com.milaboratory.core.mutations

Class MutationsBuilder<S extends Sequence<S>>

java.lang.Object

com.milaboratory.core.mutations.MutationsBuilder<S>

public final class MutationsBuilder<S extends Sequence<S>>
extends Object

Constructor Summary

Constructors

Constructor and Description
MutationsBuilder(Alphabet<S> alphabet)
MutationsBuilder(Alphabet<S> alphabet, boolean reversed)
MutationsBuilder(Alphabet<S> alphabet, boolean reversed, int[] mutations, int size)

Method Summary

Methods

Modifier and Type	Method and Description
MutationsBuilder<S>	append(int mutation)
MutationsBuilder<S>	append(int[] other)
MutationsBuilder<S>	append(Mutations<S> other)
MutationsBuilder<S>	append(Mutations<S> other, int otherFrom, int length)
MutationsBuilder<S>	append(MutationsBuilder<S> other)
MutationsBuilder<S>	appendDeletion(int position, int from)
MutationsBuilder<S>	appendDeletion(int position, int length, S originalSequence)
MutationsBuilder<S>	appendInsertion(int position, int to)
MutationsBuilder<S>	appendInsertion(int position, S insert)
MutationsBuilder<S>	appendSubstitution(int position, int from, int to)
MutationsBuilder<S>	clone()
Mutations<S>	createAndDestroy()
MutationsBuilder<S>	ensureCapacity(int capacity)
int	get(int index)
int	getLast()
void	removeLast()
MutationsBuilder<S>	reverseRange(int from, int to)
void	set(int index, int mutation)
int	size()
String	toString()

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

MutationsBuilder

public MutationsBuilder(Alphabet<S> alphabet,
                boolean reversed,
                int[] mutations,
                int size)

MutationsBuilder

public MutationsBuilder(Alphabet<S> alphabet)

MutationsBuilder

public MutationsBuilder(Alphabet<S> alphabet,
                boolean reversed)

Method Detail

get

public int get(int index)

size

public int size()

set

public void set(int index,
       int mutation)

getLast

public int getLast()

removeLast

public void removeLast()

ensureCapacity

public MutationsBuilder<S> ensureCapacity(int capacity)

createAndDestroy

public Mutations<S> createAndDestroy()

append

public MutationsBuilder<S> append(Mutations<S> other)

append

public MutationsBuilder<S> append(MutationsBuilder<S> other)

append

public MutationsBuilder<S> append(Mutations<S> other,
                         int otherFrom,
                         int length)

append

public MutationsBuilder<S> append(int[] other)

append

public MutationsBuilder<S> append(int mutation)

appendSubstitution

public MutationsBuilder<S> appendSubstitution(int position,
                                     int from,
                                     int to)

appendDeletion

public MutationsBuilder<S> appendDeletion(int position,
                                 int from)

appendInsertion

public MutationsBuilder<S> appendInsertion(int position,
                                  int to)

appendInsertion

public MutationsBuilder<S> appendInsertion(int position,
                                  S insert)

appendDeletion

public MutationsBuilder<S> appendDeletion(int position,
                                 int length,
                                 S originalSequence)

reverseRange

public MutationsBuilder<S> reverseRange(int from,
                               int to)

clone

public MutationsBuilder<S> clone()

Overrides:

clone in class Object

toString

public String toString()

Overrides:

toString in class Object