pal.alignment
Class SimpleCharacterAlignment

java.lang.Object
  pal.alignment.SimpleCharacterAlignment

All Implemented Interfaces:

java.io.Serializable, CharacterAlignment, IdGroup, Report, TableReport

public class SimpleCharacterAlignment
extends java.lang.Object
implements CharacterAlignment, java.io.Serializable, IdGroup, Report

This provides a basic implementation of CharacterAlignment. This class holds quantitative character states. Each trait (a quantitative character) has two sets of labels. One is the traitName, and the second is the environmentName. Obviously any descriptor could be placed in these two labels, however for printing purposes traitName is printed first. Double.NaN is assumed to be the missing value.

Version:

$Id: SimpleCharacterAlignment.java,v 1

Author:

Ed Buckler

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface pal.misc.IdGroup

IdGroup.Utils

Field Summary

protected java.lang.String[]	environmentNames names of the traits
protected IdGroup	idGroup sequence identifiers
protected int	numSeqs number of sequences
protected int	numTraits number of traits
protected java.lang.String[]	traitNames names of the traits
protected double[][]	traitValues trait values

Fields inherited from interface pal.alignment.CharacterAlignment

MISSING

Constructor Summary

SimpleCharacterAlignment()

SimpleCharacterAlignment(Identifier[] ids, double[][] traitValues, java.lang.String[] traitNames)
Constructor for SimpleCharacterAlignment.

SimpleCharacterAlignment(IdGroup group, double[][] traitValues, java.lang.String[] traitNames)
Constructor for SimpleCharacterAlignment.

SimpleCharacterAlignment(IdGroup group, double[][] traitValues, java.lang.String[] traitNames, java.lang.String[] environNames)
Constructor for SimpleCharacterAlignment

SimpleCharacterAlignment(IdGroup group, double[] traitValue, java.lang.String traitName)
Constructor for SimpleCharacterAlignment when there is only a single trait.

Method Summary

java.lang.String	getEnvironmentName(int trait) Return name of the environments for this trait number
int	getIdCount() Returns the number of identifiers in this group
Identifier	getIdentifier(int i) Returns the ith identifier.
int	getLength() Return number of traits in this alignment
int	getSequenceCount() Return number of taxa or sequences in this alignment
java.lang.Object[]	getTableColumnNames() Return column names for the table
java.lang.Object[][]	getTableData() Return data for the table
java.lang.String	getTableTitle() Return the name for the title of the ANOVA
double	getTrait(int seq, int trait) Return the trait value for a given sequence (taxon) and trait number
int	getTraitCount() Return number of trait for each taxon in this alignment
java.lang.String	getTraitName(int trait) Return name of the trait for this trait number
void	report(java.io.PrintWriter out) print human readable report (e.g., on parameters and associated model)
void	setIdentifier(int i, Identifier ident) Sets the ith identifier.
java.lang.String	toString() returns representation of this alignment as a string
int	whichIdNumber(java.lang.String name) returns the index of the identifier with the given name.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

traitValues

protected double[][] traitValues

trait values

traitNames

protected java.lang.String[] traitNames

names of the traits

environmentNames

protected java.lang.String[] environmentNames

names of the traits

numSeqs

protected int numSeqs

number of sequences

numTraits

protected int numTraits

number of traits

idGroup

protected IdGroup idGroup

sequence identifiers

Constructor Detail

SimpleCharacterAlignment

public SimpleCharacterAlignment()

SimpleCharacterAlignment

public SimpleCharacterAlignment(Identifier[] ids,
                                double[][] traitValues,
                                java.lang.String[] traitNames)

Constructor for SimpleCharacterAlignment. Environment names if be set to default NA.

Parameters:

group - array of taxa identifiers

traitValues - matrix of trait values

traitNames - array of trait names

SimpleCharacterAlignment

public SimpleCharacterAlignment(IdGroup group,
                                double[][] traitValues,
                                java.lang.String[] traitNames)

Constructor for SimpleCharacterAlignment. Environment names if be set to default NA.

Parameters:

group - taxa names

traitValues - matrix of trait values

traitNames - array of trait names

SimpleCharacterAlignment

public SimpleCharacterAlignment(IdGroup group,
                                double[][] traitValues,
                                java.lang.String[] traitNames,
                                java.lang.String[] environNames)

Constructor for SimpleCharacterAlignment

Parameters:

group - taxa names

traitValues - matrix of trait values

traitNames - array of trait names

environNames - array of environment names

SimpleCharacterAlignment

public SimpleCharacterAlignment(IdGroup group,
                                double[] traitValue,
                                java.lang.String traitName)

Constructor for SimpleCharacterAlignment when there is only a single trait. Environment names if be set to default NA.

Parameters:

group - holds taxa names

traitValue - array of trait values

traitName - trait name

Method Detail

getTrait

public double getTrait(int seq,
                       int trait)

Return the trait value for a given sequence (taxon) and trait number

Specified by:

getTrait in interface CharacterAlignment

getLength

public final int getLength()

Return number of traits in this alignment

getSequenceCount

public final int getSequenceCount()

Return number of taxa or sequences in this alignment

Specified by:

getSequenceCount in interface CharacterAlignment

getTraitCount

public final int getTraitCount()

Return number of trait for each taxon in this alignment

Specified by:

getTraitCount in interface CharacterAlignment

getTraitName

public java.lang.String getTraitName(int trait)

Return name of the trait for this trait number

Specified by:

getTraitName in interface CharacterAlignment

getEnvironmentName

public java.lang.String getEnvironmentName(int trait)

Return name of the environments for this trait number

Specified by:

getEnvironmentName in interface CharacterAlignment

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(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

toString

public java.lang.String toString()

returns representation of this alignment as a string

Overrides:

toString in class java.lang.Object

report

public void report(java.io.PrintWriter out)

Description copied from interface: Report

print human readable report (e.g., on parameters and associated model)

Specified by:

report in interface Report

Parameters:

out - output stream

getTableColumnNames

public java.lang.Object[] getTableColumnNames()

Return column names for the table

Specified by:

getTableColumnNames in interface TableReport

Returns:

columns names

getTableData

public java.lang.Object[][] getTableData()

Return data for the table

Specified by:

getTableData in interface TableReport

Returns:

the data elements

getTableTitle

public java.lang.String getTableTitle()

Return the name for the title of the ANOVA

Specified by:

getTableTitle in interface TableReport

Returns:

a String title