compbio.data.sequence
Class Alignment

java.lang.Object
  compbio.data.sequence.Alignment

@Immutable
public final class Alignment
extends java.lang.Object

Multiple sequence alignment. Does not give any guarantees on the content of individual FastaSequece records. That is it does not guarantee that the neither the names of sequences or the sequences themselves are unique.

Author:

pvtroshin Date September 2009

See Also:

FastaSequence, AlignmentMetadata

Constructor Summary

Alignment(java.util.List<FastaSequence> sequences, AlignmentMetadata metadata)

Alignment(java.util.List<FastaSequence> sequences, Program program, char gapchar)

Method Summary

boolean	equals(java.lang.Object obj) Please note that this implementation does not take the order of sequences into account!
AlignmentMetadata	getMetadata()
java.util.List<FastaSequence>	getSequences()
int	getSize()
java.lang.String	toString()

Methods inherited from class java.lang.Object

getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Alignment

public Alignment(java.util.List<FastaSequence> sequences,
                 Program program,
                 char gapchar)

Parameters:

sequences -

program -

gapchar -

Alignment

public Alignment(java.util.List<FastaSequence> sequences,
                 AlignmentMetadata metadata)

Parameters:

sequences -

metadata -

Method Detail

getSequences

public java.util.List<FastaSequence> getSequences()

Returns:

list of FastaSequence records

getSize

public int getSize()

Returns:

a number of sequence in the alignment

getMetadata

public AlignmentMetadata getMetadata()

Returns:

AlignmentMetadata object

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

equals

public boolean equals(java.lang.Object obj)

Please note that this implementation does not take the order of sequences into account!

Overrides:

equals in class java.lang.Object