X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Farchive%2Fbinaries%2Fmac%2Fsrc%2Fmafft%2Fcore%2Fmafft.tmpl.subopt;fp=website%2Farchive%2Fbinaries%2Fmac%2Fsrc%2Fmafft%2Fcore%2Fmafft.tmpl.subopt;h=0000000000000000000000000000000000000000;hb=fb21789ba11ae9b9f6abed1b01d4542e54abfe34;hp=9096897fec8291a369ecd1f04679824ea19e78c6;hpb=7d68cf3489c816b2ed7afb1925a6de2168eccf4a;p=jabaws.git diff --git a/website/archive/binaries/mac/src/mafft/core/mafft.tmpl.subopt b/website/archive/binaries/mac/src/mafft/core/mafft.tmpl.subopt deleted file mode 100644 index 9096897..0000000 --- a/website/archive/binaries/mac/src/mafft/core/mafft.tmpl.subopt +++ /dev/null @@ -1,788 +0,0 @@ -#! /bin/sh -er=0; -myself=`dirname $0`/`basename $0`; export myself -version="version 6.00 (2005/05/01)"; export version -LANG=C; export LANG -os=`uname` -progname=`basename $0` -if [ `echo $os | grep -i cygwin` ]; then - os="cygwin" -elif [ `echo $os | grep -i darwin` ]; then - os="darwin" -elif [ `echo $os | grep -i sunos` ]; then - os="sunos" -else - os="unix" -fi -export os - -if [ $MAFFT_BINARIES ]; then - prefix=$MAFFT_BINARIES -else - prefix=_PREFIX -fi -export prefix -if [ ! -x $prefix/tbfast ]; then - echo "" - echo "correctly installed?" 2>&1 - echo "mafft binaries have to be installed in" $prefix. - echo "" - exit 1 - er=1 -fi - -defaultiterate=0 -defaultcycle=2 -defaultmodel=" -b 62 " -defaultgop="1.53" -defaultaof="0.123" -defaultfft=1 -defaultrough=0 -defaultdistance="sixtuples" -if [ $progname = "linsi" ]; then - defaultfft=0 - defaultcycle=1 - defaultiterate=1000 - defaultdistance="local" -elif [ $progname = "ginsi" ]; then - defaultfft=1 - defaultcycle=1 - defaultiterate=1000 - defaultdistance="global" -elif [ $progname = "einsi" ]; then - defaultfft=0 - defaultcycle=1 - defaultiterate=1000 - defaultdistance="genaf" -elif [ $progname = "fftns" ]; then - defaultfft=1 - defaultcycle=2 -elif [ $progname = "fftnsi" ]; then - defaultfft=1 - defaultcycle=2 - defaultiterate=2 -elif [ $progname = "nwns" ]; then - defaultfft=0 - defaultcycle=2 -elif [ $progname = "nwnsi" ]; then - defaultfft=0 - defaultcycle=2 - defaultiterate=2 -fi -model=$defaultmodel -gop=$defaultgop -aof=$defaultaof -cycle=$defaultcycle -iterate=$defaultiterate -fft=$defaultfft -rough=$defaultrough -distance=$defaultdistance -LGOP="-6.00" -LEXP="-0.000" -lgop="-2.00" -lexp="-0.100" -laof="0.100" -seqtype=" " -param_it=" -x " -weighti="2.7" -quiet=0 -sw=0 -scorecalcopt=" " -coreout=0 -corethr="0.5" -corewin="100" -coreext=" " -outputformat="pir" -outorder="input" -if [ $# -gt 0 ]; then - while [ $# -gt 1 ]; - do - if [ $1 = "--clustalout" ]; then - outputformat="clustal" - elif [ $1 = "--reorder" ]; then - outorder="aligned" - elif [ $1 = "--rough" ]; then - rough=1 - elif [ $1 = "--noscore" ]; then - scorecalcopt=" -Z " - elif [ $1 = "--fastswpair" ]; then - distance="fasta" - sw=1 - elif [ $1 = "--fastapair" ]; then - distance="fasta" - sw=0 - elif [ $1 = "--suboptpair" ]; then - distance="subopt" - elif [ $1 = "--blastpair" ]; then - distance="blast" - elif [ $1 = "--globalpair" ]; then - distance="global" - elif [ $1 = "--localpair" ]; then - distance="local" - elif [ $1 = "--genafpair" ]; then - distance="genaf" - elif [ $1 = "--nuc" ]; then - seqtype=" -D " - elif [ $1 = "--amino" ]; then - seqtype=" -P " - elif [ $1 = "--fft" ]; then - fft=1 - elif [ $1 = "--nofft" ]; then - fft=0 - elif [ $1 = "--quiet" ]; then - quiet=1 - elif [ $1 = "--nj" ]; then - param_it=" -n " - elif [ $1 = "--coreext" ]; then - coreext=" -c " - elif [ $1 = "--core" ]; then - coreout=1 - elif [ $1 = "--maxiterate" ]; then - shift - iterate=`expr $1 - 0` - elif [ $1 = "--retree" ]; then - shift - cycle=`expr $1 - 0` || er=1 - elif [ $1 = "--jtt" ]; then - shift - model=" -j "$1 - elif [ $1 = "--tm" ]; then - shift - model=" -m "$1 - elif [ $1 = "--bl" ]; then - shift - model=" -b "$1 - elif [ $1 = "--weighti" ]; then - shift - weighti=$1 - elif [ $1 = "--op" ]; then - shift - gop=$1 - elif [ $1 = "--ep" ]; then - shift - aof=$1 - elif [ $1 = "--lop" ]; then - shift - lgop=$1 - elif [ $1 = "--LOP" ]; then - shift - LGOP=$1 - elif [ $1 = "--lep" ]; then - shift - laof=$1 - elif [ $1 = "--lexp" ]; then - shift - lexp=$1 - elif [ $1 = "--LEXP" ]; then - shift - LEXP=$1 - elif [ $1 = "--corethr" ]; then - shift - corethr=$1 - elif [ $1 = "--corewin" ]; then - shift - corewin=$1 - elif [ $1 -gt 0 -a $progname = "fftns" -o $1 -gt 0 -a $progname = "nwns" ]; then - cycle=`expr $1 - 0` - else - echo "Unknown option: " $1 2>&1 - er=1; - fi - shift - done; - if [ $fft -eq 1 ]; then - param_fft=" -F " - else - param_fft=" " - fi - if [ $sw -eq 1 ]; then - swopt=" -A " - else - swopt=" " - fi - - if [ $distance = "fasta" ]; then - if [ ! $FASTA_4_MAFFT ]; then - FASTA_4_MAFFT=`which fasta34` - fi - - if [ ! -x $FASTA_4_MAFFT ]; then - echo "" - echo "== Install FASTA ========================================================" - echo "This option requires the fasta34 program (FASTA version x.xx or higher)" - echo "installed in your PATH. If you have the fasta34 program but have renamed" - echo "(like /usr/local/bin/myfasta), set the FASTA_4_MAFFT environment variable" - echo "to point your fasta34 (like setenv FASTA_4_MAFFT /usr/local/bin/myfasta)." - echo "=========================================================================" - echo "" - exit - fi - fi - if [ $distance = "sixtuples" ]; then - localparam=" " - else - cycle=1 - localparam=" -l "$weighti - fi - - if [ $distance = "fasta" -a $sw -eq 0 ]; then - strategy="F-I" - elif [ $distance = "fasta" -a $sw -eq 1 ]; then - strategy="H-I" - elif [ $distance = "subopt" ]; then - strategy="S-I" - elif [ $distance = "blast" ]; then - strategy="B-I" - elif [ $distance = "global" ]; then - strategy="G-I" - elif [ $distance = "local" ]; then - strategy="L-I" - elif [ $distance = "genaf" ]; then - strategy="E-I" - elif [ $fft -eq 1 ]; then - strategy="FFT-" - else - strategy="NW-" - fi - strategy=$strategy"NS-" - if [ $iterate -gt 0 ]; then - strategy=$strategy"i" - elif [ $rough -eq 1 ]; then - strategy=$strategy"ROUGH" - else - strategy=$strategy$cycle - fi - - explanation='?' - performance='Not tested.' - if [ $strategy = "F-INS-i" ]; then - explanation='Iterative refinement method incorporating LOCAL pairwise alignment information' - performance='Most accurate, but very slow' - elif [ $strategy = "L-INS-i" ]; then - explanation='Iterative refinement method incorporating LOCAL pairwise alignment information' - performance='Probably most