app.js

// This is an example of an angular application, using angularjs-genoverse

(function() {

angular.module("Example", ["Genoverse"]);

/**
 * Turn on html5mode only in modern browsers because
 * in the older ones html5mode rewrites urls with Hangbangs
 * which break normal Django pages.
 * With html5mode off IE lt 10 will be able to navigate the site
 * but won't be able to open deep links to Angular pages
 * (for example, a link to a search result won't load in IE 9).
 */
angular.module('Example').config(['$locationProvider', function($locationProvider) {
    if (window.history && window.history.pushState) {
        $locationProvider.html5Mode(true);
    }
}]);

angular.module('Example').controller('GenoverseGenomeBrowser', ['$scope', '$location', '$filter', function ($scope, $location, $filter) {
    // Constructor
    // -----------

    $scope.genomes = [
        // Ensembl
        {
            'ensemblSpecies': 'homo_sapiens',
            'species': 'Homo sapiens',
            'synonyms': ['human'],
            'assembly': 'GRCh38',
            'assembly_ucsc': 'hg38',
            'taxid': 9606,
            'division': 'Ensembl',
            'example_location': {
                'chromosome': 'X',
                'start': 73819307,
                'end': 73856333
            }
        },
        {
            'ensemblSpecies': 'mus_musculus',
            'species': 'Mus musculus',
            'synonyms': ['mouse'],
            'assembly': 'GRCm38',
            'assembly_ucsc': 'mm10',
            'taxid': 10090,
            'division': 'Ensembl',
            'example_location': {
                'chromosome': 1,
                'start': 86351908,
                'end': 86352200
            }
        },
        {
            'ensemblSpecies': 'danio_rerio',
            'species': 'Danio rerio',
            'synonyms': ['zebrafish'],
            'assembly': 'GRCz10',
            'assembly_ucsc': 'danRer10',
            'taxid': 7955,
            'division': 'Ensembl',
            'example_location': {
                'chromosome': 9,
                'start': 7633910,
                'end': 7634210
            }
        },
        {
            'ensemblSpecies': 'bos_taurus',
            'species': 'Bos taurus',
            'synonyms': ['cow'],
            'assembly': 'UMD3.1',
            'assembly_ucsc': 'bosTau6',
            'taxid': 9913,
            'division': 'Ensembl',
            'example_location': {
                'chromosome': 15,
                'start': 82197673,
                'end': 82197837
            }
        },
        {
            'ensemblSpecies': 'rattus_norvegicus',
            'species': 'Rattus norvegicus',
            'synonyms': ['rat'],
            'assembly': 'Rnor_6.0',
            'assembly_ucsc': 'rn6',
            'taxid': 10116,
            'division': 'Ensembl',
            'example_location': {
                'chromosome': 'X',
                'start': 118277628,
                'end': 118277850
            }
        },
        // {
        //     'ensemblSpecies': 'felis_catus',
        //     'species': 'Felis catus',
        //     'synonyms': ['cat'],
        //     'assembly': 'Felis_catus_6.2',
        //     'assembly_ucsc': 'felCat5',
        //     'taxid': 9685,
        //     'division': 'Ensembl',
        //     'example_location': {
        //         'chromosome': 'X',
        //         'start': 18058223,
        //         'end': 18058546
        //     }
        // },
        // {
        //     'ensemblSpecies': 'macaca_mulatta',
        //     'species': 'Macaca mulatta',
        //     'synonyms': ['macaque'],
        //     'assembly': 'MMUL_1',
        //     'assembly_ucsc': '', # no matching assembly
        //     'taxid': 9544,
        //     'division': 'Ensembl',
        //     'example_location': {
        //         'chromosome': 1,
        //         'start': 146238837,
        //         'end': 146238946
        //     }
        // },
        {
            'ensemblSpecies': 'pan_troglodytes',
            'species': 'Pan troglodytes',
            'synonyms': ['chimp'],
            'assembly': 'CHIMP2.1.4',
            'assembly_ucsc': 'panTro4',
            'taxid': 9598,
            'division': 'Ensembl',
            'example_location': {
                'chromosome': 11,
                'start': 78369004,
                'end': 78369219
            }
        },
        {
            'ensemblSpecies': 'canis_lupus_familiaris',
            'species': 'Canis familiaris',
            'synonyms': ['dog', 'Canis lupus familiaris'],
            'assembly': 'CanFam3.1',
            'assembly_ucsc': 'canFam3',
            'taxid': 9615,
            'division': 'Ensembl',
            'example_location': {
                'chromosome': 19,
                'start': 22006909,
