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)`
`static int`	`getStateCount(Sequence sequence, State state)`	Counts the number of occurances of a state
`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`	`replaceStates(Sequence sequence, java.util.List<State> searchStates, State replaceState)`	Searchers and replaces a sequence of any states given
`static Sequence`	`stripGaps(Sequence sequence)`	Strips a sequence of gaps
`static Sequence`	`stripStates(Sequence sequence, java.util.List<State> stripStates)`	Strips a sequence of any states given
`static Sequence`	`trimSequence(Sequence sequence, java.util.List<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,
                             java.util.List<State> trimStates)
```
  - stripGaps
```
static Sequence stripGaps(Sequence sequence)
```
    Strips a sequence of gaps
    
    Parameters:
    
    sequence - the sequence
    
    Returns:
    
    the stripped sequence
  - stripStates
```
static Sequence stripStates(Sequence sequence,
                            java.util.List<State> stripStates)
```
    Strips a sequence of any states given
    
    Parameters:
    
    sequence - the sequence
    
    stripStates - the states to strip
    
    Returns:
    
    an array of states
  - replaceStates
```
static Sequence replaceStates(Sequence sequence,
                              java.util.List<State> searchStates,
                              State replaceState)
```
    Searchers and replaces a sequence of any states given
    
    Parameters:
    
    sequence - the sequence
    
    searchStates - the states to search for
    
    Returns:
    
    an array of states
  - getStateCount
```
static int getStateCount(Sequence sequence,
                         State state)
```
    Counts the number of occurances of a state
    
    Parameters:
    
    sequence - the sequence string to count
    
    state - the state
    
    Returns:
    
    the number of occurances

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

stripGaps

stripStates

replaceStates

getStateCount