Package jebl.evolution.sequences
Interface SequenceType
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public interface SequenceType
Interface for sequences data types.- Version:
- $Id: SequenceType.java 849 2007-12-06 00:10:14Z twobeers $
- Author:
- Andrew Rambaut, Alexei Drummond
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Nested Class Summary
Nested Classes Modifier and Type Interface Description static class
SequenceType.Utils
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Field Summary
Fields Modifier and Type Field Description static SequenceType
AMINO_ACID
static SequenceType
CODON
static SequenceType
NUCLEOTIDE
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description int
getCanonicalStateCount()
Get number of canonical statesjava.util.List<? extends State>
getCanonicalStates()
Get a list of canonical states ordered by their indices.int
getCodeLength()
State
getGapState()
Get state corresponding to a gapjava.lang.String
getName()
name of data typejava.lang.String
getNexusDataType()
State
getState(char code)
Get state whose code is the one-character string consisting only of code.State
getState(int index)
Get state corresponding to a state indexState
getState(java.lang.String code)
Get state corresponding to a string codeint
getStateCount()
Get number of states including ambiguous statesjava.util.List<? extends State>
getStates()
Get a list of states ordered by their indices.State
getUnknownState()
Get state corresponding to an unknownboolean
isGap(State state)
boolean
isUnknown(State state)
State[]
toStateArray(byte[] indexArray)
Converts an array of state indices into an array of State objects for this SequenceTypeState[]
toStateArray(java.lang.String sequenceString)
Converts a string of state codes into an array of State objects for this SequenceType
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Field Detail
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NUCLEOTIDE
static final SequenceType NUCLEOTIDE
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AMINO_ACID
static final SequenceType AMINO_ACID
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CODON
static final SequenceType CODON
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Method Detail
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getStateCount
int getStateCount()
Get number of states including ambiguous states- Returns:
- number of states
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getStates
java.util.List<? extends State> getStates()
Get a list of states ordered by their indices.- Returns:
- a list of states
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getCanonicalStateCount
int getCanonicalStateCount()
Get number of canonical states- Returns:
- number of states
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getCanonicalStates
java.util.List<? extends State> getCanonicalStates()
Get a list of canonical states ordered by their indices.- Returns:
- a list of states
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getState
State getState(java.lang.String code)
Get state corresponding to a string code- Parameters:
code
- a string code- Returns:
- the state with the given code, or null if there is no such state
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getState
State getState(char code)
Get state whose code is the one-character string consisting only of code.- Parameters:
code
-- Returns:
- the state with the given code, or null if there is no such state
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getCodeLength
int getCodeLength()
- Returns:
- the length, in characters, of a state, when encoded as a string. i.e. 1 for Nucleotides and AminoAcids and 3 for Codons.
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getState
State getState(int index)
Get state corresponding to a state index- Parameters:
index
- a state index- Returns:
- the state
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getUnknownState
State getUnknownState()
Get state corresponding to an unknown- Returns:
- the state
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getGapState
State getGapState()
Get state corresponding to a gap- Returns:
- state
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isUnknown
boolean isUnknown(State state)
- Returns:
- true if this state is an unknown state
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isGap
boolean isGap(State state)
- Returns:
- true if this state is a gap
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getName
java.lang.String getName()
name of data type- Returns:
- string describing the data type
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getNexusDataType
java.lang.String getNexusDataType()
- Returns:
- datatype inside a nexus characters block, if any.
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toStateArray
State[] toStateArray(java.lang.String sequenceString)
Converts a string of state codes into an array of State objects for this SequenceType- Parameters:
sequenceString
-- Returns:
- the State array
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toStateArray
State[] toStateArray(byte[] indexArray)
Converts an array of state indices into an array of State objects for this SequenceType- Parameters:
indexArray
-- Returns:
- the State array
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