|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectjebl.evolution.sequences.BasicSequence
public class BasicSequence
A default implementation of the Sequence interface.
Nested Class Summary |
---|
Nested classes/interfaces inherited from interface jebl.util.Attributable |
---|
Attributable.Utils |
Constructor Summary | |
---|---|
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 |
Method Summary | |
---|---|
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()
|
Methods inherited from class java.lang.Object |
---|
getClass, notify, notifyAll, wait, wait, wait |
Constructor Detail |
---|
public BasicSequence(SequenceType sequenceType, Taxon taxon, java.lang.CharSequence sequenceString)
taxon
- sequenceString
- public BasicSequence(SequenceType sequenceType, Taxon taxon, State[] states)
taxon
- sequenceType
- states
- Method Detail |
---|
public SequenceType getSequenceType()
getSequenceType
in interface Sequence
public java.lang.String getString()
getString
in interface Sequence
public java.lang.String getCleanString()
public State[] getStates()
getStates
in interface Sequence
public byte[] getStateIndices()
getStateIndices
in interface Sequence
public byte[] getSequenceCharacters()
public State getState(int site)
getState
in interface Sequence
public int getLength()
getLength
in interface Sequence
public Taxon getTaxon()
getTaxon
in interface Sequence
public int compareTo(java.lang.Object o)
compareTo
in interface java.lang.Comparable
o
- another sequence
public 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
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |