Package pal.misc

Class TimeOrderCharacterData

    • Field Detail

      • timeOrdinals

        protected int[] timeOrdinals
        Order of times

      • times

        protected double[] times
        Actual times of each sample

      • taxa

        protected IdGroup taxa
        the identifier group

      • units

        protected int units

      • subgroups_

        protected pal.misc.TimeOrderCharacterData.SubgroupHandler[] subgroups_

    • Constructor Detail

      • TimeOrderCharacterData

        protected TimeOrderCharacterData()
        Parameterless constructor for superclasses.

      • TimeOrderCharacterData

        public TimeOrderCharacterData​(IdGroup taxa,
                              int units)
        Constructor taking only IdGroup. Beware! This constructor does not initialize any time ordinals or times.
        Parameters:
        taxa - the taxa that this time data relates to.
        units - the units of the times.

      • TimeOrderCharacterData

        public TimeOrderCharacterData​(IdGroup taxa,
                              int units,
                              boolean contemp)
        Constructor taking only IdGroup.
        Parameters:
        taxa - the taxa that this time data relates to.
        units - the units of the times.
        contemp - if true, all times are set to zero, else times are not set.

      • TimeOrderCharacterData

        public TimeOrderCharacterData​(int numSeqsPerSample,
                              int numSamples,
                              double timeBetweenSamples,
                              int units)
        Constructs a TimeOrderCharacterData with a number of equal-sized, evenly-spaced sampling times.
        Parameters:
        numSeqsPerSample - the number of taxa/sequences per sample time.
        numSamples - the number of sample times.
        timeBetweenSamples - the time between each pair of consecutive samples.
        units - the units in which the times are expressed.

    • Method Detail

      • getUnits

        public int getUnits()
        Specified by:
        getUnits in interface UnitsProvider
        Returns:
        the units relating to this object.

      • setSubgroups

        public final void setSubgroups​(int[][] subgroups)
        A means for define a subgroup.
        Parameters:
        subgroups - an array of integer arrays. Each array holds the indexes of the members that for that subgroup

      • setSubgroup

        public final void setSubgroup​(int[] subgroup)
        A means for define a subgroup.
        Parameters:
        subgroups - an array indexes of the members that for the subgroup

      • setSubgroup

        public final void setSubgroup​(java.lang.String[] subgroup)
        A means for define a subgroup.
        Parameters:
        subgroups - an array of names that represent the members of the subgroup.Non existent memebers are ignored

      • setSubgroups

        public final void setSubgroups​(java.lang.String[][] subgroups)
        A means for define subgroups.
        Parameters:
        subgroups - an array of String arrays. Each array holds the members for a particular subgroup. Nonexistent members are ignored.

      • hasSubgroups

        public final boolean hasSubgroups()

      • getNumberOfSubgroups

        public final int getNumberOfSubgroups()

      • createSubgroup

        public final TimeOrderCharacterData createSubgroup​(int subgroupNumber)
        Creates a TimeOrderCharacterData which is a subset of this sub group. Different subgroups may contain the same members

      • getSubgroupMembers

        public final Identifier[] getSubgroupMembers​(int subgroupNumber)

      • setTimes

        public void setTimes​(double[] times,
                     int units)
        Sets the times, and works out what the ordinals should be.

      • setTimes

        public void setTimes​(double[] times,
                     int units,
                     boolean recalculateOrdinals)
        Sets the times.
        Parameters:
        recalculateOrdinals - true if ordinals should be recalculated from the times.

      • setOrdinals

        public void setOrdinals​(int[] ordinals)
        Sets ordinals.

      • getMaximumTime

        public double getMaximumTime()
        Returns:
        the maximum time

      • getMinimumTime

        public double getMinimumTime()
        Returns:
        the minimum time

      • getOrdinals

        public int[] getOrdinals()
        Gets ordinals.

      • getCopyOfTimes

        public double[] getCopyOfTimes()
        Returns a copy of the times in the form of an array.

      • getReordered

        public TimeOrderCharacterData getReordered​(IdGroup base)
        Creates a new TimeOrderCharacterData object with the same properites as this one but the identifier positions match that of base (ie whichIdNumber(Name) returns the same as for base)
        Throws:
        java.lang.IllegalArgumentException - if the base ids don't match the ids of this tocd

      • removeTimes

        public void removeTimes()
        Remove time character data.

      • generateExpectedSubsitutionsTimedTOCD

        public TimeOrderCharacterData generateExpectedSubsitutionsTimedTOCD​(double[] sampleRates)
        Given an array of rates between samples (matching exactly the samples in order) then produces a TimeOrderCharacterData object that is timed by Expected Substitutions. Needs only sample information so no real time information required.

      • generateDummyTimedTOCD

        public TimeOrderCharacterData generateDummyTimedTOCD​(double[] sampleRates)
        Returns:
        a dummy time order character data base on this that does have times, but the times are set to match the sample number. Eg. Ids in sample 0 have time 0, ids in sample 1 have time 1, and so on. The Units are UNKNOWN

      • setOrdinals

        public void setOrdinals​(TimeOrderCharacterData tocd)
        Set time ordinals from another TimeOrderCharacterData. Select ordinals by matching names.
        Parameters:
        tocd - to take ordinals from.

      • setOrdinals

        public void setOrdinals​(TimeOrderCharacterData tocd,
                        IdGroup standard,
                        boolean doTimes)
        Set time ordinals from another TimeOrderCharacterData. Select ordinals by matching names.
        Parameters:
        tocd - to take ordinals from
        idgroup - use these labels to match indices in given tocd.
        doTimes - if set then sets times as well

      • getNumChars

        public int getNumChars()
        Returns the number of characters per identifier

      • getName

        public java.lang.String getName()
        Returns a name for this character data.

      • setName

        public void setName​(java.lang.String name)
        Sets the name of this character data.

      • getTime

        public double getTime​(int taxon)

      • getOrdinalTime

        public double getOrdinalTime​(int ordinal)
        Obtain the time of a particular ordinal
        Parameters:
        ordinal - The ordinal of interest
        Returns:
        The time of the input ordinal
        Throws:
        java.lang.IllegalArgumentException - If no such ordinal

      • getTime

        public double getTime​(java.lang.String taxonName)

      • getHeight

        public double getHeight​(int taxon,
                        double rate)
        NOTE: currently assumes times exist!

      • getTimeOrdinal

        public int getTimeOrdinal​(int taxon)

      • getTimeOrdinal

        public int getTimeOrdinal​(java.lang.String taxonName)

      • getTimeOrdinal

        public int getTimeOrdinal​(Identifier taxonName)

      • hasTimes

        public boolean hasTimes()

      • getUniqueTimeArray

        public double[] getUniqueTimeArray()
        Returns an ordered vector of unique times in this time order character data.

      • getUniqueTimeMatrix

        public double[][] getUniqueTimeMatrix()
        Returns a matrix of times between samples. A sample is any set of identifiers that have the same times.

      • getSampleCount

        public int getSampleCount()
        Deprecated.
        Use getOrdinalCount()
        A sample is any set of identifiers that have the same times.
        Returns:
        the number of unique times in this data.

      • getOrdinalCount

        public int getOrdinalCount()
        Returns:
        the number of unique times in this data.

      • toString

        public java.lang.String toString()
        Returns a string representation of this time order character data.
        Overrides:
        toString in class java.lang.Object

      • shuffleTimes

        public void shuffleTimes()

      • setIdentifier

        public void setIdentifier​(int i,
                          Identifier ident)
        Description copied from interface: IdGroup
        Sets the ith identifier.
        Specified by:
        setIdentifier in interface IdGroup

      • getIdCount

        public int getIdCount()
        Description copied from interface: IdGroup
        Returns the number of identifiers in this group
        Specified by:
        getIdCount in interface IdGroup

      • whichIdNumber

        public int whichIdNumber​(java.lang.String name)
        Description copied from interface: IdGroup
        returns the index of the identifier with the given name.
        Specified by:
        whichIdNumber in interface IdGroup

      • getIdGroup

        public IdGroup getIdGroup()
        Deprecated.
        TimeOrderCharacterData now implements IdGroup
        Return id group of this alignment.

      • getSuggestedMaximumMutationRate

        public final double getSuggestedMaximumMutationRate()
        A simple utility method for generating a maximu mutation rate based on times. This is not guarranteed to be the best method. If the times are small (ie total differenct < 1), the maximum Mutation Rate is high. If the times are large (eg total differenct > 1) the maximum Mutation Rate is low. IE. the aim is to keep the Expected substitutions (mu*t) range reasonable (<1)