--- /dev/null
+#! /bin/bash
+
+er=0;
+myself=`dirname "$0"`/`basename "$0"`; export myself
+version="v7.310 (2017/Mar/17)"; 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 mingw` ]; then
+ os="mingw"
+elif [ `echo $os | grep -i darwin` ]; then
+ os="darwin"
+elif [ `echo $os | grep -i sunos` ]; then
+ os="sunos"
+elif [ `echo $os | grep -i linux` ]; then
+ os="linux"
+else
+ os="unix"
+fi
+export os
+
+if [ "$MAFFT_BINARIES" ]; then
+ prefix="$MAFFT_BINARIES"
+else
+ prefix=/usr/local/libexec/mafft
+fi
+export prefix
+
+if [ $# -gt 0 ]; then
+ if [ "$1" = "--man" ]; then
+ man "$prefix/mafft.1"
+ exit 0;
+ fi
+fi
+
+if [ -x "$prefix/version" ]; then
+ versionbin=`"$prefix/version"` # for cygwin 2.7
+ else
+ versionbin="0.000"
+fi
+
+if ! expr "$version" : v"$versionbin" > /dev/null ; then
+ echo "" 1>&2
+ echo "v$versionbin != $version" 1>&2
+ echo "" 1>&2
+ echo "There is a problem in the configuration of your shell." 1>&2
+ echo "Check the MAFFT_BINARIES environmental variable by" 1>&2
+ echo "$ echo \$MAFFT_BINARIES" 1>&2
+ echo "" 1>&2
+ echo "This variable must be *unset*, unless you have installed MAFFT" 1>&2
+ echo "with a special configuration. To unset this variable, type" 1>&2
+ echo "$ unset MAFFT_BINARIES" 1>&2
+ echo "or" 1>&2
+ echo "% unsetenv MAFFT_BINARIES" 1>&2
+ echo "Then retry" 1>&2
+ echo "$ mafft input > output" 1>&2
+ echo "" 1>&2
+ echo "To keep this change permanently, edit setting files" 1>&2
+ echo "(.bash_profile, .profile, .cshrc, etc) in your home directory" 1>&2
+ echo "to delete the MAFFT_BINARIES line." 1>&2
+ echo "On MacOSX, also edit or remove the .MacOSX/environment.plist file" 1>&2
+ echo "and then re-login (MacOSX 10.6) or reboot (MacOSX 10.7)." 1>&2
+ echo "" 1>&2
+ echo "Please send a problem report to kazutaka.katoh@aist.go.jp," 1>&2
+ echo "if this problem remains." 1>&2
+ echo "" 1>&2
+ exit 1
+ er=1
+fi
+
+defaultiterate=0
+defaultcycle=2
+defaultgop="1.53"
+#defaultaof="0.123"
+defaultaof="0.000"
+defaultlaof="0.100"
+defaultlgop="-2.00"
+defaultfft=1
+defaultrough=0
+defaultdistance="ktuples"
+#defaultdistance="local"
+defaultweighti="2.7"
+defaultweightr="0.0"
+defaultweightm="1.0"
+defaultdafs=0
+defaultmccaskill=0
+defaultcontrafold=0
+defaultalgopt=" "
+defaultalgoptit=" "
+defaultsbstmodel=" -b 62 "
+defaultfmodel=" "
+defaultkappa=" "
+if [ $progname = "xinsi" -o $progname = "mafft-xinsi" ]; then
+ defaultfft=1
+ defaultcycle=1
+ defaultiterate=1000
+ defaultdistance="scarna"
+ defaultweighti="3.2"
+ defaultweightr="8.0"
+ defaultweightm="2.0"
+ defaultmccaskill=1
+ defaultcontrafold=0
+ defaultdafs=0
+ defaultalgopt=" -A "
+ defaultalgoptit=" -AB " ## chui
+ defaultaof="0.0"
+ defaultsbstmodel=" -b 62 "
+ defaultkappa=" "
+ defaultfmodel=" " # 2013/06/18
+elif [ $progname = "qinsi" -o $progname = "mafft-qinsi" ]; then
+ defaultfft=1
+ defaultcycle=1
+ defaultiterate=1000
+ defaultdistance="global"
+ defaultweighti="3.2"
+ defaultweightr="8.0"
+ defaultweightm="2.0"
+ defaultmccaskill=1
+ defaultcontrafold=0
+ defaultdafs=0
+ defaultalgopt=" -A "
+ defaultalgoptit=" -AB " ## chui
+ defaultaof="0.0"
+ defaultsbstmodel=" -b 62 "
+ defaultkappa=" "
+ defaultfmodel=" " # 2013/06/18
+elif [ $progname = "linsi" -o $progname = "mafft-linsi" ]; then
+ defaultfft=0
+ defaultcycle=1
+ defaultiterate=1000
+ defaultdistance="local"
+elif [ $progname = "ginsi" -o $progname = "mafft-ginsi" ]; then
+ defaultfft=1
+ defaultcycle=1
+ defaultiterate=1000
+ defaultdistance="global"
+elif [ $progname = "einsi" -o $progname = "mafft-einsi" ]; then
+ defaultfft=0
+ defaultcycle=1
+ defaultiterate=1000
+ defaultdistance="localgenaf"
+elif [ $progname = "fftns" -o $progname = "mafft-fftns" ]; then
+ defaultfft=1
+ defaultcycle=2
+ defaultdistance="ktuples"
+elif [ $progname = "fftnsi" -o $progname = "mafft-fftnsi" ]; then
+ defaultfft=1
+ defaultcycle=2
+ defaultiterate=2
+ defaultdistance="ktuples"
+elif [ $progname = "nwns" -o $progname = "mafft-nwns" ]; then
+ defaultfft=0
+ defaultcycle=2
+ defaultdistance="ktuples"
+elif [ $progname = "nwnsi" -o $progname = "mafft-nwnsi" ]; then
+ defaultfft=0
+ defaultcycle=2
+ defaultiterate=2
+ defaultdistance="ktuples"
+fi
+outputfile=""
+namelength=-1
+anysymbol=0
+parallelizationstrategy="BAATARI2"
+kappa=$defaultkappa
+sbstmodel=$defaultsbstmodel
+fmodel=$defaultfmodel
+nmodel=" "
+gop=$defaultgop
+gopdist=$defaultgop
+aof=$defaultaof
+cycle=$defaultcycle
+iterate=$defaultiterate
+fft=$defaultfft
+rough=$defaultrough
+distance=$defaultdistance
+forcefft=0
+memopt=" "
+weightopt=" "
+GGOP="-6.00"
+LGOP="-6.00"
+LEXP="-0.000"
+GEXP="-0.000"
+lgop=$defaultlgop
+lexp="-0.100"
+laof=$defaultlaof
+pggop="-2.00"
+pgexp="-0.10"
+pgaof="0.10"
+rgop="-1.530"
+rgep="-0.000"
+seqtype=" "
+weighti=$defaultweighti
+weightr=$defaultweightr
+weightm=$defaultweightm
+rnaalifold=0
+dafs=$defaultdafs
+mccaskill=$defaultmccaskill
+contrafold=$defaultcontrafold
+progressfile="/dev/stderr"
+debug=0
+sw=0
+algopt=$defaultalgopt
+algoptit=$defaultalgoptit
+#algspecified=0
+pairspecified=0
+scorecalcopt=" "
+coreout=0
+corethr="0.5"
+corewin="100"
+coreext=" "
+outputformat="pir"
+f2clext="-N"
+outorder="input"
+seed="x"
+seedtable="x"
+auto=0
+groupsize=-1
+partsize=50
+partdist="ktuples"
+partorderopt=" -x "
+treeout=0
+distout=0
+treein=0
+topin=0
+treeinopt=" "
+seedfiles="/dev/null"
+seedtablefile="/dev/null"
+pdblist="/dev/null"
+ownlist="/dev/null"
+strdir="$PWD"
+aamatrix="/dev/null"
+treeinfile="/dev/null"
+rnascoremtx=" "
+laraparams="/dev/null"
+foldalignopt=" "
+treealg=" -X 0.1 "
+sueff="1.0"
+scoreoutarg=" "
+numthreads=0
+numthreadsit=-1
+numthreadstb=-1
+randomseed=0
+addfile="/dev/null"
+addarg0=" "
+addarg=" "
+addsinglearg=" "
+add2ndhalfarg=" "
+mapoutfile="/dev/null"
+fragment=0
+legacygapopt=" "
+mergetable="/dev/null"
+mergearg=" "
+seedoffset=0
+outnum=" "
+last_e=5000
+last_m=3
+last_subopt=" "
+last_once=" "
+adjustdirection=0
+tuplesize=6
+termgapopt=" -O "
+#termgapopt=" " # gap/gap ga kakenai node
+similarityoffset="0.0"
+unalignlevel="0.0"
+unalignspecified=0
+spfactor="100.0"
+shiftpenaltyspecified=0
+opdistspecified=0
+allowshift=0
+enrich=0
+enrichseq=0
+enrichstr=0
+seektarget=""
+fixthreshold="0.0"
+bunkatsuopt=" "
+npickup=0
+minimumweight="0.00001" # 2016/Mar
+usenaivepairscore=" "
+oldgenafparam=0
+sprigorous=0
+pileuporshuffle="l"
+initialramusage="20GB"
+focusarg=" "
+if [ $# -gt 0 ]; then
+ if [ "$1" = "--version" ]; then
+ echo "$version" 1>&2
+ exit 0;
+ elif [ "$1" = "--help" -o "$1" = "--info" ]; then
+ shift
+ er=1;
+ fi
+ while [ $# -gt 1 ];
+ do
+ if [ "$1" = "--auto" ]; then
+ auto=1
+ elif [ "$1" = "--anysymbol" ]; then
+ anysymbol=1
+ elif [ "$1" = "--preservecase" ]; then
+ anysymbol=1
+ elif [ "$1" = "--clustalout" ]; then
+ outputformat="clustal"
+ elif [ "$1" = "--phylipout" ]; then
+ outputformat="phylip"
+ elif [ "$1" = "--reorder" ]; then
+ outorder="aligned"
+ partorderopt=" "
+ elif [ "$1" = "--inputorder" ]; then
+ outorder="input"
+ partorderopt=" -x "
+ elif [ "$1" = "--unweight" ]; then
+ weightopt=" -u "
+ elif [ "$1" = "--termgappenalty" ]; then
+ termgapopt=" "
+ elif [ "$1" = "--alga" ]; then
+ algopt=" "
+ algoptit=" "
+# algspecified=1
+ elif [ "$1" = "--algq" ]; then
+ algopt=" -Q "
+ algoptit=" "
+ echo "" 1>&2
+ echo "--algq is no longer supported!" 1>&2
+ echo "" 1>&2
+ exit 1;
+# algspecified=1
+ elif [ "$1" = "--namelength" ]; then
+ shift
+ namelength=`expr "$1" - 0`
+ if ! expr "$1" : "[0-9]" > /dev/null ; then
+ echo "Specify the length of name in clustal format output!" 1>&2
+ exit
+ fi
+ elif [ "$1" = "--groupsize" ]; then
+ shift
+ groupsize=`expr "$1" - 0`
+ if ! expr "$1" : "[0-9]" > /dev/null ; then
+ echo "Specify groupsize!" 1>&2
+ exit
+ fi
+ elif [ "$1" = "--partsize" ]; then
+ shift
+ partsize=`expr "$1" - 0`
+ if ! expr "$1" : "[0-9]" > /dev/null ; then
+ echo "Specify partsize!" 1>&2
+ exit
+ fi
+ elif [ "$1" = "--parttree" ]; then
+ distance="parttree"
+ partdist="ktuples"
+ elif [ "$1" = "--dpparttree" ]; then
+ distance="parttree"
+ partdist="localalign"
+ elif [ "$1" = "--fastaparttree" ]; then
+ distance="parttree"
+ partdist="fasta"
+ elif [ "$1" = "--treeout" ]; then
+ treeout=1
+ elif [ "$1" = "--distout" ]; then
+ distout=1
+ elif [ "$1" = "--fastswpair" ]; then
+ distance="fasta"
+ pairspecified=1
+ sw=1
+ elif [ "$1" = "--fastapair" ]; then
+ distance="fasta"
+ pairspecified=1
+ sw=0
+ elif [ "$1" = "--averagelinkage" ]; then
+ treealg=" -X 1.0 "
+ sueff="1.0"
+ elif [ "$1" = "--minimumlinkage" ]; then
+ treealg=" -X 0.0 "
+ sueff="0.0"
+ elif [ "$1" = "--mixedlinkage" ]; then
+ shift
+ sueff="$1"
+ treealg=" -X $1"
+ elif [ "$1" = "--noscore" ]; then
+ scorecalcopt=" -Z "
+ elif [ "$1" = "--6mermultipair" ]; then
+ distance="ktuplesmulti"
+ tuplesize=6
+ pairspecified=1
+ elif [ "$1" = "--10mermultipair" ]; then
+ distance="ktuplesmulti"
+ tuplesize=10
+ pairspecified=1
+ elif [ "$1" = "--6merpair" ]; then
+ distance="ktuples"
+ tuplesize=6
+ pairspecified=1
+ elif [ "$1" = "--10merpair" ]; then
+ distance="ktuples"
+ tuplesize=10
+ pairspecified=1
+ elif [ "$1" = "--blastpair" ]; then
+ distance="blast"
+ pairspecified=1
+ elif [ "$1" = "--lastmultipair" ]; then
+ distance="lastmulti"
+ pairspecified=1
+ elif [ "$1" = "--globalpair" ]; then
+ distance="global"
+ pairspecified=1
+ elif [ "$1" = "--shortlongpair" ]; then
+ distance="local"
+ usenaivepairscore="-Z"
+ laof=0.0 # addfull no tokini tsukawareru.
