org.biojava.nbio.core.sequence.template

Class AbstractSequence<C extends Compound>

java.lang.Object

org.biojava.nbio.core.sequence.template.AbstractSequence<C>

Type Parameters:

C -

All Implemented Interfaces:

Iterable<C>, Accessioned, Sequence<C>

Direct Known Subclasses:

BasicSequence, DNASequence, ProteinSequence, RNASequence

public abstract class AbstractSequence<C extends Compound>
extends Object
implements Sequence<C>

The base class for DNA, RNA and Protein sequences.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	AbstractSequence.AnnotationType

Constructor Summary

Constructors

Constructor and Description
AbstractSequence()
AbstractSequence(SequenceReader<C> proxyLoader, CompoundSet<C> compoundSet) A ProxySequenceReader allows abstraction of both the storage of the sequence data and the location of the sequence data.
AbstractSequence(String seqString, CompoundSet<C> compoundSet) Create a Sequence from a simple string where the values should be found in compoundSet

Method Summary

Modifier and Type	Method and Description
void	addFeature(FeatureInterface<AbstractSequence<C>,C> feature) Add a feature to this sequence.
void	addFeature(int bioStart, int bioEnd, FeatureInterface<AbstractSequence<C>,C> feature) Method to help set the proper details for a feature as it relates to a sequence where the feature needs to have a location on the sequence
void	addNote(String note) Add notes about this sequence that will get exported for GFF3
int	countCompounds(C... compounds) Returns the number of times we found a compound in the Sequence
AccessionID	getAccession() Returns the AccessionID this location is currently bound with
AbstractSequence.AnnotationType	getAnnotationType()
List<C>	getAsList() Returns the Sequence as a List of compounds
Integer	getBioBegin()
Integer	getBioEnd()
C	getCompoundAt(int position) Returns the Compound at the given biological index
CompoundSet<C>	getCompoundSet() Gets the compound set used to back this Sequence
DatabaseReferenceInterface	getDatabaseReferences()
String	getDescription()
FeatureRetriever	getFeatureRetriever()
List<FeatureInterface<AbstractSequence<C>,C>>	getFeatures()
List<FeatureInterface<AbstractSequence<C>,C>>	getFeatures(int bioSequencePosition) Return features at a sequence position
List<FeatureInterface<AbstractSequence<C>,C>>	getFeatures(String featureType, int bioSequencePosition) Return features at a sequence position by type
List<FeatureInterface<AbstractSequence<C>,C>>	getFeaturesByType(String type)
FeaturesKeyWordInterface	getFeaturesKeyWord()
int	getIndexOf(C compound) Scans through the Sequence looking for the first occurrence of the given compound
SequenceView<C>	getInverse() Does the right thing to get the inverse of the current Sequence.
int	getLastIndexOf(C compound) Scans through the Sequence looking for the last occurrence of the given compound
int	getLength() Returns the length of the Sequence
ArrayList<String>	getNotesList()
String	getOriginalHeader()
AbstractSequence<?>	getParentSequence()
SequenceReader<C>	getProxySequenceReader()
String	getSequenceAsString() Default case is to assume strand is positive because only CDSSequence can be either positive or negative Strand.
String	getSequenceAsString(Integer bioStart, Integer bioEnd, Strand strand)
Double	getSequenceScore() Provide place holder for a metric that indicate a score associated with the sequence
String	getSource() Added support for the source of this sequence for GFF3 export If a sub sequence doesn't have source then check for parent source
SequenceView<C>	getSubSequence(Integer bioStart, Integer bioEnd) Returns a portion of the sequence from the different positions.
TaxonomyID	getTaxonomy()
Collection<Object>	getUserCollection() Provided for convince if the developer needs to associate data with a sequence
Iterator<C>	iterator()
void	removeFeature(FeatureInterface<AbstractSequence<C>,C> feature) Remove a feature from the sequence
void	removeNote(String note)
void	setAccession(AccessionID accession)
void	setAnnotationType(AbstractSequence.AnnotationType annotationType)
void	setBioBegin(Integer begin)
void	setBioEnd(Integer end)
void	setCompoundSet(CompoundSet<C> compoundSet)
void	setDatabaseReferences(DatabaseReferenceInterface databaseReferences)
void	setDescription(String description)
void	setFeatureRetriever(FeatureRetriever featureRetriever)
void	setFeaturesKeyWord(FeaturesKeyWordInterface featuresKeyWord)
void	setNotesList(ArrayList<String> notesList)
void	setOriginalHeader(String originalHeader)
void	setParentSequence(AbstractSequence<?> parentSequence)
void	setProxySequenceReader(SequenceReader<C> proxyLoader) Very important method that allows external mappings of sequence data and features.
void	setSequenceScore(Double sequenceScore)
void	setSource(String source) Added support for the source of this sequence for GFF3 export
void	setTaxonomy(TaxonomyID taxonomy)
void	setUserCollection(Collection<Object> userCollection)
String	toString()

