Eskil

    foreach line1 $block1 {
        set bestscore -100000
        set bestline 0
        set i 0
        foreach line2 $block2 {
            set x [compareLines2 $line1 $line2]
            lset scores $j $i $x
            #puts "Score $j $i : $x"
            if {$x > $bestscore} {
                set bestscore $x
                set bestline $i
            }
            incr i
        }
        #puts "Best for $j is $bestline : $bestscore"
        lset origresult $j $bestline
        lset scoresbest $j $bestscore
        incr bestsum $bestscore
        incr j
    }
    #puts "Bestsum: $bestsum"

    # origresult holds a mapping between blocks where each row
    # is paired with its best match. This may not be a possible
    # result since it has to be in order.

    set bestresult $origresult
    set bestscoresum -100000

    #puts "Origresult: $origresult"

    # If the size is 1, it is automatically in order so we
    # don't need further processing.

    if {$size1 > 1} {
        # Start with a check if the theoretical best works, since often that
        # is the case.
        set order 1
        set result $origresult
        for {set i 0} {$i < ($size1 - 1)} {incr i} {
            if {[lindex $result $i] >= [lindex $result [expr {$i + 1}]]} {
                set order 0
                break
            }
        }
        #if {$order} {puts "ORDER"}
    }
    if {$size1 > 1 && $order == 0} {
        # Look through the obvious "subblock" alternatives


        for {set startj 0} {$startj < ($size2 - $size1 + 1)} {incr startj} {
	    set sum 0
	    set result $emptyResult
	    for {set i 0 ; set j $startj} {$i < $size1} {incr i ; incr j} {
		lset result $i $j
		incr sum [lindex $scores $i $j]
	    }
	    #puts "Subblock $startj sum: $sum"
            if {$sum > $bestscoresum} {
                #puts "New best: $sum ($bestscoresum)"
                set bestresult $result
                set bestscoresum $sum
            }
	}

        # If we reach 75% if the theoretical best, we take it
        while {$bestscoresum < (3 * $bestsum / 4)} {
            #puts "Outer: $scoresbest"
	    # The outer loop restarts from the "best mapping"
	    set result $origresult
            set mark [Linit 0 $size1]
            set high $mark

            # If result is in order, no problem.
            # Otherwise, try to adjust result to make it ordered

            while {1} {
                #puts "Inner: $scoresbest"
		# The inner loop tries to get the result in order
                set besti 0
                set bestscore -100000
                set order 1
                for {set i 0} {$i < $size1} {incr i} {
                    if {[lindex $mark $i] == 0} {
                        for {set j [expr {$i + 1}]} {$j < $size1} {incr j} {
                            if {[lindex $mark $j] == 0} break
                        }
                        if {$j < $size1 && \
                                [lindex $result $i] >= [lindex $result $j]} {
                            set order 0
                        }
                        set x [lindex $scoresbest $i]
                        if {$x > $bestscore} {
                            set bestscore $x
                            set besti $i
                        }
                    }
                }
                #puts "Best $besti order $order sc $bestscore"
                if {$order} break
                lset mark $besti 1
                set bestr [lindex $result $besti]
                for {set i 0} {$i < $besti} {incr i} {
                    if {[lindex $mark $i] == 0 && \
                            [lindex $result $i] >= $bestr} {
                        lset mark $i 2

                }
            }
            set scoresum 0
            for {set i 0} {$i < $size1} {incr i} {
                set j [lindex $result $i]
                set sc [lindex $scores $i $j] ;# FIXA: can this fail?
                if {[string is integer -strict $sc]} {
                    #puts "Score: $i $j [lindex $scores $i $j]"
                    incr scoresum $sc
                }
            }
            #puts "Scoresum: $scoresum ($bestscoresum)"

	    # If it was not an improvement over previous iteration, quit
            if {$scoresum <= $bestscoresum} {
                break
	    }

	    set bestresult $result
	    set bestscoresum $scoresum





	    # We are redoing from start, but try to improve by
	    # ignoring the most awkwardly placed line.
	    set mostp -1
	    set mosti 0
	    for {set i 0} {$i < $size1} {incr i} {
		if {[lindex $mark $i] == 1} {
		    if {abs([lindex $result $i] - $i) > $mostp} {
			set mostp [expr {abs([lindex $result $i] - $i)}]
                        set mosti $i
		    }
		}
	    }
	    #puts "Most $mosti $mostp"
	    lset scoresbest $mosti 0
        }
    }

    set result $bestresult

    # Collect the result into diff-like codes to use as display info.