javagene.seq
Class SeqBig

java.lang.Object
  javagene.seq.SeqBig

All Implemented Interfaces:

SeqI

public class SeqBig
extends java.lang.Object
implements SeqI

A SeqI implementation capable of handling large sequences that do not fit into memory. The sequence data is kept on disk and accessed as a memory-mapped file. The sequence file must be in Fasta format. Assumes all data lines (except last) are of equal length. (This is checked when the file is opened.)

Constructor Summary

SeqBig(java.lang.String filename)
Construct SeqBig object given Fasta filename.

Method Summary

Location	bounds() Get the bounding location of this sequence.
java.lang.String	description() Get the text description of the sequence.
java.lang.String	id() Get the (single-word) identifier of the sequence.
SeqBig	subseq(Location location) Create a new sequence containing only the portion specified by the location parameter.
SeqBig	subseq(Location location, java.lang.String id, java.lang.String description) Create a new sequence containing only the portion specified by the location parameter, with the specified id and description.
java.lang.String	toString() Get the IUPAC character string representation of this entire sequence.
java.lang.String	toString(Location location) Get the IUPAC character string representation of the subsequence specified by the location parameter.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

SeqBig

public SeqBig(java.lang.String filename)
       throws java.io.IOException

Construct SeqBig object given Fasta filename. This is usually done through the Fasta class.

Parameters:

filename - The path and name of the Fasta file.

Throws:

java.io.IOException - - Check the exception text for details.

Method Detail

bounds

public Location bounds()

Get the bounding location of this sequence. SeqBig objects always start at index 0. To use a coordinate system that starts at a non-zero genomic location, wrap the SeqBig object in a SeqStranded object.

Specified by:

bounds in interface SeqI

Returns:

The bounding location.

description

public java.lang.String description()

Description copied from interface: SeqI

Get the text description of the sequence. This is all the text on the description line of a Fasta file after the id.

Specified by:

description in interface SeqI

Returns:

The text description.

id

public java.lang.String id()

Description copied from interface: SeqI

Get the (single-word) identifier of the sequence. This is the first identifier in a Fasta file.

Specified by:

id in interface SeqI

Returns:

The single-word identifier.

subseq

public SeqBig subseq(Location location)

Create a new sequence containing only the portion specified by the location parameter. Shares the underlying data (does not make a copy).

Specified by:

subseq in interface SeqI

Parameters:

location - The portion of the sequence to get.

Returns:

The subsequence.

Throws:

java.lang.IndexOutOfBoundsException - The location parameter was not within the bounding location of the sequence.

subseq

public SeqBig subseq(Location location,
                     java.lang.String id,
                     java.lang.String description)

Create a new sequence containing only the portion specified by the location parameter, with the specified id and description. Shares the underlying data (does not make a copy).

Specified by:

subseq in interface SeqI

Parameters:

location - The portion of the sequence to get.

id - The new single-word id.

description - The new description line.

Returns:

The subsequence.

Throws:

java.lang.IndexOutOfBoundsException - The location parameter was not within the bounding location of the sequence.

toString

public java.lang.String toString()

Get the IUPAC character string representation of this entire sequence. Makes a copy of the underlying data.

Specified by:

toString in interface SeqI

Overrides:

toString in class java.lang.Object

Returns:

The text string.

toString

public java.lang.String toString(Location location)

Get the IUPAC character string representation of the subsequence specified by the location parameter. Makes a copy of the underlying data.

Specified by:

toString in interface SeqI

Parameters:

location - The portion of the sequence to get.

Returns:

The string.

Throws:

java.lang.IndexOutOfBoundsException - The location parameter was not within the bounding location of the sequence.