org.biojava.bio.seq.impl
Class SubSequence

java.lang.Object
  org.biojava.bio.seq.impl.SubSequence

All Implemented Interfaces:

Serializable, Annotatable, FeatureHolder, Sequence, SymbolList, Changeable

public class SubSequence
extends Object
implements Sequence, Serializable

View a sub-section of a given sequence object, including all the features intersecting that region.

All features entirely contained within the region are projected by just translating their locations. The features that overlap the region are replaced by RemoteFeature instances with fuzzy locations that are trunchated to fit inside the sub-section. All features not contained by the region are not projected.

Since:

1.2

Author:

Thomas Down, Matthew Pocock

See Also:

Serialized Form

Nested Class Summary

static class

SubSequence.SubProjectedFeatureContext TargetContext that implements the mapping between the parent sequence and this sub-sequence.

Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder

FeatureHolder.EmptyFeatureHolder

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable

Annotatable.AnnotationForwarder

Field Summary

protected ChangeForwarder

annotationForwarder

Fields inherited from interface org.biojava.bio.symbol.SymbolList

EDIT, EMPTY_LIST

Fields inherited from interface org.biojava.bio.seq.FeatureHolder

EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Constructor Summary

SubSequence(Sequence seq, int start, int end)
Construct a new SubSequence of the specified sequence.

SubSequence(Sequence seq, int start, int end, String name)
Construct a new SubSequence of the specified sequence.

Method Summary

void	addChangeListener(ChangeListener cl) Add a listener that will be informed of all changes.
void	addChangeListener(ChangeListener cl, ChangeType ct) Add a listener that will be informed of changes of a given type.
boolean	containsFeature(Feature f) Check if the feature is present in this holder.
int	countFeatures() Count how many features are contained.
Feature	createFeature(Feature.Template templ) Create a new Feature, and add it to this FeatureHolder.
void	edit(Edit edit) Apply an edit to the SymbolList as specified by the edit object.
Iterator	features() Iterate over the features in no well defined order.
FeatureHolder	filter(FeatureFilter ff) Query this set of features using a supplied FeatureFilter.
FeatureHolder	filter(FeatureFilter ff, boolean recurse) Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
Alphabet	getAlphabet() The alphabet that this SymbolList is over.
Annotation	getAnnotation() Should return the associated annotation object.
int	getEnd()
protected ProjectedFeatureHolder	getFeatures()
String	getName() The name of this sequence.
FeatureFilter	getSchema() Return a schema-filter for this FeatureHolder.
Sequence	getSequence() Return the parent sequence of which this is a partial view
int	getStart()
String	getURN() A Uniform Resource Identifier (URI) which identifies the sequence represented by this object.
boolean	isUnchanging(ChangeType ct) A particular ChangeType can never be raised by this Changeable.
Iterator	iterator() An Iterator over all Symbols in this SymbolList.
int	length() The number of symbols in this SymbolList.
void	removeChangeListener(ChangeListener cl) Remove a listener that was interested in all types of changes.
void	removeChangeListener(ChangeListener cl, ChangeType ct) Remove a listener that was interested in a specific types of changes.
void	removeFeature(Feature f) Remove a feature from this FeatureHolder.
String	seqString() Stringify this symbol list.
SymbolList	subList(int start, int end) Return a new SymbolList for the symbols start to end inclusive.
String	subStr(int start, int end) Return a region of this symbol list as a String.
Symbol	symbolAt(int pos) Return the symbol at index, counting from 1.
List	toList() Returns a List of symbols.

Methods inherited from class java.lang.Object

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

Field Detail

annotationForwarder

protected transient ChangeForwarder annotationForwarder

Constructor Detail

SubSequence

public SubSequence(Sequence seq,
                   int start,
                   int end,
                   String name)

Construct a new SubSequence of the specified sequence. Generally you would use the SequenceTools.subSequence() methods to get an instance of this class.

Parameters:

seq - A sequence to view

start - The start of the range to view

end - The end of the range to view

name - Name for the subsequence

Throws:

IndexOutOfBoundsException - is the start or end position is illegal.

SubSequence

public SubSequence(Sequence seq,
                   int start,
                   int end)

Construct a new SubSequence of the specified sequence. Generally you would use the SequenceTools.subSequence() methods to get an instance of this class.

Parameters:

seq - A sequence to view

start - The start of the range to view

end - The end of the range to view

Throws:

IndexOutOfBoundsException - if the start or end position is illegal.

Method Detail

symbolAt

public Symbol symbolAt(int pos)

Description copied from interface: SymbolList

Return the symbol at index, counting from 1.

Specified by:

symbolAt in interface SymbolList

Parameters:

pos - the offset into this SymbolList

Returns:

the Symbol at that index

getAlphabet

public Alphabet getAlphabet()

Description copied from interface: SymbolList

The alphabet that this SymbolList is over.

Every symbol within this SymbolList is a member of this alphabet. alphabet.contains(symbol) == true for each symbol that is within this sequence.

