//define a constructor for a Species object.
function Species(displayName, intergenicParameterFile, fixedParameterFile, availableLengths, comment){
	this.name = displayName;
	this.fixedParamFile = fixedParameterFile;
	this.intergenicParamFile = intergenicParameterFile;
	this.lengths = availableLengths;
	this.comment = comment;
}

function rSpecies(displayName, parameterFilePrefix, fivePrimeUtrAvailable, threePrimeUtrAvailable, bothUtrAvailable, repeatFilterAvailable, nonAutoAvailable, availableLengths, comment) {
	this.name = displayName;
	this.parameterFilePrefix = parameterFilePrefix;
	this.fivePrimeUtrAvailable = fivePrimeUtrAvailable;
	this.threePrimeUtrAvailable = threePrimeUtrAvailable;
	this.bothUtrAvailable = bothUtrAvailable;
	this.repeatFilterAvailable = repeatFilterAvailable;
	this.nonAutoAvailable = nonAutoAvailable;
	this.lengths = availableLengths;
	this.comment = comment;
}

var rSCOPESpecies = new Object;

	rSCOPESpecies['Homo sapiens']						= new rSpecies('Homo sapiens','Homo_sapiens',
													true,true,false,false,true,
													'full,1000',
													'from original rScope');

	rSCOPESpecies['Danio rerio']						= new rSpecies('Danio rerio','Danio_rerio',
													true,true,false,false,true,
													'full,1000',
													'from original rScope');

	rSCOPESpecies['Mus musculus']						= new rSpecies('Mus musculus','Mus_musculus',
													true,true,false,false,true,
													'full,1000',
													'from original rScope');

// *!*!*!*!*!*!*!*!*!*!**!*!*!*!*!*!*!*!*!*!**!*!*!*!*!*!*!*!*!*!**!*!*!*!*!*!*!*!*!*!*!!!!*!*!*!*!*!*!*!*!*!*!*!
// 										ADD NEW ORGANISMS HERE
// *!*!*!*!*!*!*!*!*!*!**!*!*!*!*!*!*!*!*!*!**!*!*!*!*!*!*!*!*!*!**!*!*!*!*!*!*!*!*!*!*!!!!*!*!*!*!*!*!*!*!*!*!*!
// the SCOPESpecies variable is an associative array that holds all the species we have available.
// To add a new species, copy one of these lines and set the files accordingly. The parameters to the Species constructor are as follows:

// new Species(name to be displayed, name of parameter file, list of available lengths ([may include 'intergenic'])

// SCOPESpecies is an associative array (hash table) which means that each object is referenced by a string in the brackets.
// This string MUST MATCH THE DISPLAY NAME. See below for examples.
// New species may go anywhere in the list. The display list will have the options in sorted order by display name.

var SCOPESpecies = new Object;
	SCOPESpecies['Agrobacterium tumefaciens']				= new Species('Agrobacterium tumefaciens',
													'Agrobacterium_tumefaciens_C58_intergenic.param','Agrobacterium_tumefaciens_C58_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'C58 June 24, 2002 (ftp.tigr.org)');
													
	SCOPESpecies['Anopheles gambiae']						= new Species('Anopheles gambiae', null,'Anopheles_gambiae_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'Ensembl 49 03/18/2008 based on AgamP3, February 2006 PEST strain (http://www.ensembl.org/Anopheles_gambiae/index.html)');
													
	SCOPESpecies['Apis mellifera']						= new Species('Apis mellifera', null,'Apis_mellifera_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'2006/08/28 (http://rsat.ccb.sickkids.ca/ based on ncbi)');
													
	SCOPESpecies['Arabidopsis thaliana']					= new Species('Arabidopsis thaliana',
													'Arabidopsis_thaliana_TAIR6_intergenic.param','Arabidopsis_thaliana_TAIR6_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'September 7, 2006 (ftp://ftp.arabidopsis.org/home/taie/Genes/)');
													
