TwoBit.spec.js

require([
            'JBrowse/Store/SeqFeature/TwoBit',
            'JBrowse/Browser',
            'dojo/aspect',
            'JBrowse/Model/XHRBlob'

        ], function(
            TwoBitStore,
            Browser,
            aspect,
            XHRBlob
        ) {

describe(".2bit data store with T_ko.2bit", function() {

    var t = new TwoBitStore({
            browser: new Browser({ unitTestMode: true }),
            refSeq: { name: 'chr1', start: 1, end: 500001 },
            blob: new XHRBlob("../data/T_ko.2bit")
        });

    it("constructs", function() {
        expect(t).toBeTruthy();
    });

    it("loads some data", function() {
        var done;
        var features = [];

        var pythonReaderOutput = "ATGATCCTCGACACTGACTACATAACCGAGGATGGAAAGCCTGTCATAAGAATTTTCAAG AAGGAAAACGGCGAGTTTAAGATTGAGTACGACCGGACTTTTGAACCCTACTTCTACGCC CTCCTGAAGGACGATTCTGCCATTGAGGAAGTCAAGAAGATAACCGCCGAGAGGCACGGG ACGGTTGTAACGGTTAAGCGGGTTGAAAAGGTTCAGAAGAAGTTCCTCGGGAGACCAGTT GAGGTCTGGAAACTCTACTTTACTCATCCGCAGGACGTCCCAGCGATAAGGGACAAGATA CGAGAGCATCCAGCAGTTATTGACATCTACGAGTACGACATACCCTTCGCCAAGCGCTAC CTCATAGACAAGGGATTAGTGCCAATGGAAGGCGACGAGGAGCTGAAAATGCTCGCCTTC GACATTGAAACTCTCTACCATGAGGGCGAGGAGTTCGCCGAGGGGCCAATCCTTATGATA AGCTACGCCGACGAGGAAGGGGCCAGGGTGATAACTTGGAAGAACGTGGATCTCCCCTAC GTTGACGTCGTCTCGACGGAGAGGGAGATGATAAAGCGCTTCCTCCGTGTTGTGAAGGAG AAAGACCCGGACGTTCTCATAACCTACAACGGCGACAACTTCGACTTCGCCTATCTGAAA AAGCGCTGTGAAAAGCTCGGAATAAACTTCGCCCTCGGAAGGGATGGAAGCGAGCCGAAG ATTCAGAGGATGGGCGACAGGTTTGCCGTCGAAGTGAAGGGACGGATACACTTCGATCTC TATCCTGTGATAAGACGGACGATAAACCTGCCCACATACACGCTTGAGGCCGTTTATGAA GCCGTCTTCGGTCAGCCGAAGGAGAAGGTTTACGCTGAGGAAATAACCACAGCCTGGGAA ACCGGCGAGAACCTTGAGAGAGTCGCCCGCTACTCGATGGAAGATGCGAAGGTCACATAC GAGCTTGGGAAGGAGTTCCTTCCGATGGAGGCCCAGCTTTCTCGCTTAATCGGCCAGTCC CTCTGGGACGTCTCCCGCTCCAGCACTGGCAACCTCGTTGAGTGGTTCCTCCTCAGGAAG GCCTATGAGAGGAATGAGCTGGCCCCGAACAAGCCCGATGAAAAGGAGCTGGCCAGAAGA CGGCAGAGCTATGAAGGAGGCTATGTAAAAGAGCCCGAGAGAGGGTTGTGGGAGAACATA GTGTACCTAGATTTTAGATGCCATCCAGCCGATACGAAGGTTGTCGTCAAGGGGAAGGGG ATTATAAACATCAGCGAGGTTCAGGAAGGTGACTATGTCCTTGGGATTGACGGCTGGCAG AGAGTTAGAAAAGTATGGGAATACGACTACAAAGGGGAGCTTGTAAACATAAACGGGTTA AAGTGTACGCCCAATCATAAGCTTCCCGTTGTTACAAAGAACGAACGACAAACGAGAATA AGAGACAGTCTTGCTAAGTCTTTCCTTACTAAAAAAGTTAAGGGCAAGATAATAACCACT CCCCTTTTCTATGAAATAGGCAGAGCGACAAGTGAGAATATTCCAGAAGAAGAGGTTCTC AAGGGAGAGCTCGCTGGCATACTATTGGCTGAAGGAACGCTCTTGAGGAAAGACGTTGAA TACTTTGATTCATCCCGCAAAAAACGGAGGATTTCACACCAGTATCGTGTTGAGATAACC ATTGGGAAAGACGAGGAGGAGTTTAGGGATCGTATCACATACATTTTTGAGCGTTTGTTT GGGATTACTCCAAGCATCTCGGAGAAGAAAGGAACTAACGCAGTAACACTCAAAGTTGCG AAGAAGAATGTTTATCTTAAAGTCAAGGAAATTATGGACAACATAGAGTCCCTACATGCC CCCTCGGTTCTCAGGGGATTCTTCGAAGGCGACGGTTCAGTAAACAGGGTTAGGAGGAGT ATTGTTGCAACCCAGGGTACAAAGAACGAGTGGAAGATTAAACTGGTGTCAAAACTGCTC TCCCAGCTTGGTATCCCTCATCAAACGTACACGTATCAGTATCAGGAAAATGGGAAAGAT CGGAGCAGGTATATACTGGAGATAACTGGAAAGGACGGATTGATACTGTTCCAAACACTC ATTGGATTCATCAGTGAAAGAAAGAACGCTCTGCTTAATAAGGCAATATCTCAGAGGGAA ATGAACAACTTGGAAAACAATGGATTTTACAGGCTCAGTGAATTCAATGTCAGCACGGAA TACTATGAGGGCAAGGTCTATGACTTAACTCTTGAAGGAACTCCCTACTACTTTGCCAAT GGCATATTGACCCATAACTCCCTGTACCCCTCAATCATCATCACCCACAACGTCTCGCCG GATACGCTCAACAGAGAAGGATGCAAGGAATATGACGTTGCCCCACAGGTCGGCCACCGC TTCTGCAAGGACTTCCCAGGATTTATCCCGAGCCTGCTTGGAGACCTCCTAGAGGAGAGG CAGAAGATAAAGAAGAAGATGAAGGCCACGATTGACCCGATCGAGAGGAAGCTCCTCGAT TACAGGCAGAGGGCCATCAAGATCCTGGCAAACAGCATCCTACCCGAGGAATGGCTTCCA GTCCTCGAGGAAGGGGAGGTTCACTTCGTCAGGATTGGAGAGCTCATAGACCGGATGATG GAGGAAAATGCTGGGAAAGTAAAGAGAGAGGGCGAGACGGAAGTGCTTGAGGTCAGTGGG CTTGAAGTCCCGTCCTTTAACAGGAGAACTAAGAAGGCCGAGCTCAAGAGAGTAAAGGCC CTGATTAGGCACGATTATTCTGGCAAGGTCTACACCATCAGACTGAAGTCGGGGAGGAGA ATAAAGATAACCTCTGGCCACAGCCTCTTCTCTGTGAGAAACGGGGAGCTCGTTGAAGTT