java.lang.Comparable
, Sequence
, Attributable
public class BasicSequence extends java.lang.Object implements Sequence
Attributable.Utils
Constructor | Description |
---|---|
BasicSequence(SequenceType sequenceType,
Taxon taxon,
java.lang.CharSequence sequenceString) |
Creates a sequence with a name corresponding to the taxon name.
|
BasicSequence(SequenceType sequenceType,
Taxon taxon,
State[] states) |
Creates a sequence with a name corresponding to the taxon name
|
Modifier and Type | Method | Description |
---|---|---|
int |
compareTo(java.lang.Object o) |
Sequences are compared by their taxa
|
boolean |
equals(java.lang.Object o) |
|
java.lang.Object |
getAttribute(java.lang.String name) |
|
java.util.Map<java.lang.String,java.lang.Object> |
getAttributeMap() |
Gets the entire attribute map.
|
java.util.Set<java.lang.String> |
getAttributeNames() |
|
java.lang.String |
getCleanString() |
|
int |
getLength() |
Returns the length of the sequence
|
byte[] |
getSequenceCharacters() |
Get the sequence characters representing the sequence.
|
SequenceType |
getSequenceType() |
|
State |
getState(int site) |
|
byte[] |
getStateIndices() |
|
State[] |
getStates() |
|
java.lang.String |
getString() |
|
Taxon |
getTaxon() |
|
int |
hashCode() |
|
void |
removeAttribute(java.lang.String name) |
|
void |
setAttribute(java.lang.String name,
java.lang.Object value) |
Sets an named attribute for this object.
|
java.lang.String |
toString() |
public BasicSequence(SequenceType sequenceType, Taxon taxon, java.lang.CharSequence sequenceString)
taxon
- sequenceString
- public BasicSequence(SequenceType sequenceType, Taxon taxon, State[] states)
taxon
- sequenceType
- states
- public SequenceType getSequenceType()
getSequenceType
in interface Sequence
public java.lang.String getString()
public java.lang.String getCleanString()
public State[] getStates()
public byte[] getStateIndices()
getStateIndices
in interface Sequence
public byte[] getSequenceCharacters()
public State getState(int site)
public int getLength()
public Taxon getTaxon()
public int compareTo(java.lang.Object o)
compareTo
in interface java.lang.Comparable
o
- another sequencepublic java.lang.String toString()
toString
in class java.lang.Object
public 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
public boolean equals(java.lang.Object o)
equals
in class java.lang.Object
public int hashCode()
hashCode
in class java.lang.Object
http://code.google.com/p/jebl2/