Package org.biojava.bio.seq

Class SequenceTools

java.lang.Object

org.biojava.bio.seq.SequenceTools

public final class SequenceTools
extends Object

Methods for manipulating sequences.

Author:

Matthew Pocock

Method Summary

Modifier and Type	Method	Description
static void	addAllFeatures(Sequence seq, FeatureHolder fh)	Add features to a sequence that contain the same information as all those in a feature holder.
static Sequence	createDummy(String uri, String name)	Create a new Sequence that has no annotation, no features and a zero-length symbol list.
static Sequence	createDummy(Alphabet alpha, int length, Symbol sym, String uri, String name)	Create a new Sequence that contains a single symbol repeated over and over.
static Sequence	createSequence(SymbolList syms, String uri, String name, Annotation ann)
static GappedSequence	gappedView(Sequence seq)	Create a new gapped sequence for a sequence.
static Sequence	maskSequence(Sequence seq, RangeLocation loc)	Mask of a sequence.
static Sequence	reverseComplement(Sequence seq)	Reverse-complement a sequence, and flip all of its features.
static Sequence	subSequence(Sequence seq, int start, int end)	Extract a sub-sequence from a sequence.
static Sequence	subSequence(Sequence seq, int start, int end, String name)	Extract a sub-sequence from a sequence.
static Sequence	subSequence(Sequence seq, int start, int end, String name, StrandedFeature.Strand strand)	Extract a sub-sequence from a sequence.
static ViewSequence	view(Sequence seq)	Create a new sequence that has all of the data in the original, but allows new features and top-level annotations to be added independantly.
static ViewSequence	view(Sequence seq, String name)	Create a new sequence that has all of the data in the original, but allows new features and top-level annotations to be added independantly.
static ViewSequence	view(Sequence seq, FeatureRealizer fr)	Creates a new Sequence with the data of the old but with a different FeatureRealizer that will be applied to new Features.

Methods inherited from class java.lang.Object

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

Method Detail

createSequence

public static Sequence createSequence(SymbolList syms,
                                      String uri,
                                      String name,
                                      Annotation ann)

subSequence

public static Sequence subSequence(Sequence seq,
                                   int start,
                                   int end)
                            throws IndexOutOfBoundsException

Extract a sub-sequence from a sequence.

The sub-sequence will be indexed from 1 through to (end-start+1). An index of i in the sub-sequence corresponds to (i+start-1) in the original. All features from the original sequence will be projected down into this co-ordinate system. All features overlapping the edges will be given fuzzy locations.

Parameters:

seq - the sequence to sub-sequence

start - the first index to include in the sub-sequence

end - the last index to include in the sub-sequence

Returns:

a view Sequence for this region

Throws:

IndexOutOfBoundsException - if start or end are not in seq, or if end < start

subSequence

public static Sequence subSequence(Sequence seq,
                                   int start,
                                   int end,
                                   String name)
                            throws IndexOutOfBoundsException

Extract a sub-sequence from a sequence.

The sub-sequence will be indexed from 1 through to (end-start+1). An index of i in the sub-sequence corresponds to (i+start-1) in the original. All features from the original sequence will be projected down into this co-ordinate system. All features overlapping the edges will be given fuzzy locations.

Parameters:

seq - the sequence to sub-sequence

start - the first index to include in the sub-sequence

end - the last index to include in the sub-sequence

name - a new name to give to this sub-sequence

Returns:

a view Sequence for this region

Throws:

IndexOutOfBoundsException - if start or end are not in seq, or if end < start

subSequence

public static Sequence subSequence(Sequence seq,
                                   int start,
                                   int end,
                                   String name,
                                   StrandedFeature.Strand strand)
                            throws IndexOutOfBoundsException,
                                   IllegalAlphabetException

Extract a sub-sequence from a sequence.

The sub-sequence will be indexed from 1 through to (end-start+1). If the strand is NEGATIVE, all features will be flipped in the same manner as the reverseComplement method. If it is UNKNOWN or POSITIVE, then this is identical to the other subSequence methods.