ACGGGCGATGAACTAAAGCCAGGTGACCTCGTTGCAGTCCCGCGGAGATTGGAGCTTCCT GAGAGAAACCACGTGCTGAACCTCGTTGAACTGCTCCTTGGAACGCCAGAAGAAGAAACT TTGGACATCGTCATGACGATCCCAGTCAAGGGTAAGAAGAACTTCTTTAAAGGGATGCTC AGGACTTTGCGCTGGATTTTCGGAGAGGAAAAGAGGCCCAGAACCGCGAGACGCTATCTC AGGCACCTTGAGGATCTGGGCTATGTCCGGCTTAAGAAGATCGGCTACGAAGTCCTCGAC TGGGACTCACTTAAGAACTACAGAAGGCTCTACGAGGCGCTTGTCGAGAACGTCAGATAC AACGGCAACAAGAGGGAGTACCTCGTTGAATTCAATTCCATCCGGGATGCAGTTGGCATA ATGCCCCTAAAAGAGCTGAAGGAGTGGAAGATCGGCACGCTGAACGGCTTCAGAATGAGC CCGCTCATTGAAGTGGACGAGTCGTTAGCAAAGCTCCTCGGCTACTACGTGAGCGAGGGC TATGCAAGAAAGCAGAGGAATCCCAAAAACGGCTGGAGCTACAGCGTGAAGCTCTACAAC GAAGACCCTGAAGTGCTGGACGATATGGAGAGACTCGCCAGCAGGTTTTTCGGGAAGGTG AGGCGGGGCAGGAACTACGTTGAGATACCGAAGAAGATCGGCTACCTGCTCTTTGAGAAC ATGTGCGGTGTCCTAGCGGAGAACAAGAGGATTCCCGAGTTCGTCTTCACGTCCCCGAAA GGGGTTCGGCTGGCCTTCCTTGAGGGGTACTTCATCGGCGATGGCGACGTCCACCCGAAC AAGAGACTCAGGCTCTCAACGAAAAGCGAGCTTTTAGCGAACCAGCTCGTCCTCCTCTTG AACTCGGTGGGGGTCTCTGCTGTAAAACTTGGGCACGACAGCGGCGTTTACAGGGTCTAT ATAAACGAGGAGCTCCCGTTCGTAAAGCTGGACAAGAAAAAGAACGCCTACTACTCACAC GTGATCCCCAAGGAAGTCCTGAGCGAGGTCTTTGGGAAGGTTTTCCAGAAAAACGTCAGT CCTCAGACCTTCAGGAAGATGGTCGAGGACGGAAGACTCGATCCCGAAAAGGCCCAGAGG CTCTCCTGGCTCATTGAGGGGGACGTAGTGCTCGACCGCGTTGAGTCCGTTGATGTGGAA GACTACGATGGTTATGTCTATGACCTGAGCGTCGAGGACAACGAGAACTTCCTCGTTGGC TTTGGGTTGGTCTATGCTCACAACAGCTACTACGGTTACTACGGCTATGCAAGGGCGCGC TGGTACTGCAAGGAGTGTGCAGAGAGCGTAACGGCCTGGGGAAGGGAGTACATAACGATG ACCATCAAGGAGATAGAGGAAAAGTACGGCTTTAAGGTAATCTACAGCGACACCGACGGA TTTTTTGCCACAATACCTGGAGCCGATGCTGAAACCGTCAAAAAGAAGGCTATGGAGTTC CTCAAGTATATCAACGCCAAACTTCCGGGCGCGCTTGAGCTCGAGTACGAGGGCTTCTAC AAACGCGGCTTCTTCGTCACGAAGAAGAAGTATGCGGTGATAGACGAGGAAGGCAAGATA ACAACGCGCGGACTTGAGATTGTGAGGCGTGACTGGAGCGAGATAGCGAAAGAGACGCAG GCGAGGGTTCTTGAAGCTTTGCTAAAGGACGGTGACGTCGAGAAGGCCGTGAGGATAGTC AAAGAAGTTACCGAAAAGCTGAGCAAGTACGAGGTTCCGCCGGAGAAGCTGGTGATCCAC