	SCOPESpecies['Ashbya gossypii']					= new Species('Ashbya gossypii',
													'Ashbya_gossypii_intergenic.param','Ashbya_gossypii_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'June 1, 2006 (http://agd.unibas.ch/Ashbya_gossypii/download_ashbya)');
													
	SCOPESpecies['Aspergillus fumigatus']				= new Species('Aspergillus fumigatus','Aspergillus_fumigatus_Af293_intergenic.param',
													'Aspergillus_fumigatus_Af293_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'Af293, October 2, 2006 (ftp://ftp.ncbi.nih.gov/)');
													
	SCOPESpecies['Aspergillus terreus']					= new Species('Aspergillus terreus',
													null,'Aspergillus_terreus_fixed1000.param',
													'1000,800,600,500,400,200,100',
													'(www.broad.mit.edu/annotation/genome)');
													
	SCOPESpecies['Aspergillus nidulans']					= new Species('Aspergillus nidulans',
													null,'Aspergillus_nidulans_fixed1000.param',
													'1000,800,400,200,100',
													'June 19, 2006 (http://www.broad.mit.edu/annotation/genome');
													
	SCOPESpecies['Bacillus subtilis']					= new Species('Bacillus subtilis',
													'Bacillus_subtilis_intergenic.param','Bacillus_subtilis_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'2002 (ftp.tigr.org)');
													
	SCOPESpecies['Bos taurus']					= new Species('Bos taurus',
													null,'Bos_taurus_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'Ensembl 49 03/18/2008 based on Btau 3.1 Hereford breed (http://www.ensembl.org/Bos_taurus/index.html)');
													
	SCOPESpecies['Botrytis cinerea']					= new Species('Botrytis cinerea',
													null,'Botrytis_cinerea_fixed1000.param',
													'1000,800,600,500,400,200,100',
													'version 1 5/08/2007 (www.broad.mit.edu/annotation/genome)');
													
	SCOPESpecies['Caenorhabditis elegans']					= new Species('Caenorhabditis elegans',
													'Caenorhabditis_elegans_intergenic.param','Caenorhabditis_elegans_fixed2500.param',
													'2500,1500,800,400,200,100',
													'WB170 February 10, 2007 (www.wormbase.org)');
													
	SCOPESpecies['Candida albicans']					= new Species('Candida albicans',
													null,'Candida_albicans_fixed1000.param',
													'1000,800,600,500,400,200,100',
													'version 1 08-Mar-07 (www.broad.mit.edu/annotation/genome/)');
													
	SCOPESpecies['Candida glabrata']					= new Species('Candida glabrata',
													null,'Candida_glabrata_CBS138_fixed2500.param',
													'2500,1500,800,400,200,100',
													'release 90 08-Mar-07 (www.ebl.ac.uk/embl/)');
													
	SCOPESpecies['Candida guilliermondii']					= new Species('Candida guilliermondii',
													null,'Candida_guilliermondii_fixed1000.param',
													'1000,800,600,500,400,200,100',
													'version 1 4/26/2006 (www.broad.mit.edu/annotation/genome/)');
													
	SCOPESpecies['Candida lusitaniae']					= new Species('Candida lusitaniae',
													null,'Candida_lusitaniae_fixed1000.param',
													'1000,800,600,500,400,200,100',
													'version 1 07-May-07 (www.broad.mit.edu/annotation/genome/)');
													
	SCOPESpecies['Candida tropicalis']					= new Species('Candida tropicalis',
													null,'Candida_tropicalis_fixed1000.param',
													'1000,800,600,500,400,200,100',
													'version 3 31-May-06 (www.broad.mit.edu/annotation/genome/)');
													
	SCOPESpecies['Canis familiaris']					= new Species('Canis familiaris',
													null,'Canis_familiaris_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'Ensembl 49 03/18/2008 based on CanFam2.0 2005 (http://www.ensembl.org/Canis_familiaris/index.html)');
													
	SCOPESpecies['Chlamydia trachomatis']					= new Species('Chlamydia trachomatis',
													'Chlamydia_trachomatis_intergenic.param','Chlamydia_trachomatis_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'January 26, 2006 (ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/Chlamydia_trachomatis/AE001273.gbk)');
													