                'end': 22007119
            }
        },
        // {
        //     'ensemblSpecies': 'gallus_gallus',
        //     'species': 'Gallus gallus',
        //     'synonyms': ['chicken'],
        //     'assembly': 'Galgal4',
        //     'assembly_ucsc': 'galGal4',
        //     'taxid': 9031,
        //     'division': 'Ensembl',
        //     'example_location': {
        //         'chromosome': 9,
        //         'start': 15676031,
        //         'end': 15676160
        //     }
        // },
        // {
        //     'ensemblSpecies': 'xenopus_tropicalis',
        //     'species': 'Xenopus tropicalis',
        //     'synonyms': ['frog'],
        //     'assembly': 'JGI_4.2',
        //     'assembly_ucsc': 'xenTro3',
        //     'taxid': 8364,
        //     'division': 'Ensembl',
        //     'example_location': {
        //         'chromosome': 'NC_006839',
        //         'start': 11649,
        //         'end': 11717
        //     }
        // },
        // Ensembl Fungi
        // {
        //     'ensemblSpecies': 'saccharomyces_cerevisiae',
        //     'species': 'Saccharomyces cerevisiae',
        //     'synonyms': ['budding yeast', 'Saccharomyces cerevisiae S288c'],
        //     'assembly': 'R64-1-1',
        //     'assembly_ucsc': '',
        //     'taxid': 559292,
        //     'division': 'Ensembl Fungi',
        //     'example_location': {
        //         'chromosome': 'XII',
        //         'start': 856709,
        //         'end': 856919
        //     }
        // },
        {
            'ensemblSpecies': 'schizosaccharomyces_pombe',
            'species': 'Schizosaccharomyces pombe',
            'synonyms': ['fission yeast'],
            'assembly': 'ASM294v2',
            'assembly_ucsc': '',
            'taxid': 4896,
            'division': 'Ensembl Fungi',
            'example_location': {
                'chromosome': 'I',
                'start': 540951,
                'end': 544327
            }
        },
        // Ensembl Metazoa
        {
            'ensemblSpecies': 'caenorhabditis_elegans',
            'species': 'Caenorhabditis elegans',
            'synonyms': ['worm'],
            'assembly': 'WBcel235',
            'assembly_ucsc': 'ce11',
            'taxid': 6239,
            'division': 'Ensembl Metazoa',
            'example_location': {
                'chromosome': 'III',
                'start': 11467363,
                'end': 11467705
            }
        },
        {
            'ensemblSpecies': 'drosophila_melanogaster',
            'species': 'Drosophila melanogaster',
            'synonyms': ['fly'],
            'assembly': 'BDGP6',
            'assembly_ucsc': 'dm6',
            'taxid': 7227,
            'division': 'Ensembl Metazoa',
            'example_location': {
                'chromosome': '3R',
                'start': 7474331,
                'end': 7475217
            }
        },
        {
            'ensemblSpecies': 'bombyx_mori',
            'species': 'Bombyx mori',
            'synonyms': ['silkworm'],
            'assembly': 'GCA_000151625.1',
            'assembly_ucsc': '',
            'taxid': 7091,
            'division': 'Ensembl Metazoa',
            'example_location': {
                'chromosome': 'scaf16',
                'start': 6180018,
                'end': 6180422
            }
        },
        // {
        //     'ensemblSpecies': 'anopheles_gambiae',
        //     'species': 'Anopheles gambiae',
        //     'synonyms': [],
        //     'assembly': 'AgamP4',
        //     'assembly_ucsc': '',
        //     'taxid': 7165,
        //     'division': 'Ensembl Metazoa',
        //     'example_location': {
        //         'chromosome': '2R',
        //         'start': 34644956,
        //         'end': 34645131
        //     }
        // },

        // Ensembl Protists
        {
            'ensemblSpecies': 'dictyostelium_discoideum',
            'species': 'Dictyostelium discoideum',
            'synonyms': [],
            'assembly': 'dictybase.01',
            'assembly_ucsc': '',
            'taxid': 44689,
            'division': 'Ensembl Protists',
            'example_location': {
                'chromosome': 2,
                'start': 7874546,
                'end': 7876498
            }
        },
        // {
        //     'ensemblSpecies': 'plasmodium_falciparum',
        //     'species': 'Plasmodium falciparum',
        //     'synonyms': [],
        //     'assembly': 'ASM276v1',
        //     'assembly_ucsc': '',
        //     'taxid': 5833,
        //     'division': 'Ensembl Protists',
        //     'example_location': {
        //         'chromosome': 13,
        //         'start': 2796339,
        //         'end': 2798488
        //     }
        // },

