Class TimeOrderCharacterData

Method Details

• clone

  public static TimeOrderCharacterData clone(TimeOrderCharacterData tocd)

  Returns a clone of the specified TimeOrderCharacterData

• subset

  public TimeOrderCharacterData subset(IdGroup staxa)

  Extracts a subset of a TimeOrderCharacterData.

• 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(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(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.

• scale

  public TimeOrderCharacterData scale(double rate, int newUnits)

• 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:

  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.

• setTimesAndOrdinals

  public void setTimesAndOrdinals(TimeOrderCharacterData tocd)

• 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 String getName()

  Returns a name for this character data.

• setName

  public void setName(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:

  IllegalArgumentException - If no such ordinal

• getTime

  public double getTime(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(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 String toString()

  Returns a string representation of this time order character data.

  Overrides:

  toString in class Object

• shuffleTimes

  public void shuffleTimes()

• getIdentifier

  public Identifier getIdentifier(int i)

  Description copied from interface: IdGroup

  Returns the ith identifier.

  Specified by:

  getIdentifier in interface IdGroup

• 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(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)