systemic
Class KernelList

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.ArrayList<Kernel>
              systemic.KernelList

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Iterable<Kernel>, java.util.Collection<Kernel>, java.util.List<Kernel>, java.util.RandomAccess

public class KernelList
extends java.util.ArrayList<Kernel>

A collection of Kernel objects, usually representing the output of bootstrap or MCMC. Each Kernel object may contain orbital elements corresponding to the element of a particular chain.

See Also:

Serialized Form

Field Summary

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

KernelList()

Method Summary

Kernel	average() Returns a Kernel, the orbital elements (and voffs) of which represent the average (set by setAverageType(int)) of the corresponding orbital element.
KernelList	clone() Returns a clone of the list.
java.util.ArrayList<double[][]>	getAllElements() Returns an ArrayList containing the orbital elements of each item.
int	getAverageType() Returns the current numerical average (0 = mean, 1 = median).
int	getNOffsets() Returns the number of offsets in each Kernel
int	getNPlanets() Returns the number of planets in each Kernel
double[]	getParSlice(int index, java.lang.String what) Returns an array of doubles with the parameters derived for each model for planet index / offset index
Kernel	percentile(double p)
java.lang.Object[]	predictTransits(double time1, double time2, int intMethod)
void	printSummary() Prints a summary table to the standard output.
protected void	readBinary(java.io.FileInputStream fos)
protected void	readXML(java.io.FileInputStream fos)
void	reduce() Reduces the size in memory (and on disk) of the Kernel list, losing some data (e.g.
void	restore(java.lang.String fn, int type) Reads the contents of a previously saved Kernel list, in binary (type = 0) or XML (type = 1) format.
void	save(java.lang.String fn, int type) Saves the list to a file, using a binary (type = 0) or XML (type = 1) format.
protected void	saveBinary(java.io.FileOutputStream fos)
protected void	saveXML(java.io.FileOutputStream fos)
void	setAverageType(int averageType) Sets the numerical average (0 = mean, 1 = median)
Kernel	stdDev() Returns a Kernel, the orbital elements (and voffs) of which represent the standard deviation of the corresponding orbital element.
KernelList	subset(int step)

Methods inherited from class java.util.ArrayList

add, add, addAll, addAll, clear, contains, ensureCapacity, get, indexOf, isEmpty, lastIndexOf, remove, remove, removeRange, set, size, toArray, toArray, trimToSize

Methods inherited from class java.util.AbstractList

equals, hashCode, iterator, listIterator, listIterator, subList

Methods inherited from class java.util.AbstractCollection

containsAll, removeAll, retainAll, toString

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.List

containsAll, equals, hashCode, iterator, listIterator, listIterator, removeAll, retainAll, subList

Constructor Detail

KernelList

public KernelList()

Method Detail

save

public void save(java.lang.String fn,
                 int type)
          throws java.io.FileNotFoundException,
                 java.io.IOException

Saves the list to a file, using a binary (type = 0) or XML (type = 1) format.

Parameters:

fn - File path

type - Output format

Throws:

java.io.FileNotFoundException

java.io.IOException

saveBinary

protected void saveBinary(java.io.FileOutputStream fos)
                   throws java.io.IOException

Throws:

java.io.IOException

saveXML

protected void saveXML(java.io.FileOutputStream fos)
                throws java.io.IOException

Throws:

java.io.IOException

readXML

protected void readXML(java.io.FileInputStream fos)

readBinary

protected void readBinary(java.io.FileInputStream fos)
                   throws java.io.IOException,
                          java.lang.ClassNotFoundException

Throws:

java.io.IOException

java.lang.ClassNotFoundException

restore

public void restore(java.lang.String fn,
                    int type)
             throws java.io.FileNotFoundException,
                    java.io.IOException,
                    java.lang.ClassNotFoundException

Reads the contents of a previously saved Kernel list, in binary (type = 0) or XML (type = 1) format.

Parameters:

fn - Path of file to be read.

type - File format.

Throws:

java.io.FileNotFoundException

java.io.IOException

java.lang.ClassNotFoundException

printSummary

public void printSummary()

Prints a summary table to the standard output.

getAverageType

public int getAverageType()

Returns the current numerical average (0 = mean, 1 = median).

Returns:

setAverageType

public void setAverageType(int averageType)

Sets the numerical average (0 = mean, 1 = median)

Parameters:

averageType -

getNOffsets

public int getNOffsets()

Returns the number of offsets in each Kernel

Returns:

getNPlanets

public int getNPlanets()

Returns the number of planets in each Kernel

Returns:

reduce

public void reduce()

Reduces the size in memory (and on disk) of the Kernel list, losing some data (e.g. RV/transits data generated from bootstrap).

clone

public KernelList clone()

Returns a clone of the list.

Overrides:

clone in class java.util.ArrayList<Kernel>

Returns:

getAllElements

public java.util.ArrayList<double[][]> getAllElements()

Returns an ArrayList containing the orbital elements of each item.

Returns:

stdDev

public Kernel stdDev()

Returns a Kernel, the orbital elements (and voffs) of which represent the standard deviation of the corresponding orbital element.

Returns:

average

public Kernel average()

Returns a Kernel, the orbital elements (and voffs) of which represent the average (set by setAverageType(int)) of the corresponding orbital element.

Returns:

percentile

public Kernel percentile(double p)

Parameters:

p -

Returns:

subset

public KernelList subset(int step)

Parameters:

step -

Returns:

getParSlice

public double[] getParSlice(int index,
                            java.lang.String what)

Returns an array of doubles with the parameters derived for each model for planet index / offset index

Parameters:

index -

what - is one of: "P", "M", "e", "MA", "LOP", "INC", "NODE", "OFFS"

Returns:

predictTransits

public java.lang.Object[] predictTransits(double time1,
                                          double time2,
                                          int intMethod)

Parameters:

time1 -

time2 -

intMethod -

Returns: