uk.ac.roslin.ensembl.datasourceaware.core

Class DADNASequence

java.lang.Object

org.biojava3.core.sequence.template.AbstractSequence<NucleotideCompound>

org.biojava3.core.sequence.DNASequence

uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

All Implemented Interfaces:

Serializable, Iterable<NucleotideCompound>, Accessioned, Sequence<NucleotideCompound>, CoreObject, DNASequence, IdentifiableObject, MappableObject

Direct Known Subclasses:

DAAssembledDNASequence, GapSequence

public class DADNASequence
extends DNASequence
implements CoreObject, DNASequence

Author:

paterson

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class org.biojava3.core.sequence.DNASequence

DNASequence.DNAType

Nested classes/interfaces inherited from class org.biojava3.core.sequence.template.AbstractSequence

AbstractSequence.AnnotationType

Field Summary

Fields

Modifier and Type	Field and Description
protected Integer	codonTableID
protected HashMap<EnsemblComparaDivision,DAOComparaFactory>	comparaFactories
protected CoordinateSystem	coordSystem
protected Integer	csID
protected DAOFactory	daoFactory
protected Integer	DBSeqLength
protected String	dbSpeciesName
protected String	dbVersion
protected Integer	id
protected boolean	lazyLoaded
protected HashMap<ObjectType,CoordinateSet>	mappedRegions
protected MappingSet	mappings
protected String	name
protected HashMap<ObjectType,MappingSet>	objectTypeMappings
protected Registry	registry
protected String	schemaVersion
protected Integer	seqRegionID
protected Species	species

Constructor Summary

Constructors

Constructor and Description
DADNASequence()
DADNASequence(DAEnsemblDNASequenceReader proxyLoader)
DADNASequence(DAOCoreFactory factory)
DADNASequence(String sequence)

Method Summary

Methods

Modifier and Type	Method and Description
void	addAttribute(String key, String value)
Boolean	addMapping(Mapping mapping)
void	clearAllMappings()
String	getAssembly()
String	getAttribute(String key)
HashMap<String,String>	getAttributes()
Integer	getBioEnd()
Integer	getCodonTableID()
EnsemblComparaDivision	getComparaDivision() Note the special case for Bacteria in collections in DB >16
DAOComparaFactory	getComparaFactory()
DAOComparaFactory	getComparaFactory(EnsemblComparaDivision comparaDivision)
CoordinateSystem	getCoordSystem()
Integer	getCsID()
DAOCoreFactory	getDaoFactory()
String	getDBName()
Integer	getDBSeqLength()
String	getDBVersion()
List<DAGene>	getGenesOnRegion(Coordinate coord) Returns a List of Genes on the specified Coordinate region.
List<DAGene>	getGenesOnRegion(Integer start, Integer stop) Returns a List of Genes on the specified Region.
List<DAGene>	getGenesOnRegion(Integer start, Integer stop, Coordinate.Strand strand) Returns a List of Genes on the specified Region.
String	getHashID()
Integer	getId()
int	getLength()
MappingSet	getLoadedMappings()
MappingSet	getLoadedMappings(ObjectType targetType)
HashMap<ObjectType,CoordinateSet>	getMappedRegions()
String	getName()
HashMap<ObjectType,MappingSet>	getObjectTypeMappings()
String	getPaddedReverseComplementSequenceAsString(Integer begin, Integer end) Method to get a string representation of the reverse complement of the sequence for the given range.
String	getPaddedSequenceAsString(Integer begin, Integer end) Method to get a string representation of the sequence for the given range.
HashMap<DADNASequence,MappingSet>	getRegionsOfConservedSynteny(Coordinate range, Species target) Specifies method to retrieve all potential regions of conserved synteny (i.e. multiple chromosome regions) in the specified target Species
HashMap<DADNASequence,MappingSet>	getRegionsOfConservedSynteny(Coordinate range, Species target, String chrName) Method to retrieve a single potential region of conserved synteny for the named chromosome in the specified target Species.
Registry	getRegistry()
String	getReverseComplementSequenceAsString() Method to get a string representation of the reverse complement of the sequence.
String	getReverseComplementSequenceAsString(Integer begin, Integer end) Method to get a string representation of the reverse complement of the sequence for the given range.
String	getSchemaVersion()
String	getSequenceAsString(Integer begin, Integer end) Method to get a string representation of the sequence for the given range.
String	getSequenceAsString(Integer bioStart, Integer bioEnd, Strand strand) Deprecated.
Species	getSpecies()
ObjectType	getType()
List<? extends Mapping>	getVariationMappingsOnRegion(Coordinate coord) Returns List of Mappings of Variations on specified Coordinate Region.
List<? extends Mapping>	getVariationMappingsOnRegion(Integer start, Integer stop) Returns List of Mappings of Variations on specified Coordinate Region.
List<DAVariation>	getVariationsOnRegion(Coordinate coord) Returns list of Variations on specified Coordinate Region.
List<DAVariation>	getVariationsOnRegion(Integer start, Integer stop) Returns list of Variations on specified Region.
void	setAttributes(HashMap<String,String> attribs)
void	setCodonTableID(Integer id)
void	setCoordSystem(CoordinateSystem coordSystem)
void	setCsID(Integer csID)
void	setDaoFactory(DAOFactory daoFactory)
void	setDBSeqLength(Integer seqLength)
void	setId(Integer id)
void	setLazyLoaded(boolean b)
void	setName(String name)
void	setRegistry(Registry datasource)
void	setSequenceStorage(DAEnsemblDNASequenceReader proxyLoader)
void	setSpecies(Species species)
String	toString()

