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#!/usr/bin/env perl
use strict;
use warnings;
use feature qw/state say/;
use 5.010;
use Getopt::Long;
use Pod::Usage;
use Finnigan;
my $option_help = 0;
my $option_man = 0;
my $option_dump = 0;
my $option_html = 0;
my $option_wiki = 0;
my $option_size = 0;
my $option_si = 0;
my $option_relative = 0;
Getopt::Long::Configure ("bundling");
GetOptions(
           'help|?' => \$option_help,
           'man' => \$option_man,
           'dump|d' => \$option_dump,
           'size|s' => \$option_size,
           'html|h' => \$option_html,
           'wiki|w' => \$option_wiki,
           'sample_info|i' => \$option_si,
           'relative|r' => \$option_relative,
          ) or pod2usage(2);
pod2usage(1) if $option_help;
pod2usage(-existstatus => 0, -verbose => 2) if $option_man;
@ARGV == 1 or do{ say STDERR "Expecting a single input file\n"; pod2usage(2) };
my $file = shift @ARGV;
-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);
# fast-forward to RunHeader
my $run_header_addr = $rfi->preamble->run_header_addr;
seek INPUT, $run_header_addr, 0;
my $run_header = Finnigan::RunHeader->decode(\*INPUT, $header->version);
if ( $option_size ) {
  if ( $option_si ) {
    say "size: " . $run_header->sample_info->size;
  }
  else {
    say "size: " . $run_header->size;
  }
}
if ( $option_dump ) {
  if ( $option_html ) {
    if ( $option_si ) {
      $run_header->sample_info->dump(style => 'html', relative => $option_relative);
    }
    else {
      $run_header->dump(style => 'html', relative => $option_relative);
    }
  }
  elsif ( $option_wiki ) {
    if ( $option_si ) {
      $run_header->sample_info->dump(style => 'wiki', relative => $option_relative);
    }
    else {
      $run_header->dump(style => 'wiki', relative => $option_relative);
    }
  }
  else {
    if ( $option_si ) {
      $run_header->sample_info->dump(relative => $option_relative);
    }
    else {
      $run_header->dump(relative => $option_relative);
    }
  }
}
else {
  say "$file: "
    . "scan range: ["
      . $run_header->sample_info->low_mz . ".."
        . $run_header->sample_info->high_mz . "]; "
          . "scan numbers: ["
            . $run_header->sample_info->first_scan . ".."
              . $run_header->sample_info->last_scan . "]; "
                . "number of segments: "
                  . $run_header->nsegs . "; "
                    . "inst. status samples: "
                      . $run_header->sample_info->inst_log_length . "; "
                        . "max. ion current: "
                          . $run_header->sample_info->max_ion_current . "; "
                            . "retention time: ["
                              . $run_header->sample_info->start_time . ".."
                                . $run_header->sample_info->end_time . "]; "
                                  . "ntrailer: "
                                    . $run_header->ntrailer . "; "
                                      . "nparams: "
                                        . $run_header->nparams . "; "
                                          . "unknown[1]: "
                                            . $run_header->u1 . "; "
                                              . "unknown[2]: "
                                                . $run_header->u2 . "; "
                                                  ;
}
HideShow 94 lines of Pod
__END__
=head1 NAME
uf-runheader - decode the RunHeader structure in a Finnigan raw file
=head1 SYNOPSIS
uf-runheader [options] file
 Options:
   --help            brief help message
   --man             full documentation
   --html            format as HTML
   --wiki            format as a wiki table
   --size            tell object size
   --sample_info     dump the content of SampleInfo instead of RunHeader itself
   --relative        show relative addresses
=head1 OPTIONS
=over 8
=item B<--help>
Print a brief help message and exit.
=item B<--man>
Prints the manual page and exit.
=item B<--dump>
Prints the table listing all fields in the structure with their seek
addresses, sizes, names and values.
=item B<--html>
Dump as html table.
=item B<--wiki>
Dump as a wiki table.
=item B<--size>
Show structure size in bytes.
=item B<--smple_info>
Dump the contents of SampleInfo instead of the parent object.
=item B<--relative>
Show relative addresses of all itmes. The default is to show the
absolute seek address.
=back
=head1 DESCRIPTION
B<uf-runheader> will display the contents of RunHeader structure,
or its component SampleInfo.
It will return an error message if its input is not a Finnigan raw
file.
By default, it prints a summary of the object's data on a single line.
=head1 SEE ALSO
Finnigan::Runheader
Finnigan::SampleInfo
=head1 EXAMPLES
=over 4
=item Print a single line listing a few important numbres in RunHeader:
  uf-runheader sample.raw
=item Dump the entire RunHeader with absolute addresses:
  uf-runheader -d sample.raw
=item Dump the SampleInfo structure with relative addresses in a wiki
table format and show its size:
 uf-runheader -sdrwi sample.raw
=back
=cut