calhoun.seq
Class SimpleFastaSequence

java.lang.Object
  calhoun.seq.SimpleFastaSequence

All Implemented Interfaces:

FastaSequence, java.io.Serializable

Direct Known Subclasses:

FastaIterator.ReaderSequence

public class SimpleFastaSequence
extends java.lang.Object
implements FastaSequence, java.io.Serializable

See Also:

Serialized Form

Constructor Summary

SimpleFastaSequence()

SimpleFastaSequence(java.lang.String header, java.lang.String sequence)

Method Summary

java.lang.String	getHeader() Gets the fasta header (with leading and trailing spaces trimmed)
int	getLength() The number of sequence characters
byte[]	getQuality() Returns the quality scores for this sequence.
java.lang.String	getSequence() Returns the entire sequence.
java.lang.String	getSequence(int start, int stop) Returns a portions of the sequence.
boolean	hasQuality()
boolean	hasSequence()
void	setHeader(java.lang.String s)
void	setQuality(byte[] q)
void	setSequence(java.lang.String s)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SimpleFastaSequence

public SimpleFastaSequence()

SimpleFastaSequence

public SimpleFastaSequence(java.lang.String header,
                           java.lang.String sequence)

Method Detail

setHeader

public void setHeader(java.lang.String s)

setSequence

public void setSequence(java.lang.String s)

getHeader

public java.lang.String getHeader()

Description copied from interface: FastaSequence

Gets the fasta header (with leading and trailing spaces trimmed)

Specified by:

getHeader in interface FastaSequence

hasSequence

public boolean hasSequence()

hasQuality

public boolean hasQuality()

getSequence

public java.lang.String getSequence()

Description copied from interface: FastaSequence

Returns the entire sequence.

Specified by:

getSequence in interface FastaSequence

getSequence

public java.lang.String getSequence(int start,
                                    int stop)

Description copied from interface: FastaSequence

Returns a portions of the sequence.

Specified by:

getSequence in interface FastaSequence

Parameters:

start - 1-based index of the first character to return. Can be from 1 to the length of the sequence.

stop - 1-based index of the last charater to return. Can be from 1 to the length of the sequence.

getLength

public int getLength()

Description copied from interface: FastaSequence

The number of sequence characters

Specified by:

getLength in interface FastaSequence

getQuality

public byte[] getQuality()

Description copied from interface: FastaSequence

Returns the quality scores for this sequence. May be null if no quality is present.

Specified by:

getQuality in interface FastaSequence

setQuality

public void setQuality(byte[] q)