+ lexp=0.0 # addfull no tokini tsukawareru.
+ pgaof=0.0 # local nara iranai
+ pgexp=0.0 # local nara iranai
+ pairspecified=1
+ elif [ "$1" = "--longshortpair" ]; then
+ distance="local"
+ usenaivepairscore="-Z"
+ laof=0.0 # addfull no tokini tsukawareru.
+ lexp=0.0 # addfull no tokini tsukawareru.
+ pgaof=0.0 # local nara iranai
+ pgexp=0.0 # local nara iranai
+ pairspecified=1
+ elif [ "$1" = "--localpair" ]; then
+ distance="local"
+ pairspecified=1
+ elif [ "$1" = "--lastpair" ]; then
+ distance="last"
+ pairspecified=1
+ elif [ "$1" = "--multipair" ]; then
+ distance="multi"
+ pairspecified=1
+ elif [ "$1" = "--hybridpair" ]; then
+ distance="hybrid"
+ pairspecified=1
+ elif [ "$1" = "--scarnapair" ]; then
+ distance="scarna"
+ pairspecified=1
+ elif [ "$1" = "--dafspair" ]; then
+ distance="dafs"
+ pairspecified=1
+ elif [ "$1" = "--larapair" ]; then
+ distance="lara"
+ pairspecified=1
+ elif [ "$1" = "--slarapair" ]; then
+ distance="slara"
+ pairspecified=1
+ elif [ "$1" = "--foldalignpair" ]; then
+ distance="foldalignlocal"
+ pairspecified=1
+ elif [ "$1" = "--foldalignlocalpair" ]; then
+ distance="foldalignlocal"
+ pairspecified=1
+ elif [ "$1" = "--foldalignglobalpair" ]; then
+ distance="foldalignglobal"
+ pairspecified=1
+ elif [ "$1" = "--globalgenafpair" ]; then
+ distance="globalgenaf"
+ pairspecified=1
+ echo "" 1>&2
+ echo "--globalgenaf is no longer supported!" 1>&2
+ echo "" 1>&2
+ exit 1;
+ elif [ "$1" = "--localgenafpair" ]; then
+ distance="localgenaf"
+ pairspecified=1
+ elif [ "$1" = "--genafpair" ]; then
+ distance="localgenaf"
+ pairspecified=1
+ elif [ "$1" = "--oldgenafpair" ]; then
+ distance="localgenaf"
+ pairspecified=1
+ oldgenafparam=1
+ elif [ "$1" = "--memsave" ]; then
+ memopt=" -M -B " # -B (bunkatsunashi no riyu ga omoidasenai)
+ elif [ "$1" = "--nomemsave" ]; then
+ memopt=" -N "
+ elif [ "$1" = "--nuc" ]; then
+ seqtype=" -D "
+ elif [ "$1" = "--amino" ]; then
+ seqtype=" -P "
+ elif [ "$1" = "--fft" ]; then
+ fft=1
+ forcefft=1
+ elif [ "$1" = "--nofft" ]; then
+ fft=0
+ elif [ "$1" = "--quiet" ]; then
+ if [ $os = "mingw" ]; then
+ progressfile="nul"
+ else
+ progressfile="/dev/null"
+ fi
+ elif [ "$1" = "--debug" ]; then
+ debug=1
+ elif [ "$1" = "--coreext" ]; then
+ coreext=" -c "
+ elif [ "$1" = "--core" ]; then
+ coreout=1
+ elif [ "$1" = "--adjustdirection" ]; then
+ adjustdirection=1
+ elif [ "$1" = "--adjustdirectionaccurately" ]; then
+ adjustdirection=2
+ elif [ "$1" = "--progress" ]; then
+ shift
+ progressfile="$1"
+ if ! ( expr "$progressfile" : "\/" > /dev/null || expr "$progressfile" : "[A-Za-z]\:" > /dev/null ) ; then
+ echo "Specify a progress file name with the absolute path!" 1>&2
+ exit
+ fi
+ elif [ "$1" = "--out" ]; then
+ shift
+ outputfile="$1"
+ elif [ "$1" = "--thread" ]; then
+ shift
+ if ! expr "$1" : "[0-9\-]" > /dev/null ; then
+ echo "Specify the number of threads. Or, use --thread -1" 1>&2
+ exit
+ fi
+ numthreads=`expr "$1" - 0`
+ elif [ "$1" = "--threadtb" ]; then
+ shift
+ if ! expr "$1" : "[0-9\-]" > /dev/null ; then
+ echo "Specify the number of threads for the iterative step!" 1>&2
+ exit
+ fi
+ numthreadstb=`expr "$1" - 0`
+ elif [ "$1" = "--threadit" ]; then
+ shift
+ if ! expr "$1" : "[0-9\-]" > /dev/null ; then
+ echo "Specify the number of threads for the iterative step!" 1>&2
+ exit
+ fi
+ numthreadsit=`expr "$1" - 0`
+ elif [ "$1" = "--last_subopt" ]; then
+ last_subopt="-S"
+ elif [ "$1" = "--last_once" ]; then
+ last_once="-U"
+ elif [ "$1" = "--last_m" ]; then
+ shift
+ last_m=`expr "$1" - 0`
+ elif [ "$1" = "--last_e" ]; then
+ shift
+ last_e=`expr "$1" - 0`
+ elif [ "$1" = "--randomseed" ]; then
+ shift
+ randomseed=`expr "$1" - 0`
+ elif [ "$1" = "--bestfirst" ]; then
+ parallelizationstrategy="BESTFIRST"
+ elif [ "$1" = "--adhoc0" ]; then
+ parallelizationstrategy="BAATARI0"
+ elif [ "$1" = "--adhoc1" ]; then
+ parallelizationstrategy="BAATARI1"
+ elif [ "$1" = "--adhoc2" ]; then
+ parallelizationstrategy="BAATARI2"
+ elif [ "$1" = "--simplehillclimbing" ]; then
+ parallelizationstrategy="BAATARI2"
+ elif [ "$1" = "--scoreout" ]; then
+ scoreoutarg="-S -B"
+ elif [ "$1" = "--outnum" ]; then
+ outnum="-n"
+ elif [ "$1" = "--leavegappyregion" ]; then
+ legacygapopt="-L"
+ elif [ "$1" = "--legacygappenalty" ]; then
+ legacygapopt="-L"
+ elif [ "$1" = "--merge" ]; then
+ shift
+ mergetable="$1"
+ if [ ! -e "$mergetable" ]; then
+ echo "Cannot open $mergetable" 1>&2
+ echo "" 1>&2
+ exit
+ fi
+ elif [ "$1" = "--addprofile" ]; then
+ shift
+ addarg0="-I"
+ addfile="$1"
+ elif [ "$1" = "--add" ]; then
+ shift
+ addarg0="-K -I"
+ addfile="$1"
+ elif [ "$1" = "--addfragments" ]; then
+ shift
+ addarg0="-K -I"
+ addfile="$1"
+ fragment=1
+ elif [ "$1" = "--addfull" ]; then
+ shift
+ addarg0="-K -I"
+ addfile="$1"
+ fragment=-1
+ elif [ "$1" = "--addlong" ]; then
+ shift
+ addarg0="-K -I"
+ addfile="$1"
+ fragment=-2
+ elif [ "$1" = "--smoothing" ]; then
+ add2ndhalfarg=$add2ndhalfarg" -p "
+ elif [ "$1" = "--keeplength" ]; then
+ add2ndhalfarg=$add2ndhalfarg" -Y "
+ elif [ "$1" = "--mapout" ]; then
+ add2ndhalfarg=$add2ndhalfarg" -Z -Y "
+ elif [ "$1" = "--mapoutfile" ]; then
+ shift
+ add2ndhalfarg=$add2ndhalfarg" -Z -Y "
+ mapoutfile="$1"
+ elif [ "$1" = "--maxiterate" ]; then
+ shift
+ iterate=`expr "$1" - 0`
+ if ! expr "$1" : "[0-9]" > /dev/null ; then
+ echo "Specify the number of iterations!" 1>&2
+ exit
+ fi
+ elif [ "$1" = "--retree" ]; then
+ shift
+ cycle=`expr "$1" - 0`
+ if ! expr "$1" : "[0-9]" > /dev/null ; then
+ echo "Specify the number of tree rebuilding!" 1>&2
+ exit
+ fi
+ elif [ "$1" = "--text" ]; then
+ sbstmodel=" -b -2 -a "
+ f2clext="-E"
+ seqtype="-P"
+ fft=0
+ elif [ "$1" = "--aamatrix" ]; then
+ shift
+ sbstmodel=" -b -1 "
+ aamatrix="$1"
+ if [ ! -e "$aamatrix" ]; then
+ echo "Cannot open $aamatrix" 1>&2
+ echo "" 1>&2
+ exit
+ fi
+ elif [ "$1" = "--treein" ]; then
+ shift
+ treeinopt=" -U "
+ treein=1
+ treeinfile="$1"
+ if [ ! -e "$treeinfile" ]; then
+ echo "Cannot open $treeinfile" 1>&2
+ echo "" 1>&2
+ exit
+ fi
+ elif [ "$1" = "--pileup" ]; then
+ treeinopt=" -U "
+ treein=1
+ pileuporshuffle="p"
+ elif [ "$1" = "--randomchain" ]; then
+ treeinopt=" -U "
+ treein=1
+ pileuporshuffle="s"
+ elif [ "$1" = "--topin" ]; then
+ shift
+ treeinopt=" -V "
+ treein=1
+ treeinfile="$1"
+ echo "The --topin option has been disabled." 1>&2
+ echo "There was a bug in version < 6.530." 1>&2
+ echo "This bug has not yet been fixed." 1>&2
+ exit 1
+ elif [ "$1" = "--memsavetree" ]; then
+ treeinopt=" -U "
+ treein=1
+ pileuporshuffle="C"
+ elif [ "$1" = "--memsavetreex" ]; then
+ treeinopt=" -U "
+ treein=1
+ pileuporshuffle="c"
+ elif [ "$1" = "--initialramusage" ]; then
+ shift
+ treeinopt=" -U "
+ treein=1
+ initialramusage="$1"
+ pileuporshuffle="c"
+ elif [ "$1" = "--kappa" ]; then
+ shift
+ kappa=" -k $1 "
+ if ! expr "$1" : "[0-9]" > /dev/null ; then
+ echo "Specify kappa value!" 1>&2
+ exit
+ fi
+ elif [ "$1" = "--fmodel" ]; then
+ fmodel=" -a "
+ elif [ "$1" = "--nwildcard" ]; then
+ nmodel=" -: "
+ elif [ "$1" = "--nzero" ]; then
+ nmodel=" "
+ elif [ "$1" = "--jtt" ]; then
+ shift
+ sbstmodel=" -j $1"
+# if ! expr "$1" : "[0-9]" > /dev/null ; then
+# echo "Specify pam value!" 1>&2
+# exit
+# fi
+ elif [ "$1" = "--kimura" ]; then
+ shift
+ sbstmodel=" -j $1"
+# if ! expr "$1" : "[0-9]" > /dev/null ; then
+# echo "Specify pam value!" 1>&2
+# exit
+# fi
+ elif [ "$1" = "--tm" ]; then
+ shift
+ sbstmodel=" -m $1"
+# if ! expr "$1" : "[0-9]" > /dev/null ; then
+# echo "Specify pam value!" 1>&2
+# exit
+# fi
+ elif [ "$1" = "--bl" ]; then
+ shift
+ sbstmodel=" -b $1"
+ if ! expr "$1" : "[0-9]" > /dev/null ; then
+ echo "blosum $1?" 1>&2
+ exit
+ fi
+ elif [ "$1" = "--weighti" ]; then
+ shift
+ weighti="$1"
+ if ! expr "$1" : "[0-9]" > /dev/null ; then
+ echo "Specify weighti value!" 1>&2
+ exit
+ fi
+ elif [ "$1" = "--weightr" ]; then
+ shift
+ weightr="$1"
+ if ! expr "$1" : "[0-9]" > /dev/null ; then
+ echo "Specify weightr value!" 1>&2
+ exit
+ fi
+ elif [ "$1" = "--weightm" ]; then
+ shift
+ weightm="$1"
+ if ! expr "$1" : "[0-9]" > /dev/null ; then
+ echo "Specify weightm value!" 1>&2
+ exit
+ fi
+ elif [ "$1" = "--rnaalifold" ]; then
+ rnaalifold=1
+ elif [ "$1" = "--mccaskill" ]; then
+ mccaskill=1
+ contrafold=0
+ dafs=0
+ elif [ "$1" = "--contrafold" ]; then
+ mccaskill=0
+ contrafold=1
+ dafs=0
+ elif [ "$1" = "--dafs" ]; then
+ mccaskill=0
+ contrafold=0
+ dafs=1
+ elif [ "$1" = "--ribosum" ]; then
+ rnascoremtx=" -s "
+ elif [ "$1" = "--op" ]; then
+ shift
+ gop="$1"
+ if ! expr "$1" : "[0-9]" > /dev/null ; then
+ echo "Specify op!" 1>&2
+ exit
+ fi
+ elif [ "$1" = "--opdist" ]; then
+ shift
+ gopdist="$1"
+ if ! expr "$1" : "[0-9]" > /dev/null ; then
+ echo "Specify opdist!" 1>&2
+ exit
+ fi
+ opdistspecified=1
+ elif [ "$1" = "--allowshift" ]; then
