pal.alignment

Interface CharacterAlignment

All Superinterfaces:

IdGroup, Report, java.io.Serializable, TableReport

All Known Implementing Classes:

SimpleCharacterAlignment

public interface CharacterAlignment
extends java.io.Serializable, IdGroup, Report, TableReport

This interface is designed to hold 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: CharacterAlignment.java,v 1.2 2001/09/02 13:19:41 korbinian Exp $

Author:

Ed Buckler

Nested Class Summary

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

IdGroup.Utils

Field Summary

Fields

Modifier and Type	Field and Description
static double	MISSING

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.String	getEnvironmentName(int trait) Return name of the environments for this trait number
int	getSequenceCount() Return number of sequences(taxa) in this alignment
double	getTrait(int seq, int trait) Return the trait value for a given sequence (taxon) and trait number
int	getTraitCount() Return number of traits for each sequence in this alignment
java.lang.String	getTraitName(int trait) Return name of the trait for this trait number

Methods inherited from interface pal.misc.IdGroup

getIdCount, getIdentifier, setIdentifier, whichIdNumber

Methods inherited from interface pal.misc.Report

report

Methods inherited from interface pal.misc.TableReport

getTableColumnNames, getTableData, getTableTitle

Field Detail

MISSING

static final double MISSING

See Also:

Constant Field Values

Method Detail

getTraitName

java.lang.String getTraitName(int trait)

Return name of the trait for this trait number

getEnvironmentName

java.lang.String getEnvironmentName(int trait)

Return name of the environments for this trait number

getTrait

double getTrait(int seq,
              int trait)

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

getSequenceCount

int getSequenceCount()

Return number of sequences(taxa) in this alignment

getTraitCount

int getTraitCount()

Return number of traits for each sequence in this alignment