org.biojava.nbio.core.sequence

Class MultipleSequenceAlignment<S extends Sequence<C>,C extends Compound>

java.lang.Object

org.biojava.nbio.core.sequence.MultipleSequenceAlignment<S,C>

All Implemented Interfaces:

LightweightProfile<S,C>

public class MultipleSequenceAlignment<S extends Sequence<C>,C extends Compound>
extends Object
implements LightweightProfile<S,C>

Implements a minimal data structure for reading and writing a sequence alignment. The full Profile data structure in the alignment module provides additional functionality.

Author:

Scooter Willis, Mark Chapman

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.nbio.core.sequence.template.LightweightProfile

LightweightProfile.StringFormat

Constructor Summary

Constructors

Constructor and Description
MultipleSequenceAlignment()

Method Summary

Modifier and Type	Method and Description
void	addAlignedSequence(S sequence) A sequence that has been aligned to other sequences will have inserts.
S	getAlignedSequence(int listIndex) Uses bioIndex starting at 1 instead of 0
List<S>	getAlignedSequences() Get the list of sequences
List<C>	getCompoundsAt(int alignmentIndex) Get a list of compounds at a sequence position
CompoundSet<C>	getCompoundSet() Get the Compounds defined in the first sequence
int	getLength() Get the length of the MSA where it is assumed that all sequence position
int	getSize() Get the number of sequences in the MSA
boolean	removeAlignedSequence(S sequence) Remove a sequence
String	toString() String representation of the MSA
String	toString(int width) Get a string representation of the MSA with a fixed width
String	toString(LightweightProfile.StringFormat format) Support for different MSA formats

Methods inherited from class java.lang.Object

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

Constructor Detail

MultipleSequenceAlignment

public MultipleSequenceAlignment()

Method Detail

addAlignedSequence

public void addAlignedSequence(S sequence)

A sequence that has been aligned to other sequences will have inserts.

Parameters:

sequence -

removeAlignedSequence

public boolean removeAlignedSequence(S sequence)

Remove a sequence

Parameters:

sequence -

Returns:

flag

getAlignedSequence

public S getAlignedSequence(int listIndex)

Uses bioIndex starting at 1 instead of 0

Specified by:

getAlignedSequence in interface LightweightProfile<S extends Sequence<C>,C extends Compound>

Parameters:

listIndex -

Returns:

sequence

getAlignedSequences

public List<S> getAlignedSequences()

Get the list of sequences

Specified by:

getAlignedSequences in interface LightweightProfile<S extends Sequence<C>,C extends Compound>

Returns:

list of sequences

getCompoundsAt

public List<C> getCompoundsAt(int alignmentIndex)

Get a list of compounds at a sequence position

Specified by:

getCompoundsAt in interface LightweightProfile<S extends Sequence<C>,C extends Compound>

Parameters:

alignmentIndex -

Returns:

compounds

getCompoundSet

public CompoundSet<C> getCompoundSet()

Get the Compounds defined in the first sequence

Specified by:

getCompoundSet in interface LightweightProfile<S extends Sequence<C>,C extends Compound>

Returns:

get compound set

getLength

public int getLength()

Get the length of the MSA where it is assumed that all sequence position

Specified by:

getLength in interface LightweightProfile<S extends Sequence<C>,C extends Compound>

Returns:

length of MSA

getSize

public int getSize()

Get the number of sequences in the MSA

Specified by:

getSize in interface LightweightProfile<S extends Sequence<C>,C extends Compound>

Returns:

nr of sequences

toString

public String toString(int width)

Get a string representation of the MSA with a fixed width

Specified by:

toString in interface LightweightProfile<S extends Sequence<C>,C extends Compound>

Parameters:

width -

Returns:

String

toString

public String toString(LightweightProfile.StringFormat format)

Support for different MSA formats

Specified by:

toString in interface LightweightProfile<S extends Sequence<C>,C extends Compound>

Parameters:

format -

Returns:

String in one of the supported file formats.

toString

public String toString()

String representation of the MSA

Specified by:

toString in interface LightweightProfile<S extends Sequence<C>,C extends Compound>

Overrides:

toString in class Object

Returns:

String