+ allowshift=1
+ elif [ "$1" = "--shiftpenalty" ]; then
+ shift
+ spfactor="$1"
+ if ! expr "$1" : "[0-9]" > /dev/null ; then
+ echo "Specify sf!" 1>&2
+ exit
+ fi
+ shiftpenaltyspecified=1
+ elif [ "$1" = "--ep" ]; then
+ shift
+# aof="$1"
+ tmpval="$1"
+ aof=`awk "BEGIN{ print -1.0 * \"$tmpval\"}"`
+ if ! expr "$aof" : "[0-9\-]" > /dev/null ; then
+ printf "\nSpecify a number for ep, like --ep 0.1\n" 1>&2
+ printf "'$1' cannot be interpreted as a number..\n\n" 1>&2
+ exit
+ fi
+ elif [ "$1" = "--rop" ]; then
+ shift
+ rgop="$1"
+# Atode check
+ elif [ "$1" = "--rep" ]; then
+ shift
+ rgep="$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" = "--GEXP" ]; then
+ shift
+ GEXP="$1"
+ elif [ "$1" = "--GOP" ]; then
+ shift
+ GGOP="$1"
+ elif [ "$1" = "--gop" ]; then
+ shift
+ pggop="$1"
+ elif [ "$1" = "--gep" ]; then
+ shift
+ pgaof="$1"
+ elif [ "$1" = "--gexp" ]; then
+ shift
+ pgexp="$1"
+ elif [ "$1" = "--laraparams" ]; then
+ shift
+ laraparams="$1"
+ elif [ "$1" = "--corethr" ]; then
+ shift
+ corethr="$1"
+ elif [ "$1" = "--corewin" ]; then
+ shift
+ corewin="$1"
+ elif [ "$1" = "--strdir" ]; then
+ shift
+ strdir="$1"
+ elif [ "$1" = "--pdbidlist" ]; then
+ shift
+ pdblist="$1"
+ if [ ! -e "$pdblist" ]; then
+ echo "Cannot open $pdblist" 1>&2
+ echo "" 1>&2
+ exit
+ fi
+ elif [ "$1" = "--pdbfilelist" ]; then
+ shift
+ ownlist="$1"
+ if [ ! -e "$ownlist" ]; then
+ echo "Cannot open $ownlist" 1>&2
+ echo "" 1>&2
+ exit
+ fi
+ elif [ "$1" = "--enrich" ]; then
+ enrich=1
+ enrichseq=1
+ enrichstr=1
+ seektarget=""
+ elif [ "$1" = "--enrichseq" ]; then
+ enrich=1
+ enrichseq=1
+ enrichstr=0
+ seektarget="-seq"
+ elif [ "$1" = "--enrichstr" ]; then
+ enrich=1
+ enrichseq=0
+ enrichstr=1
+ seektarget="-str"
+ elif [ "$1" = "--seedtable" ]; then
+ shift
+ seedtable="y"
+ seedtablefile="$1"
+ elif [ "$1" = "--seed" ]; then
+ shift
+ seed="m"
+ seedfiles="$seedfiles $1"
+ elif [ "$1" = "--minimumweight" ]; then
+ shift
+ minimumweight="$1"
+ elif [ "$1" = "--similaritylevel" ]; then
+ shift
+ similarityoffset="$1"
+ elif [ "$1" = "--unalignlevel" ]; then
+ shift
+ unalignlevel="$1"
+ unalignspecified=1
+ elif [ "$1" = "--skipiterate" ]; then
+ shift
+ fixthreshold="$1"
+ elif [ "$1" = "--bunkatsunashi" ]; then
+ bunkatsuopt=" -B "
+ elif [ "$1" = "--sp" ]; then
+ sprigorous=1
+ elif [ "$1" = "--focus" ]; then
+ focusarg=" -= "
+ elif [ "$1" = "--sparsepickup" ]; then
+ shift
+ npickup="$1"
+ elif [ $progname = "fftns" -o $progname = "nwns" ]; then
+ if [ "$1" -gt 0 ]; then
+ cycle=`expr "$1" - 0`
+ fi
+ else
+ echo "Unknown option: $1" 1>&2
+ er=1;
+# exit 1;
+ fi
+ shift
+ done;
+
+
+ echo "" 1>"$progressfile"
+
+# TMPFILE=/tmp/$progname.$$
+ TMPFILE=`mktemp -dt $progname.XXXXXXXXXX`
+ if [ $? -ne 0 ]; then
+ echo "mktemp seems to be obsolete. Re-trying without -t" 1>&2
+ TMPFILE=`mktemp -d /tmp/$progname.XXXXXXXXXX`
+ fi
+
+# if [ $os = "cygwin" ]; then
+# TMPFILE=`cygpath -w $TMPFILE` unnecessary for cygwin2.7
+# fi
+
+ umask 077
+# mkdir $TMPFILE || er=1
+ if [ $debug -eq 1 ]; then
+# trap "tar cfvz debuginfo.tgz $TMPFILE; rm -rf $TMPFILE " 0 # does not work in msys
+ trap "tar cfv - $TMPFILE | gzip -c > debuginfo.tgz; rm -rf $TMPFILE " 0
+ else
+ trap "rm -rf $TMPFILE" 0
+ fi
+ if [ $# -eq 1 ]; then
+ if [ -r "$1" -o "$1" = - ]; then
+
+ if [ -r "$addfile" ]; then
+ printf '';
+ else
+ echo "$0": Cannot open "$addfile". 1>&2
+ echo "" 1>&2
+ exit 1;
+ fi
+
+ cat "$1" | tr "\r" "\n" > $TMPFILE/infile
+ echo "" >> $TMPFILE/infile
+ cat "$addfile" | tr "\r" "\n" | grep -v "^$" >> $TMPFILE/infile
+ cat "$addfile" | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_addfile
+ cat "$aamatrix" | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_aamtx
+ cat "$mergetable" | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_subalignmentstable
+ cat "$treeinfile" | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_guidetree
+ cat "$seedtablefile" | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_seedtablefile
+ cat "$laraparams" | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_lara.params
+ cat "$pdblist" | tr "\r" "\n" | grep -v "^$" > $TMPFILE/pdblist
+ cat "$ownlist" | tr "\r" "\n" | grep -v "^$" > $TMPFILE/ownlist
+
+# echo $seedfiles
+ infilename="$1"
+ seedfilesintmp="/dev/null"
+ seednseq="0"
+ set $seedfiles > /dev/null
+ while [ $# -gt 1 ];
+ do
+ shift
+ if [ -r "$1" ]; then
+ cat "$1" | tr "\r" "\n" > $TMPFILE/seed$#
+ else
+ echo "$0": Cannot open "$1". 1>&2
+ echo "" 1>&2
+ exit 1;
+ fi
+ seednseq=$seednseq" "`grep -c '^[>|=]' $TMPFILE/seed$#`
+ seedfilesintmp=$seedfilesintmp" "seed$#
+ done
+# ls $TMPFILE
+# echo $seedfilesintmp
+# echo $seednseq
+
+
+ else
+ echo "$0": Cannot open "$1". 1>&2
+ echo "" 1>&2
+ er=1
+# exit 1;
+ fi
+ else
+# echo '$#'"=$#" 1>&2
+ er=1
+ fi
+
+
+
+ if [ $numthreads -lt 0 ]; then
+ if [ $os = "linux" ]; then
+ nlogicalcore=`cat /proc/cpuinfo | grep "^processor" | uniq | wc -l`
+ ncoresinacpu=`cat /proc/cpuinfo | grep 'cpu cores' | uniq | awk '{print $4}'`
+ nphysicalcpu=`cat /proc/cpuinfo | grep 'physical id' | sort | uniq | wc -l`
+ if [ $nlogicalcore -eq 0 ]; then
+ echo "Cannot get the number of processors from /proc/cpuinfo" 1>>"$progressfile"
+ exit 1
+ fi
+ if [ ${#ncoresinacpu} -gt 0 -a $nphysicalcpu -gt 0 ]; then
+ numthreads=`expr $ncoresinacpu '*' $nphysicalcpu`
+# if [ $nlogicalcore -gt $numthreads ]; then # Hyperthreading
+# numthreads=`expr $numthreads '+' 1`
+# fi
+ else
+ numthreads=$nlogicalcore
+ fi
+ elif [ $os = "darwin" ]; then
+ numthreads=`sysctl -n hw.physicalcpu`
+ if [ -z $numthreads ]; then
+ echo "Cannot get the number of physical cores from sysctl" 1>>"$progressfile"
+ exit 1
+ fi
+# nlogicalcore=`sysctl -n hw.logicalcpu`
+# if [ $nlogicalcore -gt $numthreads ]; then # Hyperthreading
+# numthreads=`expr $numthreads '+' 1`
+# fi
+ elif [ $os = "mingw" -o $os = "cygwin" ]; then
+ numthreads=`wmic cpu get NumberOfCores | head -2 | tail -1 | awk '{print $1}'`
+ else
+ echo "Cannot count the number of physical cores." 1>>"$progressfile"
+ exit 1
+ fi
+ echo "OS = "$os 1>>"$progressfile"
+ echo "The number of physical cores = " $numthreads 1>>"$progressfile"
+ fi
+
+ if [ $numthreadstb -lt 0 ]; then
+ numthreadstb=$numthreads
+ fi
+
+ if [ $numthreadsit -lt 0 ]; then
+ if [ $numthreads -lt 11 ]; then
+ numthreadsit=$numthreads
+ else
+ numthreadsit=10
+ fi
+ fi
+
+ if [ $numthreadsit -eq 0 -a $parallelizationstrategy = "BESTFIRST" ]; then
+ echo 'Impossible' 1>&2;
+ exit 1;
+ fi
+
+ if [ "$addarg0" != " " ]; then
+ iterate=0 # 2013/03/23
+ "$prefix/countlen" < $TMPFILE/_addfile > $TMPFILE/addsize 2>>"$progressfile"
+ nadd=`awk '{print $1}' $TMPFILE/addsize`
+ if [ $nadd -eq "0" ]; then
+ echo Check $addfile 1>&2
+ exit 1;
+ fi
+ if [ $seed != "x" -o $seedtable != "x" ]; then
+ echo 'Impossible' 1>&2;
+ echo 'Use either ONE of --seed, --seedtable, --addprofile and --add.' 1>&2
+ exit 1;
+ fi
+ else
+ nadd="0"
+ fi
+
+ if [ $auto -eq 1 ]; then
+ "$prefix/countlen" < $TMPFILE/infile > $TMPFILE/size 2>>"$progressfile"
+ nseq=`awk '{print $1}' $TMPFILE/size`
+ nlen=`awk '{print $3}' $TMPFILE/size`
+
+ if [ $nlen -lt 3000 -a $nseq -lt 100 ]; then
+ distance="local"
+ iterate=1000
+ cycle=1
+ elif [ $nlen -lt 1000 -a $nseq -lt 200 ]; then
+ distance="local"
+ iterate=2
+ cycle=1
+ elif [ $nlen -lt 10000 -a $nseq -lt 500 ]; then
+ distance="ktuples"
+ iterate=2
+ cycle=2
+ elif [ $nseq -lt 50000 ]; then # changed from 10000 2014/Oct/4
+ distance="ktuples"
+ iterate=0
+ cycle=2
+ elif [ $nseq -lt 90000 ]; then # changed from 30000 2014/Oct/4
+ distance="ktuples"
+ iterate=0
+ cycle=1
+ elif [ $nlen -lt 3000 ]; then
+ distance="parttree"
+ partdist="localalign"
+ algopt=" "
+ algoptit=" "
+# algspecified=1
+ cycle=1
+ else
+ distance="parttree"
+ partdist="ktuples"
+ algopt=" "
+ algoptit=" "
+# algspecified=1
+ cycle=1
+ fi
+
+
+# if [ $nlen -lt 3000 -a $nseq -lt 100 ]; then
+# distance="local"
+# iterate=1000
+# cycle=1
+# elif [ $nlen -lt 1000 -a $nseq -lt 200 ]; then
+# distance="local"
+# iterate=2
+# cycle=1
+# elif [ $nlen -lt 10000 -a $nseq -lt 500 ]; then
+# distance="ktuples"
+# iterate=2
+# cycle=2
+# elif [ $nseq -lt 200000 ]; then
+# distance="ktuples"
+# iterate=0
+# treeinopt=" -U "
+# treein=1
+# pileuporshuffle="a"
+# elif [ $nlen -lt 3000 ]; then
+# distance="parttree"
+# partdist="localalign"
+# algopt=" "
+# algoptit=" "
+## algspecified=1
+# cycle=1
+# else
+# distance="parttree"
+# partdist="ktuples"
+# algopt=" "
+# algoptit=" "
+## algspecified=1
+# cycle=1
+# fi
+
+
+ if [ $fragment -ne 0 ]; then
+ norg=`expr $nseq '-' $nadd`
+ npair=`expr $norg '*' $nadd`
+ echo "nadd = " $nadd 1>>"$progressfile"
+ echo "npair = " $npair 1>>"$progressfile"
+ echo "nseq = " $nseq 1>>"$progressfile"
+ echo "nlen = " $nlen 1>>"$progressfile"
+# nagasa check!
