Examples of Genome

au.org.intersect.samifier.domain.Genome
com.heatonresearch.aifh.evolutionary.genome.Genome
A genome is the basic blueprint for creating an phenome (organism) in Encog. Some genomes also function as phenomes.
de.mh4j.solver.genetic.Genome
TODO write class description
org.broad.igv.feature.genome.Genome
Simple model of a genome. Keeps an ordered list of Chromosomes, an alias table, and genome position offsets for each chromosome to support a whole-genome view.
org.digibots.genetique.Genome
The Genome of a digibot @author Amos Wenger (aka BlueSky)
org.encog.ml.ea.genome.Genome
A genome is the basic blueprint for creating an phenome (organism) in Encog. Some genomes also function as phenomes.
org.encog.ml.genetic.genome.Genome
A genome is the basic blueprint for creating an organism in Encog. A genome is made up of one or more chromosomes, which are in turn made up of genes.
versusSNP.genome.Genome

Examples of org.broad.igv.feature.genome.Genome


    @Test
    public void testFilesHeaded() throws Exception {


        String ex_filename = "/vcf/example4-last-gsnap-2_fixed.vcf";
        Genome genome = TestUtils.loadGenome();
        List<String> finames = new ArrayList<String>(Arrays.asList(TrackLoaderTest.filenamesTryIndex));


        finames.add(ex_filename);


        for (String finame : finames) {

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Examples of org.broad.igv.feature.genome.Genome

        igvTools.run(cmd_withdups.split("\\s+"));


        assertTrue((new File(outputFileND).exists()));
        assertTrue((new File(outputFileWithDup).exists()));


        Genome genome = TestUtils.loadGenome();


        //Have to read back in using aliased chromosome names
        String readChr = genome.getChromosomeAlias(queryChr);


        int noDupCount = (int) getCount(outputFileND, readChr, 23, pos, genome);
        int dupCount = (int) getCount(outputFileWithDup, readChr, 23, pos, genome);


        assertEquals(noDupCount + 4, dupCount);

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Examples of org.broad.igv.feature.genome.Genome

        String indexFile = infile + ".idx";
        File idxFi = new File(indexFile);
        assertTrue(idxFi.exists());
        idxFi.deleteOnExit();


        Genome genome = IgvTools.loadGenome(fasta_file);
        FeatureCodec codec = CodecFactory.getCodec(infile, genome);
        AbstractFeatureReader<Feature, ?> reader = AbstractFeatureReader.getFeatureReader(infile, codec, true);
        String chr = "NC_000913_bb";
        Iterator<Feature> features = reader.query(chr, 5085, 5091);
        int count = 0;

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Examples of org.broad.igv.feature.genome.Genome

    }


    @Test
    public void testLoadGFFAliasedChrs() throws Exception {
        String filepath = TestUtils.DATA_DIR + "gff/aliased.unsorted.gff";
        Genome genome = IgvTools.loadGenome(TestUtils.DATA_DIR + "genomes/hg18_truncated_aliased.genome");
        List<Track> tracks = trackLoader.load(new ResourceLocator(filepath), genome);
        assertEquals(1, tracks.size());
        FeatureTrack track = (FeatureTrack) tracks.get(0);


        assertEquals("aliased.unsorted.gff", track.getName());

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Examples of org.broad.igv.feature.genome.Genome

        assertTrue("VCF file loaded incorrect track type", tracks.get(0) instanceof VariantTrack);


    }


    private List<Track> tstLoadFi(String filepath, Integer expected_tracks, boolean makeIndex) throws Exception {
        Genome genome = TestUtils.loadGenome();
        return tstLoadFi(filepath, expected_tracks, genome, makeIndex);
    }

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Examples of org.broad.igv.feature.genome.Genome

        tmp.add("/sam/test_2.sam");
        filenamesTryIndex = tmp.toArray(new String[tmp.size()]);
    }


    public void tstFilesHeadless(String[] filenames, boolean tryIndex) throws Exception {
        Genome genome = TestUtils.loadGenome();
        for (String finame : filenames) {
            tstLoadFi(TestUtils.DATA_DIR + finame, null, genome, tryIndex);
        }
    }

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Examples of org.broad.igv.feature.genome.Genome

 */
public class EQTLCodecTest {
    @Test
    public void testDecode() throws Exception {


        Genome genome = null;  // Genome not needed for this test


        EQTLCodec codec = new EQTLCodec(genome);


        String line = "rs4700772\t5\t180341845\tENSG00000168903.7\tBTNL3\t180415845\t129.858921455635\t1.61918925670937e-27";

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Examples of org.broad.igv.feature.genome.Genome


    @Test
    public void testGetSummaryScoresForSNPs() throws Exception {


        ResourceLocator locator = new ResourceLocator(TestUtils.DATA_DIR + "cn/multi_snp.cn");
        Genome genome = TestUtils.loadGenome();
        IGVDataset ds = new IGVDataset(locator, genome);
        DatasetDataSource dataSource = new DatasetDataSource("Sample1", ds, genome);
        String chr = "chr10";


        dataSource.cacheSummaryTiles = false;

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Examples of org.broad.igv.feature.genome.Genome

public class FreqDataTest extends AbstractHeadlessTest {


    @Test
    public void test() throws IOException {


        Genome genome = TestUtils.loadGenome();


        String segfile = TestUtils.DATA_DIR + "seg/canFam2_hg18.seg";




        SegmentedDataSet sd = new SegmentedAsciiDataSet(new ResourceLocator(segfile), genome);

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Examples of org.digibots.genetique.Genome

     * @param angle Z-Angle
     */
    public void addDigibot(float posX, float posY, float angle) {
        
        // Create a random genome
        Genome genome = new Genome();
        genome.alleleB1 = rnd.nextBoolean();
        genome.alleleB2 = rnd.nextBoolean();
        genome.alleleD1 = rnd.nextBoolean();
        genome.alleleD2 = rnd.nextBoolean();
        genome.alleleM1 = rnd.nextBoolean();

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