uk.ac.roslin.ensembl.datasourceaware.core

Class DAAssembledDNASequence

java.lang.Object

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

org.biojava3.core.sequence.DNASequence

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

uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence

All Implemented Interfaces:

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

Direct Known Subclasses:

DAChromosome

public class DAAssembledDNASequence
extends DADNASequence
implements AssembledDNASequence

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 inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

codonTableID, comparaFactories, coordSystem, csID, daoFactory, DBSeqLength, dbSpeciesName, dbVersion, id, lazyLoaded, mappedRegions, mappings, name, objectTypeMappings, registry, schemaVersion, seqRegionID, species

Constructor Summary

Constructors

Constructor and Description
DAAssembledDNASequence()
DAAssembledDNASequence(DAOCoreFactory factory)

Method Summary

Methods

Modifier and Type	Method and Description
DAAssembly	getCompleteAssembly()
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.
String	getReverseComplementSequenceAsString() Default case is to assume strand is positive because only CDSSequence can be either positive or negative Strand.
String	getReverseComplementSequenceAsString(Integer begin, Integer end) Method to get a string representation of the reverse complement of the sequence for the given range.
String	getSequenceAsString() Default case is to assume strand is positive because only CDSSequence can be either positive or negative Strand.
String	getSequenceAsString(Integer begin, Integer end) Method to get a string representation for the given range of the assembled sequence.
String	getSequenceAsString(Integer begin, Integer end, Strand strand) Deprecated.

Methods inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

addAttribute, addMapping, clearAllMappings, getAssembly, getAttribute, getAttributes, getBioEnd, getCodonTableID, getComparaDivision, getComparaFactory, getComparaFactory, getCoordSystem, getCsID, getDaoFactory, getDBName, getDBSeqLength, getDBVersion, getGenesOnRegion, getGenesOnRegion, getGenesOnRegion, getHashID, getId, getLength, getLoadedMappings, getLoadedMappings, getMappedRegions, getName, getObjectTypeMappings, getRegionsOfConservedSynteny, getRegionsOfConservedSynteny, getRegistry, getSchemaVersion, getSpecies, getType, getVariationMappingsOnRegion, getVariationMappingsOnRegion, getVariationsOnRegion, getVariationsOnRegion, setAttributes, setCodonTableID, setCoordSystem, setCsID, setDaoFactory, setDBSeqLength, setId, setLazyLoaded, setName, setRegistry, setSequenceStorage, setSpecies, 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, 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 uk.ac.roslin.ensembl.model.core.DNASequence

getCodonTableID, getCoordSystem, getDBSeqLength, getGenesOnRegion, getGenesOnRegion, getGenesOnRegion, getMappedRegions, getName, getObjectTypeMappings, getRegionsOfConservedSynteny, getRegionsOfConservedSynteny, getVariationMappingsOnRegion, getVariationMappingsOnRegion, getVariationsOnRegion, getVariationsOnRegion, setCoordSystem, setDBSeqLength, setName

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, getSubSequence

Methods inherited from interface java.lang.Iterable

iterator

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

getAccession

Constructor Detail

DAAssembledDNASequence

public DAAssembledDNASequence()

DAAssembledDNASequence

public DAAssembledDNASequence(DAOCoreFactory factory)

Method Detail

getCompleteAssembly

public DAAssembly getCompleteAssembly()

Specified by:

getCompleteAssembly in interface AssembledDNASequence

getSequenceAsString

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

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

Specified by:

getSequenceAsString in interface DNASequence

Overrides:

getSequenceAsString in class DADNASequence

Parameters:

begin -

end -

Returns:

String representation of the Sequence

Throws:

RangeException

getPaddedSequenceAsString

public String getPaddedSequenceAsString(Integer begin,
                               Integer end)

Description copied from class: DADNASequence

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

Overrides:

getPaddedSequenceAsString in class DADNASequence

getSequenceAsString

@Deprecated
public String getSequenceAsString(Integer begin,
                                    Integer end,
                                    Strand strand)
                           throws RangeException

Deprecated.

Don't use: It is ambiguous to use Strands for getting sequence strings. Always use getSequenceAsString or getReverseComplementSequenceAsString to guarantee polarity.

Overrides:

getSequenceAsString in class DADNASequence

Parameters:

begin -

end -

strand -

Returns:

String representation of the Sequence

Throws:

RangeException

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<NucleotideCompound>

Overrides:

getSequenceAsString in class AbstractSequence<NucleotideCompound>

Returns:

String representation of the Sequence

getReverseComplementSequenceAsString

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

Description copied from class: DADNASequence

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

Overrides:

getReverseComplementSequenceAsString in class DADNASequence

Parameters:

begin -

end -

Returns:

String representation of the reverse complement Sequence

Throws:

RangeException

getPaddedReverseComplementSequenceAsString

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

Description copied from class: DADNASequence

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

Overrides:

getPaddedReverseComplementSequenceAsString in class DADNASequence

Throws:

RangeException

getReverseComplementSequenceAsString

public String getReverseComplementSequenceAsString()

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

Specified by:

getReverseComplementSequenceAsString in interface DNASequence

Overrides:

getReverseComplementSequenceAsString in class DADNASequence

Returns:

String representation of the reverse complement Sequence