+#
+ if [ $npair -gt 10000000 -o $nlen -gt 500000 ]; then # 2015/Jun
+ distance="ktuples"
+ echo "use ktuples, size=$tuplesize!" 1>>"$progressfile"
+ elif [ $npair -gt 3000000 -o $nlen -gt 100000 ]; then # 2015/Jun
+ distance="multi"
+ weighti="0.0"
+ echo "use multipair, weighti=0.0!" 1>>"$progressfile"
+ else
+ distance="multi"
+ echo "use multipair, weighti=$weighti!" 1>>"$progressfile"
+ fi
+ pairspecified=1
+ fi
+ fi
+
+ if [ `awk "BEGIN {print( 0.0+\"$sueff\" < 0.0 || 0.0+\"$sueff\" > 1.0 )}"` -gt 0 ]; then
+ printf "\n%s\n\n" "The argument of --mixedlinkage must be between 0.0 and 1.0" 1>>"$progressfile"
+ exit 1;
+ fi
+
+ if [ $allowshift -eq 1 ]; then
+ if [ $unalignspecified -ne 1 ]; then
+ unalignlevel="0.8"
+ fi
+ if [ $shiftpenaltyspecified -ne 1 ]; then
+ spfactor="2.00"
+ fi
+ fi
+
+ if [ $opdistspecified -ne 1 ]; then
+ gopdist=$gop
+ fi
+
+ if [ $unalignlevel != "0.0" -o `awk "BEGIN {print( 0.0+\"$spfactor\" < 100.0 )}"` -gt 0 ]; then
+ nmodel=" -: "
+ termgapopt=" "
+ if [ $distance = "localgenaf" ]; then
+ printf "\n%s\n" "The combination of --allowshift and --genafpair (E-INS-i/-1) is not supported." 1>>"$progressfile"
+ printf "%s\n" "Instead, please try --allowshift --globalpair (G-INS-i/-1 in the web version)," 1>>"$progressfile"
+ printf "%s\n\n" "which covers the situation for --genafpair (E-INS-i/-1), too." 1>>"$progressfile"
+ exit 1;
+ fi
+ if [ $distance != "global" -o `awk "BEGIN {print( 0.0+\"$weighti\" < 1.0 )}"` -gt 0 ]; then
+ printf "\n%s\n\n" "At present, --unalignlevel # or --allowshift is supported only with the --globalpair option." 1>>"$progressfile"
+ exit 1;
+ fi
+ if [ $fragment -ne 0 ]; then
+ printf "\n%s\n\n" "At present, --unalignlevel # or --allowshift is not supported with the --addfragments option." 1>>"$progressfile"
+ exit 1;
+ fi
+ fi
+
+ if [ `awk "BEGIN {print( 0.0+\"$spfactor\" < 1.0 )}"` -gt 0 ]; then
+ printf "\n%s\n" "shiftpenalty must be >1." 1>>"$progressfile"
+ exit 1;
+ fi
+
+ if [ `awk "BEGIN {print( 0.0+\"$fixthreshold\" < 0.0 )}"` -gt 0 ]; then
+ printf "\n%s\n\n" "The 'fix' parameter must be >= 0.0" 1>>"$progressfile"
+ exit 1;
+ fi
+
+ if [ `awk "BEGIN {print( 0.0+\"$unalignlevel\" < 0.0 || 0.0+\"$unalignlevel\" > 1.0 )}"` -gt 0 ]; then
+ printf "\n%s\n\n" "The 'unalignlevel' parameter must be between 0.0 and 1.0" 1>>"$progressfile"
+ exit 1;
+ fi
+ if [ `awk "BEGIN {print( 0.0+\"$unalignlevel\" > 0.0 )}"` -gt 0 ]; then
+ laof="0"
+ lexp="0"
+ pgaof="0"
+ pgexp="0"
+ LEXP="0"
+ GEXP="0"
+ termgapopt=" "
+# if [ $auto -eq 1 -o $fragment -ne 0 -o $iterate -gt 0 ]; then
+ if [ $fragment -ne 0 ]; then
+ printf "\n%s\n\n" "At present, the 'unalignlevel > 0' mode is not supported with the --addfragments option." 1>>"$progressfile"
+ exit 1;
+ fi
+ if [ $distance = "parttree" ]; then
+ printf "\n%s\n\n" "At present, the 'unalignlevel > 0' mode is not supported in the (dp)parttree option." 1>>"$progressfile"
+ exit 1;
+ fi
+ if [ $distance = "localgenaf" ]; then
+ printf "\n%s\n" "The --genafpair is not supported in the 'unalignlevel > 0' mode." 1>>"$progressfile"
+ printf "%s\n" "Instead, please try --unalignlevel xx --globalpair," 1>>"$progressfile"
+ printf "%s\n\n" "which covers the situation for --genafpair (E-INS-i), too." 1>>"$progressfile"
+ exit 1;
+ fi
+# if [ $distance != "ktuples" -a `awk "BEGIN {print( 0.0+\"$weighti\" > 0.0 )}"` -gt 0 -a $iterate -gt 0 ]; then
+# printf "\n%s\n\n" "Please add --weighti 0.0, for now." 1>>"$progressfile"
+# exit 1;
+# fi
+ fi
+
+ if [ `awk "BEGIN {print( 0.0+\"$similarityoffset\" != 0.0 && 0.0+\"$unalignlevel\" != 0.0 )}"` -gt 0 ]; then
+ printf "\n%s\n\n" "Do not simultaneously specify --similaritylevel and --unalignlevel" 1>>"$progressfile"
+ exit 1;
+ fi
+
+ if [ `awk "BEGIN {print( 0.0+\"$similarityoffset\" < -1.0 || 0.0+\"$similarityoffset\" > 1.0 )}"` -gt 0 ]; then
+ printf "\n%s\n\n" "Similarity must be between -1.0 and +1.0" 1>>"$progressfile"
+ exit 1;
+ fi
+ aof=`awk "BEGIN{print 0.0 + \"$similarityoffset\" + $aof}"`
+ laof=`awk "BEGIN{print 0.0 + \"$similarityoffset\" + $laof}"`
+ pgaof=`awk "BEGIN{print 0.0 + \"$similarityoffset\" + $pgaof}"`
+
+
+ if [ $parallelizationstrategy = "BESTFIRST" -o $parallelizationstrategy = "BAATARI0" ]; then
+ iteratelimit=254
+ else
+ iteratelimit=16
+ fi
+ if [ $iterate -gt $iteratelimit ]; then #??
+ iterate=$iteratelimit
+ fi
+
+ if [ $rnaalifold -eq 1 ]; then
+ rnaopt=" -e $rgep -o $rgop -c $weightm -r $weightr -R $rnascoremtx "
+# rnaoptit=" -o $rgop -BT -c $weightm -r $weightr -R "
+ rnaoptit=" -o $rgop -F -c $weightm -r $weightr -R "
+ elif [ $mccaskill -eq 1 -o $dafs -eq 1 -o $contrafold -eq 1 ]; then
+ rnaopt=" -o $rgop -c $weightm -r $weightr "
+# rnaoptit=" -e $rgep -o $rgop -BT -c $weightm -r $weightr $rnascoremtx "
+ rnaoptit=" -e $rgep -o $rgop -F -c $weightm -r $weightr $rnascoremtx "
+ else
+ rnaopt=" "
+ rnaoptit=" -F "
+ fi
+
+# if [ $algspecified -eq 0 ]; then
+# if [ $distance = "parttree" ]; then
+# algopt=" -Q "
+# algoptit=" "
+# else
+# algopt=" "
+# algoptit=" "
+# fi
+# fi
+
+ if [ $sprigorous -eq 1 ]; then
+ algopt=" -@ "
+ if [ $iterate -gt 0 ]; then
+ if [ $numthreadsit -eq 0 ]; then
+ algoptit=" -@ -B -Z -z 1000 "
+ else
+ echo "" 1>>"$progressfile"
+ echo "At present, the combination of --sp and iterative refinement is supported only in a single thread." 1>>"$progressfile"
+ echo "Please try \"--thread -1 --threadit 0\", which runs the iterative refinment calculation on a single thread." 1>>"$progressfile"
+ echo "" 1>>"$progressfile"
+ exit 1;
+# algoptit=" -@ -B -z 1000 "
+ fi
+ fi
+ termgapopt=" "
+ fft=0
+ memopt=" -N "
+ fi
+
+ model="$sbstmodel $kappa $fmodel $nmodel"
+
+ if [ $er -eq 1 ]; then
+ echo "------------------------------------------------------------------------------" 1>&2
+ echo " MAFFT" $version 1>&2
+# echo "" 1>&2
+# echo " Input format: fasta" 1>&2
+# echo "" 1>&2
+# echo " Usage: `basename $0` [options] inputfile > outputfile" 1>&2
+ echo " http://mafft.cbrc.jp/alignment/software/" 1>&2
+ echo " MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)" 1>&2
+# echo "------------------------------------------------------------------------------" 1>&2
+# echo " % mafft in > out" 1>&2
+ echo "------------------------------------------------------------------------------" 1>&2
+# echo "" 1>&2
+ echo "High speed:" 1>&2
+ echo " % mafft in > out" 1>&2
+ echo " % mafft --retree 1 in > out (fast)" 1>&2
+ echo "" 1>&2
+ echo "High accuracy (for <~200 sequences x <~2,000 aa/nt):" 1>&2
+ echo " % mafft --maxiterate 1000 --localpair in > out (% linsi in > out is also ok)" 1>&2
+ echo " % mafft --maxiterate 1000 --genafpair in > out (% einsi in > out)" 1>&2
+ echo " % mafft --maxiterate 1000 --globalpair in > out (% ginsi in > out)" 1>&2
+ echo "" 1>&2
+ echo "If unsure which option to use:" 1>&2
+ echo " % mafft --auto in > out" 1>&2
+ echo "" 1>&2
+# echo "Other options:" 1>&2
+ echo "--op # : Gap opening penalty, default: 1.53" 1>&2
+ echo "--ep # : Offset (works like gap extension penalty), default: 0.0" 1>&2
+ echo "--maxiterate # : Maximum number of iterative refinement, default: 0" 1>&2
+ echo "--clustalout : Output: clustal format, default: fasta" 1>&2
+ echo "--reorder : Outorder: aligned, default: input order" 1>&2
+ echo "--quiet : Do not report progress" 1>&2
+ echo "--thread # : Number of threads (if unsure, --thread -1)" 1>&2
+# echo "" 1>&2
+# echo " % mafft --maxiterate 1000 --localpair in > out (L-INS-i)" 1>&2
+# echo " most accurate in many cases, assumes only one alignable domain" 1>&2
+# echo "" 1>&2
+# echo " % mafft --maxiterate 1000 --genafpair in > out (E-INS-i)" 1>&2
+# echo " works well if many unalignable residues exist between alignable domains" 1>&2
+# echo "" 1>&2
+# echo " % mafft --maxiterate 1000 --globalpair in > out (G-INS-i)" 1>&2
+# echo " suitable for globally alignable sequences " 1>&2
+# echo "" 1>&2
+# echo " % mafft --maxiterate 1000 in > out (FFT-NS-i)" 1>&2
+# echo " accurate and slow, iterative refinement method " 1>&2
+# echo "" 1>&2
+# echo "If the input sequences are long (~1,000,000nt)," 1>&2
+# echo " % mafft --retree 1 --memsave --fft in > out (FFT-NS-1-memsave, new in v5.8)" 1>&2
+# echo "" 1>&2
+# echo "If many (~5,000) sequences are to be aligned," 1>&2
+# echo "" 1>&2
+# echo " % mafft --retree 1 [--memsave] --nofft in > out (NW-NS-1, new in v5.8)" 1>&2
+# echo "" 1>&2
+# echo " --localpair : All pairwise local alignment information is included" 1>&2
+# echo " to the objective function, default: off" 1>&2
+# echo " --globalpair : All pairwise global alignment information is included" 1>&2
+# echo " to the objective function, default: off" 1>&2
+# echo " --op # : Gap opening penalty, default: $defaultgop " 1>&2
+# echo " --ep # : Offset (works like gap extension penalty), default: $defaultaof " 1>&2
+# echo " --bl #, --jtt # : Scoring matrix, default: BLOSUM62" 1>&2
+# echo " Alternatives are BLOSUM (--bl) 30, 45, 62, 80, " 1>&2
+# echo " or JTT (--jtt) # PAM. " 1>&2
+# echo " --nuc or --amino : Sequence type, default: auto" 1>&2
+# echo " --retree # : The number of tree building in progressive method " 1>&2
+# echo " (see the paper for detail), default: $defaultcycle " 1>&2
+# echo " --maxiterate # : Maximum number of iterative refinement, default: $defaultiterate " 1>&2
+# if [ $defaultfft -eq 1 ]; then
+# echo " --fft or --nofft: FFT is enabled or disabled, default: enabled" 1>&2
+# else
+# echo " --fft or --nofft: FFT is enabled or disabled, default: disabled" 1>&2
+# fi
+# echo " --memsave: Memory saving mode" 1>&2
+# echo " (for long genomic sequences), default: off" 1>&2
+# echo " --clustalout : Output: clustal format, default: fasta" 1>&2
+# echo " --reorder : Outorder: aligned, default: input order" 1>&2
+# echo " --quiet : Do not report progress" 1>&2
+# echo "-----------------------------------------------------------------------------" 1>&2
+ exit 1;
+ fi
+ if [ $sw -eq 1 ]; then
+ swopt=" -A "
+ else
+ swopt=" "
+ fi
+
+ if [ $distance = "fasta" -o $partdist = "fasta" ]; then
+ if [ ! "$FASTA_4_MAFFT" ]; then
+ FASTA_4_MAFFT=`which fasta34`
+ fi
+
+ if [ ! -x "$FASTA_4_MAFFT" ]; then
+ echo "" 1>&2
+ echo "== Install FASTA ========================================================" 1>&2
+ echo "This option requires the fasta34 program (FASTA version x.xx or higher)" 1>&2
