Package com.biomatters.geneious.publicapi.documents.sequence

Class ValueAndFrequencyDistribution

    • Constructor Detail

      • ValueAndFrequencyDistribution

        public ValueAndFrequencyDistribution()
        Construct a new empty distribution.

      • ValueAndFrequencyDistribution

        public ValueAndFrequencyDistribution​(ValueAndFrequencyDistribution distribution1,
                                     ValueAndFrequencyDistribution distribution2)
                              throws java.io.IOException
        Constructs a new distribution by adding 2 distributions together
        Parameters:
        distribution1 - the first distribution to add
        distribution2 - the second distribution to add
        Throws:
        java.io.IOException - if we can't write the data to disk.

      • ValueAndFrequencyDistribution

        public ValueAndFrequencyDistribution​(org.jdom.Element e)
                              throws XMLSerializationException
        Construct a new empty distribution from some previously serialized data.
        Parameters:
        e - the element returned frmo a previous call to toXML()
        Throws:
        XMLSerializationException - if it can't be deserialized.

    • Method Detail

      • toXML

        public org.jdom.Element toXML()
        Description copied from interface: XMLSerializable
        Convert object to a JDOM element. The representation should be complete so that XMLSerializable.fromXML(org.jdom.Element) can completely restore the object's representation.

        It is recommended that the returned element use XMLSerializable.ROOT_ELEMENT_NAME as its name, in which case it must not define an attribute called "type". In this case, fromXML, will be called with an element whose name may differ from the element return from this function. This recommendation allows a more compact representation of the XML can be stored.

        This method generally should not be called directly. Instead, you should usually call XMLSerializer.classToXML(String, XMLSerializable) which calls this method internally.

        PluginDocument implementations of this method may choose to throw an XMLSerializationException, enclosed in a RuntimeException.

        Specified by:
        toXML in interface XMLSerializable
        Returns:
        object encoded as a JDOM element

      • toXML

        public org.jdom.Element toXML​(Geneious.MajorVersion majorVersion,
                              jebl.util.ProgressListener progressListener)
        Description copied from interface: XMLSerializable.OldVersionCompatible
        Serializes this class to XML format, potentially to a format readable by an earlier version of Geneious. It is acceptable for the XML to include unnecessary tags that will be ignored by the earlier version. For example if the implementation has only extended the XML since the earlier version, then the XML returned may be identical to the XML returned for the current version.

        See XMLSerializable.toXML() for a more detailed description of what it means to serialize to XML.

        All classes that implement this method must also implement XMLSerializable.toXML() and should delegate back to this method using Geneious.getMajorVersion() and ProgressListener.EMPTY as parameters.

        Specified by:
        toXML in interface XMLSerializable.OldVersionCompatible
        Parameters:
        majorVersion - the major version of Geneious to serialize to XML for. For example "6.0" but not "6.0.0". This must be a version returned greater or equal to a version returned from getVersionSupport(VersionSupportType.OldestVersionSerializableTo) and must never be greater than the current version (Geneious.getMajorVersion())
        progressListener - for reporting progress and cancelling
        Returns:
        object encoded as a JDOM element

      • fromXML

        public void fromXML​(org.jdom.Element element)
             throws XMLSerializationException
        Description copied from interface: XMLSerializable
        Restore the object from the JDOM Element returned by XMLSerializable.toXML().

        This method generally should not be called directly. Instead, you should usually call XMLSerializer.classFromXML(org.jdom.Element) or XMLSerializer.classFromXML(org.jdom.Element, Class) which calls this method internally.

        It is optional to implement this method. Instead of implementing an empty constructor and implementing this method properly, the implementation may instead throw an UnsupportedOperationException and implement a constructor that takes a single Element as a parameter. This allows for cleaner code such as support for final fields in the XMLSerializable class.

        The element parameter should not be modified since it may be reused. If you need a modified version of it, take a copy with Element.clone().

        Specified by:
        fromXML in interface XMLSerializable
        Parameters:
        element - representation from a previous call to XMLSerializable.toXML()
        Throws:
        XMLSerializationException - if the Element can't be converted into this type of object

      • addValue

        public void addValue​(long value,
                     long frequency)
              throws java.io.IOException
        Adds a new value. finishedAddingValues(jebl.util.ProgressListener) must be called once all values have been added.
        Parameters:
        value - the value to add
        frequency - the number of occurrences of the value to add
        Throws:
        java.io.IOException - if we can't write the data to disk.
        java.lang.IllegalStateException - if finishedAddingValues(jebl.util.ProgressListener) has already been called.

      • finishedAddingValues

        public void finishedAddingValues​(jebl.util.ProgressListener progressListener)
                          throws java.io.IOException
        Called to finalize and sort the data. This method must be called after adding values using addValue(long, long) before many of the getter methods can be used.
        Parameters:
        progressListener - for handling progress and cancelling.
        Throws:
        java.io.IOException - if we can't write the data to disk or if the progress listener requests we cancel
        java.lang.IllegalStateException - if this method is called more than once

      • getMin

        public long getMin()
        Returns:
        the minimum value in this distribution, or 0 if there are no values

      • getMax

        public long getMax()
        Returns:
        the maximum value in this distribution, or 0 if there are no values

      • getMedian

        public double getMedian()
        Returns:
        the median value in this distribution, or 0 if there are no values. This method calculates the median each time it is called, so may not be fast on large data sets
        Since:
        API 4.1020 (Geneious 10.2.0)

      • getMean

        public double getMean()
        Returns:
        the mean value in this distribution, or 0 if there are no values. This method calculates the mean each time it is called, so may not be fast on large data sets
        Since:
        API 4.1020 (Geneious 10.2.0)