org.biojavax.bio.seq

Class ThinRichSequence

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojavax.bio.SimpleBioEntry

org.biojavax.bio.seq.ThinRichSequence

All Implemented Interfaces:

Comparable, Annotatable, FeatureHolder, Sequence, SymbolList, Changeable, BioEntry, RichSequence, RankedCrossRefable, RichAnnotatable

Direct Known Subclasses:

SimpleRichSequence

public class ThinRichSequence
extends SimpleBioEntry
implements RichSequence

A simple implementation of RichSequence. It has no sequence data, and delegates to a RichSequenceHandler to do sequence handling.

Since:

1.5

Author:

Richard Holland

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojavax.bio.seq.RichSequence

RichSequence.IOTools, RichSequence.Terms, RichSequence.Tools

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

Annotatable.AnnotationForwarder

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

FeatureHolder.EmptyFeatureHolder

Field Summary

Fields inherited from interface org.biojavax.bio.seq.RichSequence

CIRCULAR, SYMLISTVERSION

Fields inherited from interface org.biojavax.bio.BioEntry

COMMENT, DESCRIPTION, DIVISION, IDENTIFIER, RANKEDCROSSREF, RANKEDDOCREF, RELATIONS, SEQVERSION, TAXON

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

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

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	ThinRichSequence()
	ThinRichSequence(Namespace ns, String name, String accession, int version, Alphabet alpha, Double seqversion) Creates a new instance of ThinRichSequence.

Method Summary

Modifier and Type	Method and Description
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 ft) 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<Feature>	features() Iterate over the features in no well defined order.
FeatureHolder	filter(FeatureFilter filter) Query this set of features using a supplied FeatureFilter.
FeatureHolder	filter(FeatureFilter fc, 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.
protected String	getAlphabetName()
boolean	getCircular() Is the sequence circular?
Set<Feature>	getFeatureSet() The features for this sequence.
SymbolList	getInternalSymbolList() A special function that returns the SymbolList that this RichSequence is based around.
FeatureFilter	getSchema() Return a schema-filter for this FeatureHolder.
protected int	getSequenceLength()
Double	getSeqVersion() The version of the associated symbol list.
String	getURN() A Uniform Resource Identifier (URI) which identifies the sequence represented by this object.
Iterator	iterator() An Iterator over all Symbols in this SymbolList.
int	length() The number of symbols in this SymbolList.
void	removeFeature(Feature f) Remove a feature from this FeatureHolder.
String	seqString() Stringify this symbol list.
protected void	setAlphabetName(String alphaname)
void	setCircular(boolean circular) Circularises the Sequence.
void	setFeatureSet(Set<Feature> features) Sets the features of this sequence.
protected void	setSequenceLength(int length)
void	setSeqVersion(Double seqVersion) Sets the version of the associated 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 index) Return the symbol at index, counting from 1.
List	toList() Returns a List of symbols.

Methods inherited from class org.biojavax.bio.SimpleBioEntry

addComment, addRankedCrossRef, addRankedDocRef, addRelationship, compareTo, equals, getAccession, getAnnotation, getComments, getDescription, getDivision, getId, getIdentifier, getName, getNamespace, getNoteSet, getRankedCrossRefs, getRankedDocRefs, getRelationships, getRichAnnotation, getTaxon, getVersion, hashCode, removeComment, removeRankedCrossRef, removeRankedDocRef, removeRelationship, setDescription, setDivision, setId, setIdentifier, setNoteSet, setRankedCrossRefs, setTaxon, toString

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biojavax.bio.BioEntry

addComment, addRankedDocRef, addRelationship, getAccession, getComments, getDescription, getDivision, getIdentifier, getName, getNamespace, getRankedDocRefs, getRelationships, getTaxon, getVersion, removeComment, removeRankedDocRef, removeRelationship, setDescription, setDivision, setIdentifier, setTaxon

Methods inherited from interface org.biojavax.RichAnnotatable

getNoteSet, getRichAnnotation, setNoteSet

Methods inherited from interface org.biojava.bio.Annotatable

getAnnotation

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface org.biojavax.RankedCrossRefable

addRankedCrossRef, getRankedCrossRefs, removeRankedCrossRef, setRankedCrossRefs

Methods inherited from interface java.lang.Comparable

compareTo

Methods inherited from interface org.biojava.bio.seq.Sequence

getName

Constructor Detail

ThinRichSequence

public ThinRichSequence(Namespace ns,
                        String name,
                        String accession,
                        int version,
                        Alphabet alpha,
                        Double seqversion)

Creates a new instance of ThinRichSequence. Note the use of Double for seqversion, which indicates that it is nullable.

Parameters:

ns - the namespace for this sequence.

name - the name of the sequence.

accession - the accession of the sequence.

version - the version of the sequence.

seqversion - the version of the symbols for the sequence.

ThinRichSequence

protected ThinRichSequence()

Method Detail

getSeqVersion

public Double getSeqVersion()

The version of the associated symbol list. Note the use of an object for the value means that it can be nulled.