+ echo "installed in your PATH. If you have the fasta34 program but have renamed" 1>&2
+ echo "(like /usr/local/bin/myfasta), set the FASTA_4_MAFFT environment variable" 1>&2
+ echo "to point your fasta34 (like setenv FASTA_4_MAFFT /usr/local/bin/myfasta)." 1>&2
+ echo "=========================================================================" 1>&2
+ echo "" 1>&2
+ exit 1
+ fi
+ fi
+ if [ $distance = "last" -o $distance = "lastmulti" ]; then
+ if [ ! -x "$prefix/lastal" -o ! -x "$prefix/lastdb" ]; then
+ echo "" 1>&2
+ echo "== Install LAST ============================================================" 1>&2
+ echo "LAST (Kielbasa, Wan, Sato, Horton, Frith 2011 Genome Res. 21:487) is required." 1>&2
+ echo "http://last.cbrc.jp/" 1>&2
+ echo "http://mafft.cbrc.jp/alignment/software/xxxxxxx.html " 1>&2
+ echo "============================================================================" 1>&2
+ echo "" 1>&2
+ exit 1
+ fi
+ fi
+ if [ $distance = "lara" -o $distance = "slara" ]; then
+ if [ ! -x "$prefix/mafft_lara" ]; then
+ echo "" 1>&2
+ echo "== Install LaRA =========================================================" 1>&2
+ echo "This option requires LaRA (Bauer et al. http://www.planet-lisa.net/)." 1>&2
+ echo "The executable have to be renamed to 'mafft_lara' and installed into " 1>&2
+ echo "the $prefix directory. " 1>&2
+ echo "A configuration file of LaRA also have to be given" 1>&2
+ echo "mafft-xinsi --larapair --laraparams parameter_file" 1>&2
+ echo "mafft-xinsi --slarapair --laraparams parameter_file" 1>&2
+ echo "=========================================================================" 1>&2
+ echo "" 1>&2
+ exit 1
+ fi
+ if [ ! -s "$laraparams" ]; then
+ echo "" 1>&2
+ echo "== Configure LaRA =======================================================" 1>&2
+ echo "A configuration file of LaRA have to be given" 1>&2
+ echo "mafft-xinsi --larapair --laraparams parameter_file" 1>&2
+ echo "mafft-xinsi --slarapair --laraparams parameter_file" 1>&2
+ echo "=========================================================================" 1>&2
+ echo "" 1>&2
+ exit 1
+ fi
+ fi
+ if [ $distance = "foldalignlocal" -o $distance = "foldalignglobal" ]; then
+ if [ ! -x "$prefix/foldalign210" ]; then
+ echo "" 1>&2
+ echo "== Install FOLDALIGN ====================================================" 1>&2
+ echo "This option requires FOLDALIGN (Havgaard et al. http://foldalign.ku.dk/)." 1>&2
+ echo "The executable have to be renamed to 'foldalign210' and installed into " 1>&2
+ echo "the $prefix directory. " 1>&2
+ echo "=========================================================================" 1>&2
+ echo "" 1>&2
+ exit 1
+ fi
+ fi
+ if [ $distance = "scarna" -o $mccaskill -eq 1 ]; then
+ if [ ! -x "$prefix/mxscarnamod" ]; then
+ echo "" 1>&2
+ echo "== Install MXSCARNA ======================================================" 1>&2
+ echo "MXSCARNA (Tabei et al. BMC Bioinformatics 2008 9:33) is required." 1>&2
+ echo "Please 'make' at the 'extensions' directory of the MAFFT source package," 1>&2
+ echo "which contains the modified version of MXSCARNA." 1>&2
+ echo "http://mafft.cbrc.jp/alignment/software/source.html " 1>&2
+ echo "==========================================================================" 1>&2
+ echo "" 1>&2
+ exit 1
+ fi
+ fi
+ if [ $distance = "dafs" -o $dafs -eq 1 ]; then
+ if [ ! -x "$prefix/dafs" ]; then
+ echo "" 1>&2
+ echo "== Install DAFS===========================================================" 1>&2
+ echo "DAFS (Sato et al. Journal 2012 issue:page) is required." 1>&2
+ echo "http://www.ncrna.org/ " 1>&2
+ echo "==========================================================================" 1>&2
+ echo "" 1>&2
+ exit 1
+ fi
+ fi
+ if [ $contrafold -eq 1 ]; then
+ if [ ! -x "$prefix/contrafold" ]; then
+ echo "" 1>&2
+ echo "== Install CONTRAfold ===================================================" 1>&2
+ echo "This option requires CONTRAfold" 1>&2
+ echo "(Do et al. http://contra.stanford.edu/contrafold/)." 1>&2
+ echo "The executable 'contrafold' have to be installed into " 1>&2
+ echo "the $prefix directory. " 1>&2
+ echo "=========================================================================" 1>&2
+ echo "" 1>&2
+ exit 1
+ fi
+ fi
+
+#old
+# if [ $treeout -eq 1 ]; then
+# parttreeoutopt="-t"
+# if [ $cycle -eq 0 ]; then
+# treeoutopt="-t -T"
+# groupsize=1
+# iterate=0
+# if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
+# distance="distonly"
+# fi
+# else
+# treeoutopt="-t"
+# fi
+# else
+# parttreeoutopt=" "
+# if [ $cycle -eq 0 ]; then
+# treeoutopt="-t -T"
+# iterate=0
+# if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
+# distance="distonly"
+# fi
+# else
+# treeoutopt=" "
+# fi
+# fi
+
+#new
+ if [ $cycle -eq 0 ]; then
+ treeoutopt="-t -T"
+ iterate=0
+ weighti="0.0" # 2016Jul31, tbfast.c kara idou
+# if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then # 2012/04, localpair --> local alignment distance
+# if [ $distance = "global" ]; then
+# distance="distonly"
+# fi
+ if [ $treeout -eq 1 ]; then
+ parttreeoutopt="-t"
+ groupsize=1
+ else
+ parttreeoutopt=" "
+ fi
+ if [ $distout -eq 1 ]; then
+ distoutopt="-y -T"
+ if [ $treeout -eq 0 ]; then
+ treeoutopt=""
+ fi
+ fi
+ else
+ if [ $treeout -eq 1 ]; then
+ parttreeoutopt="-t"
+ treeoutopt="-t"
+ else
+ parttreeoutopt=" "
+ treeoutopt=" "
+ fi
+ if [ $distout -eq 1 ]; then
+ distoutopt="-y"
+ fi
+ fi
+#
+
+ formatcheck=`grep -c '^[[:blank:]]\+>' $TMPFILE/infile | head -1 `
+ if [ $formatcheck -gt 0 ]; then
+ echo "The first character of a description line must be " 1>&2
+ echo "the greater-than (>) symbol, not a blank." 1>&2
+ echo "Please check the format around the following line(s):" 1>&2
+ grep -n '^[[:blank:]]\+>' $TMPFILE/infile 1>&2
+ exit 1
+ fi
+
+ nseq=`grep -c '^[>|=]' $TMPFILE/infile | head -1 `
+ if [ $nseq -eq 2 ]; then
+ cycle=1
+ fi
+ if [ $cycle -gt 3 ]; then
+ cycle=3
+ fi
+
+ if [ $nseq -gt 60000 -a $iterate -gt 1 ]; then # 2014/Oct/22, test
+ echo "Too many sequences to perform iterative refinement!" 1>&2
+ echo "Please use a progressive method." 1>&2
+ exit 1
+ fi
+ if [ $distance = "lastmulti" -o $distance = "multi" ]; then
+ if [ $fragment -eq 0 ]; then
+ echo 'Specify --addfragments too' 1>&2
+ exit 1
+ fi
+ fi
+
+ if [ $fragment -ne 0 ]; then
+ if [ $pairspecified -eq 0 ]; then
+ distance="multi"
+ fi
+ if [ $distance != "multi" -a $distance != "hybrid" -a $distance != "lastmulti" -a $distance != "local" -a $distance != "last" -a $distance != "ktuples" -a $distance != "ktuplesmulti" ]; then
+ echo 'Specify --multipair, --lastmultipair, --lastpair, --localpair, --6merpair, --6mermultipair or --hybridpair' 1>&2
+ exit 1
+ fi
+ fi
+
+ if [ "$memopt" = " -M -B " -a "$distance" != "ktuples" ]; then
+ echo "Impossible" 1>&2
+ exit 1
+ fi
+
+ if [ $distance = "parttree" ]; then
+ if [ $mergetable != "/dev/null" ]; then
+ echo "The combination of (dp)parttree and merge is Impossible. " 1>&2
+ exit 1
+ fi
+ if [ $addfile != "/dev/null" ]; then
+ echo "The combination of (dp)parttree and add(fragments) is Impossible. " 1>&2
+ exit 1
+ fi
+ if [ $seed != "x" -o $seedtable != "x" ]; then
+ echo "Impossible" 1>&2
+ exit 1
+ fi
+ if [ $iterate -gt 1 ]; then
+ echo "Impossible" 1>&2
+ exit 1
+ fi
+ if [ $outorder = "aligned" ]; then
+ outorder="input"
+ fi
+ outorder="input" # partorder ga kiku
+ if [ $partdist = "localalign" ]; then
+ splitopt=" -U " # -U -l -> fast
+ cycle=1
+ elif [ $partdist = "fasta" ]; then
+ splitopt=" -S "
+ cycle=1
+ else
+ splitopt=" "
+ fi
+ fi
+
+
+ if [ \( $distance = "ktuples" -o $distance = "ktuplesmulti" \) -a \( $seed = "x" -a $seedtable = "x" -a $ownlist = "/dev/null" -a $pdblist = "/dev/null" -a $enrichstr -eq 0 \) ]; then
+ localparam=""
+ weighti="0.0"
+ elif [ \( $distance = "ktuples" -o $distance = "ktuplesmulti" \) -a \( $seed != "x" -o $seedtable != "x" -o $ownlist != "/dev/null" -o $pdblist != "/dev/null" -o $enrichstr -eq 1 \) ]; then
+ if [ $cycle -lt 2 ]; then
+ cycle=2 # disttbfast ha seed hi-taiou # chuui 2014Aug21
+ fi
+ if [ $iterate -lt 2 ]; then
+ echo "############################################################################" 1>&2
+ echo "# Warning:" 1>&2
+ echo "# Progressive alignment method is incompatible with the --seed option." 1>&2
+ echo "# Automatically switched to the iterative refinement method." 1>&2
+ echo "# " 1>&2
+ echo "# Also consider using the '--add' option, which is compatible with" 1>&2
+ echo "# the progressive method and FASTER than the '--seed' option." 1>&2
+ echo "# Usage is:" 1>&2
+ echo "# % mafft --add newSequences existingAlignment > output" 1>&2
+ echo "############################################################################" 1>&2
+ iterate=2
+ fi
+ localparam="-l "$weighti
+ elif [ $distance = "parttree" ]; then
+ localparam=""
+ weighti="0.0"
+ if [ $groupsize -gt -1 ]; then
+ cycle=1
+ fi
+ else
+ localparam="-B -l "$weighti # weighti=0 demo bunkatsu nashi
+ if [ $cycle -gt 1 ]; then # 09/01/08
+ cycle=1
+ fi
+ fi
+
+
+ if [ $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
+ aof="0.000"
+ if [ $oldgenafparam -ne 1 ]; then
+ laof="0.0"
+ lexp="0.0"
+# LEXP="0.0" # default = 0.0
+ usenaivepairscore="-Z"
+ fi
+ fi
+
+
+# if [ $nseq -gt 5000 ]; then
+# fft=0
+# fi
+ if [ $forcefft -eq 1 ]; then
+ param_fft=" -G "
+ fft=1
+ elif [ $fft -eq 1 ]; then
+ param_fft=" -F "
+ else
+ param_fft=" "
+ fi
+
+ if [ $seed != "x" -a $seedtable != "x" ]; then
+ echo 'Use either one of seedtable and seed. Not both.' 1>&2
+ exit 1
+ fi
+ if [ $f2clext = "-E" -a $anysymbol -gt 0 ]; then
+ echo '' 1>&2
+ echo 'At present, the combination of --text and ( --anysymbol or --preservecase ) is impossible.' 1>&2
+ echo '' 1>&2
+ exit 1
+ fi
+
+ if [ $f2clext = "-E" -a $aamatrix != "/dev/null" ]; then
+ echo '' 1>&2
+ echo 'At present, the combination of --text and (--aamatrix) is impossible.' 1>&2
+ echo '' 1>&2
+ exit 1
+ fi
+
+ if [ $treein -eq 1 ]; then
+# if [ $iterate -gt 0 ]; then
+# echo 'Not supported yet.' 1>&2
+# exit 1
+# fi
+ if [ ! -s $TMPFILE/_guidetree ]; then
+ if [ $distance != "ktuples" ]; then
+ echo "Not supported yet" 1>>"$progressfile"
+ exit 1
+ fi
+ if [ $pileuporshuffle = "p" ]; then
+ echo "pileup" > $TMPFILE/_guidetree
+# weightopt=" -u " -> disttbfast.c?