        // Ensembl Plants
        {
            'ensemblSpecies': 'arabidopsis_thaliana',
            'species': 'Arabidopsis thaliana',
            'synonyms': [],
            'assembly': 'TAIR10',
            'assembly_ucsc': '',
            'taxid': 3702,
            'division': 'Ensembl Plants',
            'example_location': {
                'chromosome': 2,
                'start': 18819643,
                'end': 18822629
            }
        }
    ];

    $scope.genomeNames = [];
    for (var i = 0; i < $scope.genomes.length; i++) {
        $scope.genomeNames.push($scope.genomes[i].ensemblSpecies);
    }

    $scope.exampleLocations = {};
    for (var i = 0; i < $scope.genomes.length; i++) {
        $scope.exampleLocations[$scope.genomes[i].ensemblSpecies] = {
            'chr': $scope.genomes[i].example_location.chromosome,
            'start': $scope.genomes[i].example_location.start,
            'end': $scope.genomes[i].example_location.end
        }
    }

    $scope.genome = $scope.genomes[0].ensemblSpecies;

    // get domain for Ensembl links
    $scope.domain = getEnsemblSubdomainByDivision($scope.genome, $scope.genomes);

    $scope.chromosome = "X";
    $scope.start = 73819307;
    $scope.end = 73856333;

    $scope.Genoverse = Genoverse;

    $scope.urls = {
        sequence: function () { // Sequence track configuration
            var species = $filter('urlencodeSpecies')($scope.genome);
            var endpoint = getEndpoint(species);
            return '__ENDPOINT__/sequence/region/__SPECIES__/__CHR__:__START__-__END__?content-type=text/plain'
                .replace('__ENDPOINT__', endpoint)
                .replace('__SPECIES__', species);
        },
        genes: function() { // Genes track configuration
            var species = $filter('urlencodeSpecies')($scope.genome);
            var endpoint = getEndpoint(species);
            return '__ENDPOINT__/overlap/region/__SPECIES__/__CHR__:__START__-__END__?feature=gene;content-type=application/json'
                .replace('__ENDPOINT__', endpoint)
                .replace('__SPECIES__', species);
        },
        transcripts: function() { // Transcripts track configuration
            var species = $filter('urlencodeSpecies')($scope.genome);
            var endpoint = getEndpoint(species);
            return '__ENDPOINT__/overlap/region/__SPECIES__/__CHR__:__START__-__END__?feature=transcript;feature=exon;feature=cds;content-type=application/json'
                .replace('__ENDPOINT__', endpoint)
                .replace('__SPECIES__', species);
        }
    };

    // reflect any changes in genome in address bar
    $scope.$watch('genome', setUrl);
    $scope.$watch('chromosome', setUrl);
    $scope.$watch('start', setUrl);
    $scope.$watch('stop', setUrl);

    $scope.$watch('genome', setDomain);


    $scope.getGenomeObject = getGenomeObject;

    // Method definitions
    // ------------------

    /**
     * Sets the url in address bar to reflect the changes in browser location
     */
    function setUrl(newValue, oldValue) {
        // set the full url
        $location.search({
            species: $scope.genome,
            chromosome: $scope.chromosome,
            start: $scope.start,
            end: $scope.end
        });
        $location.replace();
    }

    function setDomain(newValue, oldValue) {
        $scope.domain = getEnsemblSubdomainByDivision(newValue, $scope.genomes);
    }