Specified by:

getAlphabet in interface SymbolList

Returns:

the alphabet

subList

public SymbolList subList(int start,
                          int end)

Description copied from interface: SymbolList

Return a new SymbolList for the symbols start to end inclusive.

The resulting SymbolList will count from 1 to (end-start + 1) inclusive, and refer to the symbols start to end of the original sequence.

Specified by:

subList in interface SymbolList

Parameters:

start - the first symbol of the new SymbolList

end - the last symbol (inclusive) of the new SymbolList

seqString

public String seqString()

Description copied from interface: SymbolList

Stringify this symbol list.

It is expected that this will use the symbol's token to render each symbol. It should be parsable back into a SymbolList using the default token parser for this alphabet.

Specified by:

seqString in interface SymbolList

Returns:

a string representation of the symbol list

subStr

public String subStr(int start,
                     int end)

Description copied from interface: SymbolList

Return a region of this symbol list as a String.

This should use the same rules as seqString.

Specified by:

subStr in interface SymbolList

Parameters:

start - the first symbol to include

end - the last symbol to include

Returns:

the string representation

toList

public List toList()

Description copied from interface: SymbolList

Returns a List of symbols.

This is an immutable list of symbols. Do not edit it.

Specified by:

toList in interface SymbolList

Returns:

a List of Symbols

length

public int length()

Description copied from interface: SymbolList

The number of symbols in this SymbolList.

Specified by:

length in interface SymbolList

Returns:

the length

iterator

public Iterator iterator()

Description copied from interface: SymbolList

An Iterator over all Symbols in this SymbolList.

This is an ordered iterator over the Symbols. It cannot be used to edit the underlying symbols.

Specified by:

iterator in interface SymbolList

Returns:

an iterator

edit

public void edit(Edit edit)
          throws ChangeVetoException

Description copied from interface: SymbolList

Apply an edit to the SymbolList as specified by the edit object.

Description

All edits can be broken down into a series of operations that change contiguous blocks of the sequence. This represent a one of those operations.

When applied, this Edit will replace 'length' number of symbols starting a position 'pos' by the SymbolList 'replacement'. This allow to do insertions (length=0), deletions (replacement=SymbolList.EMPTY_LIST) and replacements (length>=1 and replacement.length()>=1).

The pos and pos+length should always be valid positions on the SymbolList to:

• be edited (between 0 and symL.length()+1).
• To append to a sequence, pos=symL.length()+1, pos=0.
• To insert something at the beginning of the sequence, set pos=1 and length=0.

Examples

 SymbolList seq = DNATools.createDNA("atcaaaaacgctagc");
 System.out.println(seq.seqString());

 // delete 5 bases from position 4
 Edit ed = new Edit(4, 5, SymbolList.EMPTY_LIST);
 seq.edit(ed);
 System.out.println(seq.seqString());

 // delete one base from the start
 ed = new Edit(1, 1, SymbolList.EMPTY_LIST);
 seq.edit(ed);

 // delete one base from the end
 ed = new Edit(seq.length(), 1, SymbolList.EMPTY_LIST);
 seq.edit(ed);
 System.out.println(seq.seqString());

 // overwrite 2 bases from position 3 with "tt"
 ed = new Edit(3, 2, DNATools.createDNA("tt"));
 seq.edit(ed);
 System.out.println(seq.seqString());

 // add 6 bases to the start
 ed = new Edit(1, 0, DNATools.createDNA("aattgg");
 seq.edit(ed);
 System.out.println(seq.seqString());

 // add 4 bases to the end
 ed = new Edit(seq.length() + 1, 0, DNATools.createDNA("tttt"));
 seq.edit(ed);
 System.out.println(seq.seqString());

 // full edit
 ed = new Edit(3, 2, DNATools.createDNA("aatagaa");
 seq.edit(ed);
 System.out.println(seq.seqString());
 

Specified by:

edit in interface SymbolList

Parameters:

edit - the Edit to perform

Throws:

ChangeVetoException - if either the SymboList does not support the edit, or if the change was vetoed

countFeatures

public int countFeatures()

Description copied from interface: FeatureHolder

Count how many features are contained.

Specified by:

countFeatures in interface FeatureHolder

Returns:

a positive integer or zero, equal to the number of features contained

features

public Iterator features()

Description copied from interface: FeatureHolder

Iterate over the features in no well defined order.

Specified by:

features in interface FeatureHolder

Returns:

an Iterator

filter

public FeatureHolder filter(FeatureFilter ff,
                            boolean recurse)

Description copied from interface: FeatureHolder

Return a new FeatureHolder that contains all of the children of this one that passed the filter fc. This method is scheduled for deprecation. Use the 1-arg filter instead.

Specified by:

filter in interface FeatureHolder

Parameters:

ff - the FeatureFilter to apply

recurse - true if all features-of-features should be scanned, and a single flat collection of features returned, or false if just immediate children should be filtered.

filter

public FeatureHolder filter(FeatureFilter ff)

Description copied from interface: FeatureHolder

Query this set of features using a supplied FeatureFilter.