+# numthreadstb=0 -> disttbfast.c
+ cycle=1 # disttbfast. shitei
+ elif [ $pileuporshuffle = "s" ]; then
+ echo "shuffle $randomseed" > $TMPFILE/_guidetree
+# numthreadstb=0 -> disttbfast.c
+# weightopt=" -u " -> disttbfast.c?
+ cycle=1 # disttbfast.c dem shitei
+ elif [ $pileuporshuffle = "C" ]; then
+ echo "very compact" > $TMPFILE/_guidetree
+ elif [ $pileuporshuffle = "c" ]; then
+ echo "compact " "$initialramusage" > $TMPFILE/_guidetree
+ elif [ $pileuporshuffle = "a" ]; then
+ echo "auto $randomseed 200" > $TMPFILE/_guidetree
+ fi
+ fi
+ fi
+
+ if [ $nadd -gt "0" ]; then
+ if [ $fragment -eq "1" ]; then
+ addarg="$addarg0 $nadd -g -0.01"
+ addsinglearg=""
+ cycle=1 # chuui 2014Aug25
+ elif [ $fragment -eq "-1" ]; then
+ addarg="$addarg0 $nadd"
+ addsinglearg="-V" # allowlongadds, 2014/04/02
+ cycle=1 # chuui 2014Aug25
+ elif [ $fragment -eq "-2" ]; then
+ addarg="$addarg0 $nadd"
+ addsinglearg="-V" # allowlongadds + smoothing
+ add2ndhalfarg=$add2ndhalfarg" -p "
+ cycle=1 # chuui 2014Aug25
+ usenaivepairscore="-Z" # 2015Jun01
+ laof=0.0 # 2015Jun01
+ lexp=0.0 # 2015Jun01
+ else
+ addarg="$addarg0 $nadd"
+ addsinglearg=""
+ fi
+
+# cycle=1 # chuui 2014Aug19
+ iterate=0
+# treealg=" -q " ## 2012/01/24 ## removed 2012/02/06
+ fi
+
+
+ if [ -z "$localparam" -a $fragment -eq 0 -a $distance != "parttree" ]; then
+# echo "use disttbfast"
+# echo cycle = $cycle
+ cycletbfast=1 # tbfast wo jikkou shinai
+ cycledisttbfast=$cycle # disttbfast ni -E cycle wo watasu
+ if [ $cycledisttbfast -eq 0 ]; then # --treeout de tsukau
+ cycledisttbfast=1
+ fi
+ else
+# echo "use tbfast"
+# echo cycle = $cycle
+ cycletbfast=$cycle # 1 ijou nara jikkou
+ cycledisttbfast=1 # disttbfast ha ikkai dake
+ fi
+
+# echo localparam=
+# echo $localparam
+# echo cycletbfast=
+# echo $cycletbfast
+# echo cycledisttbfast=
+# echo $cycledisttbfast
+
+#exit
+
+ if [ $adjustdirection -gt 0 -a $seed != "x" ]; then
+ echo '' 1>&2
+ echo 'The combination of --adjustdirection(accurately) and --seed is not supported.' 1>&2
+ echo '' 1>&2
+ exit 1
+ fi
+
+
+ if [ $mccaskill -eq 1 -o $dafs -eq 1 -o $rnaalifold -eq 1 -o $contrafold -eq 1 ]; then
+ if [ $distance = "ktuples" ]; then
+ echo 'Not supported.' 1>&2
+ echo 'Please add --globalpair, --localpair, --scarnapair, --dafspair' 1>&2
+ echo '--larapair, --slarapair, --foldalignlocalpair or --foldalignglobalpair' 1>&2
+ exit 1
+ fi
+ if [ $f2clext = "-E" ]; then
+ echo '' 1>&2
+ echo 'For RNA alignment, the --text mode is impossible.' 1>&2
+ echo '' 1>&2
+ exit 1
+ fi
+ fi
+
+# cycle ga atode henkou sareru node koko de strategy no namae wo kimeru.
+# kokokara
+ if [ $pileuporshuffle = "p" ]; then
+ strategy="Pileup-"
+ elif [ $pileuporshuffle = "s" ]; then
+ strategy="Randomchain-"
+ elif [ $mccaskill -eq 1 -o $dafs -eq 1 -o $rnaalifold -eq 1 -o $contrafold -eq 1 ]; then
+ if [ $distance = "scarna" -o $distance = "dafs" -o $distance = "lara" -o $distance = "slara" -o $distance = "foldalignlocal" -o $distance = "foldalignglobal" ]; then
+ strategy="X-"
+ elif [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o "globalgenaf" ]; then
+ strategy="Q-"
+ fi
+ elif [ $distance = "fasta" -a $sw -eq 0 ]; then
+ strategy="F-"
+ elif [ $distance = "fasta" -a $sw -eq 1 ]; then
+ strategy="H-"
+ elif [ $distance = "blast" ]; then
+ strategy="B-"
+ elif [ $distance = "global" -o $distance = "distonly" ]; then
+ strategy="G-"
+ elif [ $distance = "local" ]; then
+ strategy="L-"
+ elif [ $distance = "last" ]; then
+ strategy="Last-"
+ elif [ $distance = "hybrid" ]; then
+ strategy="Hybrid-"
+ elif [ $distance = "multi" ]; then
+ strategy="Multi-"
+ elif [ $distance = "lastmulti" ]; then
+ strategy="LastMulti-"
+ elif [ $distance = "localgenaf" ]; then
+ strategy="E-"
+ elif [ $distance = "globalgenaf" ]; then
+ strategy="K-"
+ elif [ $fft -eq 1 ]; then
+ strategy="FFT-"
+ else
+ strategy="NW-"
+ fi
+# if [ `echo "$weighti>0.0" | bc` -gt 0 ]; then
+ if [ `awk "BEGIN {print(0.0+\"$weighti\">0.0)}"` -gt 0 ]; then
+ strategy=$strategy"I"
+ fi
+ strategy=$strategy"NS-"
+ if [ $iterate -gt 0 ]; then
+ strategy=$strategy"i"
+ elif [ $distance = "parttree" ]; then
+ if [ $partdist = "fasta" ]; then
+ strategy=$strategy"FastaPartTree-"$cycle
+ elif [ $partdist = "localalign" ]; then
+ strategy=$strategy"DPPartTree-"$cycle
+ else
+ strategy=$strategy"PartTree-"$cycle
+ fi
+ elif [ $fragment -eq 1 ]; then
+ strategy=$strategy"fragment"
+ elif [ $fragment -eq -1 ]; then
+ strategy=$strategy"full"
+ elif [ $fragment -eq -2 ]; then
+ strategy=$strategy"long"
+ else
+ strategy=$strategy$cycle
+ fi
+
+ explanation='?'
+ performance='Not tested.'
+ if [ $strategy = "F-INS-i" ]; then
+ explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment information'
+ performance='Most accurate, but very slow'
+ elif [ $strategy = "L-INS-i" ]; then
+ explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment information'
+ performance='Probably most accurate, very slow'
+ elif [ $strategy = "E-INS-i" ]; then
+ explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment with generalized affine gap costs (Altschul 1998)'
+ performance='Suitable for sequences with long unalignable regions, very slow'
+ elif [ $strategy = "G-INS-i" ]; then
+ explanation='Iterative refinement method (<'$iterate') with GLOBAL pairwise alignment information'
+ performance='Suitable for sequences of similar lengths, very slow'
+ elif [ $strategy = "X-INS-i" ]; then
+ explanation='RNA secondary structure information is taken into account.'
+ performance='For short RNA sequences only, extremely 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
+ outputopt=" -c $strategy -r $TMPFILE/order $f2clext "
+ elif [ $outputformat = "clustal" -a $outorder = "input" ]; then
+ outputopt=" -c $strategy $f2clext "
+ elif [ $outputformat = "phylip" -a $outorder = "aligned" ]; then
+ outputopt=" -y -r $TMPFILE/order "
+ elif [ $outputformat = "phylip" -a $outorder = "input" ]; then
+ outputopt=" -y "
+ elif [ $outputformat = "pir" -a $outorder = "aligned" ]; then
+ outputopt=" -f -r $TMPFILE/order "
+ else
+ outputopt="null"
+ fi
+# kokomade
+
+
+
+# ( # 2017/Mar/17
+ pushd $TMPFILE > /dev/null;
+
+ cat /dev/null > pre
+
+# echo "nseq = " $nseq 1>>"$progressfile"
+# echo "distance = " $distance 1>>"$progressfile"
+# echo "iterate = " $iterate 1>>"$progressfile"
+# echo "cycle = " $cycle 1>>"$progressfile"
+
+ if [ $anysymbol -eq 1 ]; then
+ mv infile orig
+ "$prefix/replaceu" $seqtype -i orig > infile 2>>"$progressfile" || exit 1
+ fi
+
+ if [ $mergetable != "/dev/null" ]; then
+ if [ $nadd -gt "0" ]; then
+ echo "Impossible" 1>&2
+ exit 1
+ fi
+# if [ $seed != "x" -o $seedtable != "x" ]; then
+# echo "This version does not support the combination of merge and seed." 1>&2
+# exit 1
+# fi
+# iterate=0 # 2013/04/16
+ mergearg="-H $seedoffset"
+ fi
+
+ if [ $adjustdirection -gt 0 ]; then
+ if [ $fragment -ne 0 ]; then
+ fragarg="-F" #
+ else
+ fragarg="-F" # 2014/02/06, do not consider other additional sequences, even in the case of --add
+ fi
+ if [ $adjustdirection -eq 1 ]; then
+ "$prefix/makedirectionlist" $fragarg -C $numthreads -m -I $nadd -i infile -t 0.00 -r 5000 -o a > _direction 2>>"$progressfile"
+ elif [ $adjustdirection -eq 2 ]; then
+ "$prefix/makedirectionlist" $fragarg -C $numthreads -m -I $nadd -i infile -t 0.00 -r 100 -o a -d > _direction 2>>"$progressfile"
+ fi
+ "$prefix/setdirection" $mergearg -d _direction -i infile > infiled 2>>"$progressfile" || exit
+ mv infiled infile
+ if [ $anysymbol -eq 1 ]; then
+ "$prefix/setdirection" $mergearg -d _direction -i orig -r > origd 2>>"$progressfile" || exit
+ mv origd orig
+ fi
+ fi
+
+ if [ $seed != "x" -o $seedtable != "x" ]; then
+ if [ $pdblist != "/dev/null" -o $ownlist != "/dev/null" ]; then
+ echo "The combination of --seed and (--pdbidlist or --pdbfilelist) is impossible." 1>>"$progressfile"
+ exit 1
+ fi
+ if [ $enrich -eq 1 ]; then
+ echo "The combination of --seed and (--enrich, --enrichseq or --enrichstr) is impossible at present." 1>>"$progressfile"
+ exit 1
+ fi
+ fi
+
+ if [ $enrich -eq 1 ]; then
+ if [ $ownlist != "/dev/null" ]; then
+ echo "Warning: Sequence homologs of the structures given with the --pdbfilelist option cannot be collected.\n" 1>>"$progressfile"
+ fi
+ echo "SEEKQUENCER (http://sysimm.ifrec.osaka-u.ac.jp/seekquencer/) is" 1>>"$progressfile"
+ if [ $pdblist != "/dev/null" ]; then
+ echo "collecting homoplogs of the input sequences and the structures given with the --pdbidlist option." 1>>"$progressfile"
+ perl "$prefix/seekquencer_premafft.pl" $seektarget -run thread -trd 2 -seqd uniref90 -blim 1000 -noin -seqf infile -idf pdblist -out seekout -mod mafftash-split 2>>"seekerr"
+ seekres="$?"
+ else
+ echo "collecting homologs of the input sequences." 1>>"$progressfile"
+ perl "$prefix/seekquencer_premafft.pl" $seektarget -run thread -trd 2 -seqd uniref90 -blim 1000 -noin -seqf infile -out seekout -mod mafftash-split 2>>"seekerr"
+ seekres="$?"
+ fi
+ cat seekerr 1>>"$progressfile"
+
+ if [ $seekres -ne "0" ]; then
+ echo "Error in SEEKQUENCER" 1>>"$progressfile"
+ exit 1;
+ fi
+ echo "Done." 1>>"$progressfile"
+
+ if [ $enrichseq -eq 1 ]; then
+# cat seekout.seq >> infile
+ if [ $anysymbol -eq 1 ]; then
+ "$prefix/replaceu" $seqtype -i seekout.seq -o $nseq >> infile
+ cat seekout.seq >> orig
+ else
+ "$prefix/replaceu" $seqtype -i seekout.seq | sed 's/_os_[0-9]*_oe_//' >> infile
+ fi
+
+ fi
+ if [ $enrichstr -eq 1 ]; then
+ nseekstr=`wc -l < seekout.str`
+ if [ $nseekstr -gt 1 ]; then
+ cat seekout.str >> pdblist
+ pdblist="tsukaimasu"
+ fi
+ fi
+ fi
+
+ if [ $seed != "x" ]; then
+ mv infile infile2
+ if [ $anysymbol -eq 1 ]; then
+ mv orig orig2
+ cat /dev/null > orig
+ fi
+ cat /dev/null > infile
+ cat /dev/null > hat3.seed
+ seedoffset=0
+# echo "seednseq="$seednseq
+# echo "seedoffset="$seedoffset
+ set $seednseq >> "$progressfile"
+# echo $#
+ while [ $# -gt 1 ]
+ do
+ shift
+# echo "num="$#
+
+ if [ $anysymbol -eq 1 ]; then
+ cat seed$# >> orig
+ "$prefix/replaceu" $seqtype -i seed$# -o $seedoffset > clean 2>>"$progressfile" || exit 1
+ mv clean seed$#
+ fi
+ "$prefix/multi2hat3s" -t $nseq -o $seedoffset -i seed$# >> infile 2>>"$progressfile" || exit 1
+ cat hat3 >> hat3.seed
+# echo "$1"
+ seedoffset=`expr $seedoffset + $1`
+# echo "$1"
+# echo "seedoffset="$seedoffset
+ done;
+# echo "seedoffset="$seedoffset
+ if [ $anysymbol -eq 1 ]; then
+ "$prefix/replaceu" $seqtype -i orig2 -o $seedoffset >> infile 2>>"$progressfile" || exit 1 # yarinaoshi
+ cat orig2 >> orig
+ else
+ cat infile2 >> infile
+ fi
+ elif [ $seedtable != "x" ]; then
+ cat _seedtablefile > hat3.seed
+ elif [ $pdblist != "/dev/null" -o $ownlist != "/dev/null" ]; then
+ mv infile infile2
+ if [ $anysymbol -eq 1 ]; then
+ mv orig orig2
+ cat /dev/null > orig
+ fi
+ cat /dev/null > infile
+
+ echo "strdir = " 1>>"$progressfile"
+ echo $strdir 1>>"$progressfile"
+
+ echo "Calling DASH (http://sysimm.ifrec.osaka-u.ac.jp/dash/)" 1>>"$progressfile"
+ perl "$prefix/mafftash_premafft.pl" -p pdblist -o ownlist -d "$strdir" 2>>"dasherr"
+ dashres="$?"
+ cat dasherr 1>>"$progressfile"
+
+ if [ $dashres -ne "0" ]; then
+ echo "Error in DASH" 1>>"$progressfile"
+ exit 1;
+ fi
+ echo "Done." 1>>"$progressfile"
+
+ seedoffset=`grep -c '^[>|=]' instr | head -1 `
+
+ echo "# of structures = " 1>>"$progressfile"
+ echo $seedoffset 1>>"$progressfile"
+ mv hat3 hat3.seed
+
+ if [ $anysymbol -eq 1 ]; then
+ cat instr >> orig
+ "$prefix/replaceu" $seqtype -i instr -o 0 > clean 2>>"$progressfile" || exit 1
+ mv clean infile
+
+ "$prefix/replaceu" $seqtype -i orig2 -o $seedoffset >> infile 2>>"$progressfile" || exit 1 # yarinaoshi
+ cat orig2 >> orig
+ else
+ cat instr > infile
+ cat infile2 >> infile
+ fi
+ else
+ cat /dev/null > hat3.seed
+ fi
+# cat hat3.seed
+
+
+
+
+ if [ $mccaskill -eq 1 ]; then
+ "$prefix/mccaskillwrap" -s -C $numthreads -d "$prefix" -i infile > hat4 2>>"$progressfile" || exit 1
+ elif [ $dafs -eq 1 ]; then
+ "$prefix/mccaskillwrap" -G -C $numthreads -d "$prefix" -i infile > hat4 2>>"$progressfile" || exit 1
+ elif [ $contrafold -eq 1 ]; then
+ "$prefix/contrafoldwrap" -d "$prefix" -i infile > hat4 2>>"$progressfile" || exit 1
+ fi
+ if [ $distance = "fasta" ]; then
+ "$prefix/dndfast7" $swopt < infile > /dev/null 2>>"$progressfile" || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ elif [ $distance = "blast" ]; then
+ "$prefix/dndblast" < infile > /dev/null 2>>"$progressfile" || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ elif [ $distance = "foldalignlocal" ]; then
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $foldalignopt $model -g $lexp -f $lgop -Q $spfactor -h $laof -H -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ elif [ $distance = "foldalignglobal" ]; then
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $foldalignopt $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof -H -o -global -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ elif [ $distance = "slara" ]; then
+ "$prefix/pairlocalalign" -C $numthreads -p $laraparams $seqtype $model -f $lgop -Q $spfactor -T -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ elif [ $distance = "lara" ]; then
+ "$prefix/pairlocalalign" -C $numthreads -p $laraparams $seqtype $model -f $lgop -Q $spfactor -B -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ elif [ $distance = "scarna" ]; then
+# "$prefix/pairlocalalign" -C $numthreads $seqtype $model -f $pggop -Q $spfactor -s -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1
+# cat hat3.seed hat3 > hatx
+# mv hatx hat3
+# "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ "$prefix/tbfast" _ -C $numthreads $seqtype $model -f $pggop -Q $spfactor -s -d "$prefix" _ -+ $iterate -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ elif [ $distance = "dafs" ]; then
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $model -f $pggop -Q $spfactor -G -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ elif [ $distance = "global" ]; then
+# "$prefix/pairlocalalign" -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof -A $usenaivepairscore $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1
+# cat hat3.seed hat3 > hatx
+# mv hatx hat3
+# "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ "$prefix/tbfast" _ -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof -A $usenaivepairscore $focusarg _ -+ $iterate -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1
+
+ elif [ $distance = "local" ]; then
+ if [ $fragment -ne 0 ]; then
+ "$prefix/pairlocalalign" $localparam $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -L $usenaivepairscore < infile > /dev/null 2>>"$progressfile" || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/addsingle" -Q 100 $legacygapopt -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ else
+# "$prefix/pairlocalalign" -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -L $usenaivepairscore $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1
+# addarg wo watasanai
+# cat hat3.seed hat3 > hatx
+# mv hatx hat3
+# "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ "$prefix/tbfast" _ -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -L $usenaivepairscore $focusarg _ -+ $iterate -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ fi
+ elif [ $distance = "globalgenaf" ]; then
+ "$prefix/pairlocalalign" -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof -O $GGOP -E $GEXP -K $usenaivepairscore < infile > /dev/null 2>>"$progressfile" || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ elif [ $distance = "localgenaf" ]; then
+# "$prefix/pairlocalalign" -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -O $LGOP -E $LEXP -N $usenaivepairscore $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1
+# cat hat3.seed hat3 > hatx
+# mv hatx hat3
+# "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ "$prefix/tbfast" _ -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -O $LGOP -E $LEXP -N $usenaivepairscore $focusarg _ -+ $iterate -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ elif [ $distance = "last" ]; then
+ if [ $fragment -ne 0 ]; then
+ "$prefix/pairlocalalign" $addarg -C $numthreads $seqtype $model -e $last_e -w $last_m -g $lexp -f $lgop -Q $spfactor -h $laof -R $last_subopt $last_once -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/addsingle" -Q 100 $legacygapopt -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ else
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $model -e $last_e -w $last_m -g $lexp -f $lgop -Q $spfactor -h $laof -R $last_subopt $last_once -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1
+# addarg wo watasanai
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ fi
+ elif [ $distance = "lastmulti" ]; then
+ "$prefix/dndpre" $model -M 2 $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof < infile > /dev/null 2>>"$progressfile" || exit 1
+ mv hat2 hat2i
+ "$prefix/pairlocalalign" $addarg -C $numthreads $seqtype $model -e $last_e -w $last_m -g $lexp -f $lgop -Q $spfactor -h $laof -r $last_subopt $last_once -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hat2 hat2n
+ mv hatx hat3
+ if [ $fragment -ne 0 ]; then
+ "$prefix/addsingle" -Q 100 $legacygapopt -d -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ else
+ echo "Impossible" 1>&2
+ exit 1
+ fi
+ elif [ $distance = "multi" ]; then
+ "$prefix/dndpre" $model -M 2 $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -h $laof $usenaivepairscore < infile > /dev/null 2>>"$progressfile" || exit 1
+ mv hat2 hat2i
+ "$prefix/pairlocalalign" $localparam $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -Y $usenaivepairscore < infile > /dev/null 2>>"$progressfile" || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hat2 hat2n
+ mv hatx hat3
+ if [ $fragment -ne 0 ]; then
+ "$prefix/addsingle" -Q 100 $legacygapopt -d -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ else
+ echo "Impossible" 1>&2
+ exit 1
+ fi
+ elif [ $distance = "hybrid" ]; then
+ "$prefix/pairlocalalign" $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -Y < infile > /dev/null 2>>"$progressfile" || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/disttbfast" -E 1 -s $unalignlevel $legacygapopt -W $tuplesize $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $memopt $weightopt $treeinopt $treeoutopt -T -y $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ if [ $fragment -ne 0 ]; then
+ "$prefix/addsingle" -Q 100 $legacygapopt -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ else
+ "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ fi
+# elif [ $distance = "distonly" ]; then
+# "$prefix/pairlocalalign" -C $numthreads $seqtype $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof -t < infile > /dev/null 2>>"$progressfile" || exit 1
+# "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ elif [ $distance = "parttree" ]; then
+ "$prefix/splittbfast" $legacygapopt $algopt $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof -p $partsize -s $groupsize $treealg $outnum -i infile > pre 2>>"$progressfile" || exit 1
+ mv hat3.seed hat3
+ elif [ $distance = "ktuplesmulti" ]; then
+# "$prefix/dndpre" $model -M 1 $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -h $laof < infile > /dev/null 2>>"$progressfile" || exit 1
+# mv hat2 hat2i
+# "$prefix/disttbfast" -E 1 -s $unalignlevel $legacygapopt -W $tuplesize $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $memopt $weightopt $treeinopt $treeoutopt -T -y $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+# mv hat2 hat2n
+ if [ $fragment -ne 0 ]; then
+ "$prefix/addsingle" -Q 100 $legacygapopt -d -W $tuplesize -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+# "$prefix/addsingle" -Q 100 $legacygapopt -d -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ else
+ echo "Impossible" 1>&2
+ exit 1
+ fi
+ else
+ if [ $fragment -ne 0 ]; then
+ "$prefix/addsingle" -Q 100 $legacygapopt -W $tuplesize -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ else
+ "$prefix/disttbfast" -q $npickup -E $cycledisttbfast -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg -W $tuplesize $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $algopt $treealg $scoreoutarg < infile > pre 2>>"$progressfile" || exit 1
+ mv hat3.seed hat3
+ fi
+ fi
+ while [ $cycletbfast -gt 1 ]
+ do
+ if [ $distance = "parttree" ]; then
+ mv pre infile
+ "$prefix/splittbfast" $legacygapopt -Z $algopt $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof -p $partsize -s $groupsize $treealg $outnum -i infile > pre 2>>"$progressfile" || exit 1
+ else
+ "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum -C $numthreadstb $rnaopt $weightopt $treeoutopt $distoutopt $memopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt -J $treealg $scoreoutarg < pre > /dev/null 2>>"$progressfile" || exit 1
+# fragment>0 no baai, nanimoshinai
+# seed youchuui!!
