help.html#C PICTURE", $CWIDTH ); } else { printPar( "Comparison picture width" , "help.html#C PICTURE", $CWIDTH . " (adjusted to ".$cwid.")" ); } if( $auto_hei_c ) { //printPar( "Comparison picture height", "help.html#CPICTURE", "AUTO: " . $chei); //CHEIGHT ); printPar( "Comparison picture height", "help.html#CPICTURE", "AUTO" ); //CHEIGHT ); } else { if( $CHEIGHT == $chei ) { printPar( "Comparison picture height", "help.html#CPICTURE", $CHEIGHT ); } else { printPar( "Comparison picture height", "help.html#CPICTURE", $CHEIGHT." (adjusted to ".$chei.")" ); } } printPar( "Offset scale", "help.html#CPICTURE", ($OSCALE == "ABS" ? "1 - Max" : "Min - Max" ) ); printPar( "Compare mismatched sequences", "help.html#CPICTURE", $MISMATCH ); printPar( "Comparison picture types" , "help.html#CPICTURE", $sCPicLine ); // Separate align options: if( (isset( $PICTURE[0] ) && $PICTURE[0] != "NONE") || (isset( $SELGROUP[0] ) && $SELGROUP[0] != "UNSELECTED") ) { f_outAlignSpecOpt(); } //+printPar( "Picture types" , "help.html#PICTURE", $sPicLine ); //printPar( "Normalize weight matrix","help.html#mfr",( $NORM == 1 ) ? "ON" : "OFF" ); //printPar( "Weight matrices","help.html#type",$WM_LINE ); echo "

Name

Value

"; #___________________________________ molType & other errors function f_outErrors( $f ) { //echo "

";
   readfile ( $f );
   echo "

", substr($seq1,0, $iP), "\n
";
 //+echo substr( $seq1, $iP ),"

";
 echo $ALIGN_SOU1 . "

";
 echo $ALIGN_SOU2 . "

"; *****/ ## ## Picture (Form) ## $fn = $IMAGE_PREF; ## Load Images ## (not the case - needed for rolling pictures - if any, some other day...) print "\n"; //++ echo " cwid/chei = " . $cwid . "/" . $chei . "
\n"; echo "

---

\n"; echo "

Comparison 1: 1st Alignment Versus 2nd Alignment

"; //print " //
\n"; //print ""; // Tags for( $i = 0; $i < $numCPic; $i++ ){ $ty = $CPicType [ $CPICTURE[$i] ]; $tail = $CImageTail[ $CPICTURE[$i] ]; print "

". $CPicTitle[$CPICTURE[$i]] . "

\n"; print "
\n"; } echo "

Comparison 2: 2nd Alignment Versus 1st Alignment

"; //print " //
\n"; //print ""; // Tags for( $i = 0; $i < $numCPic; $i++ ){ $ty = $CPicType [ $CPICTURE[$i] ]; $tail = $CImageTail[ $CPICTURE[$i] ]; print "

". $CPicTitle[$CPICTURE[$i]] . "

\n"; print "
\n"; } #_________________________ Mismatch Display. function f_outMismatch( $f ) { echo "

---

\n"; echo "

Mismatch Errors

"; echo "

Some sequences with same names are found to have different lengths or different letters at same positions:\n"; echo "

";
   readfile ( $f );
   echo "

\n"; } if( file_exists( $MISFILE ) ) { f_outMismatch( $MISFILE ); if( $Windows ) { unlink( $MISFILE ); } } /***** // Tags for( $i = 0; $i < $numPic; $i++ ){ $ty = $PicType [ $PICTURE[$i] ]; if( $ty > 10 ) continue; $tail = $ImageTail[ $PICTURE[$i] ]; print "

". $PicTitle[$PICTURE[$i]] . "

\n"; //print "

// // //

print " \n"; //

\n"; } for( $i = 0; $i < $numPic; $i++ ){ $ty = $PicType [ $PICTURE[$i] ]; if( $ty <= 10 ) continue; $tail = $ImageTail[ $PICTURE[$i] ]; print "

". $PicTitle[$PICTURE[$i]] . "

// // //

print " \n"; //