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

AbstractSequence

public AbstractSequence()

AbstractSequence

public AbstractSequence(String seqString,
                        CompoundSet<C> compoundSet)
                 throws CompoundNotFoundException

Create a Sequence from a simple string where the values should be found in compoundSet

Parameters:

seqString -

compoundSet -

Throws:

CompoundNotFoundException

AbstractSequence

public AbstractSequence(SequenceReader<C> proxyLoader,
                        CompoundSet<C> compoundSet)

A ProxySequenceReader allows abstraction of both the storage of the sequence data and the location of the sequence data. A variety of use cases are possible. A ProxySequenceReader that knows the offset and of the sequence in a large fasta file. A ProxySequenceReader that can pull Sequence data from UniProt, NCBI or a custom database. If the ProxySequenceReader implements various interfaces then the sequence will set those interfaces so that calls to various methods will be valid.

Parameters:

proxyLoader -

compoundSet -

Method Detail

setProxySequenceReader

public void setProxySequenceReader(SequenceReader<C> proxyLoader)

Very important method that allows external mappings of sequence data and features. This method will gain additional interface inspection that allows external data sources with knowledge of features for a sequence to be supported.

Parameters:

proxyLoader -

getProxySequenceReader

public SequenceReader<C> getProxySequenceReader()

getBioBegin

public Integer getBioBegin()

Returns:

the bioBegin

setBioBegin

public void setBioBegin(Integer begin)

Parameters:

bioBegin - the bioBegin to set

getBioEnd

public Integer getBioEnd()

Returns:

the bioEnd

setBioEnd

public void setBioEnd(Integer end)

Parameters:

bioEnd - the bioEnd to set

getUserCollection

public Collection<Object> getUserCollection()

Provided for convince if the developer needs to associate data with a sequence

Returns:

setUserCollection

public void setUserCollection(Collection<Object> userCollection)

Parameters:

userCollection -

getAnnotationType

public AbstractSequence.AnnotationType getAnnotationType()

Returns:

the annotation

setAnnotationType

public void setAnnotationType(AbstractSequence.AnnotationType annotationType)

Parameters:

annotation - the annotation to set

getDescription

public String getDescription()

Returns:

the description

setDescription

public void setDescription(String description)

Parameters:

description - the description to set

getOriginalHeader

public String getOriginalHeader()

Returns:

the originalHeader

setOriginalHeader

public void setOriginalHeader(String originalHeader)

Parameters:

originalHeader - the originalHeader to set

getParentSequence

public AbstractSequence<?> getParentSequence()

Returns:

the parentSequence

setParentSequence

public void setParentSequence(AbstractSequence<?> parentSequence)

Parameters:

parentSequence - the parentSequence to set

getSource

public String getSource()

Added support for the source of this sequence for GFF3 export If a sub sequence doesn't have source then check for parent source

Returns:

the source

setSource

public void setSource(String source)

Added support for the source of this sequence for GFF3 export

Parameters:

source - the source to set

addNote

public void addNote(String note)

Add notes about this sequence that will get exported for GFF3

Parameters:

note -

removeNote

public void removeNote(String note)

getNotesList

public ArrayList<String> getNotesList()

Returns:

the notesList

setNotesList

public void setNotesList(ArrayList<String> notesList)

Parameters:

notesList - the notesList to set

getSequenceScore

public Double getSequenceScore()

Provide place holder for a metric that indicate a score associated with the sequence

Returns:

the sequenceScore

setSequenceScore

public void setSequenceScore(Double sequenceScore)

Parameters:

sequenceScore - the sequenceScore to set

getFeatures

public List<FeatureInterface<AbstractSequence<C>,C>> getFeatures(String featureType,
                                                                 int bioSequencePosition)

Return features at a sequence position by type

Parameters:

featureType -

bioSequencePosition -

Returns:

getFeatures

public List<FeatureInterface<AbstractSequence<C>,C>> getFeatures(int bioSequencePosition)

Return features at a sequence position

Parameters:

featureType -

bioSequencePosition -

Returns:

getFeatures

public List<FeatureInterface<AbstractSequence<C>,C>> getFeatures()

Returns:

addFeature

public void addFeature(int bioStart,
                       int bioEnd,
                       FeatureInterface<AbstractSequence<C>,C> feature)

Method to help set the proper details for a feature as it relates to a sequence where the feature needs to have a location on the sequence

Parameters:

bioStart -

bioEnd -

feature -

addFeature

public void addFeature(FeatureInterface<AbstractSequence<C>,C> feature)