GAGCAGATAACGAGGGATTTAAAGGACTACAAGGCAACCGGTCCCCACGTTGCCGTTGCC AAGAGGTTGGCCGCGAGAGGAGTCAAAATACGCCCTGGAACGGTGATAAGCTACATCGTG CTCAAGGGCTCTGGGAGGATAGGCGACAGGGCGATACCGTTCGACGAGTTCGACCCGACG AAGCACAAGTACGACGCCGAGTACTACATTGAGAACCAGGTTCTCCCAGCCGTTGAGAGA ATTCTGAGAGCCTTCGGTTACCGCAAGGAAGACCTGCGCTACCAGAAGACGAGACAGGTT GGTTTGAGTGCTTGGCTGAAGCCGAAGGGAACTTGACCTTTCCATTTGTTTTCCAGCGGA TAACCCTTTAACTTCCCTTTCAAAAACTCCCTTTAGGGAAAGACCATGAAGATAGAAATC CGGCGGCGCCCGGTTAAATACGCTAGGATAGAAGTGAAGCCAGACGGCAGGGTAGTCGTC ACTGCCCCCGAGGGGTTCAACGTTGAGAAGTTCATAGCAAAGAACGCCGCCTGGCTGGAG GGGAAGCTGGCCCAGATTGAAGGTCTGAAAGAGCTTGCAGAGTCGGGCTTTCCCCTGAAC GGCGAGTTCTACAAGGTCATACACGGAAGGAGGGCGAAAGTTCATGACAGCTTTAGGACC GTTGTTCTCCCCCCTTATCCCGAAGACATGCGGGAAGAACTGAAAAGGCTTCTCCGGCCG GAGATATTTGGGCTTATTGAAAAATACGCAGGAAAAATGGGAGTATCCCCCGGCAAGGTC TTCATCCGTTCGCAGAGGACAAGGTGGGGCAGCTGTTCTGGAAAGGGCAACCTGAACTTC AACCTTCGCCTGATAGCCCTTCCGCCGGAGCTCAGGGAGTACGTTGTCGTCCACGAGCTT GCTCACCTTAAGCACAGAAACCACTCAAAGGCCTTCTGGAGCCTTGTCTCCCGCTTCTAC CCGGACTACCGCTCCGCAAGGGAAGAGCTGAAGAAGTGGTGGAGCATTCTGGAGCTGAAC CCGTACTGGCGGTGGCTGGAGGGAAGGGAGTGACGCTGAAGGGAGTTTTAAAGCTCCTCC TTCTTTCAGCGGACGAAATAGCTGTCGCGGTCTTTATCTTTGTAGTTCTCCCCGGATTTG GGGTTGATGTGCCCTTGAAAGTATCCGTTCCACTTTTGGTGCTCCTGCTCCTCAAGGATA TTTTAATCGCCCCATACGTCCTCGGAGGCGGACTCGAAAAGAGGCCTTTAACTGGCCCTG AGGCTTTGATAGGGATGGAGGCGGTGGTCGTTGAAGACCTATCTCCAGAGGGTATCGTCA AAGTTGGGAACGAGCTGTGGAGAGGGGTCTGCTTAAACGGAAGGGCCAAGAGGGGAGAAA AAGTCAGGATCGTTGGATTCAGGGGGAACCTCCTACTACTGGAACGCCCAGAGTCCTGAG AACCTCTGCCAGCTCTTCGGGCCTGTTGGTGGTGAATGAGATGCTCCAGCCTTTAGTTCT TTCAATGAGAACGCAGGCCTTCCCTGGGTAAGTGTAGTGTATCGTCCCGCTGCAGCTCAT CCAGCCCTCTGAAATTCTGACGAGCTTTATCTCGTCGAGCCGGATCGTCTTTCTGGCGAG GAGACCGAGGGCACTTCTGATTTTCAGTCTCTCCTCATCCACTTCAATCTTTAGCTGCAT CAGGTCAAGGGCTATTGCCACAAACGGAAGAAGAAAAACGAGGAGAAACGTCATGTCTTC GCCTGCCAGGTATGAAGCTCCTATTCCTATGGTCATTCCTAGGAAGGCTGGGAGCATTAT