#!/bin/bash -x
# ------------------------------------------------------------
# (C) 2003 Lehrstuhl fuer Mikrobiologie TU Muenchen
# Coded by Ralf Westram
# ------------------------------------------------------------
#
# usage: arb_bootstrap count treeprog [keys for treeprog]
#
# 'count'                  is the number of generated trees
# 'treeprog'               calculates the trees (e.g. dnapars, protpars)
# 'keys for treeprog'      is arb_echo'ed to stdin of 'treeprog'
#
# expects input data in "infile"
# output data is written to "outtree"
#
# ------------------------------------------------------------

COUNT=$1
TREEPROG=$2
shift
shift
# additional arguments are pushed to arb_echo

RANDOMSEED1=$(($RANDOM|1)) # a odd number
RANDOMSEED2=$(($RANDOM|1)) # a odd number

echo "-consense $COUNT" >arb_read_tree_args

# arb_echo $RANDOMSEED r $COUNT y | seqboot
arb_echo r "$COUNT" y $RANDOMSEED1 | seqboot

if [ \! -f outfile ] ; then
    echo "Error in seqboot: 'outfile' not generated"
else
    mv -f outfile infile
    TREED=0
    if [ \( "$TREEPROG" = "dnapars" \) -o \
         \( "$TREEPROG" = "protpars" \) -o \
         \( "$TREEPROG" = "proml" \) \
         ]; then
        arb_echo m d $COUNT $RANDOMSEED2 1 $* y | $TREEPROG
        # $TREEPROG
        TREED=1
    fi

    if [ "$TREED" = 0 ]; then
        echo "treeprogram '$TREEPROG' is unknown by arb_bootstrap"
    else
        if [ \! -f outtree ] ; then
            echo "Error running $TREEPROG: 'outtree' not generated"
        else
            if [ \! -s outtree ] ; then
                echo "Error running $TREEPROG: 'outtree' is empty"
                rm outtree
            else
                mv -f outtree intree
                rm outfile
                arb_echo y | consense
                #consense

                if [ \! -f outtree ] ; then
                    echo "Error running consense: 'outtree' not generated"
                fi
            fi
        fi
    fi
fi