MultipleSequenceAlignment (biojava 5.2.0 API)

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 Description

MultipleSequenceAlignment()

Constructors
Constructor	Description
`MultipleSequenceAlignment()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	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

Nested Class Summary

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

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

MultipleSequenceAlignment

Method Detail

addAlignedSequence

removeAlignedSequence

getAlignedSequence

getAlignedSequences

getCompoundsAt

getCompoundSet

getLength

getSize

toString

toString

toString