GAGGAGCATCTTCCAGCTCCTGACGGTCTCGGAGTAGATGGCCACCACCGAGGGATTTTC CACTACCTCTTTAAAGCCCTTTTCCAAAGGTTACCAGGTGATAAGATGGTTCGGATAATG CCCGTTGACAGGCTGAGCGATGAGGAGGTAAGAGAAATTCTCACAAAGTACCGGAAGATA GCGCTCGTCGGCGCCTCACCAAAGCCGGAGCGCGATGCTAACAGGGTCATGCGCTATCTC CTCGAACACGGCTATGAGGTCTATCCCGTGAACCCGCGCTACGATGAGGTTCTCGGGAGG AAGTGCTATCCTAGCGTTCTTGACATCCCGGATGAGGTTGAAATCGTTGACCTCTTCGTT AGGCCAGAGTTCACTATGGACTACGTGGAACAGGCGATAAAGAAGGGTGCGAAGGTGGTC TGGTTCCAGTTCAACACCTACAACAGGGAGGCGTTCAGGAAAGCGAAAGAAGCGGGCCTT ACAGCAGTCGCTCACAGGTGCATAAAGCAGGAGCACGAGAGGCTTATCGGGTAATTCCAA GGAGCTCAAGGAGTTCTTTGGTGTTCACCACGTCAATCTCCTCTATTTCCTTCAGTCTCT TGTCGTTGTTCCACAGGGGGCTTTTACTTTTAGGGCCAGTGCCACAAAGTCAGCGTCATC TTTGTCGGGGGTTATTCGAGTGCTAGAGGTATGAACTCGGCGTAGAACCCCTCGTTTACG AATATGACATGCTCTTTAAGAACGGACAGTATTTCCTCGAACTCTTTCTCTCCGATCTTT GCTTTTTTCAGGACTTCGTCCCTGTGCTCGTGAAGCTCTTCCAGTGCAAACTCGGGACTT ATAAGTCTCCCTGATACCAAGAACACGAGCTCTCTGGTTACTGTTGATTTCCCGAAGAAA GAGAATAGCACGTTTGTGTTAACTACGAGAAGAATATCTTCTCTCAAGGTACTCGCCCCT TCCCATTTTCGCCTTCCGTCCGAGTTCTATTGCATCCTCTTCTGAGAGTTCGGAGTTCTT GAGCATCTCATTGAGCCTTGCGAGGGTTTTCAGTCTCTCCGCGATAGTCTTTGCTATCAA ATCGGCCAGCTTTTCGTCCACACTCGGGGGGACCTTGACCACTATGTCTCCCACGCTATC ACCGCTCTTACTACGCCGCTCTGCTTATAACGGTTTATCCTCTGTACCTCAGCACGTGGA TGTCCCTTACGACCCTGTGCCTCTCCTCGTAGTCAGGGTACCTCCCGAGGACTTCAAAGC CGAGCTTCACGAGCCACTTCCTCTCCTTCCGGTATATTCCACCGCCGCTCAGCTTGTAGG CCGGGAAGACAAAGACAACCTTTCCGTTTCTTTTCAGAACGTCGGCAAAGCTCTCGAAGA CCGAATAATAGAAGCGGTCGAGCTCGTTGGCCAGCTTTATGGCCTCGCCCCTACTCGGGT GTCTTTTGAGGGGCTTTCCGAGGTAGGGTTCGGTGACTATAGCATCGAACCTCTGTCTAA AACACTTCTTCAGCTTTCTGGCGTCGCAGACTTCTAAGTGAGCCGAGTTTTTGAGCCGGA ACTCTTTCCTCAGCCAGGTGAGATTCTTCTTGGCATCCCTGATCTGCCCCTCGTCGCGGT CGCTCCCGTAGGCAGTAAGCCCCTGAAGAACGAACTCCTGAACCACCGTTCCAATGCCGC AGAACGGATCCAGGAAGCTCCCCTTTCTAACCTCCGTCAGGTTCACCATTATCCTTGCCA GTCTCGGCGGAATCGAGAGGATGGGCTTCTGGACGGGCCTCTCGACGTCGAGCTTCTTCA