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

Fields
Modifier and Type	Field and Description
`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

Constructors
Constructor and Description
`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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`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

Class SimpleCharacterAlignment

Nested Class Summary

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

Field Summary

Fields inherited from interface pal.alignment.CharacterAlignment

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

traitValues

traitNames

environmentNames

numSeqs

numTraits

idGroup

Constructor Detail

SimpleCharacterAlignment

SimpleCharacterAlignment

SimpleCharacterAlignment

SimpleCharacterAlignment

SimpleCharacterAlignment

Method Detail

getTrait

getLength

getSequenceCount

getTraitCount

getTraitName

getEnvironmentName

getIdentifier

setIdentifier

getIdCount

whichIdNumber

toString

report

getTableColumnNames

getTableData

getTableTitle