	SCOPESpecies['Chaetomium globosum']					= new Species('Chaetomium globosum',
													null,'Chaetomium_globosum_fixed1000.param',
													'1000,800,600,500,400,200,100',
													'version 1 4/26/2006 (www.broad.mit.edu/annotation/genome/)');
													
	SCOPESpecies['Clostridium tetani']					= new Species('Clostridium tetani',
													'Clostridium_tetani_E88_intergenic.param','Clostridium_tetani_E88_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'E88, August 5, 2005 (ftp.tigr.org)');
													
	SCOPESpecies['Coprinus cinereus']					= new Species('Coprinus cinereus',
													null,'Coprinus_cinereus_fixed1000.param',
													'1000,800,600,500,400,200,100',
													'version 1 5/04/2006 (www.broad.mit.edu/annotation/genome/)');
													
	SCOPESpecies['Cryptococcus neoformans']					= new Species('Cryptococcus neoformans',
													null,'Cryptococcus_neoformans_fixed1000.param',
													'1000,800,600,500,400,200,100',
													'version 1 26-Apr-06 (www.broad.mit.edu/annotation/genome/)');
													
	SCOPESpecies['Danio rerio']						= new Species('Danio rerio', 'Danio_rerio_intergenic.param','Danio_rerio_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'version 6 (Zv6), March 30, 2006 (ftp://ftp.ensembl.org/pub/current_danio_rerio/data/flatfiles/genbank/)');
													
	SCOPESpecies['Debaryomyces hansenii']						= new Species('Debaryomyces hansenii', null,'Debaryomyces_hansenii_CBS767_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'CBS767, 2007/06/08 (http://rsat.ccb.sickkids.ca/ based on ncbi)');
													
	SCOPESpecies['Drosophila melanogaster']				= new Species('Drosophila melanogaster',
													'Drosophila_melanogaster_intergenic.param','Drosophila_melanogaster_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'February 17, 2006 (ftp://flybase.net)');
													
	SCOPESpecies['Equus caballus']					= new Species('Equus caballus',
													null,'Equus_caballus_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'Ensembl 49 03/18/2008(http://www.ensembl.org/Equus_caballus/index.html)');
													
	SCOPESpecies['Escherichia coli']				= new Species('Escherichia coli',
													'Escherichia_coli_K12-MG1655_intergenic.param','Escherichia_coli_K12-MG1655_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'K12-MG1655 2000 (ftp.tigr.org)');
													
	SCOPESpecies['Fusarium verticillioides']					= new Species('Fusarium verticillioides',
													null,'Fusarium_verticillioides_fixed1000.param',
													'1000,800,600,500,400,200,100',
													'version 1 29-May-07 (www.broad.mit.edu/annotation/genome/)');
													
	SCOPESpecies['Gallus gallus']					= new Species('Gallus gallus',
													null,'Gallus_gallus_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'Ensembl 49 03/18/2008 based on May 2006 v 2.1 from Washington University in St Louis(http://www.ensembl.org/Gallus_gallus/index.html)');
													
	SCOPESpecies['Haemophilus influenzae']					= new Species('Haemophilus influenzae',
													'Haemophilus_influenzae_intergenic.param','Haemophilus_influenzae_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'January 18, 2006 (ftp.tigr.org)');
													
	SCOPESpecies['Helicobacter pylori']						= new Species('Helicobacter pylori',
													'Helicobacter_pylori_intergenic.param','Helicobacter_pylori_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'2000 (ftp.tigr.org)');
													
	SCOPESpecies['Histoplasma capsulatum']					= new Species('Histoplasma capsulatum',
													null,'Histoplasma_capsulatum_fixed1000.param',
													'1000,800,600,500,400,200,100',
													'version 1 11-May-06 (www.broad.mit.edu/annotation/genome/)');
	SCOPESpecies['Homo sapiens']						= new Species('Homo sapiens',
													'Homo_sapiens_intergenic.param','Homo_sapiens_fixed2500.param',
													'2500,1500,800,400,200,100',
													'March 2006 from UCSC: http://genome.ucsc.edu hg18 based on ncbi 36.1');
													