GCTCGAAGGGGTCCGTTACTCTGATCGTCTCGCCGACGAGGAAGCTCCCGTCTTCCCTGA ACAGAAAGACGAAGTCCTTAACCTCCGGAAAGCCCTTGAGGATGAGCTCCGCGGGCATGG CATATGTTTTTGCGGGCTTGAAGAACTTAGCTGACCCCTCCTCTTTGAACCTCTTCTTTA TCTCGCTCCCGAGCTTACGCCAGAGCTTCCAGTCGCTCTTCCCGTAGAGACTGACCGTAA AAAGCCTGGAGTACTCCAGCTCCTCCAGAGCCTCTTCTCCCTCCCCAACTATCCTGACGA GCTTGAGAGAACCGCCTATCCACCGGAAATATCTCTCCACCGAAGGCTTGGATTCAAAGA CTATCCAGTTATGCTCTTCCTCAATCGATTTAACTTTTAGTCCGAATCTTCTCCCGAAAG AGTAAAATTCAGCACGGCTGAGCTCTGAATTCTTTCCTAAGATTACTCCATACATGGATT GCGCTTTGAGTAAGCTTTTAAAAAGGTTCCGCGTAAATATAATTGGGATTTAATCAAAAA CATGAGTCCACGGTGACCACCTATGCTGACGGTTGAGGTTCTTAAATCAGCTGACATCAT ACCTGATCCATATACGCGCGCGGTAACCTACGCCCGGTTAGGTGAGACGCTTGTGCGCAG GAAGGATCCCCTTTATAAGGAGGCGTTTTTGAAGGCGTTTGACGCGTTGAACGATATAAA CGATCCCGAACTTCTACTCAGGGCAACCCTAGCCATAGGGTACCACATGGGAAAAGCTGG GATCAAAGCGTACTACAAGGTGTTTCTGAGGGTGGTTGAAGATTCCTCTGCTTTATCTCC TCCAGTTAGAGACGAAATTTTAGCACTTGCCGTCAGGTACCTAGTGAGCCTCGGGAACCT CGGACAGGCCGTAACACTCGCGACGGAAATTTCGGATAAGAAACTTGCACAGGCCACTCT CTTCTCCATAGTCCGGGCGGGGAGCAGGTTAATTCAGGACAGCTCCCTAAAGGCGGCCTA CAAGCTCAGGAAAATCAAGCTGGCGCTTGAGTATATAACTGACGAGCCATATCGCTCAAA GGCCCTGATAGAGCTGGCAAAGGCTTTTATTGCGGTGGGGAGTTATGAGAGGGCGCTGGC CACGATTAGGGAAATAGAATCCCCAGATTGGGCTAAGGTTGCCTTCAAGGAACTTACCTT TAGTTTGGGCAGGATGGGCGTCATAGACAAGTTCATAAGCGGGCTTTCTGAGCTGGCGGA TGATTTCAGCTCGCGTTTTGGTGCCGATTTTGTTGTGGAGCTTGCAGAGGCTTTTCTGCT TGCTGGGAAACCGGATATTGCCGTTGGAATGCTCCGCAATCTTGATGATTCAGTTCAGGT GATCTCTGAAGTTGCACTTGAGGTTCTGGACAAAAATCCCGCGGTTATTCCGGGTTTTCT TGAAGTTCTCTCCGATGATGAGGCACGTATCGTTGGAAAGTTGTTGATGGATAAAATCCT TGAGCATCCGACAAAGGCCCTTGAGGAAGTTGTCAAGGCCGTGGCGAGGAGGGTTAGATC AGAAGCCATGTGGGTAAAGGTCGCCAGGTACTACACTCTGCTGGGGGACGTTGAGACGGC TAGAAATATCGGGGTTGTACTCCAGAATCCCAAGCTCCGCTCGATAGTTCTTGCGGACGT TGCCAGAAGTTACTTGAAACAGAACAAAATAGAAGAGGCC"
        pythonReaderOutput = pythonReaderOutput.replace(/\s/g, '');

