CharacterAlignment

Skip navigation links

All Classes

SEARCH:

Summary:
Nested |
Field |
Constr |
Method

Detail:
Field |
Constr |
Method

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 Description

static double MISSING

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	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

Skip navigation links

All Classes

Summary:
Nested |
Field |
Constr |
Method

Detail:
Field |
Constr |
Method