    /**
     * Dynamically determine whether to use E! or EG REST API based on species.
     * If species not in E!, use EG.
     * Ensembl species list: http://www.ensembl.org/info/about/species.html
     */
    function getEndpoint(species) {
        var ensemblSpecies = [
            "ailuropoda_melanoleuca",
            "anas_platyrhynchos",
            "anolis_carolinensis",
            "astyanax_mexicanus",
            "bos_taurus",
            "callithrix_jacchus",
            "canis_lupus_familiaris",
            "cavia_porcellus",
            "ceratotherium_simum_simum",
            "chlorocebus_sabaeus",
            "choloepus_hoffmanni",
            "chrysemys_picta_bellii",
            "ciona_intestinalis",
            "ciona_savignyi",
            "cricetulus_griseus",
            "danio_rerio",
            "dasypus_novemcinctus",
            "dipodomys_ordii",
            "drosophila_melanogaster",
            "echinops_telfairi",
            "equus_caballus",
            "erinaceus_europaeus",
            "felis_catus",
            "ficedula_albicollis",
            "gadus_morhua",
            "gallus_gallus",
            "gasterosteus_aculeatus",
            "gorilla_gorilla_gorilla",
            "heterocephalus_glaber",
            "homo_sapiens",
            "ictidomys_tridecemlineatus",
            "latimeria_chalumnae",
            "lepisosteus_oculatus",
            "loxodonta_africana",
            "macaca_fascicularis",
            "macaca_mulatta",
            "macropus_eugenii",
            "meleagris_gallopavo",
            "melopsittacus_undulatus",
            "microcebus_murinus",
            "microtus_ochrogaster",
            "monodelphis_domestica",
            "mus_musculus",
            "mustela_putorius_furo",
            "myotis_lucifugus",
            "nomascus_leucogenys",
            "ochotona_princeps",
            "oreochromis_niloticus",
            "ornithorhynchus_anatinus",
            "orycteropus_afer_afer",
            "oryctolagus_cuniculus",
            "oryzias_latipes",
            "otolemur_garnettii",
            "ovis_aries",
            "pan_troglodytes",
            "papio_anubis",
            "papio_hamadryas",
            "pelodiscus_sinensis",
            "petromyzon_marinus",
            "poecilia_formosa",
            "pongo_abelii",
            "procavia_capensis",
            "pteropus_vampyrus",
            "rattus_norvegicus",
            "saimiri_boliviensis",
            "sarcophilus_harrisii",
            "sorex_araneus",
            "sus_scrofa",
            "sus_scrofa_map",
            "taeniopygia_guttata",
            "takifugu_rubripes",
            "tarsius_syrichta",
            "tetraodon_nigroviridis",
            "tupaia_belangeri",
            "tursiops_truncatus",
            "vicugna_pacos",
            "xenopus_tropicalis",
            "xiphophorus_maculatus"
        ];
        // "saccharomyces_cerevisiae", "caenorhabditis_elegans"];
        // "saccharomyces_cerevisiae", "caenorhabditis_elegans" could use either E! or EG

        var encoded = $filter('urlencodeSpecies')(species); // urlencoded species name
        return ensemblSpecies.indexOf(encoded) > -1 ? 'https://rest.ensembl.org' : 'https://rest.ensemblgenomes.org';
    }

    /**
    * @param genome {String} - e.g. 'homo_sapient'
    * @param genomes {Array} - contents of $scope.genome
    * @returns {String} element of genomes array
    */
    function getGenomeObject(genome, genomes) {
        // get genome object from Genomes
        var genomeObject;
        for (var i = 0; i < $scope.genomes.length; i++) {
            if (genome === $scope.genomes[i].ensemblSpecies) {
                genomeObject = $scope.genomes[i];
                return genomeObject;
            }
        }

        // if we're here, this is a failure
        console.log("Can't get genomeObject for genome: " + genome);
        return null;
    }

    /**
     * Takes a genome on input, looks into its division attribute and returns the corresponding Ensembl
     * subdomain
     *
     * @param genome {String}
     * @param genomes {Array} e.g.
     * [{
     *     'ensemblSpecies': 'mus_musculus', 'species': 'Mus musculus', 'synonyms': ['mouse'],
     *     'assembly': 'GRCm38', 'assembly_ucsc': 'mm10',
     *     'taxid': 10090, 'division': 'Ensembl',
     *     'example_location': {'chromosome': 1, 'start': 86351981, 'end': 86352127,}
     * }, ...]
     * @returns {String} domain name without protocol or slashes or trailing dots
     */
    function getEnsemblSubdomainByDivision(genome, genomes) {
        var subdomain;

        // get genome object from Genomes
        var genomeObject = getGenomeObject(genome, genomes);

        if (genomeObject.division == 'Ensembl') {
            subdomain = 'ensembl.org';
        } else if (genomeObject.division == 'Ensembl Plants') {
            subdomain = 'plants.ensembl.org';
        } else if (genomeObject.division == 'Ensembl Metazoa') {
            subdomain = 'metazoa.ensembl.org';
        } else if (genomeObject.division == 'Ensembl Bacteria') {
            subdomain = 'bacteria.ensembl.org';
        } else if (genomeObject.division == 'Ensembl Fungi') {
            subdomain = 'fungi.ensembl.org';
        } else if (genomeObject.division == 'Ensembl Protists') {
            subdomain = 'protists.ensembl.org';
        }

        return subdomain;
    }

}]);

})();