Specified by:

getSeqVersion in interface RichSequence

Returns:

the version

setSeqVersion

public void setSeqVersion(Double seqVersion)
                   throws ChangeVetoException

Sets the version of the associated symbol list. Note the use of an object for the value means that it can be nulled.

Specified by:

setSeqVersion in interface RichSequence

Parameters:

seqVersion - the version to set.

Throws:

ChangeVetoException - if it doesn't want to change.

setCircular

public void setCircular(boolean circular)
                 throws ChangeVetoException

Circularises the Sequence. The circular length can then be said to be the length of the sequence itself.

Specified by:

setCircular in interface RichSequence

Parameters:

circular - set to true if you want it to be circular

Throws:

ChangeVetoException - if the change is blocked. Some implementations may choose not to support circularisation and should throw an exception here. Some implementations may only support this method for certain Alphabets.

getCircular

public boolean getCircular()

Is the sequence circular? Circularity has implications for work with locations and any coordinate work eg symbolAt(int i). Classes that allow it should test this method when working with coordinates or locations / features.

Specified by:

getCircular in interface RichSequence

Returns:

true if the this is circular else false.

edit

public void edit(Edit edit)
          throws IndexOutOfBoundsException,
                 IllegalAlphabetException,
                 ChangeVetoException

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:

IndexOutOfBoundsException - if the edit does not lie within the SymbolList

IllegalAlphabetException - if the SymbolList to insert has an incompatible alphabet

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

symbolAt

public Symbol symbolAt(int index)
                throws IndexOutOfBoundsException

Return the symbol at index, counting from 1.

Specified by:

symbolAt in interface SymbolList

Parameters:

index - the offset into this SymbolList

Returns:

the Symbol at that index

Throws:

IndexOutOfBoundsException - if index is less than 1, or greater than the length of the symbol list

toList

public List toList()

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

subStr

public String subStr(int start,
                     int end)
              throws IndexOutOfBoundsException

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

Throws:

IndexOutOfBoundsException - if either start or end are not within the SymbolList

subList

public SymbolList subList(int start,
                          int end)
                   throws IndexOutOfBoundsException

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

Throws:

IndexOutOfBoundsException

seqString

public String seqString()

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

length

public int length()

The number of symbols in this SymbolList.

Specified by:

length in interface SymbolList

Returns:

the length

iterator

public Iterator iterator()

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

getAlphabet

public Alphabet getAlphabet()

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

setAlphabetName

protected void setAlphabetName(String alphaname)
                        throws IllegalSymbolException,
                               BioException

Throws:

IllegalSymbolException

BioException

getAlphabetName

protected String getAlphabetName()

setSequenceLength

protected void setSequenceLength(int length)

getSequenceLength

protected int getSequenceLength()

getURN

public String getURN()

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

filter

public FeatureHolder filter(FeatureFilter fc,
                            boolean recurse)

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:

fc - 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.

createFeature

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

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

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

containsFeature

public boolean containsFeature(Feature f)

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

filter

public FeatureHolder filter(FeatureFilter filter)

Query this set of features using a supplied FeatureFilter.

Specified by:

filter in interface FeatureHolder

Parameters:

filter - the FeatureFilter to apply.

Returns:

all features in this container which match filter.

getFeatureSet

public Set<Feature> getFeatureSet()

The features for this sequence. Warning this method gives access to the original Collection not a copy. This is required by Hibernate. If you modify the object directly the behaviour may be unpredictable.

Specified by:

getFeatureSet in interface RichSequence

Returns:

a set of RichFeature objects.

setFeatureSet

public void setFeatureSet(Set<Feature> features)
                   throws ChangeVetoException

Sets the features of this sequence. Note that it is not checked to see if the features actually belong to this sequence, you'd best check that yourself and make changes using feature.setParent() if necessary. Warning this method gives access to the original Collection not a copy. This is required by Hibernate. If you modify the object directly the behaviour may be unpredictable.

Specified by:

setFeatureSet in interface RichSequence

Parameters:

features - the features to assign to this sequence, replacing all others. Must be a set of RichFeature objects.

Throws:

ChangeVetoException - if they could not be assigned.

getSchema

public FeatureFilter getSchema()

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

features

public Iterator<Feature> features()

Iterate over the features in no well defined order. Warning this method gives access to the original Collection not a copy. This is required by Hibernate. If you modify the object directly the behaviour may be unpredictable.

Specified by:

features in interface FeatureHolder

Returns:

an Iterator

countFeatures

public int countFeatures()

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

getInternalSymbolList

public SymbolList getInternalSymbolList()

A special function that returns the SymbolList that this RichSequence is based around. This should _not_ be the RichSequence object itself, as this function is used to perform actions on the symbol list without referring to the RichSequence object directly.

Specified by:

getInternalSymbolList in interface RichSequence

Returns:

the internal SymbolList of the RichSequence, NOT the RichSequence object itself.