	SCOPESpecies['Kluyveromyces lactis']					= new Species('Kluyveromyces lactis',
													null,'Kluyveromyces_lactis_NRRL_fixed2500.param',
													'2500,1500,800,400,200,100',
													'14-Nov-06 (ftp.ncbi.nih.gov)');
													
	SCOPESpecies['Macaca mulatta']					= new Species('Macaca mulatta',
													null,'Macaca_mulatta_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'Ensembl 49 03/18/2008(http://www.ensembl.org/Macaca_mulatta/index.html)');
													
	SCOPESpecies['Magnaporthe grisea']					= new Species('Magnaporthe grisea',
													null,'Magnaporthe_grisea_fixed1000.param',
													'1000,800,600,500,400,200,100',
													'version 5 07-May-07 (www.broad.mit.edu/annotation/genome/)');
													
	SCOPESpecies['Methanococcus jannaschii']					= new Species('Methanococcus jannaschii',
													'Methanococcus_jannaschii_intergenic.param','Methanococcus_jannaschii_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'2000 (ftp.tigr.org)');
													
	SCOPESpecies['Mus musculus']					= new Species('Mus musculus',
													null,'Mus_musculus_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'Ensembl 48 based on NCBI m37 April 2007, strain C57BL/6J (http://www.ensembl.org/Mus_musculus)');
													
	SCOPESpecies['Mycobacterium tuberculosis']		= new Species('Mycobacterium tuberculosis',
													'Mycobacterium_tuberculosis_CDC1551_intergenic.param','Mycobacterium_tuberculosis_CDC1551_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'CDC1551, 2000 (ftp.tigr.org)');
													
	SCOPESpecies['Mycobacterium tuberculosis']			= new Species('Mycobacterium tuberculosis',
													'Mycobacterium_tuberculosis_H37Rv_intergenic.param','Mycobacterium_tuberculosis_H37Rv_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'H37Rv, 2000 (ftp.tigr.org)');
													
	SCOPESpecies['Neurospora crassa']						= new Species('Neurospora crassa',
													'Neurospora_crassa_intergenic.param','Neurospora_crassa_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'July 18, 2006 (http://www.broad.mit.edu/annotation/genome/neurospora/Downloads.html/direct)');
													
	SCOPESpecies['Plasmodium falciparum']				= new Species('Plasmodium falciparum',
													'Plasmodium_falciparum_3D7_intergenic.param','Plasmodium_falciparum_3D7_fixed2500.param',
													'2500,1500,800,400,200,100',
													'3D7, November 9, 2006');
													
	SCOPESpecies['Porphyromonas gingivalis']				= new Species('Porphyromonas gingivalis',
													'Porphyromonas_gingivalis_W83_intergenic.param','Porphyromonas_gingivalis_W83_fixed800.param',
													'800,400,200,100',
													'W83, 03-DEC-2007 (http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=34539880)');
													
	SCOPESpecies['Pseudomonas aeruginosa']				= new Species('Pseudomonas aeruginosa',
													'Pseudomonas_aeruginosa_PA01_intergenic.param','Pseudomonas_aeruginosa_PA01_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'PA01, January 19, 2005');
													
	SCOPESpecies['Rattus norvegicus']					= new Species('Rattus norvegicus',
													'Rattus_norvegicus_intergenic.param','Rattus_norvegicus_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'December 1, 2006 (http://www.ensembl.org/info/data/download.html)');
													
	SCOPESpecies['Rhizopus oryzae']					= new Species('Rhizopus oryzae',
													null,'Rhizopus_oryzae_fixed1000.param',
													'1000,800,600,500,400,200,100',
													'14-Nov-06 (www.broad.mit.edu/annotation/genome/)');
													
	SCOPESpecies['Saccharomyces cerevisiae'] 					= new Species('Saccharomyces cerevisiae',
													'Saccharomyces_cerevisiae_intergenic.param', 'Saccharomyces_cerevisiae_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'November 21, 2006 (ftp://ftp.ncbi.nih.gov/)');
													
