Package htsjdk.samtools.metrics

Class MetricsFile<BEAN extends MetricBase,​HKEY extends Comparable>

  • All Implemented Interfaces:
    Serializable
    public class MetricsFile<BEAN extends MetricBase,​HKEY extends Comparable>
extends Object
implements Serializable
    Contains a set of metrics that can be written to a file and parsed back again. The set of metrics is composed of zero or more instances of a class, BEAN, that extends MetricBase (all instances must be of the same type) and may optionally include one or more histograms that share the same key set.
    See Also:
    Serialized Form

    • Constructor Detail

      • MetricsFile

        public MetricsFile()

    • Method Detail

      • addHeader

        public void addHeader​(Header h)
        Adds a header to the collection of metrics.

      • getHeaders

        public List<Header> getHeaders()
        Returns the list of headers.

      • addMetric

        public void addMetric​(BEAN bean)
        Adds a bean to the collection of metrics.

      • addAllMetrics

        public void addAllMetrics​(Iterable<BEAN> beanz)
        Add multiple metric beans at once.

      • getMetrics

        public List<BEAN> getMetrics()
        Returns the list of headers.

      • getMetricsColumnLabels

        public Set<String> getMetricsColumnLabels()

      • getHistogram

        public Histogram<HKEY> getHistogram()
        Returns the histogram contained in the metrics file if any.

      • setHistogram

        public void setHistogram​(Histogram<HKEY> histogram)
        Sets the histogram contained in the metrics file.

      • addHistogram

        public void addHistogram​(Histogram<HKEY> histogram)
        Adds a histogram to the list of histograms in the metrics file.

      • getNumHistograms

        public int getNumHistograms()
        Returns the number of histograms added to the metrics file.

      • getHeaders

        public List<Header> getHeaders​(Class<? extends Header> type)
        Returns the list of headers with the specified type.

      • write

        public void write​(File f)
        Writes out the metrics file to the supplied file. The file is written out headers first, metrics second and histogram third.
        Parameters:
        f - a File into which to write the metrics

      • write

        public void write​(Writer w)
        Writes out the metrics file to the supplied writer. The file is written out headers first, metrics second and histogram third.
        Parameters:
        w - a Writer into which to write the metrics

      • read

        public void read​(Reader r)
        Reads the Metrics in from the given reader.

      • equals

        public boolean equals​(Object o)
        Checks that the headers, metrics and histogram are all equal.
        Overrides:
        equals in class Object

      • areHeadersEqual

        public boolean areHeadersEqual​(MetricsFile that)

      • areMetricsEqual

        public boolean areMetricsEqual​(MetricsFile that)

      • areHistogramsEqual

        public boolean areHistogramsEqual​(MetricsFile that)

      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class Object

      • readBeans

        public static <T extends MetricBase> List<T> readBeans​(File file)
        Convenience method to read all the Metric beans from a metrics file.
        Parameters:
        file - to be read.
        Returns:
        list of beans from the file.

      • readHeaders

        public static List<Header> readHeaders​(File file)
        Method to read the header from a metrics file.

      • areMetricsEqual

        public static boolean areMetricsEqual​(File file1,
                                      File file2)
        Compare the metrics in two files, ignoring headers and histograms.

      • areMetricsAndHistogramsEqual

        public static boolean areMetricsAndHistogramsEqual​(File file1,
                                                   File file2)
        Compare the metrics and histograms in two files, ignoring headers.