#!/usr/local/bin/perl5 -w
#
# format_prediction
# Builds a CASP3 prediction file, delimited by PFRMAT and END
#
# Arguments:
# REQUIRED:
#	-target <targetname>
#	-method <method_description_file>
#	-al	<alignment file as produced by fasta2al or other converter>
#       -registration <registration code file>
#       -model <model number>        this is optional, by default 1
#       -targetoffset <target offset> optional, by default 0
#
# OPTIONAL:
#	-remark	<file containing remarks>
#

# Get inputs from command line

    &process_command_line;

#
# Step 1: put in the header information: PFRMAT, TARGET, and AUTHOR.
#
    print "PFRMAT AL\n";
    print "TARGET $targetId\n";
    open REGISTRATION, $registrationFilename 
        || die "Could not read registration file $registrationFilename\n"; 
    print "AUTHOR ", <REGISTRATION>;
    close REGISTRATION;

#
# Step 2: echo the contents of the remark file, if there is one.
#
    if (defined($remarkFile)) {
	open REMARK, $remarkFile 
	    || die "Could not read remark file $remarkFile\n";
 	while ( <REMARK> ) {
 	    print "REMARK $_";
 	}
	close REMARK;
    }

#
# Step 3: echo the contents of the method file
#
   open METHOD, $methodFile || die "Could not read method file $methodFile\n";
   while (<METHOD>) {
       print "METHOD $_";
   }
   close METHOD;

#
# Step 4: echo the contents of the AL alignment file
#
    open AL, $alFile || die "Could not open alignment file $alFile\n";
    $al_line = <AL>;
    while ($al_line)
    {
        if ($model ne ""
            && $al_line =~ /^MODEL/)
        {
            print "MODEL $model\n";
        }
        elsif ($target_offset != 0
               && $al_line =~ /^\s*(\S)\s+(\d+)\s+(\S)\s+(\d+)\s*$/)
	{
            $target_aa = $1;
            $target_ind = $2;
            $parent_aa = $3;
            $parent_ind = $4;
            $offset_target_ind = $target_ind + $target_offset;
            print "$target_aa $offset_target_ind $parent_aa $parent_ind\n";
        }
        else
        {
             print $al_line;
        }
        $al_line = <AL>;
    }
    close AL;


#
# Step 5: put on the footer
#
    print "END\n";

#--------------------------------------------------
# subroutines

# parse arguments

sub process_command_line
{
    my($arg_i) = 0;

    $model = "";
    $target_offset = 0;

    while ($arg_i <= $#ARGV)
    {
        my($cur_arg) = $ARGV[$arg_i];
        $arg_i++;

        if ($cur_arg eq "-target")
  	{   $targetId = $ARGV[$arg_i++]; }
        elsif ($cur_arg eq "-method")
        {   $methodFile = $ARGV[$arg_i++];}
        elsif ($cur_arg eq "-al")
        {   $alFile = $ARGV[$arg_i++]; }
        elsif ($cur_arg eq "-registration")
        {   $registrationFilename = $ARGV[$arg_i++]; }
        elsif ($cur_arg eq "-remark")
        {   $remarkFile = $ARGV[$arg_i++]; }
        elsif ($cur_arg eq "-model")
        {   $model = $ARGV[$arg_i++]; }
        elsif ($cur_arg eq "-targetoffset")
        {   $target_offset = $ARGV[$arg_i++]; }
        else
	{
            die "Error: bad command line switch: $cur_arg\n";
        }
    }

    defined($targetId) || die "Error: must specify '-target <target_ID>'\n";
    defined($methodFile) 
	|| die "Error: must specify '-method <method_description_file>'\n";
    defined($alFile) 
	|| die "Error: must specify '-al <al_formatted_alignment_file>'\n";
    defined($registrationFilename)
        || die "Error: must specify '-registration <registration code file>'\n";
    return;
}