silico Code

156 lines (117 with data), 3.9 kB

#!/usr/bin/perl -w

#  COPYRIGHT NOTICE
#  
#  Silico - A Perl Molecular Toolkit
#  Copyright (C) 2008 David K. Chalmers and Benjamin P. Roberts,
#  Department of Medicinal Chemistry, Monash University
#  
#  This program is free software: you can redistribute it and/or modify
#  it under the terms of the GNU General Public License as published by
#  the Free Software Foundation, either version 3 of the License, or
#  (at your option) any later version.
#  
#  This program is distributed in the hope that it will be useful,
#  but WITHOUT ANY WARRANTY; without even the implied warranty of
#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#  GNU General Public License for more details.
#  
#  You should have received a copy of the GNU General Public License
#  along with this program.  If not, see <http://www.gnu.org/licenses/>.


#<
#! makedoc
#? Generate Silico documentation using a simple markup scheme to extract
#  comments from Silico programs, libraries and data files.  
#
#. See silico_doc.pm for a description of the simple Silico markup syntax
#  for documentation.
#>

use strict;
package Silico;

#########################
# Variable declarations #
#########################

use vars qw($SUBHASH);

################
# Start script #
################

silico_setup();
print_title("makedoc");

require silico_doc;

get_arguments2();

my $version = `pwd`;
chomp $version;
$version =~ s/\/doc//;
$version =~ s/.*\///;

my $file_tagged .= "<STD>File documentation generated on ".`date`."";
my $sub_tagged .= "<STD>Subroutine documentation generated on ".`date`."";

$file_tagged .= read_doc('0intro');
$file_tagged .= read_doc('0subroutines');

my @dirs = qw(../bin ../local ../data ../lib);

foreach my $dir (@dirs) {

	my @files = glob("$dir/*");

	$file_tagged .= "<HEAD2>Directory: $dir";

	# Print file information
	foreach my $file (@files) {

		
		next if $file eq '0intro';
		next if $file eq '0subroutines';
		next if $file eq 'README';
		next if $file =~ /\.new$/;
		next if $file =~ /\.old$/;

		# Read file information
		my $t = read_doc($file);
		$file_tagged .= $t;

		read_doc_subroutine($file);
	}
}

# Subroutine index
$sub_tagged .= "<HEAD2>Subroutine Index";
my $i = 0;
foreach (sort keys %$SUBHASH) {
	$sub_tagged .= "<LIST><LINK#$i>$_";
	++$i;
}

# Subroutine descriptions
$sub_tagged .= "<HEAD2>Subroutine descriptions";
$i = 0;
foreach (sort keys %$SUBHASH) {

	$sub_tagged .= "<HEAD3><ANCH$i>$_";
	$sub_tagged .= $SUBHASH->{$_};
	++$i;
}

writetext($file_tagged, 'doc', 'txt');
writetext($file_tagged, 'doc', 'html');
writetext($sub_tagged, 'subroutines', 'txt');
writetext($sub_tagged, 'subroutines', 'html');

sub writetext {

	my $tagged = $_[0];
	my $filebase = $_[1];
	my $format = $_[2];

	my $filename = "$filebase.$format";

	print "Writing $filename\n";
	my $form = format_doc_txt($tagged) if $format eq 'txt';
	$form = format_doc_html($tagged) if $format eq 'html';
	open (OUTFILE, ">$filename")
		|| silico_msg('d', "Can not create or open file $filename for writing!");
	print OUTFILE $form;
	close OUTFILE;
}

sub silico_setup {

        #<
        #? Locates the Silico libraries and reads in the parent library, silico.pm
        #; Sets: $Silico::home_dir, $Silico::lib_dir, $Silico::data_dir, $Silico::FS
        #; Requires: nothing
        #; Returns: nothing
        #>
	
	use vars qw($data_dir);

        if ($ENV{SILICO_HOME}) {

                # Look for Silico location by environment variable
		$Silico::FS = "/";
                $Silico::home_dir = $ENV{SILICO_HOME}.$Silico::FS;
		$Silico::data_dir = $Silico::home_dir."data".$Silico::FS;
		$Silico::lib_dir = $Silico::home_dir."lib".$Silico::FS;
                push @INC, substr($Silico::lib_dir, 0, -1);
		
        } else {

                die "Error: The environment variable SILICO_HOME is not set\n";
        }

        require silico;
}