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  • Committer: Package Import Robot
  • Author(s): Charles Plessy
  • Date: 2014-01-19 08:25:50 UTC
  • mfrom: (18.1.2 sid)
  • Revision ID: package-import@ubuntu.com-20140119082550-y9m1g39vel5jjm1t
Tags: 7.130-1
* New upstream release.
* Correct ‘XS-Testsuite’ to ‘Testsuite’ in debian/control.

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Lines of Context:
core/mafft.tmpl
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er=0;
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myself=`dirname "$0"`/`basename "$0"`; export myself
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version="v7.127b (2013/10/29)"; export version
 
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version="v7.130b (2013/12/05)"; export version
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LANG=C; export LANG
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os=`uname`
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progname=`basename "$0"`
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                elif [ "$1" = "--globalgenafpair" ]; then
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                        distance="globalgenaf"
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                        pairspecified=1
 
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                        echo "No longer supported!" 1>&2
 
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                        exit;
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                elif [ "$1" = "--localgenafpair" ]; then
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                        distance="localgenaf"
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                        pairspecified=1
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                exit;
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        fi
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        if [ `awk "BEGIN {print( 0.0+\"$specificityconsideration\" > 0.0 )}"` -gt 0 ]; then
 
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                laof="0"
 
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                lexp="0"
 
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                pgaof="0"
 
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                pgexp="0"
 
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                LEXP="0"
 
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                GEXP="0"
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#               if [ $auto -eq 1 -o $fragment -ne 0 -o $iterate -gt 0 ]; then
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                if [ $auto -eq 1 -o $fragment -ne 0 ]; then
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                        printf "\n%s\n\n" "At present, the 'unalignlevel > 0' mode is supported in the progressive options only." 1>>"$progressfile"
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                        printf "\n%s\n\n" "At present, the 'unalignlevel > 0' mode is not supported in the (dp)parttree option." 1>>"$progressfile"
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                        exit;
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                fi
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                if [ $distance != "ktuples" -a `awk "BEGIN {print( 0.0+\"$weighti\" > 0.0 )}"` -gt 0 ]; then
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                        printf "\n%s\n\n" "Please add --weighti 0.0, for now." 1>>"$progressfile"
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                        exit;
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                fi
 
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#               if [ $distance != "ktuples" -a `awk "BEGIN {print( 0.0+\"$weighti\" > 0.0 )}"` -gt 0 -a $iterate -gt 0 ]; then
 
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#                       printf "\n%s\n\n" "Please add --weighti 0.0, for now." 1>>"$progressfile"
 
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#                       exit;
 
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#               fi
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        fi
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        if [ $parallelizationstrategy = "BESTFIRST" -o  $parallelizationstrategy = "BAATARI0" ]; then
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                        mv hatx hat3
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                        "$prefix/tbfast" -s $specificityconsideration $legacygapopt $mergearg $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
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                elif [ $distance = "global" ]; then
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                        "$prefix/pairlocalalign" $localparam  -C $numthreads $seqtype $model -g $pgexp -f $pggop  -h $pgaof  -A < infile > /dev/null  2>>"$progressfile"      || exit 1
 
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                        "$prefix/pairlocalalign" -u $specificityconsideration $localparam  -C $numthreads $seqtype $model -g $pgexp -f $pggop  -h $pgaof  -A < infile > /dev/null  2>>"$progressfile"      || exit 1
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                        cat hat3.seed hat3 > hatx
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                        mv hatx hat3
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                        "$prefix/tbfast" -s $specificityconsideration $legacygapopt $mergearg $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
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                                mv hatx hat3
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                                "$prefix/addsingle" $legacygapopt -O $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
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                        else
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                                "$prefix/pairlocalalign" $localparam -C $numthreads $seqtype $model  -g $lexp -f $lgop  -h $laof -L < infile > /dev/null  2>>"$progressfile"      || exit 1
 
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                                "$prefix/pairlocalalign" -u $specificityconsideration $localparam -C $numthreads $seqtype $model  -g $lexp -f $lgop  -h $laof -L < infile > /dev/null  2>>"$progressfile"      || exit 1
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#                               addarg wo watasanai
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                                cat hat3.seed hat3 > hatx
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                                mv hatx hat3
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                                "$prefix/tbfast" -s $specificityconsideration $legacygapopt $mergearg $termgapopt $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
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                        fi
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                elif [ $distance = "globalgenaf" ]; then
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                        "$prefix/pairlocalalign" $localparam -C $numthreads $seqtype $model  -g $pgexp -f $pggop  -h $pgaof -O $GGOP -E $GEXP -K  < infile > /dev/null 2>>"$progressfile"    || exit 1
 
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                        "$prefix/pairlocalalign"  -u $specificityconsideration $localparam -C $numthreads $seqtype $model  -g $pgexp -f $pggop  -h $pgaof -O $GGOP -E $GEXP -K  < infile > /dev/null 2>>"$progressfile"    || exit 1
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                        cat hat3.seed hat3 > hatx
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                        mv hatx hat3
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                        "$prefix/tbfast" -s $specificityconsideration $legacygapopt $mergearg $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
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                elif [ $distance = "localgenaf" ]; then
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                        "$prefix/pairlocalalign" $localparam -C $numthreads $seqtype $model -g $lexp -f $lgop  -h $laof -O $LGOP -E $LEXP -N < infile > /dev/null  2>>"$progressfile"      || exit 1
 
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                        "$prefix/pairlocalalign"  -u $specificityconsideration $localparam -C $numthreads $seqtype $model -g $lexp -f $lgop  -h $laof -O $LGOP -E $LEXP -N < infile > /dev/null  2>>"$progressfile"      || exit 1
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                        cat hat3.seed hat3 > hatx
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                        mv hatx hat3
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                        "$prefix/tbfast" -s $specificityconsideration $legacygapopt $mergearg $termgapopt $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1