Methods inherited from class org.biojava3.core.sequence.DNASequence

getComplement, getDNAType, getGCCount, getReverse, getReverseComplement, getRNASequence, getRNASequence, getRNASequence, getRNASequence, main, setDNAType

Methods inherited from class org.biojava3.core.sequence.template.AbstractSequence

addFeature, addFeature, addNote, countCompounds, getAccession, getAnnotationType, getAsList, getBioBegin, getCompoundAt, getCompoundSet, getDatabaseReferences, getDescription, getFeatures, getFeatures, getFeatures, getFeaturesByType, getFeaturesKeyWord, getIndexOf, getInverse, getLastIndexOf, getNotesList, getOriginalHeader, getParentSequence, getProxySequenceReader, getSequenceAsString, getSequenceScore, getSource, getSubSequence, getTaxonomy, getUserCollection, iterator, removeFeature, removeNote, setAccession, setAnnotationType, setBioBegin, setBioEnd, setCompoundSet, setDatabaseReferences, setDescription, setFeaturesKeyWord, setNotesList, setOriginalHeader, setParentSequence, setProxySequenceReader, setSequenceScore, setSource, setTaxonomy, setUserCollection

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biojava3.core.sequence.template.Sequence

countCompounds, getAsList, getCompoundAt, getCompoundSet, getIndexOf, getInverse, getLastIndexOf, getSequenceAsString, getSubSequence

Methods inherited from interface java.lang.Iterable

iterator

Methods inherited from interface org.biojava3.core.sequence.template.Accessioned

getAccession

Field Detail

daoFactory

protected DAOFactory daoFactory

schemaVersion

protected String schemaVersion

dbVersion

protected String dbVersion

registry

protected Registry registry

id

protected Integer id

seqRegionID

protected Integer seqRegionID

name

protected String name

dbSpeciesName

protected String dbSpeciesName

species

protected Species species

DBSeqLength

protected Integer DBSeqLength

coordSystem

protected CoordinateSystem coordSystem

mappings

protected MappingSet mappings

mappedRegions

protected HashMap<ObjectType,CoordinateSet> mappedRegions

objectTypeMappings

protected HashMap<ObjectType,MappingSet> objectTypeMappings

comparaFactories

protected HashMap<EnsemblComparaDivision,DAOComparaFactory> comparaFactories

codonTableID

protected Integer codonTableID

lazyLoaded

protected boolean lazyLoaded

csID

protected Integer csID

Constructor Detail

DADNASequence

public DADNASequence()

DADNASequence

public DADNASequence(DAEnsemblDNASequenceReader proxyLoader)

DADNASequence

public DADNASequence(String sequence)

DADNASequence

public DADNASequence(DAOCoreFactory factory)

Method Detail

setSequenceStorage

public void setSequenceStorage(DAEnsemblDNASequenceReader proxyLoader)

getDaoFactory

public DAOCoreFactory getDaoFactory()

setDaoFactory

public void setDaoFactory(DAOFactory daoFactory)

getSchemaVersion

public String getSchemaVersion()

Specified by:

getSchemaVersion in interface IdentifiableObject

getDBVersion

public String getDBVersion()

Specified by:

getDBVersion in interface IdentifiableObject

getRegistry

public Registry getRegistry()

setRegistry

public void setRegistry(Registry datasource)

getId

public Integer getId()

Specified by:

getId in interface IdentifiableObject

setId

public void setId(Integer id)

Specified by:

setId in interface IdentifiableObject

getDBName

public String getDBName()

getSpecies

public Species getSpecies()

