jebl.evolution.sequences
public interface SequenceType
Modifier and Type | Interface and Description |
---|---|
static class |
SequenceType.Utils |
Modifier and Type | Field and Description |
---|---|
static SequenceType |
AMINO_ACID |
static SequenceType |
CODON |
static SequenceType |
NUCLEOTIDE |
Modifier and Type | Method and Description |
---|---|
int |
getCanonicalStateCount()
Get number of canonical states
|
java.util.List<? extends State> |
getCanonicalStates()
Get a list of canonical states ordered by their indices.
|
int |
getCodeLength() |
State |
getGapState()
Get state corresponding to a gap
|
java.lang.String |
getName()
name of data type
|
java.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 index
|
State |
getState(java.lang.String code)
Get state corresponding to a string code
|
int |
getStateCount()
Get number of states including ambiguous states
|
java.util.List<? extends State> |
getStates()
Get a list of states ordered by their indices.
|
State |
getUnknownState()
Get state corresponding to an unknown
|
boolean |
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 SequenceType
|
State[] |
toStateArray(java.lang.String sequenceString)
Converts a string of state codes into an array of State objects for this SequenceType
|
static final SequenceType NUCLEOTIDE
static final SequenceType AMINO_ACID
static final SequenceType CODON
int getStateCount()
java.util.List<? extends State> getStates()
int getCanonicalStateCount()
java.util.List<? extends State> getCanonicalStates()
State getState(java.lang.String code)
code
- a string codeState getState(char code)
code
- int getCodeLength()
State getState(int index)
index
- a state indexState getUnknownState()
State getGapState()
boolean isUnknown(State state)
boolean isGap(State state)
java.lang.String getName()
java.lang.String getNexusDataType()
State[] toStateArray(java.lang.String sequenceString)
sequenceString
- State[] toStateArray(byte[] indexArray)
indexArray
- http://code.google.com/p/jebl2/