compbio.data.sequence

Class Alignment

java.lang.Object

compbio.data.sequence.Alignment

public class Alignment
extends java.lang.Object

Multiple sequence alignment. Does not give any guarantees on the content of individual FastaSequece records. It does not guarantee neither the uniqueness of the names of sequences nor it guarantees the uniqueness of the sequences.

Version:

1.0 September 2009

Author:

pvtroshin

See Also:

FastaSequence, AlignmentMetadata

Field Summary

Fields

Modifier and Type	Field and Description
protected AlignmentMetadata	metadata
protected java.util.List<FastaSequence>	sequences

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	Alignment()
	Alignment(java.util.List<FastaSequence> sequences, AlignmentMetadata metadata)
	Alignment(java.util.List<FastaSequence> sequences, Program program, char gapchar)

Method Summary

Modifier and Type	Method and Description
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()
int	hashCode()
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

metadata

protected AlignmentMetadata metadata

sequences

protected java.util.List<FastaSequence> sequences

Constructor Detail

Alignment

protected Alignment()

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

hashCode

public int hashCode()

Overrides:

hashCode 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