accurate, very slow' - elif [ $strategy = "E-INS-i" ]; then - explanation='Iterative refinement method incorporating LOCAL pairwise alignment with generalized affine gap costs (Altshul 1998)' - performance='Suitable for sequences with long unalignable regions, very slow' - elif [ $strategy = "G-INS-i" ]; then - explanation='Iterative refinement method incorporating GLOBAL pairwise alignment information' - performance='Suitable for sequences of similar lengths, very slow' - elif [ $strategy = "F-INS-1" ]; then - explanation='Progressive method incorporating LOCAL pairwise alignment information' - elif [ $strategy = "L-INS-1" ]; then - explanation='Progressive method incorporating LOCAL pairwise alignment information' - elif [ $strategy = "G-INS-1" ]; then - explanation='Progressive method incorporating GLOBAL pairwise alignment information' - elif [ $strategy = "FFT-NS-i" -o $strategy = "NW-NS-i" ]; then - explanation='Iterative refinement method (max. '$iterate' iterations)' - if [ $iterate -gt 2 ]; then - performance='Accurate but slow' - else - performance='Standard' - fi - elif [ $strategy = "FFT-NS-2" -o $strategy = "NW-NS-2" ]; then - explanation='Progressive method (guide trees were built '$cycle' times.)' - performance='Fast but rough' - elif [ $strategy = "FFT-NS-1" -o $strategy = "NW-NS-1" ]; then - explanation='Progressive method (rough guide tree was used.)' - performance='Very fast but very rough' - fi - - if [ $outputformat = "clustal" -a $outorder = "aligned" ]; then - outputcommand="$prefix/f2cl -c $strategy -r order " - elif [ $outputformat = "clustal" -a $outorder = "input" ]; then - outputcommand="$prefix/f2cl -c $strategy " - elif [ $outputformat = "pir" -a $outorder = "aligned" ]; then - outputcommand="$prefix/f2cl -f -r order " - else - outputcommand=" cat " - fi - - TMPFILE=/tmp/`basename $0`.`whoami`.$$.`date +%y%m%d%H%M%S` - TMPFILE=/tmp/$progname.$$ - umask 077 - mkdir $TMPFILE || er=1 - trap "rm -r $TMPFILE " 0 - if [ $# -eq 1 ]; then - if [ -s "$1" -o "$1" = - ]; then - cat "$1" | tr "\r" "\n" > $TMPFILE/infile - else - echo "Cannot open $1." 2>&1 - er=1 - fi - else - echo '$#'"=$#" 2>&1 - er=1 - fi - - - if [ $er -eq 1 ]; then - echo "" 2>&1 - echo "MAFFT" $version 2>&1 - echo "" 2>&1 - echo " References: " 2>&1 - echo " Katoh et al., 2002, NAR 30: 3059-3066" 2>&1 - echo " Katoh et al., 2005, NAR 33: 511-518" 2>&1 - echo " http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft" 2>&1 - echo "" 2>&1 -# echo "Usage: `basename $0` [options] inputfile > outputfile" 2>&1 - echo " Options: " 2>&1 - echo " --globalpair : All pairwise global alignment information is included." 2>&1 - echo " default: off" 2>&1 - echo " --localpair : All pairwise local alignment information is included." 2>&1 - echo " default: off" 2>&1 - echo " --op # : Gap opening penalty (>0). default: $defaultgop " 2>&1 - echo " --ep # : Offset (>0, works like gap extension penalty). " 2>&1 - echo " default: $defaultaof " 2>&1 - echo " --bl #, --jtt # : Scoring matrix. default: BLOSUM62" 2>&1 - echo " Alternatives are BLOSUM (--bl) 30, 45, 62, 80, " 2>&1 - echo " or JTT (--jtt) # PAM. " 2>&1 - echo " --nuc or --amino : Sequence type. default: auto" 2>&1 - echo " --retree # : The number of tree building in progressive