Specified by:

filter in interface FeatureHolder

Parameters:

ff - the FeatureFilter to apply.

Returns:

all features in this container which match filter.

containsFeature

public boolean containsFeature(Feature f)

Description copied from interface: FeatureHolder

Check if the feature is present in this holder.

Specified by:

containsFeature in interface FeatureHolder

Parameters:

f - the Feature to check

Returns:

true if f is in this set

createFeature

public Feature createFeature(Feature.Template templ)
                      throws BioException,
                             ChangeVetoException

Description copied from interface: FeatureHolder

Create a new Feature, and add it to this FeatureHolder. This method will generally only work on Sequences, and on some Features which have been attached to Sequences.

Specified by:

createFeature in interface FeatureHolder

Throws:

BioException - if something went wrong during creating the feature

ChangeVetoException - if this FeatureHolder does not support creation of new features, or if the change was vetoed

removeFeature

public void removeFeature(Feature f)
                   throws ChangeVetoException,
                          BioException

Description copied from interface: FeatureHolder

Remove a feature from this FeatureHolder.

Specified by:

removeFeature in interface FeatureHolder

Throws:

ChangeVetoException - if this FeatureHolder does not support feature removal or if the change was vetoed

BioException - if there was an error removing the feature

getSchema

public FeatureFilter getSchema()

Description copied from interface: FeatureHolder

Return a schema-filter for this FeatureHolder. This is a filter which all Features immediately contained by this FeatureHolder will match. It need not directly match their child features, but it can (and should!) provide information about them using FeatureFilter.OnlyChildren filters. In cases where there is no feature hierarchy, this can be indicated by including FeatureFilter.leaf in the schema filter.

For the truly non-informative case, it is possible to return FeatureFilter.all. However, it is almost always possible to provide slightly more information that this. For example, Sequence objects should, at a minimum, return FeatureFilter.top_level. Feature objects should, as a minimum, return FeatureFilter.ByParent(new FeatureFilter.ByFeature(this)).

Specified by:

getSchema in interface FeatureHolder

Returns:

the schema filter

getFeatures

protected ProjectedFeatureHolder getFeatures()

getName

public String getName()

Description copied from interface: Sequence

The name of this sequence.

The name may contain spaces or odd characters.

Specified by:

getName in interface Sequence

Returns:

the name as a String

getURN

public String getURN()

Description copied from interface: Sequence

A Uniform Resource Identifier (URI) which identifies the sequence represented by this object. For sequences in well-known database, this may be a URN, e.g.

 urn:sequence/embl:AL121903
 

It may also be a URL identifying a specific resource, either locally or over the network

 file:///home/thomas/myseq.fa|seq22
 http://www.mysequences.net/chr22.seq
 

Specified by:

getURN in interface Sequence

Returns:

the URI as a String

getAnnotation

public Annotation getAnnotation()

Description copied from interface: Annotatable

Should return the associated annotation object.

Specified by:

getAnnotation in interface Annotatable

Returns:

an Annotation object, never null

getSequence

public Sequence getSequence()

Return the parent sequence of which this is a partial view

Since:

1.3

getStart

public int getStart()

getEnd

public int getEnd()

addChangeListener

public void addChangeListener(ChangeListener cl,
                              ChangeType ct)

Description copied from interface: Changeable

Add a listener that will be informed of changes of a given type.

Specified by:

addChangeListener in interface Changeable

Parameters:

cl - the ChangeListener

ct - the ChangeType it is to be informed of

addChangeListener

public void addChangeListener(ChangeListener cl)

Description copied from interface: Changeable

Add a listener that will be informed of all changes.

Specified by:

addChangeListener in interface Changeable

Parameters:

cl - the ChangeListener to add

removeChangeListener

public void removeChangeListener(ChangeListener cl,
                                 ChangeType ct)

Description copied from interface: Changeable

Remove a listener that was interested in a specific types of changes.

Specified by:

removeChangeListener in interface Changeable

Parameters:

cl - a ChangeListener to remove

ct - the ChangeType that it was interested in

removeChangeListener

public void removeChangeListener(ChangeListener cl)

Description copied from interface: Changeable

Remove a listener that was interested in all types of changes.

Specified by:

removeChangeListener in interface Changeable

Parameters:

cl - a ChangeListener to remove

isUnchanging

public boolean isUnchanging(ChangeType ct)

Description copied from interface: Changeable

A particular ChangeType can never be raised by this Changeable.

If this returns true, then it is guaranteed that change events of this type (and all child types) can never under any circumstances be fired by this Changeable instance. If it returns false, that does not mean that this type of event will or even can be raised, but that it is worth registering listeners incase.

Specified by:

isUnchanging in interface Changeable

Parameters:

ct - the ChangeType to check

Returns:

true if ChangeEvents of this type are guaranteed to never be fired