Parameters:

seq - the sequence to sub-sequence

start - the first index to include in the sub-sequence

end - the last index to include in the sub-sequence

name - a new name to give to this sub-sequence

strand - a StrandedFeature.Strand indicating which strand the sub-sequence should be on

Returns:

a view Sequence for this region

Throws:

IndexOutOfBoundsException - if start or end are not in seq, or if end < start

IllegalAlphabetException

reverseComplement

public static Sequence reverseComplement(Sequence seq)
                                  throws IllegalAlphabetException

Reverse-complement a sequence, and flip all of its features.

Parameters:

seq - the Sequence to reverse-complement

Returns:

the flipped Sequence

Throws:

IllegalAlphabetException - if the symbols in the sequence can not be complemented

view

public static ViewSequence view(Sequence seq)

Create a new sequence that has all of the data in the original, but allows new features and top-level annotations to be added independantly. Use this as a scratch-space.

Parameters:

seq - the Sequence to view

Returns:

a new ViewSequence

view

public static ViewSequence view(Sequence seq,
                                String name)

Create a new sequence that has all of the data in the original, but allows new features and top-level annotations to be added independantly. Use this as a scratch-space.

Parameters:

seq - the Sequence to view

name - a new name for the sequence

Returns:

a new ViewSequence with the new name

view

public static ViewSequence view(Sequence seq,
                                FeatureRealizer fr)

Creates a new Sequence with the data of the old but with a different FeatureRealizer that will be applied to new Features.

Parameters:

seq - the Sequence to wrap

fr - the new FeatureRealizer

Returns:

the new ViewSequence

gappedView

public static GappedSequence gappedView(Sequence seq)

Create a new gapped sequence for a sequence.

The gapped sequence can be used to insert gaps. The features on the underlying sequence will be projected onto the view taking the gaps into account.

Parameters:

seq -

Returns:

a GappedSequence view of seq

maskSequence

public static Sequence maskSequence(Sequence seq,
                                    RangeLocation loc)
                             throws IndexOutOfBoundsException,
                                    IllegalArgumentException

Mask of a sequence.

This will return a view of a sequence where everything outside loc is dropped. This includes all symbols, which become gaps, and all features, which behave in a similar manner to those produced by subSequence().

Parameters:

seq - the Sequence to mask

loc - the region to retain

Returns:

a Sequence viewing just the retained portion of seq

Throws:

IndexOutOfBoundsException - if loc is not totaly within seq

IllegalArgumentException - fixme: not sure where this comes from

createDummy

public static Sequence createDummy(String uri,
                                   String name)

Create a new Sequence that has no annotation, no features and a zero-length symbol list. Instantiate this if an API requres a sequence, but you can't be bothered or are not able to provide full sequence information. It is sometimes usefull to create a dummy sequence and then wrap this in a view.

Parameters:

uri - the URI to give the dummy sequence

name - the name of the dummy sequence

Returns:

a dummy Sequence

createDummy

public static Sequence createDummy(Alphabet alpha,
                                   int length,
                                   Symbol sym,
                                   String uri,
                                   String name)
                            throws IllegalSymbolException

Create a new Sequence that contains a single symbol repeated over and over.

Parameters:

alpha - the Alphabet this sequence is over

length - the length of the sequence

sym - the symbol returned by every call to symbolAt

uri - the URI of the sequence

name - the name of the sequence

Returns:

a new sequence of the right length

Throws:

IllegalSymbolException - if sym is not in alpha

Since:

1.4

addAllFeatures

public static void addAllFeatures(Sequence seq,
                                  FeatureHolder fh)
                           throws ChangeVetoException,
                                  BioException

Add features to a sequence that contain the same information as all those in a feature holder.

Parameters:

seq - the Sequence to add features to

fh - the features to add

Throws:

ChangeVetoException - if the sequence could not be modified

BioException - if there was an error creating the features