|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectpal.alignment.AlignmentBuilder
public class AlignmentBuilder
A class for the gradual construction of an alignment. To supersede simular classes hidden away in PAL History
Constructor Summary | |
---|---|
AlignmentBuilder(int initialCapacity)
The constructor |
Method Summary | |
---|---|
void |
addSequence(int[] states,
java.lang.String name)
Add sequence data to store |
void |
clearAll()
Remove all currently stored sequences. |
Alignment |
generateAlignment(DataType dt)
Build an alignment based on sequences stored. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
---|
public AlignmentBuilder(int initialCapacity)
initialCapacity
- The initial amount of space to allocate for sequence storage (dynamically adjusts if number of sequences exceeds capacity)Method Detail |
---|
public void clearAll()
public Alignment generateAlignment(DataType dt)
dt
- The datatype of the sequence data
public void addSequence(int[] states, java.lang.String name)
states
- The states of the sequence (builder assumes all state arrays are equal length)name
- The name of the sequence
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |