Package org.biojavax.bio.seq

Class RichSequence.Tools

java.lang.Object

org.biojavax.bio.seq.RichSequence.Tools

Enclosing interface:

RichSequence

public static class RichSequence.Tools
extends Object

Some useful tools for working with RichSequence objects.

Since:

1.5

Method Summary

Modifier and Type	Method	Description
static RichSequence	createRichSequence(String namespace, String name, String seqString, Alphabet alpha)	Create a new RichSequence in the specified namespace.
static RichSequence	createRichSequence(String name, String seqString, Alphabet alpha)	Create a new RichSequence in the default namespace.
static RichSequence	createRichSequence(String name, SymbolList syms)	Create a new RichSequence in the default namespace.
static RichSequence	createRichSequence(Namespace ns, String name, String seqString, Alphabet alpha)	Create a new RichSequence in the specified namespace.
static RichSequence	createRichSequence(Namespace ns, String name, SymbolList syms)	Create a new RichSequence in the specified namespace.
static RichSequence	enrich(Sequence s)	Boldly attempts to convert a Sequence into a RichSequence.
static RichSequence	subSequence(RichSequence s, int from, int to, Namespace newNamespace, String newName, String newAccession, String newIdentifier, int newVersion, Double seqVersion)	Creates a new sequence from a subregion of another sequence.

Methods inherited from class java.lang.Object

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

Method Detail

createRichSequence

public static RichSequence createRichSequence(String name,
                                              String seqString,
                                              Alphabet alpha)
                                       throws BioException

Create a new RichSequence in the default namespace.

Parameters:

name - The name for the sequence. Will also be used for the accession.

seqString - The sequence string

alpha - The Alphabet for the sequence

Returns:

A new RichSequence. All versions are 1 or 1.0

Throws:

BioException - If the symbols in seqString are not valid in alpha

createRichSequence

public static RichSequence createRichSequence(String namespace,
                                              String name,
                                              String seqString,
                                              Alphabet alpha)
                                       throws BioException

Create a new RichSequence in the specified namespace.

Parameters:

namespace - the namespace to create the sequence in. A singleton Namespace will be created or retrieved as appropriate.

name - The name for the sequence. Will also be used for the accession.

seqString - The sequence string

alpha - The Alphabet for the sequence

Returns:

A new RichSequence. All versions are 1 or 1.0

Throws:

BioException - If the symbols in seqString are not valid in alpha

createRichSequence

public static RichSequence createRichSequence(Namespace ns,
                                              String name,
                                              String seqString,
                                              Alphabet alpha)
                                       throws BioException

Create a new RichSequence in the specified namespace.

Parameters:

ns - The namespace to create the sequence in.

name - The name for the sequence. Will also be used for the accession.

seqString - The sequence string

alpha - The Alphabet for the sequence

Returns:

A new RichSequence. All versions are 1 or 1.0

Throws:

BioException - If the symbols in seqString are not valid in alpha

createRichSequence

public static RichSequence createRichSequence(String name,
                                              SymbolList syms)

Create a new RichSequence in the default namespace.

Parameters:

syms - The symbols to add to the sequence.

name - The name for the sequence. Will also be used for the accession.

Returns:

A new RichSequence. All versions are 1 or 1.0

createRichSequence

public static RichSequence createRichSequence(Namespace ns,
                                              String name,
                                              SymbolList syms)

Create a new RichSequence in the specified namespace.

Parameters:

ns - the namespace to create the sequence in.

syms - The symbols to add to the sequence.

name - The name for the sequence. Will also be used for the accession.

Returns:

A new RichSequence. All versions are 1 or 1.0

enrich

public static RichSequence enrich(Sequence s)
                           throws ChangeVetoException

Boldly attempts to convert a Sequence into a RichSequence. Sequences will be assigned to the default namespace. The accession will be assumed to be the name of the old sequence. The version of the sequence will be set to 0 and the seqversion set to 0.0. Features are converted to RichFeatures. The old Annotation bundle is converted to a RichAnnotation

Parameters:

s - The Sequence to enrich

Returns:

a new RichSequence

Throws:

ChangeVetoException - if s is locked or the conversion fails.

subSequence

public static RichSequence subSequence(RichSequence s,
                                       int from,
                                       int to,
                                       Namespace newNamespace,
                                       String newName,
                                       String newAccession,
                                       String newIdentifier,
                                       int newVersion,
                                       Double seqVersion)
                                throws IndexOutOfBoundsException

Creates a new sequence from a subregion of another sequence. The sequence is not a view. The sequence can be given a new Namespace, Accession, Name, Identifier etc. or you can copy over the old values. For unique identification in databases we recommend you change at least the name and identifier.

The new sequence will retain all features that are fully contained by the new subsequence, the note set (annotation), Taxon, and description, modified to reflect the subsequence as follows:

 seq.setDescription("subsequence (" + from + ":" + to + ") of "
                + s.getDescription());
 

No other properties are copied.

Parameters:

newVersion - the new version number

seqVersion - the new sequence version

s - the original RichSequence.

from - the 1st subsequence coordinate (inclusive)

to - the last subsequence coordinate (inclusive)

newNamespace - the new Namespace

newName - the new name

newAccession - the new accession number

newIdentifier - the new identifier

Returns:

A new RichSequence

Throws:

IndexOutOfBoundsException - if from or to lie outside of the bounds of s.