uk.ac.roslin.ensembl.model.core

Interface DNASequence

All Superinterfaces:

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

All Known Subinterfaces:

AssembledDNASequence, Chromosome

All Known Implementing Classes:

DAAssembledDNASequence, DAChromosome, DADNASequence, GapSequence

public interface DNASequence
extends CoreObject, MappableObject, Sequence<NucleotideCompound>

Author:

paterson

Method Summary

Methods

Modifier and Type	Method and Description
Integer	getCodonTableID()
CoordinateSystem	getCoordSystem()
Integer	getDBSeqLength()
List<? extends Gene>	getGenesOnRegion(Coordinate coord)
List<? extends Gene>	getGenesOnRegion(Integer start, Integer stop)
List<? extends Gene>	getGenesOnRegion(Integer start, Integer stop, Coordinate.Strand strand)
HashMap<ObjectType,CoordinateSet>	getMappedRegions()
String	getName()
HashMap<ObjectType,? extends MappingSet>	getObjectTypeMappings()
String	getPaddedReverseComplementSequenceAsString(Integer begin, Integer end)
String	getPaddedSequenceAsString(Integer begin, Integer end)
HashMap<? extends DNASequence,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<? extends DNASequence,MappingSet>	getRegionsOfConservedSynteny(Coordinate range, Species target, String chrName) Specifies method to retrieve a single potential region of conserved synteny for the named chromosome in the specified target Species.
String	getReverseComplementSequenceAsString()
String	getReverseComplementSequenceAsString(Integer begin, Integer end)
String	getSequenceAsString(Integer begin, Integer end)
List<? extends Mapping>	getVariationMappingsOnRegion(Coordinate coord)
List<? extends Mapping>	getVariationMappingsOnRegion(Integer start, Integer stop)
List<? extends Variation>	getVariationsOnRegion(Coordinate coord)
List<? extends Variation>	getVariationsOnRegion(Integer start, Integer stop)
void	setCoordSystem(CoordinateSystem coordSystem)
void	setDBSeqLength(Integer seqLength)
void	setName(String name)

Methods inherited from interface uk.ac.roslin.ensembl.model.core.CoreObject

getAssembly, getSpecies, setSpecies

Methods inherited from interface uk.ac.roslin.ensembl.model.MappableObject

addMapping, clearAllMappings, getLoadedMappings, getLoadedMappings

Methods inherited from interface uk.ac.roslin.ensembl.model.IdentifiableObject

getDBVersion, getHashID, getId, getSchemaVersion, getType, setId

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

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

Methods inherited from interface java.lang.Iterable

iterator

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

getAccession

Method Detail

getDBSeqLength

Integer getDBSeqLength()

setDBSeqLength

void setDBSeqLength(Integer seqLength)

getCoordSystem

CoordinateSystem getCoordSystem()

setCoordSystem

void setCoordSystem(CoordinateSystem coordSystem)

getName

String getName()

setName

void setName(String name)

getGenesOnRegion

List<? extends Gene> getGenesOnRegion(Coordinate coord)
                                      throws DAOException

Throws:

DAOException

getGenesOnRegion

List<? extends Gene> getGenesOnRegion(Integer start,
                                    Integer stop)
                                      throws DAOException

Throws:

DAOException

getGenesOnRegion

List<? extends Gene> getGenesOnRegion(Integer start,
                                    Integer stop,
                                    Coordinate.Strand strand)
                                      throws DAOException

Throws:

DAOException

getRegionsOfConservedSynteny

HashMap<? extends DNASequence,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

Parameters:

range -

target -

Returns:

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

Throws:

DAOException

getRegionsOfConservedSynteny

HashMap<? extends DNASequence,MappingSet> getRegionsOfConservedSynteny(Coordinate range,
                                                                     Species target,
                                                                     String chrName)
                                                                       throws DAOException

Specifies 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.

Parameters:

range -

target -

chrName -

Returns:

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

Throws:

DAOException

getVariationsOnRegion

List<? extends Variation> getVariationsOnRegion(Coordinate coord)
                                                throws DAOException

Throws:

DAOException

getVariationMappingsOnRegion

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

Throws:

DAOException

getVariationsOnRegion

List<? extends Variation> getVariationsOnRegion(Integer start,
                                              Integer stop)
                                                throws DAOException

Throws:

DAOException

getVariationMappingsOnRegion

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

Throws:

DAOException

getSequenceAsString

String getSequenceAsString(Integer begin,
                         Integer end)
                           throws RangeException

Throws:

RangeException

getPaddedSequenceAsString

String getPaddedSequenceAsString(Integer begin,
                               Integer end)

getReverseComplementSequenceAsString

String getReverseComplementSequenceAsString(Integer begin,
                                          Integer end)
                                            throws RangeException

Throws:

RangeException

getPaddedReverseComplementSequenceAsString

String getPaddedReverseComplementSequenceAsString(Integer begin,
                                                Integer end)

getReverseComplementSequenceAsString

String getReverseComplementSequenceAsString()

getObjectTypeMappings

HashMap<ObjectType,? extends MappingSet> getObjectTypeMappings()

getMappedRegions

HashMap<ObjectType,CoordinateSet> getMappedRegions()

getCodonTableID

Integer getCodonTableID()