source: branches/ali/SH/arb_proml

#!/bin/bash -x

BOOTSTRAP=$1 ; shift
MODEL=$1 ; shift
REPORT=$1 ; shift
ANALYSIS=$1 ; shift
RANDOMIZE=$1 ; shift
REARRANGE=$1 ; shift
RATE_VARIATION=$1 ; shift
VARIATION_COEFF=$1 ; shift
HMM_RATES=$1 ; shift
INV_FRACTION=$1 ; shift
INTERACTIVE=$1 ; shift

if [ -z "$INTERACTIVE" ]; then
    echo "Usage: arb_proml bootstrap aachangemodel viewreport analysis randomize rearrange rate_variation variation_coeff hmm_rates inv_fraction interactive"
else
    FLAGS=""
    ADD_PARA=""

    if [ "$MODEL" = "PAM" ]; then
        FLAGS="$FLAGS p"
    fi
    if [ "$ANALYSIS" = "fine" ]; then
        FLAGS="$FLAGS s"
    fi
    if [ "$RANDOMIZE" = "1" ]; then
        RANDOMSEED=$(($RANDOM|1)) # a odd number
        FLAGS="$FLAGS j $RANDOMSEED 1"
    fi
    if [ "$REARRANGE" = "1" ]; then
        FLAGS="$FLAGS g"
    fi

    case $RATE_VARIATION in
        0) ;;
        1) FLAGS="$FLAGS r"
           ADD_PARA="$ADD_PARA $VARIATION_COEFF $HMM_RATES"
           ;;
        2) FLAGS="$FLAGS r r"
           ADD_PARA="$ADD_PARA $VARIATION_COEFF $HMM_RATES $INV_FRACTION"
           ;;
        *) arb_message "Illegal value for 'rate_variation'"
           exit 1
           ;;
    esac

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