net.sf.jfasta

Interface FASTAElement

All Known Implementing Classes:

FASTAElementImpl

public interface FASTAElement

A FASTAElement represents one entry in a (multi) fasta file.

Example:

 >gi|40806168|ref|NM_014946.3| Homo sapiens spastin (SPAST), transcript variant 1, mRNA
 GGCCCGAGCCACCGACTGCAGGAGGAGAAGGGGTTGTGCTCCTGGCCGAGGAAGGAGAAAGGGGCGGGGC
 CGGC[...]
 

last reviewed: 2013-04-29

Version:

2010-11-04

Author:

Alexander Kerner

See Also:

FASTAFile

Method Summary

Methods

Modifier and Type	Method and Description
String	getHeader() Retrieves this FASTAElement's header string.
int	getLineLength() Retrieves this FASTAElement's default line length.
String	getSequence() Gets this FASTAElements sequence.
int	getSequenceLength() Retrieves this FASTAElement's sequence length.
void	setLineLength(int length) Sets this FASTAElement's default line length.

Method Detail

getHeader

String getHeader()

Retrieves this FASTAElement's header string. Meaning string starting right after HEADER_IDENT and continuing until first subsequent NEW_LINE_STRING

Returns:

this FASTAElement's header string

getLineLength

int getLineLength()

Retrieves this FASTAElement's default line length.

Returns:

this FASTAElement's default line length

getSequence

String getSequence()

Gets this FASTAElements sequence.

Returns:

String view of this FASTAElements sequence

getSequenceLength

int getSequenceLength()

Retrieves this FASTAElement's sequence length.

Returns:

this FASTAElement's sequence length

setLineLength

void setLineLength(int length)

Sets this FASTAElement's default line length. When invoking toString() or #toString(boolean) after length characters written to one line, a NEW_LINE_STRING will be appended.

Parameters:

length - the new default line length