        t.getFeatures({ref: "chr1", start: 0, end: 10000 },
            function(feature) {
                features.push(feature);
            },
            function() { done = true; });

        waitsFor( function() { return done; }, 2000);
        runs(function(){
            expect(features.length).toEqual(1);
            expect(features[0].get('seq').length).toEqual(10000);
            expect(features[0].get('seq')).toEqual(pythonReaderOutput);
        });
    });

    it("has correct behavior when refSeq not defined in file", function() {
        var done;
        var features = [];

        t.getFeatures({ref: "chr2", start: 0, end: 50000 },
            function(feature) {
                features.push(feature);
                console.log(feature);
            },
            function() { done = true; });

        waitsFor( function() { return done; }, 2000);
        runs(function(){
            expect(features.length).toEqual(0);
        });
    });

});

describe(".2bit data store with volvox.2bit", function() {

    var t2 = new TwoBitStore({
            browser: new Browser({ unitTestMode: true }),
            refSeq: { name: 'chr1', start: 1, end: 500001 },
            blob: new XHRBlob("../data/volvox.2bit")
        });

    it("constructs", function() {
        expect(t2).toBeTruthy();
    });

    it("loads some data", function() {
        var done;
        var features = [];

        t2.getFeatures({ref: "ctgA", start: 0, end: 50000 },
            function(feature) {
                features.push(feature);
            },
            function() { done = true; });

        waitsFor( function() { return done; }, 2000);


        runs(function(){
            expect(features.length).toEqual(1);
            expect(features[0].get('seq').length).toEqual(50000);
        });
    });

    it("loads some more data", function() {
        var done;
        var features = [];

        var seqFromFasta = "ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT";
        t2.getFeatures({ref: "ctgB", start: 0, end: 5000 },
            function(feature) {
                features.push(feature);
            },
            function() { done = true; });

        waitsFor( function() { return done; }, 2000);
        runs(function(){
            expect(features.length).toEqual(1);
            expect(features[0].get('seq').length).toEqual(5000);
            expect(features[0].get('seq')).toEqual(seqFromFasta);
        });
    });

    it("has correct behavior when refSeq not defined in file", function() {
        var done;
        var features = [];

        t2.getFeatures({ref: "nonexistent", start: 0, end: 50000 },
            function(feature) {
                features.push(feature);
            },
            function() { done = true; });

        waitsFor( function() { return done; }, 2000);
        runs(function(){
            expect(features.length).toEqual(0);
        });
    });

});

    var seqString = "NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACTCTATCTATCTATCTATCTATCTTTTTCCCCCCGGGGGGagagagagactctagcatcctcctacctcacNNacCNctTGGACNCcCaGGGatttcNNNcccNNCCNCgN";

describe(".2bit data store with random data foo.2bit", function() {

    var t3 = new TwoBitStore({
        browser: new Browser({unitTestMode: true }),
        refSeq: { name: 'chr1', start: 1, end: 500001 },
        blob: new XHRBlob("../data/foo.2bit")
    });

    it("constructs", function() {
        expect(t3).toBeTruthy();
    });

    it("loads data properly (even with masks and N blocks)", function(){
        var done;
        var features = [];

        t3.getFeatures({ref: "chr1", start: 0, end: 159 },
            function(feature) {
                features.push(feature);
            },
            function() { done = true; });

        waitsFor( function() { return done; }, 2000);
        runs(function(){
            expect(features.length).toEqual(1);
            expect(features[0].get('seq').length).toEqual(159);
            expect(features[0].get('seq')).toEqual(seqString);
        });
    });

    it("isn't fazed by being asked to look past the beginning or end of a sequence", function() {
        var done;
        var features = [];
        t3.getFeatures({ref: "chr1", start: -17, end: 300},
            function(feature) {
                features.push(feature);
            },
            function(){ done = true; });

        waitsFor( function() { return done; }, 2000);
        runs( function() {
            expect(features.length).toEqual(1);
            expect(features[0].get('seq').length).toEqual(159);
            expect(features[0].get('seq')).toEqual(seqString);
        });

    });
});

describe("empty 2bit", function() {
    var t4 = new TwoBitStore({
        browser: new Browser({ unitTestMode: true }),
        refSeq: { name: 'chr1', start: 1, end: 500001 },
        blob: new XHRBlob("../data/empty.2bit")
    });

    it("constructs", function() {
        expect(t4).toBeTruthy();
    });

    it("returns no data, but doesn't crash", function() {
        var done;
        var features = [];
        t4.getFeatures({ref: "unimportant", start: 0, end: 4000},
            function(feature) {
                features.push(feature);
            },
            function() { done = true; },
            function(err) { console.log(err); });

        waitsFor( function() { return done; }, 2000);
        runs( function() {
            expect(features.length).toEqual(0);
        });
    });

});


});