/** Gets a MetricsFile with default headers already written into it. */ protected <A extends MetricBase,B extends Comparable<?>> MetricsFile<A,B> getMetricsFile() { final MetricsFile<A,B> file = new MetricsFile<>(); for (final Header h : this.defaultHeaders) { file.addHeader(h); } return file; }
public void addMetricsToFile(final MetricsFile<QualityYieldMetrics, Integer> metricsFile) { metricsFile.addMetric(metrics); } }
/** Constructor that uses the supplied value as the value of the header. */ public StringHeader(String value) { setValue(value); }
@Test public void testFloatingPointEquality() throws IOException { MetricsFile<FloatingPointMetric,Integer> file = new MetricsFile<FloatingPointMetric,Integer>(); FloatingPointMetric metric = new FloatingPointMetric(); metric.DOUBLE_PRIMITIVE = .0000000000000000001d; metric.DOUBLE_PROP = .0000000000000000001d; metric.FLOAT_PRIMITIVE = .0000000000000000001f; metric.FLOAT_PROP = .0000000000000000001f; file.addMetric(metric); MetricsFile<FloatingPointMetric,Integer> file2 = writeThenReadBack(file); Assert.assertEquals(file, file2); }
@Override public void addMetricsToFile(final MetricsFile<RnaSeqMetrics, Integer> file) { // Compute metrics based on coverage of top 1000 genes final Histogram<Integer> normalizedCovByPos = computeCoverageMetrics(); file.addMetric(metrics); file.addHistogram(normalizedCovByPos); }
@Test public void testHashCodeWithNull(){ TestMetric metric = new TestMetric(null); metric.hashCode(); //test that it can get a hashcode without crashing }
/** Gets a MetricsFile with default headers already written into it. */ protected <A extends MetricBase,B extends Comparable<?>> MetricsFile<A,B> getMetricsFile() { final MetricsFile<A,B> file = new MetricsFile<>(); for (final Header h : this.defaultHeaders) { file.addHeader(h); } return file; }
/** Add multiple metric beans at once. */ public void addAllMetrics(final Iterable<BEAN> beanz) { for (final BEAN bean : beanz) { this.addMetric(bean); } }
@Override public void addMetricsToFile(final MetricsFile<RnaSeqMetrics, Integer> file) { // Compute metrics based on coverage of top 1000 genes final Histogram<Integer> normalizedCovByPos = computeCoverageMetrics(); file.addMetric(metrics); file.addHistogram(normalizedCovByPos); }
/** Constructor that uses the supplied value as the value of the header. */ public StringHeader(String value) { setValue(value); }
/** * Creates a new metrics file with appropriate headers for this context * @return MetricsFile */ public <A extends MetricBase,B extends Comparable<?>> MetricsFile<A,B> createMetricsFile() { final MetricsFile<A,B> file = new MetricsFile<A,B>(); for (final Header h : metricsHeaders) { file.addHeader(h); } return file; } public GridssConfiguration getConfig() {
public void addMetricsToFile(final MetricsFile<QualityYieldMetrics, Integer> metricsFile) { metricsFile.addMetric(metrics); } }
/** Constructor that uses the supplied value as the value of the header. */ public StringHeader(String value) { setValue(value); }
/** Add multiple metric beans at once. */ public void addAllMetrics(final Iterable<BEAN> beanz) { for (final BEAN bean : beanz) { this.addMetric(bean); } }
private void addIdsvMetrics(MetricsFile<IdsvMetrics, Integer> metricsFile) { metricsFile.addMetric(idsv); } private void addCigarMetrics(MetricsFile<CigarDetailMetrics, Integer> metricsFile) {
@Override public void addMetricsToFile(final MetricsFile<TotalNumberMetric, Integer> totalNumberMetricIntegerMetricsFile) { totalNumberMetricIntegerMetricsFile.addMetric(metric); } }
public void addMetricsToFile(final MetricsFile<IlluminaBasecallingMetrics, Comparable<?>> file) { onComplete(); file.addMetric(metrics); }