	SCOPESpecies['Saccharomyces cerevisiae S288C'] 					= new Species('Saccharomyces cerevisiae S288C',
													'Saccharomyces_cerevisiae_S288C_intergenic.param', 'Saccharomyces_cerevisiae_S288C_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'Tue Apr 14 19:50:11 2009 (http://www.yeastgenome.org)');
													
	SCOPESpecies['Salmonella typhimurium']	= new Species('Salmonella typhimurium',
													'Salmonella_typhimurium_LT2_SGSC1412_intergenic.param','Salmonella_typhimurium_LT2_SGSC1412_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'LT2 SGSC1412 November 8, 2001 (ftp.tigr.org)');
													
	SCOPESpecies['Schizosaccharomyces pombe']						= new Species('Schizosaccharomyces pombe',
													'Schizosaccharomyces_pombe_intergenic.param','Schizosaccharomyces_pombe_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'April 17, 2006 (ftp.ncbi.nih.gov/genbank/)');
													
	SCOPESpecies['Stagonospora nodorum']					= new Species('Stagonospora nodorum',
													null,'Stagonospora_nodorum_fixed1000.param',
													'1000,800,400,200,100',
													'February 2009 (http://www.broad.mit.edu/annotation/genome/stagonospora_nodorum/)');
													
	SCOPESpecies['Staphylococcus aureus']					= new Species('Staphylococcus aureus',
													'Staphylococcus_aureus_MW2_intergenic.param','Staphylococcus_aureus_MW2_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'MW2, August 28, 2002 (ftp.tigr.org)');
													
	SCOPESpecies['Uncinocarpus reesii']					= new Species('Uncinocarpus reesii',
													null,'Uncinocarpus_reesii_fixed1000.param',
													'1000,800,600,500,400,200,100',
													'version 1 5/12/2006 (www.broad.mit.edu/annotation/genome/)');
													
	SCOPESpecies['Ustilago maydis']					= new Species('Ustilago maydis',
													null,'Ustilago_maydis_fixed1000.param',
													'1000,800,600,500,400,200,100',
													'version 1 4/26/2006 (www.broad.mit.edu/annotation/genome)');
													
	SCOPESpecies['Vibrio cholerae']		= new Species('Vibrio cholerae',
													'Vibrio_cholerae_El_Tor_N16961_intergenic.param','Vibrio_cholerae_El_Tor_N16961_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'El Tor N16961, 2000 (ftp.ncbi.nih.gov/genbank/)');
													
	SCOPESpecies['Yarrowia lipolytica']					= new Species('Yarrowia lipolytica',
													null,'Yarrowia_lipolytica_CLIB122_fixed2500.param',
													'2500,1500,800,400,200,100',
													'14-Nov-06 (ftp.ncbi.nih.gov)');
													
	SCOPESpecies['Yersinia pestis']					= new Species('Yersinia pestis',
													'Yersinia_pestis_CO92_intergenic.param','Yersinia_pestis_CO92_fixed2500.param',
													'2500,1500,1000,800,400,200,100',
													'CO92, June 24, 2002');
													
//	SCOPESpecies['Enterobacteria phage T4']						= new Species('Enterobacteria phage T4',
//													'Enterobacteria_phage_T4_intergenic.param','Enterobacteria_phage_T4_fixed800.param',
//													'800,400,200,100',
//													'March 29, 2003 (http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NC_000866)');

// *!*!*!*!*!*!*!*!*!*!**!*!*!*!*!*!*!*!*!*!**!*!*!*!*!*!*!*!*!*!**!*!*!*!*!*!*!*!*!*!*!!!!*!*!*!*!*!*!*!*!*!*!*!
// 										END ADD NEW ORGANISMS 
// *!*!*!*!*!*!*!*!*!*!**!*!*!*!*!*!*!*!*!*!**!*!*!*!*!*!*!*!*!*!**!*!*!*!*!*!*!*!*!*!*!!!!*!*!*!*!*!*!*!*!*!*!*!