#!/bin/bash -x
# renames output to 'treefile'

if [ -f treefile ]; then
    rm treefile
fi

if [ -z "$5" ]; then
    arb_message "Usage: arb_protml modelflag searchflag rearrange calclengths inputfile"
else
    MODEL=$1
    SEARCH=$2
    REARRANGE=$3
    CALCLENGTH=$4
    INFILE=$5

    if [ \! -s $INFILE ]; then
        arb_message "Error: no or empty input file"
        ls -al $INFILE
    else
        FLAGS="-v $MODEL"
        if [ \! "$REARRANGE" = "0" ]; then
            if [ "$SEARCH" = "-s" ]; then
                arb_message "You have selected 'Star decomposition search' AND 'Rearrangement'.\n  Original protml crashed with this parameter combination.\n  We fixed protml, but we did not check the results\n  - so use them with care!"
            fi
            FLAGS="$FLAGS $REARRANGE"
        fi

        # normal tree generation with protml
        echo >arb_read_tree_args
        if [ "$SEARCH" = "-s" ]; then
            if [ "$CALCLENGTH" = "0" ]; then
                arb_message "Note: Star decomposition search always calculates branchlengths"
            fi
            # Star decomposition search (may not be the ML tree)
            protml $FLAGS -I -s $INFILE
        else
            # Exhaustive search or quickadd
            protml $FLAGS -I $SEARCH $INFILE | tail -1 >outtree # write last tree to outtree

            if [ -s outtree ]; then
                if [ "$CALCLENGTH" = "1" ]; then
                    echo "1" >intree #no of trees
                    cat outtree >>intree
                    protml -v $MODEL -u -I $INFILE intree # calculates branch lengths
                else
                    mv outtree protml.tre
                fi
            else
                arb_message "Error running protml: outtree is empty"
            fi
        fi

        if [ \! -s protml.tre ]; then
            arb_message "Error running protml: protml.tre was not generated or is empty"
        else
            mv protml.tre treefile
        fi
    fi

    # remove protml junk:
    rm protml.eps protml.tpl
fi