#!/usr/bin/env perl

use strict;
use warnings;
use feature qw/state say/;
use 5.010;

use Getopt::Declare;
use Finnigan;

my $args = new Getopt::Declare q{
  [strict]
  [mutex: -h -w]
  -d[ump]			dump the requested feature with file seek addresses
  -s[ize]			print record size [requires: -d]
  -h[tml]			format as html
  -w[iki]			format as a wiki table
  -r[elative]			show relative addersess in the dump [requires: -d]
  <file>			input file [required]
}
  or exit(-1);

my $file = $args->{"<file>"};
-e $file or die "file '$file' does not exist";
-f $file or die "'$file' is not a plain file";
-s $file or die "'$file' has zero size";

# -----------------------------------------------------------------------------
open INPUT, "<$file" or die "can't open '$file': $!";
binmode INPUT;

my $header = Finnigan::FileHeader->decode(\*INPUT);
my $seq_row = Finnigan::SeqRow->decode(\*INPUT, $header->version);
my $cas_info = Finnigan::CASInfo->decode(\*INPUT);
my $rfi = Finnigan::RawFileInfo->decode(\*INPUT, $header->version);

my $run_header_addr = $rfi->preamble->run_header_addr;

# fast-forward to RunHeader
seek INPUT, $run_header_addr, 0;
my $run_header = Finnigan::RunHeader->decode(\*INPUT, $header->version);
my $inst_id  = Finnigan::InstID->decode( \*INPUT );

if ( exists $args->{-d} ) {
  if ( exists $args->{-s} ) {
    my $size = $inst_id->size;
    say "size: $size";
  }
  if ( exists $args->{-h} ) {
    $inst_id->dump(style => 'html', relative => exists $args->{-r});
  }
  elsif ( exists $args->{-w} ) {
    $inst_id->dump(style => 'wiki', relative => exists $args->{-r});
  }
  else {
    $inst_id->dump(relative => exists $args->{-r});
  }
}
else {
  say $inst_id->stringify;
}

__END__
=head1 NAME

uf-instrument - print or dump the instrument IDs found a Finnigan raw file

=head1 SYNOPSIS

uf-log <file>

=head1 OPTIONS

=over 4

=item B<-help>

Print a brief help message and exit.

=item B<-d[ump]>

Prints a table listing all fields in the InstID structure containing
the instrument IDs, incliding their seek addresses, sizes, names and
values.

=item B<-h[tml]>

Format the dump output as an HTML table.

=item B<-w[iki]>

Format the dump output as a wiki table.

=item B<-s[ize]>

Show the structure size in bytes (works with the -d[ump] option).

=item B<-r[elative]>

Show relative addresses of all elemests in the dump. The default is to
show the absolute seek address.

=back

=head1 DESCRIPTION

If called without options, B<uf-instrument> prints all instrument ID
information on one line.

For more detailed information about all instruments involved in the
acquisition of the data, use B<uf-meth>, the method file tool.

It will exit with no output if there are no error messages.

=head1 SEE ALSO

Finnigan::InstID

L<uf-meth>

=cut