+ fi
+ cycletbfast=`expr $cycletbfast - 1`
+ done
+ if [ $iterate -gt 0 ]; then
+ if [ $distance = "ktuples" ]; then
+ "$prefix/dndpre" $model -M 2 -C $numthreads < pre > /dev/null 2>>"$progressfile" || exit 1
+ fi
+ "$prefix/dvtditr" -W $minimumweight $bunkatsuopt -E $fixthreshold -s $unalignlevel $legacygapopt $mergearg $outnum -C $numthreadsit -t $randomseed $rnaoptit $memopt $scorecalcopt $localparam -z 50 $seqtype $model -f "-"$gop -Q $spfactor -h $aof -I $iterate $weightopt $treeinopt $algoptit $treealg -p $parallelizationstrategy $scoreoutarg < pre > /dev/null 2>>"$progressfile" || exit 1
+ fi
+ if [ $coreout -eq 1 ]; then
+ "$prefix/setcore" -w $corewin -i $corethr $coreext < pre > pre2
+ mv pre2 pre
+ elif [ $anysymbol -eq 1 ]; then
+ "$prefix/restoreu" $add2ndhalfarg -a pre -i orig > restored || exit 1
+ mv restored pre
+ fi
+
+
+
+
+ echo '' 1>>"$progressfile"
+ if [ $mccaskill -eq 1 ]; then
+ echo "RNA base pairing probaility was calculated by the McCaskill algorithm (1)" 1>>"$progressfile"
+ echo "implemented in Vienna RNA package (2) and MXSCARNA (3), and then" 1>>"$progressfile"
+ echo "incorporated in the iterative alignment process (4)." 1>>"$progressfile"
+ echo "(1) McCaskill, 1990, Biopolymers 29:1105-1119" 1>>"$progressfile"
+ echo "(2) Hofacker et al., 2002, J. Mol. Biol. 319:3724-3732" 1>>"$progressfile"
+ echo "(3) Tabei et al., 2008, BMC Bioinformatics 9:33" 1>>"$progressfile"
+ echo "(4) Katoh and Toh, 2008, BMC Bioinformatics 9:212" 1>>"$progressfile"
+ echo "" 1>>"$progressfile"
+ elif [ $contrafold -eq 1 ]; then
+ echo "RNA base pairing probaility was calculated by the CONTRAfold algorithm (1)" 1>>"$progressfile"
+ echo "and then incorporated in the iterative alignment process (4)." 1>>"$progressfile"
+ echo "(1) Do et al., 2006, Bioinformatics 22:e90-98" 1>>"$progressfile"
+ echo "(2) Katoh and Toh, 2008, BMC Bioinformatics 9:212" 1>>"$progressfile"
+ echo "" 1>>"$progressfile"
+ fi
+ if [ $pdblist != "/dev/null" -o $ownlist != "/dev/null" ]; then
+ echo "Input structures are decomposed into structural domains using" 1>>"$progressfile"
+ echo "Protein Domain Parser (Alexandrov & Shindyalov 2003)." 1>>"$progressfile"
+ echo "Domain pairs are aligned using the rash function in" 1>>"$progressfile"
+ echo "the ASH structural alignment package (Standley et al. 2007)." 1>>"$progressfile"
+ fi
+ if [ $pdblist != "/dev/null" ]; then
+ echo "Pre-computed alignments stored in " 1>>"$progressfile"
+ echo "DASH (http://sysimm.ifrec.osaka-u.ac.jp/dash/) are used. " 1>>"$progressfile"
+ fi
+ if [ $distance = "fasta" -o $partdist = "fasta" ]; then
+ echo "Pairwise alignments were computed by FASTA" 1>>"$progressfile"
+ echo "(Pearson & Lipman, 1988, PNAS 85:2444-2448)" 1>>"$progressfile"
+ fi
+ if [ $distance = "blast" ]; then
+ echo "Pairwise alignments were computed by BLAST" 1>>"$progressfile"
+ echo "(Altschul et al., 1997, NAR 25:3389-3402)" 1>>"$progressfile"
+ fi
+ if [ $distance = "last" -o $distance = "lastmulti" ]; then
+ echo "Pairwise alignments were computed by LAST" 1>>"$progressfile"
+ echo "http://last.cbrc.jp/" 1>>"$progressfile"
+ echo "Kielbasa, Wan, Sato, Horton, Frith 2011 Genome Res. 21:487" 1>>"$progressfile"
+ fi
+ if [ $distance = "scarna" ]; then
+ echo "Pairwise alignments were computed by MXSCARNA" 1>>"$progressfile"
+ echo "(Tabei et al., 2008, BMC Bioinformatics 9:33)." 1>>"$progressfile"
+ fi
+ if [ $distance = "dafs" ]; then
+ echo "Pairwise alignments were computed by DAFS" 1>>"$progressfile"
+ echo "(Sato et al., 2012,,,,)." 1>>"$progressfile"
+ fi
+ if [ $distance = "lara" -o $distance = "slara" ]; then
+ echo "Pairwise alignments were computed by LaRA" 1>>"$progressfile"
+ echo "(Bauer et al., 2007, BMC Bioinformatics 8:271)." 1>>"$progressfile"
+ fi
+ if [ $distance = "foldalignlocal" ]; then
+ echo "Pairwise alignments were computed by FOLDALIGN (local)" 1>>"$progressfile"
+ echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>>"$progressfile"
+ fi
+ if [ $distance = "foldalignglobal" ]; then
+ echo "Pairwise alignments were computed by FOLDALIGN (global)" 1>>"$progressfile"
+ echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>>"$progressfile"
+ fi
+# printf "\n" 1>>"$progressfile"
+ echo 'Strategy:' 1>>"$progressfile"
+ printf ' '$strategy 1>>"$progressfile"
+ echo ' ('$performance')' 1>>"$progressfile"
+ echo ' '$explanation 1>>"$progressfile"
+ echo '' 1>>"$progressfile"
+ echo "If unsure which option to use, try 'mafft --auto input > output'." 1>>"$progressfile"
+ echo "For more information, see 'mafft --help', 'mafft --man' and the mafft page." 1>>"$progressfile"
+ echo "" 1>>"$progressfile"
+ echo "The default gap scoring scheme has been changed in version 7.110 (2013 Oct)." 1>>"$progressfile"
+ echo "It tends to insert more gaps into gap-rich regions than previous versions." 1>>"$progressfile"
+ echo "To disable this change, add the --leavegappyregion option." 1>>"$progressfile"
+# echo "If long gaps are expected, try 'mafft --ep 0.0 --auto input > output'." 1>>"$progressfile"
+# echo "If the possibility of long gaps can be excluded, add '--ep 0.123'." 1>>"$progressfile"
+ if [ $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
+ echo "" 1>>"$progressfile"
+ if [ $oldgenafparam -eq 1 ]; then
+ echo "Obsolete parameters used for this calculation." 1>>"$progressfile"
+ echo "Also try the new parameters for E-INS-i, by not specifying --oldgenafpair." 1>>"$progressfile"
+ else
+ echo "Parameters for the E-INS-i option have been changed in version 7.243 (2015 Jun)." 1>>"$progressfile"
+ echo "To switch to the old parameters, use --oldgenafpair, instead of --genafpair." 1>>"$progressfile"
+ fi
+ fi
+ echo '' 1>>"$progressfile"
+
+
+ if [ $pdblist != "/dev/null" -o $ownlist != "/dev/null" ]; then
+ cat dasherr >>"$progressfile"
+ fi
+
+# ) # 2017/Mar/17
+ popd > /dev/null;
+
+
+ if [ "$outputfile" = "" ]; then
+ if [ "$outputopt" = "null" ]; then
+ cat < $TMPFILE/pre || exit 1
+ else
+ "$prefix/f2cl" -n $namelength $outputopt < $TMPFILE/pre 2>>/dev/null || exit 1
+ fi
+ else
+ if [ "$outputopt" = "null" ]; then
+ cat < $TMPFILE/pre > "$outputfile" || exit 1
+ else
+ "$prefix/f2cl" -n $namelength $outputopt < $TMPFILE/pre > "$outputfile" 2>>/dev/null || exit 1
+ fi
+ fi
+
+ if [ $treeout -eq 1 ]; then
+ cp $TMPFILE/infile.tree "$infilename.tree"
+ fi
+
+ if [ -s $TMPFILE/GuideTree ]; then # --merge no toki dake
+ cp $TMPFILE/GuideTree .
+ fi
+
+ if [ $distout -eq 1 ]; then
+ cp $TMPFILE/hat2 "$infilename.hat2"
+ fi
+
+ if [ $npickup -ne 0 ]; then
+ cp $TMPFILE/notused "$infilename.notused"
+ fi
+
+ if [ -s $TMPFILE/_deletemap ]; then
+ if [ "$mapoutfile" = "/dev/null" ]; then
+ cp $TMPFILE/_deletemap "$addfile.map"
+ else
+ cp $TMPFILE/_deletemap "$mapoutfile"
+ fi
+ fi
+
+ exit 0;
+fi
+
+prog="awk"
+
+tmpawk=`which nawk 2>/dev/null | awk '{print $1}'`
+if [ -x "$tmpawk" ]; then
+ prog="$tmpawk"
+fi
+
+tmpawk=`which gawk 2>/dev/null | awk '{print $1}'`
+if [ -x "$tmpawk" ]; then
+ prog="$tmpawk"
+fi
+
+#echo "prog="$prog 1>&2
+
+umask 077
+(
+$prog '
+BEGIN {
+ prefix = ENVIRON["prefix"];
+ version = ENVIRON["version"];
+ myself = ENVIRON["myself"];
+ 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( " Copyright (c) 2016 Kazutaka Katoh\n" ) > "/dev/tty";
+ printf( " MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)\n" ) > "/dev/tty";
+ printf( " http://mafft.cbrc.jp/alignment/software/\n" ) > "/dev/tty";
+ printf( "---------------------------------------------------------------------\n" ) > "/dev/tty";
+ printf( "\n" ) > "/dev/tty";
+
+ 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;
+ infile = sprintf( "%s", $0 );
+
+ res = getline < infile;
+ close( infile );
+ if( res == -1 )
+ {
+ printf( "%s: No such file.\n\n", infile ) > "/dev/tty";
+ printf( "Filename extension (eg., .txt) must be typed, if any.\n\n" ) > "/dev/tty";
+ }
+ else if( res == 0 )
+ printf( "%s: Empty.\n", infile ) > "/dev/tty";
+ else
+ {
+ printf( "OK. infile = %s\n\n", infile ) > "/dev/tty";
+ 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", $0 );
+ printf( "OK. outfile = %s\n\n", outfile ) > "/dev/tty";
+ break;
+ }
+ }
+
+ while( 1 )
+ {
+ outargs = "";
+ printf( "\n" ) > "/dev/tty";
+ printf( "Output format?\n" ) > "/dev/tty";
+ printf( " 1. Clustal format / Sorted\n" ) > "/dev/tty";
+ printf( " 2. Clustal format / Input order\n" ) > "/dev/tty";
+ printf( " 3. Fasta format / Sorted\n" ) > "/dev/tty";
+ printf( " 4. Fasta format / Input order\n" ) > "/dev/tty";
+ printf( " 5. Phylip format / Sorted\n" ) > "/dev/tty";
+ printf( " 6. Phylip format / Input order\n" ) > "/dev/tty";
+ printf( "@ " ) > "/dev/tty";
+ res = getline < "/dev/tty";
+ close( "/dev/tty" );
+# printf( "res=%d, NF=%d\n", res, NF );
+
+ resnum = 0 + $1;
+# printf( "resnum=%d\n", resnum );
+
+ if( resnum < 1 || 6 < resnum )
+ continue;
+ else
+ {
+ if( resnum == 1 )
+ outargs = "--clustalout --reorder";
+ else if( resnum == 2 )
+ outargs = "--clustalout --inputorder";
+ else if( resnum == 3 )
+ outargs = "--reorder";
+ else if( resnum == 4 )
+ outargs = "--inputorder";
+ else if( resnum == 5 )
+ outargs = "--phylipout --reorder";
+ else if( resnum == 6 )
+ outargs = "--phylipout --inputorder";
+ else
+ continue;
+ printf( "OK. arguments = %s\n\n", outargs ) > "/dev/tty";
+ break;
+ }
+ }
+
+ while( 1 )
+ {
+ arguments = "";
+ printf( "\n" ) > "/dev/tty";
+ printf( "Strategy?\n" ) > "/dev/tty";
+ printf( " 1. --auto\n" ) > "/dev/tty";
+ printf( " 2. FFT-NS-1 (fast)\n" ) > "/dev/tty";
+ printf( " 3. FFT-NS-2 (default)\n" ) > "/dev/tty";
+ printf( " 4. G-INS-i (accurate)\n" ) > "/dev/tty";
+ printf( " 5. L-INS-i (accurate)\n" ) > "/dev/tty";
+ printf( " 6. E-INS-i (accurate)\n" ) > "/dev/tty";
+ printf( "@ " ) > "/dev/tty";
+ res = getline < "/dev/tty";
+ close( "/dev/tty" );
+# printf( "res=%d, NF=%d\n", res, NF );
+
+ resnum = 0 + $1;
+# printf( "resnum=%d\n", resnum );
+
+ if( resnum < 1 || 6 < resnum )
+ continue;
+ else
+ {
+ if( resnum == 1 )
+ arguments = "--auto";
+ else if( resnum == 2 )
+ arguments = "--retree 1";
+ else if( resnum == 3 )
+ arguments = "--retree 2";
+ else if( resnum == 4 )
+ arguments = "--globalpair --maxiterate 16";
+ else if( resnum == 5 )
+ arguments = "--localpair --maxiterate 16";
+ else if( resnum == 6 )
+ arguments = "--genafpair --maxiterate 16";
+ else
+ arguments = sprintf( "%s", $0 );
+ printf( "OK. arguments = %s %s\n\n", arguments, outargs ) > "/dev/tty";
+ break;
+ }
+ }
+
+
+ while( 1 )
+ {
+ printf( "\n" ) > "/dev/tty";
+ printf( "Additional arguments? (--ep # --op # --kappa # etc)\n" ) > "/dev/tty";
+ printf( "@ " ) > "/dev/tty";
+ res = getline < "/dev/tty";
+ close( "/dev/tty" );
+ if( res == 0 || NF == 0 )
+ {
+ break;
+ }
+ else
+ {
+ addargs = sprintf( "%s", $0 );
+ printf( "OK. arguments = %s %s %s\n\n", addargs, arguments, outargs ) > "/dev/tty";
+ break;
+ }
+ }
+
+ arguments = sprintf( "%s %s %s", addargs, arguments, outargs );
+
+ print ""
+ command = sprintf( "\"%s\" %s \"%s\" > \"%s\"", myself, arguments, infile, outfile );
+ gsub( /\\/, "/", command );
+
+
+ printf( "command=\n%s\n", command ) > "/dev/tty";
+
+
+ while( 1 )
+ {
+ go = 0;
+ printf( "OK?\n" ) > "/dev/tty";
+ 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" ) > "/dev/tty";
+ printf( "\n" ) > "/dev/tty";
+ }
+ system( command );
+ command = sprintf( "more \"%s\"", outfile );
+ system( command );
+ printf( "Press Enter to exit." ) > "/dev/tty";
+ res = getline < "/dev/tty";
+}
+'
+)
+exit 0;
git://source.jalview.org / jabaws.git / blobdiff