Specified by:

getSpecies in interface CoreObject

setSpecies

public void setSpecies(Species species)

Specified by:

setSpecies in interface CoreObject

getType

public ObjectType getType()

Specified by:

getType in interface IdentifiableObject

getDBSeqLength

public Integer getDBSeqLength()

Specified by:

getDBSeqLength in interface DNASequence

setDBSeqLength

public void setDBSeqLength(Integer seqLength)

Specified by:

setDBSeqLength in interface DNASequence

getBioEnd

public Integer getBioEnd()

Overrides:

getBioEnd in class AbstractSequence<NucleotideCompound>

getLength

public int getLength()

Specified by:

getLength in interface Sequence<NucleotideCompound>

Overrides:

getLength in class AbstractSequence<NucleotideCompound>

getName

public String getName()

Specified by:

getName in interface DNASequence

setName

public void setName(String name)

Specified by:

setName in interface DNASequence

getCoordSystem

public CoordinateSystem getCoordSystem()

Specified by:

getCoordSystem in interface DNASequence

setCoordSystem

public void setCoordSystem(CoordinateSystem coordSystem)

Specified by:

setCoordSystem in interface DNASequence

getLoadedMappings

public MappingSet getLoadedMappings()

Specified by:

getLoadedMappings in interface MappableObject

getLoadedMappings

public MappingSet getLoadedMappings(ObjectType targetType)

Specified by:

getLoadedMappings in interface MappableObject

addMapping

public Boolean addMapping(Mapping mapping)

Specified by:

addMapping in interface MappableObject

getGenesOnRegion

public List<DAGene> getGenesOnRegion(Coordinate coord)
                              throws DAOException

Returns a List of Genes on the specified Coordinate region.

Specified by:

getGenesOnRegion in interface DNASequence

Parameters:

coord -

Throws:

DAOException

getGenesOnRegion

public List<DAGene> getGenesOnRegion(Integer start,
                            Integer stop,
                            Coordinate.Strand strand)
                              throws DAOException

Returns a List of Genes on the specified Region. Start/Stop locations must be both Non-Null and Non-ZERO or a Runtime IllegalArgumentException will be thrown.

Specified by:

getGenesOnRegion in interface DNASequence

Parameters:

start -

stop -

strand -

Throws:

DAOException

getGenesOnRegion

public List<DAGene> getGenesOnRegion(Integer start,
                            Integer stop)
                              throws DAOException

Returns a List of Genes on the specified Region. Start/Stop locations must be both Non-Null and Non-ZERO or a Runtime IllegalArgumentException will be thrown.

Specified by:

getGenesOnRegion in interface DNASequence

Parameters:

start -

stop -

Throws:

DAOException

getSequenceAsString

public String getSequenceAsString(Integer begin,
                         Integer end)
                           throws RangeException

Method to get a string representation of the sequence for the given range. Arguments outwith the extent of the sequence (i.e. greater than its length, or less than the start site of +1) will throw a RangeException.

Specified by:

getSequenceAsString in interface DNASequence

Parameters:

begin -

end -

Throws:

RangeException

getPaddedSequenceAsString

public String getPaddedSequenceAsString(Integer begin,
                               Integer end)

Method to get a string representation of the sequence for the given range. If the requested range is outwith the sequence extent, the upstream and or downstream will be padded with N's.

Specified by:

getPaddedSequenceAsString in interface DNASequence

Parameters:

begin -

end -

getSequenceAsString

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

Deprecated.

Don't use Strands for getting sequence strings - always use getSequenceAsString or getReverseComplementSequenceAsString to guarantee polarity.

Overrides:

getSequenceAsString in class AbstractSequence<NucleotideCompound>

getReverseComplementSequenceAsString

public String getReverseComplementSequenceAsString(Integer begin,
                                          Integer end)
                                            throws RangeException

Method to get a string representation of the reverse complement of the sequence for the given range. Arguments outwith the extent of the sequence (i.e. greater than its length, or less than the start site of +1) will throw a RangeException.

Specified by:

getReverseComplementSequenceAsString in interface DNASequence

Parameters:

begin -

end -

Returns:

String

Throws:

RangeException

getPaddedReverseComplementSequenceAsString

public String getPaddedReverseComplementSequenceAsString(Integer begin,
                                                Integer end)

Method to get a string representation of the reverse complement of the sequence for the given range. If the requested range is outwith the sequence extent, the upstream and or downstream will be padded with N's.

Specified by:

getPaddedReverseComplementSequenceAsString in interface DNASequence

Parameters:

begin -

end -

getReverseComplementSequenceAsString

public String getReverseComplementSequenceAsString()

Method to get a string representation of the reverse complement of the sequence.

