#!/usr/local/bin/perl5 -w
#
# format_prediction
# Builds a CASP3 prediction file, delimited by PFRMAT and END
#
# Arguments:
# REQUIRED:
#	-target targetnum
#	-method <method_description_file>
#	-al	<alignment file as produced by fasta2al or other converter>
#
# OPTIONAL:
#	-remark	<file containing remarks>
#

    $registrationFilename 
        = "/projects/compbio/experiments/casp3/submit/registration.fold";

# 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";
    print <AL>;
    close AL;

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

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

# parse arguments

sub process_command_line
{
    local($i) = 0;

    while ($i <= $#ARGV)
    {   $_ = $ARGV[$i++];
        if (/^-target/)  	{   $targetId = $ARGV[$i++]; }
        elsif (/^-methods/) 	{   $methodFile = $ARGV[$i++]; }
        elsif (/^-al/)		{   $alFile = $ARGV[$i++]; }
        elsif (/^-remark/)	{   $remarkFile = $ARGV[$i++] } 
    }
    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";

    return;
}