public class ConsensusSequence extends java.lang.Object implements Sequence
Attributable.Utils
Constructor and Description |
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ConsensusSequence(Taxon taxon,
Alignment source)
Creates a FilteredSequence wrapper to the given source sequence.
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ConsensusSequence(Taxon taxon,
Alignment source,
boolean includeAmbiguities)
Creates a FilteredSequence wrapper to the given source sequence.
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Modifier and Type | Method and Description |
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int |
compareTo(java.lang.Object o)
Sequences are compared by their taxa
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static State[] |
constructConsensus(Alignment source,
boolean includeAmbiguities) |
java.lang.Object |
getAttribute(java.lang.String name) |
java.util.Map<java.lang.String,java.lang.Object> |
getAttributeMap()
Gets the entire attribute map.
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java.util.Set<java.lang.String> |
getAttributeNames() |
int |
getLength()
Returns the length of the sequence
|
SequenceType |
getSequenceType() |
Alignment |
getSource() |
State |
getState(int site) |
byte[] |
getStateIndices() |
State[] |
getStates() |
java.lang.String |
getString() |
Taxon |
getTaxon() |
void |
removeAttribute(java.lang.String name) |
void |
setAttribute(java.lang.String name,
java.lang.Object value)
Sets an named attribute for this object.
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public ConsensusSequence(Taxon taxon, Alignment source)
source
- public Alignment getSource()
public SequenceType getSequenceType()
getSequenceType
in interface Sequence
public java.lang.String getString()
public State[] getStates()
public byte[] getStateIndices()
getStateIndices
in interface Sequence
public State getState(int site)
public int getLength()
public static State[] constructConsensus(Alignment source, boolean includeAmbiguities)
public Taxon getTaxon()
public int compareTo(java.lang.Object o)
compareTo
in interface java.lang.Comparable
o
- another sequencepublic void setAttribute(java.lang.String name, java.lang.Object value)
Attributable
setAttribute
in interface Attributable
name
- the name of the attribute.value
- the new value of the attribute.public java.lang.Object getAttribute(java.lang.String name)
getAttribute
in interface Attributable
name
- the name of the attribute of interest, or null if the attribute doesn't exist.public void removeAttribute(java.lang.String name)
removeAttribute
in interface Attributable
name
- name of attribute to removepublic java.util.Set<java.lang.String> getAttributeNames()
getAttributeNames
in interface Attributable
public java.util.Map<java.lang.String,java.lang.Object> getAttributeMap()
Attributable
getAttributeMap
in interface Attributable
http://code.google.com/p/jebl2/