method " 2>&1 - echo " (see the paper for detail). default: $defaultcycle " 2>&1 - echo " --maxiterate # : Maximum number of iterative refinement. default: $defaultiterate " 2>&1 - echo " --nj : Tree dependent iterative refinement is performed" 2>&1 - echo " on an NJ tree. default: UPG tree" 2>&1 - if [ $defaultfft -eq 1 ]; then - echo " --fft or --nofft: FFT is enabled or disabled. default: enabled" 2>&1 - else - echo " --fft or --nofft: FFT is enabled or disabled. default: disabled" 2>&1 - fi -# if [ $defaultrough -eq 1 ]; then -# echo " --rough : Rough alignment, for >1,000 sequences. default: enabled" 2>&1 -# else -# echo " --rough : Rough alignment, for >1,000 sequences. default: disabled" 2>&1 -# i - echo " --clustalout: Output: clustal format (not tested). default: fasta" 2>&1 - echo " --reorder: Outorder: aligned (not tested). default: input order" 2>&1 - echo " --quiet : Do not report progress." 2>&1 - echo "" 2>&1 - echo " Input format: fasta format" 2>&1 - echo "" 2>&1 - echo " Typical usages:" 2>&1 - echo " % mafft --maxiterate 1000 --localpair input > output" 2>&1 - echo " L-INS-i (most accurate and very slow, iterative refinement" 2>&1 - echo " method incorporating LOCAL alignment information)" 2>&1 - echo "" 2>&1 - echo " % mafft --maxiterate 1000 --globalpair input > output" 2>&1 - echo " G-INS-i (slightly less accurate than L-INS-i and very slow," 2>&1 - echo " iterative refinement method incorporating GLOBAL alignment" 2>&1 - echo " information, suitable for sequences of similar lengths) " 2>&1 - echo "" 2>&1 - echo " % mafft --maxiterate 1000 input > output" 2>&1 - echo " FFT-NS-i (accurate and slow, iterative refinement method)" 2>&1 - echo "" 2>&1 - echo " % mafft --retree 2 input > output (DEFAULT; same as mafft input > output)" 2>&1 - echo " FFT-NS-2 (rough and fast, default, progressive method)" 2>&1 - echo "" 2>&1 - echo " % mafft --retree 1 input > output" 2>&1 - echo " FFT-NS-1 (very rough and very fast, progressive method with" 2>&1 - echo " a rough guide tree)" 2>&1 - echo "" 2>&1 - exit 1; - fi - - ( - cd $TMPFILE; - if [ $rough -gt 0 ]; then - $prefix/splitseq infile 500 - for spfile in sp-[0-9]*[0-9] - do - echo $spfile > /dev/tty - nseq=`grep -c '^[>|=]' $spfile` - echo $nseq > /dev/tty - if [ $nseq -eq 1 ]; then - cp $spfile $spfile.aln - else - $prefix/sextet5 $seqtype < $spfile > /dev/null 2>&1 || exit 1 - $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft -Ax < $spfile > /dev/null 2>&1 || exit 1 - cat pre > $spfile.aln - fi - done - ngroup=0 - for alfile in sp-[0-9]*[0-9].aln - do - ngroup=`expr $ngroup + 1` - echo $alfile > /dev/tty - if [ $ngroup -eq 1 ]; then - cp $alfile alall - else - $prefix/galn -A alall $alfile > altmp - mv altmp alall - fi - done - cat alall - else - if [ $quiet -gt 0 ]; then - if [ $distance = "subopt" ]; then - $prefix/pairlocalalign $seqtype -b 62 -g $lexp -f $lgop -h $laof -O $LGOP -E $LEXP -S < infile > /dev/null 2>&1 || exit 1 - $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null 2>&1 || exit 1 - elif [ $distance = "fasta" ]; then - $prefix/dndfast7 $swopt < infile > /dev/null 2>&1 || exit 1 - $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null 2>&1 || exit 1 - elif [ $distance = "blast" ]; then - $prefix/dndblast < infile > /dev/null 2>&1 || exit 1 - $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null 2>&1 || exit 1 - elif [ $distance = "global" ]; then - $prefix/pairlocalalign $seqtype $model -f "-"$gop -h "-"$aof -F < infile > /dev/null 2>&1 || exit 1 - $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null 2>&1 || exit 1 - elif [ $distance = "local" ]; then - $prefix/pairlocalalign $seqtype -b 62 -g $lexp -f $lgop -h $laof -L < infile > /dev/null 2>&1 || exit 1 - $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null 2>&1 || exit 1 - elif [ $distance = "genaf" ]; then - $prefix/pairlocalalign $seqtype -b 62 -g $lexp -f $lgop -h $laof -O $LGOP -E $LEXP -N < infile > /dev/null 2>&1 || exit 1 - $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null 2>&1 || exit 1 - else - $prefix/disttbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft -Ax < infile > pre 2>/dev/null || exit 1 - fi - while [ $cycle -gt 1 ] - do - $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft -JAx < pre > /dev/null 2>&1 || exit 1 - cycle=`expr $cycle - 1` - done - if [ $iterate -gt 0 ]; then - if [ $distance == "sixtuples" ]; then - $prefix/dndpre < pre > /dev/null 2>&1 || exit 1 - fi - $prefix/dvtditr $scorecalcopt $localparam -F -z 50 $seqtype $model -f "-"$gop -h "-"$aof -A -c -I $iterate $param_it < pre > /dev/null 2>&1 || exit 1 - fi - else - if [ $distance = "subopt" ]; then - $prefix/pairlocalalign $seqtype -b 62 -g $lexp -f $lgop -h $laof -O $LGOP -E $LEXP -S < infile > /dev/null || exit 1 - $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null || exit 1 - elif [ $distance = "fasta" ]; then - $prefix/dndfast7 $swopt < infile > /dev/null || exit 1 - $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null || exit 1 - elif [ $distance = "blast" ]; then - $prefix/dndblast < infile > /dev/null || exit 1 - $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null || exit 1 - elif [ $distance = "global" ]; then - $prefix/pairlocalalign $seqtype $model -f "-"$gop -h "-"$aof -F < infile > /dev/null || exit 1 - $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null || exit 1 - elif [ $distance = "local" ]; then - $prefix/pairlocalalign $seqtype -b 62 -g $lexp -f $lgop -h $laof -L < infile > /dev/null || exit 1 - $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null || exit 1 - elif [ $distance = "genaf" ]; then - $prefix/pairlocalalign $seqtype -b 62 -g $lexp -f $lgop -h $laof -O $LGOP -E $LEXP -N < infile > /dev/null || exit 1 - $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null || exit 1 - else - $prefix/disttbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft -Ax < infile > pre || exit 1 - fi - while [ $cycle -gt 1 ] - do - $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft -JAx < pre > /dev/null || exit 1 - cycle=`expr $cycle - 1` - done - if [ $iterate -gt 0 ]; then - if [ $distance = "sixtuples" ]; then - $prefix/dndpre < pre > /dev/null 2>&1 || exit 1 - fi - $prefix/dvtditr $scorecalcopt $localparam -F -z 50 $seqtype $model -f "-"$gop -h "-"$aof -A -c -I $iterate $param_it < pre > /dev/null || exit 1 - fi - fi -# cat < pre || exit 1 - if [ $coreout -eq 0 ]; then - $outputcommand < pre || exit 1 - else - $prefix/setcore -w $corewin -i $corethr $coreext < pre > pre2 - $outputcommand < pre2 || exit 1 - fi - fi - ) - echo '' >/dev/tty - if [ $distance = "fasta" ]; then - echo "Pairwise alignments were computed by FASTA" >/dev/tty - echo "(Pearson & Lipman, 1988, PNAS 85:2444-2448)" >/dev/tty - fi - if [ $distance = "blast" ]; then - echo "Pairwise alignments were computed by BLAST">/dev/tty - echo "(Altschul et al., 1997, NAR 25:3389-3402)">/dev/tty - fi - printf "\n" >/dev/tty - echo 'Strategy:' >/dev/tty - printf ' '$strategy >/dev/tty - echo ' ('$performance')' >/dev/tty - echo ' '$explanation >/dev/tty - echo '' >/dev/tty - echo "Type '$0 --help' for other options." >/dev/tty - echo '' >/dev/tty - exit 0; -fi - -prog="awk" - -if [ $os != "darwin" ]; then - echo "checking nawk" - tmpawk=`which nawk 2>/dev/null | awk '{print $1}'` - if [ -x $tmpawk ]; then - prog=$tmpawk - fi - - echo "checking gawk" - tmpawk=`which gawk 2>/dev/null | awk '{print $1}'` - if [ -x $tmpawk ]; then - prog=$tmpawk - fi -fi - -echo "prog="$prog - -umask 077 -export defaultaof -export defaultgop -export defaultfft -export defaultcycle -export defaultiterate -( -$prog ' -BEGIN { - prefix = ENVIRON["prefix"]; - version = ENVIRON["version"]; - myself = ENVIRON["myself"]; - defaultgop = ENVIRON["defaultgop"] - defaultaof = ENVIRON["defaultaof"] - defaultfft = ENVIRON["defaultfft"] - defaultcycle = ENVIRON["defaultcycle"] - defaultiterate = ENVIRON["defaultiterate"] - while( 1 ) - { - options = "" - printf( "\n" ) > "/dev/tty"; - printf( "---------------------------------------------------------------------\n" ) > "/dev/tty"; - printf( "\n" ) > "/dev/tty"; - printf( " MAFFT %s\n", version ) > "/dev/tty"; - printf( "\n" ) > "/dev/tty"; - printf( " K. Katoh, K. Misawa, K. Kuma and T. Miyata (2002)\n" ) > "/dev/tty"; - printf( " Nucleic Acids Research 30: 3059-3066.\n" ) > "/dev/tty"; - printf( " http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft\n" ) > "/dev/tty"; - printf( "---------------------------------------------------------------------\n" ) > "/dev/tty"; - printf( "\n" ); - - while( 1 ) - { - printf( "\n" ) > "/dev/tty"; - printf( "Input file? (fasta format)\n@ " ) > "/dev/tty"; - res = getline < "/dev/tty"; - close( "/dev/tty" ) - if( res == 0 || NF == 0 ) - continue; - infile0 = sprintf( "%s", $1 ); - infile = sprintf( "%s", $1 ); - - res = getline < infile; - close( infile ); - if( res == -1 ) - printf( "%s: No such file.\n\n", infile ); - else if( res == 0 ) - printf( "%s: Empty.\n", infile ); - else - { - printf( "OK. infile = %s\n\n", infile ); - break; - } - } - nseq = 0; - - while( 1 ) - { - printf( "\n" ) > "/dev/tty"; - printf( "Output file?\n" ) > "/dev/tty"; - printf( "@ " ) > "/dev/tty"; - res = getline < "/dev/tty"; - close( "/dev/tty" ); - if( res == 0 || NF == 0 ) - continue; - else - { - outfile = sprintf( "%s", $1 ); - printf( "OK. outfile = %s\n\n", outfile ); - break; - } - } - - - while( 1 ) - { - retree = defaultcycle - printf( "\n" ); - printf( "Number of tree-rebuilding?\n" ) > "/dev/tty"; - printf( "@ [%d] ", retree ) > "/dev/tty"; - res = getline < "/dev/tty"; - close( "/dev/tty" ); - if( res == 0 ) - continue; - else if( NF == 0 ) - ; - else - retree = 0 + $1; - if( retree < 1 || 10 < retree ) - ; - else - { - printf( "OK. %d\n\n", retree ); - break; - } - } - - while( 1 ) - { - niterate = defaultiterate; - printf( "\n" ); - printf( "Maximum number of iterations?