Specified by:

getReverseComplementSequenceAsString in interface DNASequence

getObjectTypeMappings

public HashMap<ObjectType,MappingSet> getObjectTypeMappings()

Specified by:

getObjectTypeMappings in interface DNASequence

getMappedRegions

public HashMap<ObjectType,CoordinateSet> getMappedRegions()

Specified by:

getMappedRegions in interface DNASequence

getHashID

public String getHashID()

Specified by:

getHashID in interface IdentifiableObject

toString

public String toString()

Overrides:

toString in class AbstractSequence<NucleotideCompound>

clearAllMappings

public void clearAllMappings()

Specified by:

clearAllMappings in interface MappableObject

getComparaDivision

public EnsemblComparaDivision getComparaDivision()

Note the special case for Bacteria in collections in DB >16

Returns:

getComparaFactory

public DAOComparaFactory getComparaFactory(EnsemblComparaDivision comparaDivision)

getComparaFactory

public DAOComparaFactory getComparaFactory()

getRegionsOfConservedSynteny

public HashMap<DADNASequence,MappingSet> getRegionsOfConservedSynteny(Coordinate range,
                                                             Species target)
                                                               throws DAOException

Specifies method to retrieve all potential regions of conserved synteny (i.e. multiple chromosome regions) in the specified target Species

Specified by:

getRegionsOfConservedSynteny in interface DNASequence

Parameters:

range -

target -

Returns:

a HashMap of each DNASequence discovered against the MappingSet of Homologous genes

Throws:

DAOException

getRegionsOfConservedSynteny

public HashMap<DADNASequence,MappingSet> getRegionsOfConservedSynteny(Coordinate range,
                                                             Species target,
                                                             String chrName)
                                                               throws DAOException

Method to retrieve a single potential region of conserved synteny for the named chromosome in the specified target Species. In effect a filter on the full query, for efficiency where the target chromosome is already known.

Specified by:

getRegionsOfConservedSynteny in interface DNASequence

Parameters:

range -

target -

chrName -

Returns:

a HashMap of each DNASequence discovered against the MappingSet of Homologous genes

Throws:

DAOException

getAssembly

public String getAssembly()

Specified by:

getAssembly in interface CoreObject

getVariationsOnRegion

public List<DAVariation> getVariationsOnRegion(Coordinate coord)
                                        throws DAOException

Returns list of Variations on specified Coordinate Region. Compare to getVariationMappingsOnRegion(Coordinate coord) methods.

Specified by:

getVariationsOnRegion in interface DNASequence

Parameters:

coord -

Throws:

DAOException

getVariationsOnRegion

public List<DAVariation> getVariationsOnRegion(Integer start,
                                      Integer stop)
                                        throws DAOException

Returns list of Variations on specified Region. Compare to getVariationMappingsOnRegion(Integer start, Integer stop) methods. Start/Stop locations must be both Non-Null and Non-ZERO or a Runtime IllegalArgumentException will be thrown.

Specified by:

getVariationsOnRegion in interface DNASequence

Parameters:

start -

stop -

Throws:

DAOException

getVariationMappingsOnRegion

public List<? extends Mapping> getVariationMappingsOnRegion(Coordinate coord)
                                                     throws DAOException

Returns List of Mappings of Variations on specified Coordinate Region. Compare to getVariationsOnRegion(Coordinate coord) methods.

Specified by:

getVariationMappingsOnRegion in interface DNASequence

Parameters:

coord -

Throws:

DAOException

getVariationMappingsOnRegion

public List<? extends Mapping> getVariationMappingsOnRegion(Integer start,
                                                   Integer stop)
                                                     throws DAOException

Returns List of Mappings of Variations on specified Coordinate Region. Compare to getVariationsOnRegion(Integer start, Integer stop) methods. Start/Stop locations must be both Non-Null and Non-ZERO or a Runtime IllegalArgumentException will be thrown.

Specified by:

getVariationMappingsOnRegion in interface DNASequence

Parameters:

start -

stop -

Throws:

DAOException

getCodonTableID

public Integer getCodonTableID()

Specified by:

getCodonTableID in interface DNASequence

setCodonTableID

public void setCodonTableID(Integer id)

addAttribute

public void addAttribute(String key,
                String value)

getAttribute

public String getAttribute(String key)

setAttributes

public void setAttributes(HashMap<String,String> attribs)

getAttributes

public HashMap<String,String> getAttributes()

setLazyLoaded

public void setLazyLoaded(boolean b)

getCsID

public Integer getCsID()

setCsID

public void setCsID(Integer csID)