net.maizegenetics.analysis.popgen

Class DiversityAnalyses

java.lang.Object

net.maizegenetics.util.AbstractTableReport

net.maizegenetics.analysis.popgen.DiversityAnalyses

All Implemented Interfaces:

Serializable, TableReport

public class DiversityAnalyses
extends AbstractTableReport
implements TableReport, Serializable

This method calculated estimates of nucleotide diversity (pi, theta, etc). In order to provide high performance, it establishes one nucleotide SitePattern, and then manipulates the weighting patterns for sliding windows and different types of sites. Total segregating sites needs to be adjusted for missing and gap data, as this will modify Theta and Tajima estimates

Version:

1.0

Author:

Ed Buckler

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
DiversityAnalyses(GenotypeTable aa, boolean slidingWindow, int start, int end, int window, int step)
DiversityAnalyses(GenotypeTable aa, boolean slidingWindow, int start, int end, int window, int step, PolymorphismDistribution thePolymorphismDistribution) Constructor that uses a sliding window

Method Summary

Modifier and Type	Method and Description
static double	estimatePi(int totalSites, double avgPairwiseDivergence, double averageSiteCoverage)
static double	estimatePiPerbp(int totalSites, double avgPairwiseDivergence, double averageSiteCoverage)
static double	estimateTajimaD(int segSites, double totalSites, double averageSiteCoverage, double taxa, double pipbp, double thetapbp)
static double	estimateTheta(int segSites, int totalSites, double averageSiteCoverage, int taxa)
static double	estimateThetaPerbp(int segSites, int totalSites, double averageSiteCoverage, int taxa)
int	getColumnCount() Get the number of the columns
long	getElementCount() Get the total number of elements in the dataset.
Object[]	getRow(long row) Returns specified row.
long	getRowCount() Get the number of rows
Object[]	getTableColumnNames() Get the names of the columns
String	getTableTitle() Get the title of the table
String	toString()

Methods inherited from class net.maizegenetics.util.AbstractTableReport

getValueAt

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface net.maizegenetics.util.TableReport

getValueAt, toStringTabDelim

Constructor Detail

DiversityAnalyses

public DiversityAnalyses(GenotypeTable aa,
                         boolean slidingWindow,
                         int start,
                         int end,
                         int window,
                         int step,
                         PolymorphismDistribution thePolymorphismDistribution)

Constructor that uses a sliding window

Parameters:

aa - an annotated alignment

slidingWindow - if true a sliding window will be run

DiversityAnalyses

public DiversityAnalyses(GenotypeTable aa,
                         boolean slidingWindow,
                         int start,
                         int end,
                         int window,
                         int step)

Method Detail

estimateTheta

public static double estimateTheta(int segSites,
                                   int totalSites,
                                   double averageSiteCoverage,
                                   int taxa)

estimateThetaPerbp

public static double estimateThetaPerbp(int segSites,
                                        int totalSites,
                                        double averageSiteCoverage,
                                        int taxa)

estimatePi

public static double estimatePi(int totalSites,
                                double avgPairwiseDivergence,
                                double averageSiteCoverage)

estimatePiPerbp

public static double estimatePiPerbp(int totalSites,
                                     double avgPairwiseDivergence,
                                     double averageSiteCoverage)

estimateTajimaD

public static double estimateTajimaD(int segSites,
                                     double totalSites,
                                     double averageSiteCoverage,
                                     double taxa,
                                     double pipbp,
                                     double thetapbp)

getTableColumnNames

public Object[] getTableColumnNames()

Description copied from interface: TableReport

Get the names of the columns

Specified by:

getTableColumnNames in interface TableReport

Returns:

columns names

getRow

public Object[] getRow(long row)

Returns specified row.

Specified by:

getRow in interface TableReport

Parameters:

row - row number

Returns:

row

getTableTitle

public String getTableTitle()

Description copied from interface: TableReport

Get the title of the table

Specified by:

getTableTitle in interface TableReport

Returns:

title

toString

public String toString()

Overrides:

toString in class Object

getRowCount

public long getRowCount()

Description copied from interface: TableReport

Get the number of rows

Specified by:

getRowCount in interface TableReport

Returns:

number of rows

getElementCount

public long getElementCount()

Description copied from interface: TableReport

Get the total number of elements in the dataset. Elements = rowCount * columnCount;

Specified by:

getElementCount in interface TableReport

Returns:

number of elements

getColumnCount

public int getColumnCount()

Description copied from interface: TableReport

Get the number of the columns

Specified by:

getColumnCount in interface TableReport

Returns:

number of columns