SimpleDataType

java.lang.Object
- pal.datatype.SimpleDataType

All Implemented Interfaces:

java.io.Serializable, DataType

Direct Known Subclasses:

AminoAcids, Codons, GapBalanced, IUPACNucleotides, Nucleotides, NumericDataType, StateRemover, TwoStates
```
public abstract class SimpleDataType
extends java.lang.Object
implements DataType
```
interface for sequence data types

Version:

$Id: SimpleDataType.java,v 1.14 2003/11/30 05:29:22 matt Exp $

Author:

Alexei Drummond

See Also:

Serialized Form

Nested Class Summary
- Nested classes/interfaces inherited from interface pal.datatype.DataType
  DataType.Utils

Field Summary
- Fields inherited from interface pal.datatype.DataType
  AMINO_ACID_DESCRIPTION, AMINOACIDS, CODON_DESCRIPTION, CODONS, GAP_BALANCED, GAP_BALANCED_DESCRIPTION, IUPAC_NUCELOTIDES_DESCRIPTION, IUPACNUCLEOTIDES, NUCLEOTIDE_DESCRIPTION, NUCLEOTIDES, NUMERIC, PRIMARY_SUGGESTED_GAP_CHARACTER, SUGGESTED_GAP_CHARACTERS, SUGGESTED_GAP_STATE, SUGGESTED_UNKNOWN_STATE, TWO_STATE_DESCRIPTION, TWOSTATES, UNKNOWN, UNKNOWN_CHARACTER, UNKNOWN_TLA

Constructor Summary

Constructors
Constructor and Description

SimpleDataType()

Constructors
Constructor and Description
`SimpleDataType()`

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`AmbiguousDataType`	`getAmbiguousVersion()`
`char`	`getChar(int state)` Handles gap state and then passes on to getStateImpl
`protected abstract char`	`getCharImpl(int state)`
`char`	`getPreferredChar(char c)` Automatically handles Gaps for sub classes
`protected char`	`getPreferredCharImpl(char c)` Can be overidden by subclasses.
`int`	`getRecommendedGapState()`
`int`	`getRecommendedUnknownState()`
`int`	`getState(char c)` Handles gap char and then passes on to getStateImpl
`protected abstract int`	`getStateImpl(char c)` For sub classes to implement main functionality of getState.
`boolean`	`hasGap()`
`boolean`	`isAmbiguous()`
`boolean`	`isGapChar(char c)`
`boolean`	`isGapState(int state)`
`boolean`	`isUnknownChar(char c)`
`boolean`	`isUnknownState(int state)` Checks if state is a gap state (then returns true), otherwise passes on to isUnknownStateImpl
`protected abstract boolean`	`isUnknownStateImpl(int state)` For subclasses to handle, without regard for gaps
`java.lang.String`	`toString()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface pal.datatype.DataType
getDescription, getNumStates, getTypeID

- Constructor Detail
  - SimpleDataType
```
public SimpleDataType()
```
- Method Detail
  - getState
```
public final int getState(char c)
```
    Handles gap char and then passes on to getStateImpl
    
    Specified by:
    
    getState in interface DataType
    
    Parameters:
    
    c - character
    
    Returns:
    
    state
  - getChar
```
public final char getChar(int state)
```
    Handles gap state and then passes on to getStateImpl
    
    Specified by:
    
    getChar in interface DataType
    
    Parameters:
    
    state - state return corresponding character
  - getStateImpl
```
protected abstract int getStateImpl(char c)
```
    For sub classes to implement main functionality of getState. Gaps do not need to be considered
  - getCharImpl
```
protected abstract char getCharImpl(int state)
```
  - getPreferredChar
```
public final char getPreferredChar(char c)
```
    Automatically handles Gaps for sub classes
    
    Specified by:
    
    getPreferredChar in interface DataType
  - getPreferredCharImpl
```
protected char getPreferredCharImpl(char c)
```
    Can be overidden by subclasses. Default implementation get's character's state and that get's the character for that state
  - isUnknownChar
```
public final boolean isUnknownChar(char c)
```
    Specified by:
    
    isUnknownChar in interface DataType
    
    Returns:
    
    true if this state is unknown (or a gap)
  - isUnknownState
```
public final boolean isUnknownState(int state)
```
    Checks if state is a gap state (then returns true), otherwise passes on to isUnknownStateImpl
    
    Specified by:
    
    isUnknownState in interface DataType
    
    Returns:
    
    true if this state is an unknown state (the same as check if a state is >= the number of states... but neater)
  - isUnknownStateImpl
```
protected abstract boolean isUnknownStateImpl(int state)
```
    For subclasses to handle, without regard for gaps
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object
  - getRecommendedUnknownState
```
public int getRecommendedUnknownState()
```
    Specified by:
    
    getRecommendedUnknownState in interface DataType
    
    Returns:
    
    -1 (not getNumStates())
  - isAmbiguous
```
public boolean isAmbiguous()
```
    Specified by:
    
    isAmbiguous in interface DataType
    
    Returns:
    
    false
  - getAmbiguousVersion
```
public AmbiguousDataType getAmbiguousVersion()
```
    Specified by:
    
    getAmbiguousVersion in interface DataType
    
    Returns:
    
    null
  - hasGap
```
public final boolean hasGap()
```
    Specified by:
    
    hasGap in interface DataType
    
    Returns:
    
    true
  - isGapChar
```
public final boolean isGapChar(char c)
```
    Specified by:
    
    isGapChar in interface DataType
    
    Returns:
    
    true if this character is a '.' or a '_'
  - isGapState
```
public final boolean isGapState(int state)
```
    Specified by:
    
    isGapState in interface DataType
    
    Returns:
    
    true if state is gap state (-2), false other wise
  - getRecommendedGapState
```
public final int getRecommendedGapState()
```
    Specified by:
    
    getRecommendedGapState in interface DataType
    
    Returns:
    
    GAP_STATE (-2)

Class SimpleDataType

Nested Class Summary

Nested classes/interfaces inherited from interface pal.datatype.DataType

Field Summary

Fields inherited from interface pal.datatype.DataType

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface pal.datatype.DataType

Constructor Detail

SimpleDataType

Method Detail

getState

getChar

getStateImpl

getCharImpl

getPreferredChar

getPreferredCharImpl

isUnknownChar

isUnknownState

isUnknownStateImpl

toString

getRecommendedUnknownState

isAmbiguous

getAmbiguousVersion

hasGap

isGapChar

isGapState

getRecommendedGapState