#!/usr/bin/perl -T
#########
# Author:     Magnus Manske (mm6@sanger.ac.uk)
# Group:      Team 112
#

package settings ;

require Exporter;
use warnings ;
use strict ;
#use AutoLoader qw(AUTOLOAD);
our @ISA = qw(Exporter);
our @EXPORT = qw( 
	$execpath $datapath $genome_file $webroot $docroot $htmlpath $tooltitle $reference_fa
	$cgi_path $annotation_file $snp_file $robots_flag $use_db_index_cutoff $uniqueness_file 
	$use_sanger_cache $use_sanger_layout $sanger_header $css_file
	$use_mysql $mysql_server $mysql_port $mysql_user $mysql_password @mysql_dbs
	%lscolor $ls_max_lines $max_window $bam_ftp $reference_ftp
	$GbrowerPath $GbrowerSuffix
);

# Tool title
our $tooltitle = 'LookSeq' ;

# The local file path to the CGI files
our $execpath = "/home/xianggan/bin/";

# The local file path to the directory containing the data (alignment databases, reference sequence etc.)
our $datapath = '/data/arabidopsis/bams_stampy/';  #'/Net/fs2/projects/arabidopsis/download_data/bams/';

our $bam_ftp = '/data/arabidopsis/bams_stampy/'; #'/Net/fs2/projects/arabidopsis/download_data/bams/';
our $sanger_header = "/WWW/SANGER_docs/htdocs/modelorgs/mousegenomes/snps-header.ini";
our $css_file  = "/modelorgs/mousegenomes/snps.css";              

# The local file path to the HTML/JavaScript/i18n files
our $htmlpath = "/data/www/arabidopsis/";

# The full URL of the directory containing the HTML/JavaScript/i18n files
our $webroot = "http://mus.well.ox.ac.uk/arabidopsis";

# The full URL of the directory containing the Perl files (this one, for example)
our $cgi_path = 'http://mus.well.ox.ac.uk/arabidopsis/cgi';

# The file name of the reference sequence in FASTA format. The file must be in the $datapath directory
our $genome_file = 'chr_all.fas' ;

# The file name of the reference sequence in SAMTOOLS .fa/.fai format. Give the .fa file only
our $reference_fa = 'chr_all.fas' ;

# The file name of the uniqueness (like FASTA, but each "base" is a digit 0-9, with 0=unique and 9=uh-oh). The file must be in the $datapath directory
#our $uniqueness_file = '3D7_pm.fastu' ;

# Internal index usage cutoff; leave unless you know what you're doing!
our $use_db_index_cutoff = 25000 ;

# The file name of the sequence annotation database. The file must be in the $datapath directory.
# Leave undefined if no annotation is given.
#our $annotation_file = 'annotation.sqlite' ;

# The file name of the known SNP database. The file must be in the $datapath directory
# Leave undefined if no known SNP data is present.
#our $snp_file = "snps.sqlite" ;

# MySQL settings, deactivated by default
our $use_mysql = 0 ;
our ( $mysql_server , $mysql_port , $mysql_user , $mysql_password , @mysql_dbs ) ;


# Allows/disallows indexing of the page by robots (set to 'noindex' if you don't want the page to show up on Google et al)
our $robots_flag = 'index, follow' ;

# Don't use index for database query if region is larger than this
$use_db_index_cutoff = 20000 ;

# Sanger-specific flags; don't change unless you know what you're doing
our $use_sanger_layout = 0 ;
our $use_sanger_cache = 0 ;


# Upper SNP display limit for SAM format; set for max number of lines, e.g. 50000
our $ls_max_lines =50000000;


our $max_window = 50000;
# Colors
our %lscolor ;

$lscolor{'white'} = [ 0xFF , 0xFF , 0xFF ] ;
$lscolor{'ltblue'} = [ 0x44 , 0xB4 , 0xD5 ] ;
$lscolor{'green'} = [ 0x00 , 0xFF , 0x00 ] ;
$lscolor{'ltgreen'} = [ 0x72 , 0xFE , 0x95 ] ;
$lscolor{'yellow'} = [ 0xED , 0xEF , 0x85 ] ;
$lscolor{'ltgrey'} = [ 0xDC , 0xDC , 0xDC ] ;
$lscolor{'grey'} = [ 0xC8 , 0xC8 , 0xC8 ] ;
$lscolor{'cyan'} = [ 0x44 , 0xB4 , 0xD5 ] ; # Cigar
$lscolor{'ltgrey'} = [ 0xDC , 0xDC , 0xDC ] ;
$lscolor{'orange'} = [ 0xff, 0x72 , 0x00 ]; 
$lscolor{'purple'} = [0xFF ,0x00, 0xCC];
$lscolor{'blue'} = [ 0x00 , 0x00 , 0xFF ] ;   #matching
$lscolor{'red'} = [ 0xFF , 0x00 , 0x00 ] ;   #SNPs
$lscolor{'black'} = [ 0x00 , 0x00 , 0x00 ] ;  #reference
$lscolor{'green2'} = [ 0x00 , 0x80 , 0x00 ] ; #single pair
$lscolor{'brown'} = [ 0xD2 , 0x69 , 0x1E ] ; # Inversion

$lscolor{'mapqual_zero'} = $lscolor{'green2'} ;   # mapping quality zero
$lscolor{'single_color'} = $lscolor{'purple'} ;   # single color
$lscolor{'gccontent_color'}= $lscolor{'blue'};

our $GbrowerPath="http://gbrowse.arabidopsis.org/cgi-bin/gbrowse_img/arabidopsis/?name=";
our $GbrowerSuffix=";type=BAC+%22Transposable%20elements%22+Locus+ProteinCoding+Pseudogene+ncRNAs+cDNA+tDNAs+Polymorphism+Marker;keystyle=between;grid=on";

1 ;