#!/usr/local/bin/perl -w

#main
{    
    use FileHandle;
    STDERR->autoflush(1);
    use English;
    use File::Basename;
    use lib dirname($PROGRAM_NAME);
    use READ_RDB;

    ($n, $alignmentsfile, $hitsfile) = @ARGV;

    print STDERR "Looking for $n hits in $hitsfile, choosing alignments from $alignmentsfile\n";

    %FSSPRepHash = ();
    %SCOPDomainHash = ();
    %rank_of_hit = ();

    $num_hits = 0;
    #get the ids of the top five hits and put in rank_of_hit
    open(HITSFILE, $hitsfile) 
    	|| die "Error: top_reported_alignments can't open $hitsfile for reading.\n";
    
    read_rdb_header(*HITSFILE{IO});
    	$idcolnum = $col_num{"Sequence_ID"};
    #	$lencolnum = $col_num{"Length"};
    #	$BEcolnum = $col_num{"Best_Evalue"};	#unused in html output
    #	$Ecolnum = $col_num{"Evalue"};
    #	$FSSPcolnum = $col_num{"FSSP-rep"};
    #	$SCOPcolnum = $col_num{"SCOP_domain"};
    #	$suidcolnum = $col_num{"SCOP_suid"};

    while($line = <HITSFILE>)
    {   chomp $line;
	@cols = split('\t', $line);
	    #skip rows with no id in the line (additional domain rows)
	next if (!($cols[$idcolnum] =~ /\w+/)); 
	$rank_of_hit{$cols[$idcolnum]} = ++$num_hits;
    }
    close(HITSFILE);
    print STDERR "read $num_hits hits\n";

    open(ALIGNMENTSFILE, "<$alignmentsfile") 
    	|| die "Error: top_reported_alignments can't open $alignmentsfile for reading.\n";

    read_rdb_header(*ALIGNMENTSFILE{IO});
    	$aligncolnum = $col_num{"Alignment"};
    #	$Ecolnum = $col_num{"Evalue"};
    	$FSSPcolnum = $col_num{"FSSP-rep"};
	$SCOPcolnum = $col_num{"SCOP-domain"};
    while($line = <ALIGNMENTSFILE>)
    {	chomp $line;
	@cols = split('\t', $line);
	# We will print the top $n different hits.
	# Conditions for printing a row:
	# the hit is from different SCOP superfamily or
	#	has a different FSSP representative from what
	#	we've already seen  AND
	#    is a local, adpstyle 5 alignment to 100-30-str HMM

	my $align = $cols[$aligncolnum];
	my $FSSP = $cols[$FSSPcolnum];
	my $SCOP = $cols[$SCOPcolnum];

	
	$align =~ /\w+-(\w+)-.*/ && ($chainID = $1);
	if(defined($rank_of_hit{$chainID}))
	{   # print STDERR "fssprep:$FSSP SCOPsuperfam:$SCOP name: $align\n"; 
	    if ( !defined($FSSPRepHash{$FSSP}) 
		&& !defined($SCOPDomainHash{$SCOP})
		&& ($align =~ /\S+-STR-local-adpstyle5.pw.a2m.gz/))
	    {   #put in hash of rows to be printed, where key is the
		# rank of the hit 
		print STDERR "adding $chainID";
		$rowsToPrint{$rank_of_hit{$chainID}} = $line;
		# mark the fssprep or superfam in hash if its not blank
		if($FSSP =~ /\S+/)
		{    $FSSPRepHash{$FSSP} = 1;
		}
		if($SCOP =~ /\S+/)
		{    $SCOPDomainHash{$SCOP} = 1;
		}
	    }

	} 
    }
    close(ALIGNMENTSFILE);

    @sorted = sort {$a <=> $b}  keys %rowsToPrint;
    print STDERR "There are 0..$#sorted keys in rowsToPrint\n";

    print "Alignment\tEvalue\tFSSP-rep\tSCOP_domain\n";
    print "50S\t10N\t5S\t10S\n";
    
    for (my $i = 0; $i<$n && $i<=$#sorted; $i++)
    {	print "$rowsToPrint{$sorted[$i]}\n";
    }
}