GapBalanced

java.lang.Object
- pal.datatype.SimpleDataType
- - pal.datatype.GapBalanced

All Implemented Interfaces:

java.io.Serializable, DataType, MolecularDataType
```
public class GapBalanced
extends SimpleDataType
implements MolecularDataType
```
implements a ResidueDataType for GapBalanced notation. The terminate character IS included as a state

Version:

$Id: GapBalanced.java,v 1.6 2003/03/23 00:04:23 matt Exp $

Author:

Matthew Goode

See Also:

Serialized Form

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

Field Summary

Fields
Modifier and Type Field and Description

static GapBalanced DEFAULT_INSTANCE
- 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

Fields
Modifier and Type	Field and Description
`static GapBalanced`	`DEFAULT_INSTANCE`

Constructor Summary

Constructors
Constructor and Description

GapBalanced(CodonTable translationTable)

Constructors
Constructor and Description
`GapBalanced(CodonTable translationTable)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected char`	`getCharImpl(int state)`
`java.lang.String`	`getDescription()` description of data type
`int[]`	`getMolecularStatesFromIUPACNucleotides(int[] nucleotideStates, int startingIndex)` Currently converts ambiguous states to a simple version (IE takes the first possible simple state for the ambiguous state)
`int[]`	`getMolecularStatesFromSimpleNucleotides(int[] nucleotideStates, int startingIndex)`
`int`	`getNucleotideLength()`
`int[]`	`getNucleotideStates(int[] residueStates)`
`int`	`getNumStates()` get number of unique states
`int`	`getStateImpl(char c)` For sub classes to implement main functionality of getState.
`int`	`getTypeID()` get numerical code describing the data type
`boolean`	`isCreatesIUPACNuecleotides()`
`protected boolean`	`isUnknownStateImpl(int state)` For subclasses to handle, without regard for gaps

Methods inherited from class pal.datatype.SimpleDataType
getAmbiguousVersion, getChar, getPreferredChar, getPreferredCharImpl, getRecommendedGapState, getRecommendedUnknownState, getState, hasGap, isAmbiguous, isGapChar, isGapState, isUnknownChar, isUnknownState, 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
getAmbiguousVersion, getChar, getPreferredChar, getRecommendedGapState, getRecommendedUnknownState, getState, hasGap, isAmbiguous, isGapChar, isGapState, isUnknownChar, isUnknownState

- Field Detail
  - DEFAULT_INSTANCE
```
public static final GapBalanced DEFAULT_INSTANCE
```
- Constructor Detail
  - GapBalanced
```
public GapBalanced(CodonTable translationTable)
```
- Method Detail
  - getNumStates
```
public int getNumStates()
```
    Description copied from interface: DataType
    
    get number of unique states
    
    Specified by:
    
    getNumStates in interface DataType
    
    Returns:
    
    number of unique states
  - getStateImpl
```
public int getStateImpl(char c)
```
    Description copied from class: SimpleDataType
    
    For sub classes to implement main functionality of getState. Gaps do not need to be considered
    
    Specified by:
    
    getStateImpl in class SimpleDataType
  - getCharImpl
```
protected char getCharImpl(int state)
```
    Specified by:
    
    getCharImpl in class SimpleDataType
  - isUnknownStateImpl
```
protected final boolean isUnknownStateImpl(int state)
```
    Description copied from class: SimpleDataType
    
    For subclasses to handle, without regard for gaps
    
    Specified by:
    
    isUnknownStateImpl in class SimpleDataType
  - getDescription
```
public java.lang.String getDescription()
```
    Description copied from interface: DataType
    
    description of data type
    
    Specified by:
    
    getDescription in interface DataType
    
    Returns:
    
    string describing the data type
  - getTypeID
```
public int getTypeID()
```
    Description copied from interface: DataType
    
    get numerical code describing the data type
    
    Specified by:
    
    getTypeID in interface DataType
    
    Returns:
    
    numerical code
  - getNucleotideStates
```
public int[] getNucleotideStates(int[] residueStates)
```
    Specified by:
    
    getNucleotideStates in interface MolecularDataType
    
    Parameters:
    
    residueStates - an array of states corresponding to states of this datatype
    
    Returns:
    
    the corresponding IUPAC states
  - getMolecularStatesFromIUPACNucleotides
```
public final int[] getMolecularStatesFromIUPACNucleotides(int[] nucleotideStates,
                                                          int startingIndex)
```
    Currently converts ambiguous states to a simple version (IE takes the first possible simple state for the ambiguous state)
    
    Specified by:
    
    getMolecularStatesFromIUPACNucleotides in interface MolecularDataType
  - getMolecularStatesFromSimpleNucleotides
```
public final int[] getMolecularStatesFromSimpleNucleotides(int[] nucleotideStates,
                                                           int startingIndex)
```
    Specified by:
    
    getMolecularStatesFromSimpleNucleotides in interface MolecularDataType
    
    Returns:
  - isCreatesIUPACNuecleotides
```
public boolean isCreatesIUPACNuecleotides()
```
    Specified by:
    
    isCreatesIUPACNuecleotides in interface MolecularDataType
    
    Returns:
    
    true
  - getNucleotideLength
```
public final int getNucleotideLength()
```
    Specified by:
    
    getNucleotideLength in interface MolecularDataType
    
    Returns:
    
    1

Class GapBalanced

Nested Class Summary

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

Field Summary

Fields inherited from interface pal.datatype.DataType

Constructor Summary

Method Summary

Methods inherited from class pal.datatype.SimpleDataType

Methods inherited from class java.lang.Object

Methods inherited from interface pal.datatype.DataType

Field Detail

DEFAULT_INSTANCE

Constructor Detail

GapBalanced

Method Detail

getNumStates

getStateImpl

getCharImpl

isUnknownStateImpl

getDescription

getTypeID

getNucleotideStates

getMolecularStatesFromIUPACNucleotides

getMolecularStatesFromSimpleNucleotides

isCreatesIUPACNuecleotides

getNucleotideLength