All Superinterfaces:

Attributable, java.lang.Comparable

All Known Implementing Classes:

BasicSequence, CanonicalSequence, CodonSequence, ConsensusSequence, FilteredSequence, GaplessSequence, TranslatedSequence
```
public interface Sequence
extends Attributable, java.lang.Comparable
```
A biomolecular sequence.

Version:

$Id: Sequence.java 365 2006-06-28 07:34:56Z pepster $

Author:

Andrew Rambaut, Alexei Drummond

Nested Class Summary
- Nested classes/interfaces inherited from interface jebl.util.Attributable
  Attributable.Utils

Method Summary

All Methods Static Methods Instance Methods Abstract Methods
Modifier and Type	Method	Description
`static Sequence`	`appendSequences(Sequence sequence1, Sequence sequence2)`	Append two sequences together to create a new sequence object.
`int`	`getLength()`	Get the length of the sequence
`SequenceType`	`getSequenceType()`
`State`	`getState(int site)`
`byte[]`	`getStateIndices()`
`State[]`	`getStates()`
`java.lang.String`	`getString()`
`static Sequence`	`getSubSequence(Sequence sequence, int from, int to)`	Returns a sub-sequence for states from, to (inclusive).
`Taxon`	`getTaxon()`
`static Sequence`	`trimSequence(Sequence sequence, State[] trimStates)`

Methods inherited from interface jebl.util.Attributable
getAttribute, getAttributeMap, getAttributeNames, removeAttribute, setAttribute

Methods inherited from interface java.lang.Comparable
compareTo

- Method Detail
  - getTaxon
```
Taxon getTaxon()
```
    Returns:
    
    the taxon that this sequence represents (primarily used to match sequences with tree nodes)
  - getSequenceType
```
SequenceType getSequenceType()
```
    Returns:
    
    the type of symbols that this sequence is made up of.
  - getString
```
java.lang.String getString()
```
    Returns:
    
    a string representing the sequence of symbols.
  - getStates
```
State[] getStates()
```
    Returns:
    
    an array of state objects.
  - getStateIndices
```
byte[] getStateIndices()
```
    Returns:
    
    an array of state indices.
  - getState
```
State getState(int site)
```
    Returns:
    
    the state at site.
  - getLength
```
int getLength()
```
    Get the length of the sequence
    
    Returns:
    
    the length
  - appendSequences
```
static Sequence appendSequences(Sequence sequence1,
                                Sequence sequence2)
```
    Append two sequences together to create a new sequence object. New sequence has the taxon of the first sequence.
    
    Parameters:
    
    sequence1 -
    
    sequence2 -
    
    Returns:
  - getSubSequence
```
static Sequence getSubSequence(Sequence sequence,
                               int from,
                               int to)
```
    Returns a sub-sequence for states from, to (inclusive).
    
    Parameters:
    
    sequence -
    
    from -
    
    to -
    
    Returns:
  - trimSequence
```
static Sequence trimSequence(Sequence sequence,
                             State[] trimStates)
```

Interface Sequence

Nested Class Summary

Nested classes/interfaces inherited from interface jebl.util.Attributable

Method Summary

Methods inherited from interface jebl.util.Attributable

Methods inherited from interface java.lang.Comparable

Method Detail

getTaxon

getSequenceType

getString

getStates

getStateIndices

getState

getLength

appendSequences

getSubSequence

trimSequence