Package jebl.evolution.sequences
Interface Sequence
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- 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
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Nested Class Summary
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Nested classes/interfaces inherited from interface jebl.util.Attributable
Attributable.Utils
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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 sequenceSequenceType
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)
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Methods inherited from interface jebl.util.Attributable
getAttribute, getAttributeMap, getAttributeNames, removeAttribute, setAttribute
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Method Detail
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getTaxon
Taxon getTaxon()
- Returns:
- the taxon that this sequence represents (primarily used to match sequences with tree nodes)
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getSequenceType
SequenceType getSequenceType()
- Returns:
- the type of symbols that this sequence is made up of.
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getString
java.lang.String getString()
- Returns:
- a string representing the sequence of symbols.
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getStates
State[] getStates()
- Returns:
- an array of state objects.
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getStateIndices
byte[] getStateIndices()
- Returns:
- an array of state indices.
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getState
State getState(int site)
- Returns:
- the state at site.
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getLength
int getLength()
Get the length of the sequence- Returns:
- the length
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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:
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getSubSequence
static Sequence getSubSequence(Sequence sequence, int from, int to)
Returns a sub-sequence for states from, to (inclusive).- Parameters:
sequence
-from
-to
-- Returns:
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