\n" ) > "/dev/tty"; - printf( "@ [%d] ", niterate ) > "/dev/tty"; - res = getline < "/dev/tty"; - close( "/dev/tty" ); - if( res == 0 ) - continue; - else if( NF == 0 ) - ; - else - niterate = 0 + $1; - if( niterate < 0 || 1000 < niterate ) - ; - else - { - printf( "OK. %d\n\n", niterate ); - break; - } - } - - while( 1 ) - { - fft = defaultfft; - printf( "\n" ); - printf( "Use fft?\n" ) > "/dev/tty"; - printf( "@ [%s] ", fft?"Yes":"No" ) > "/dev/tty"; - res = getline < "/dev/tty"; - close( "/dev/tty" ); - if( res == 0 ) - continue; - else if( NF == 0 ) - { - break; - } - else if( NF == 0 || $0 ~ /^[Yy]/ ) - { - fft = 1; - break; - } - else if( NF == 0 || $0 ~ /^[Nn]/ ) - { - fft = 0; - break; - } - } - if( fft ) - { - printf( "OK. FFT is enabled.\n\n" ); - fftparam = " --fft "; - } - else - { - printf( "OK. FFT is disabled.\n\n" ); - fftparam = " --nofft "; - } - - while( 1 ) - { - scoringmatrix = 3; - printf( "\n" ); - printf( "Scoring matrix? (ignored when DNA sequence is input.)\n" ) > "/dev/tty"; - printf( " 1. BLOSUM 30\n" ) > "/dev/tty"; - printf( " 2. BLOSUM 45\n" ) > "/dev/tty"; - printf( " 3. BLOSUM 62\n" ) > "/dev/tty"; - printf( " 4. BLOSUM 80\n" ) > "/dev/tty"; - printf( " 5. JTT 200\n" ) > "/dev/tty"; - printf( " 6. JTT 100\n" ) > "/dev/tty"; - printf( "@ [%d] ", scoringmatrix ) > "/dev/tty"; - res = getline < "/dev/tty"; - close( "/dev/tty" ); - if( res == 0 ) - continue; - else if( NF == 0 ) - ; - else - scoringmatrix = 0 + $1; - if( scoringmatrix < 1 || 6 < scoringmatrix ) - ; - else - { - break; - } - } - if( scoringmatrix == 1 ) - scoringparam = " --bl 30 "; - else if( scoringmatrix == 2 ) - scoringparam = " --bl 45 "; - else if( scoringmatrix == 3 ) - scoringparam = " --bl 62 "; - else if( scoringmatrix == 4 ) - scoringparam = " --bl 80 "; - else if( scoringmatrix == 5 ) - scoringparam = " --jtt 200 "; - else if( scoringmatrix == 6 ) - scoringparam = " --jtt 100 "; - printf( "OK. %s\n\n",scoringparam ); - - while( 1 ) - { - penalty = 0.0 + defaultgop; - offset = 0.0 + defaultaof; - printf( "\n" ); - printf( "Parameters (gap opening penalty, offset)?\n", penalty, offset ) > "/dev/tty"; - printf( "@ [%5.3f, %5.3f] ", penalty, offset ) > "/dev/tty"; - res = getline < "/dev/tty"; - close( "/dev/tty" ); - if( res == 0 ) - continue; - else if( NF == 2 ) - { - penalty = 0.0 + $1; - offset = 0.0 + $2; - } - else if( NF == 0 ) - ; - else - continue; - if( penalty <= 0.0 || 10.0 < penalty ) - ; - else if( offset <= 0.0 || 10.0 < offset ) - ; - else - { - printf( "OK. %5.3f %5.3f\n\n", penalty, offset ); - break; - } - } - - command = sprintf( "%s %s --retree %d --maxiterate %d %s --op %f --ep %f %s > %s", myself, fftparam, retree, niterate, scoringparam, penalty, offset, infile, outfile ); - printf( "%s\n\n", command ); - - - while( 1 ) - { - go = 0; - printf( "\n" ); - printf( "OK?\n" ); - printf( "@ [Y] " ) > "/dev/tty"; - res = getline < "/dev/tty"; - close( "/dev/tty" ); - if( res == 0 ) - continue; - else if( NF == 0 || $0 ~ /^[Yy]/ ) - { - go=1; - break; - } - else - break; - } - if( go ) break; - printf( "\n" ); - printf( "\n" ); - } - system( command ); -} -' -) -exit 0;