Package jebl.evolution.alignments
Interface Pattern
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public interface Pattern
An interface representing a list of states for a list of taxa (e.g. an alignment column).- Version:
- $Id: Pattern.java 658 2007-03-20 03:27:20Z twobeers $
- Author:
- Andrew Rambaut, Alexei Drummond
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description int
getLength()
State
getMostFrequentState()
Returns the most frequent state in this patternState
getMostFrequentState(boolean includeAmbiguous)
Returns the most frequent state in this pattern, optionally including ambiguous statesSequenceType
getSequenceType()
State
getState(int index)
Get the state for the ith taxonint
getStateCount(State state)
Returns the count of the given state in this patterndouble
getStateFrequency(State state)
Returns the frequent of the given state in this patternjava.util.List<State>
getStates()
java.util.Set<State>
getStateSet()
java.util.List<Taxon>
getTaxa()
double
getWeight()
Get the weight of this pattern
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Method Detail
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getSequenceType
SequenceType getSequenceType()
- Returns:
- the data type of the states in this pattern.
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getLength
int getLength()
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getTaxa
java.util.List<Taxon> getTaxa()
- Returns:
- the list of taxa that the state values correspond to.
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getState
State getState(int index)
Get the state for the ith taxon- Parameters:
index
-- Returns:
- the state
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getStates
java.util.List<State> getStates()
- Returns:
- the list of state values of this pattern.
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getStateSet
java.util.Set<State> getStateSet()
- Returns:
- the set of state values of this pattern.
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getWeight
double getWeight()
Get the weight of this pattern- Returns:
- the weight
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getMostFrequentState
State getMostFrequentState()
Returns the most frequent state in this pattern- Returns:
- the most frequent state
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getMostFrequentState
State getMostFrequentState(boolean includeAmbiguous)
Returns the most frequent state in this pattern, optionally including ambiguous states- Parameters:
includeAmbiguous
- whether to include ambiguous states- Returns:
- the most frequent state
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getStateFrequency
double getStateFrequency(State state)
Returns the frequent of the given state in this pattern- Parameters:
state
-- Returns:
- the frequency
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getStateCount
int getStateCount(State state)
Returns the count of the given state in this pattern- Parameters:
state
-- Returns:
- the count
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