Add a feature to this sequence. The feature will be added to the collection where the order is start position and if more than one feature at the same start position then longest is added first. This helps on doing feature layout for displaying features in SequenceFeaturePanel

Parameters:

feature -

removeFeature

public void removeFeature(FeatureInterface<AbstractSequence<C>,C> feature)

Remove a feature from the sequence

Parameters:

feature -

getFeaturesByType

public List<FeatureInterface<AbstractSequence<C>,C>> getFeaturesByType(String type)

Parameters:

type -

Returns:

getFeaturesKeyWord

public FeaturesKeyWordInterface getFeaturesKeyWord()

Returns:

the featuresKeyWord

setFeaturesKeyWord

public void setFeaturesKeyWord(FeaturesKeyWordInterface featuresKeyWord)

Parameters:

featuresKeyWord - the featuresKeyWord to set

getDatabaseReferences

public DatabaseReferenceInterface getDatabaseReferences()

Returns:

the databaseReferences

setDatabaseReferences

public void setDatabaseReferences(DatabaseReferenceInterface databaseReferences)

Parameters:

databaseReferences - the databaseReferences to set

getFeatureRetriever

public FeatureRetriever getFeatureRetriever()

setFeatureRetriever

public void setFeatureRetriever(FeatureRetriever featureRetriever)

getAccession

public AccessionID getAccession()

Description copied from interface: Accessioned

Returns the AccessionID this location is currently bound with

Specified by:

getAccession in interface Accessioned

Returns:

the accession

setAccession

public void setAccession(AccessionID accession)

Parameters:

accession - the accession to set

getTaxonomy

public TaxonomyID getTaxonomy()

Returns:

the species

setTaxonomy

public void setTaxonomy(TaxonomyID taxonomy)

Parameters:

species - the species to set

getCompoundSet

public CompoundSet<C> getCompoundSet()

Description copied from interface: Sequence

Gets the compound set used to back this Sequence

Specified by:

getCompoundSet in interface Sequence<C extends Compound>

setCompoundSet

public void setCompoundSet(CompoundSet<C> compoundSet)

toString

public String toString()

Overrides:

toString in class Object

getSequenceAsString

public String getSequenceAsString(Integer bioStart,
                                  Integer bioEnd,
                                  Strand strand)

Parameters:

begin -

end -

strand -

Returns:

getSequenceAsString

public String getSequenceAsString()

Default case is to assume strand is positive because only CDSSequence can be either positive or negative Strand.

Specified by:

getSequenceAsString in interface Sequence<C extends Compound>

Returns:

getAsList

public List<C> getAsList()

Description copied from interface: Sequence

Returns the Sequence as a List of compounds

Specified by:

getAsList in interface Sequence<C extends Compound>

Returns:

getCompoundAt

public C getCompoundAt(int position)

Description copied from interface: Sequence

Returns the Compound at the given biological index

Specified by:

getCompoundAt in interface Sequence<C extends Compound>

Parameters:

position - The 1-indexed position of the amino acid

Returns:

getIndexOf

public int getIndexOf(C compound)

Description copied from interface: Sequence

Scans through the Sequence looking for the first occurrence of the given compound

Specified by:

getIndexOf in interface Sequence<C extends Compound>

Parameters:

compound -

Returns:

The first index of compound in this sequence (1-based)

getLastIndexOf

public int getLastIndexOf(C compound)

Description copied from interface: Sequence

Scans through the Sequence looking for the last occurrence of the given compound

Specified by:

getLastIndexOf in interface Sequence<C extends Compound>

Parameters:

compound -

Returns:

The last index of compound in this sequence (1-based)

getLength

public int getLength()

Description copied from interface: Sequence

Returns the length of the Sequence

Specified by:

getLength in interface Sequence<C extends Compound>

Returns:

getSubSequence

public SequenceView<C> getSubSequence(Integer bioStart,
                                      Integer bioEnd)

Description copied from interface: Sequence

Returns a portion of the sequence from the different positions. This is indexed from 1

Specified by:

getSubSequence in interface Sequence<C extends Compound>

Parameters:

bioStart -

bioEnd -

Returns:

iterator

public Iterator<C> iterator()

Specified by:

iterator in interface Iterable<C extends Compound>

Returns:

countCompounds

public int countCompounds(C... compounds)

Description copied from interface: Sequence

Returns the number of times we found a compound in the Sequence

Specified by:

countCompounds in interface Sequence<C extends Compound>

Parameters:

compounds -

Returns:

getInverse

public SequenceView<C> getInverse()

Description copied from interface: Sequence

Does the right thing to get the inverse of the current Sequence. This means either reversing the Sequence and optionally complementing the Sequence.

Specified by:

getInverse in interface Sequence<C extends Compound>

Returns: