source: branches/ali/SH/arb_protpars

#!/bin/bash -x

if [ -z "$6" ]; then
    echo "Usage: arb_protpars bootstrap geneticcode viewreport randomize threshold_pars interactive"
else
    BOOTSTRAP=$1
    CODE=$2
    REPORT=$3
    RANDOMIZE=$4
    THRESHOLD_PARS=$5
    INTERACTIVE=$6

    FLAGS="c $CODE"

    if [ "$RANDOMIZE" = "1" ]; then
        RANDOMSEED=$(($RANDOM|1)) # a odd number
        FLAGS="$FLAGS j $RANDOMSEED 1"
    fi

    if [ \! "$THRESHOLD_PARS" = "0" ]; then
        FLAGS="$FLAGS t $THRESHOLD_PARS"
    fi

    if [ "$BOOTSTRAP" = "0" ]; then
        if [ "$INTERACTIVE" = "0" ]; then
            arb_echo $FLAGS y | protpars
        else
            (arb_echo $FLAGS ; cat -) | ( protpars ; echo "Press RETURN to continue.." )
        fi
        echo >arb_read_tree_args
        WHAT=protpars
    else
        arb_bootstrap $BOOTSTRAP protpars $FLAGS
        WHAT=arb_bootstrap/protpars/consense
    fi

    if [ -f outfile ]; then
        if [ -s outfile ]; then
            if [ "$REPORT" = "1" ]; then
                arb_textedit outfile &
            fi
        else
            arb_message "$WHAT: Error: generated 'outfile' is empty"
            false
        fi
    else
        arb_message "$WHAT: Error: 'outfile' has not been generated"
        false
    fi
fi