compbio.data.sequence
Class FastaSequence

java.lang.Object
  compbio.data.sequence.FastaSequence

Direct Known Subclasses:

AnnotatedSequence

@Immutable
public class FastaSequence
extends Object

A FASTA formatted sequence. Please note that this class does not make any assumptions as to what sequence it stores e.g. it could be nucleotide, protein or even gapped alignment sequence! The only guarantee it makes is that the sequence does not contain white space characters e.g. spaces, new lines etc

Version:

1.0 September 2009

Author:

pvtroshin

Constructor Summary

FastaSequence(String id, String sequence)
Upon construction the any whitespace characters are removed from the sequence

Method Summary

static int	countMatchesInSequence(String theString, String theRegExp)
boolean	equals(Object obj)
String	getFormatedSequence(int width) Format sequence per width letter in one string.
String	getFormattedFasta()
String	getId() Gets the value of id
int	getLength()
String	getOnelineFasta()
String	getSequence() Gets the value of sequence
int	hashCode()
String	toString() Same as oneLineFasta

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

FastaSequence

public FastaSequence(String id,
                     String sequence)

Upon construction the any whitespace characters are removed from the sequence

Parameters:

id -

sequence -

Method Detail

getId

public String getId()

Gets the value of id

Returns:

the value of id

getSequence

public String getSequence()

Gets the value of sequence

Returns:

the value of sequence

countMatchesInSequence

public static int countMatchesInSequence(String theString,
                                         String theRegExp)

getFormattedFasta

public String getFormattedFasta()

getOnelineFasta

public String getOnelineFasta()

Returns:

one line name, next line sequence, no matter what the sequence length is

getFormatedSequence

public String getFormatedSequence(int width)

Format sequence per width letter in one string. Without spaces.

Returns:

multiple line formated sequence, one line width letters length

getLength

public int getLength()

Returns:

sequence length

toString

public String toString()

Same as oneLineFasta

Overrides:

toString in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object obj)

Overrides:

equals in class Object