uk.ac.roslin.ensembl.datasourceaware.core

Class GapSequence

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.GapSequence

All Implemented Interfaces:

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

public class GapSequence
extends DADNASequence

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

Method Summary

Methods

Modifier and Type	Method and Description
static String	getGapString(Integer length)
static String	getGapString(Integer length, char gap)
int	getLength()
String	getPaddedReverseComplementSequenceAsString(Integer start, Integer stop) Method to get a string representation of the reverse complement of the sequence for the given range.
String	getPaddedRNASequenceAsString(Integer start, Integer stop)
String	getPaddedSequenceAsString(Integer start, Integer stop) Method to get a string representation of the sequence for the given range.
String	getReverseComplementSequenceAsString() Method to get a string representation of the reverse complement of the sequence.
String	getReverseComplementSequenceAsString(Integer start, Integer stop) Method to get a string representation of the reverse complement of the sequence for the given range.
String	getRNASequenceAsString()
String	getRNASequenceAsString(Integer start, Integer stop)
String	getSequenceAsString()
String	getSequenceAsString(Integer start, Integer stop) Method to get a string representation of the sequence for the given range.
String	getSequenceAsString(Integer start, Integer stop, Strand strand) Deprecated.
static GapSequence	makeGap(Integer length)
String	toString()

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, 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

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 org.biojava3.core.sequence.template.Sequence

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

Methods inherited from interface java.lang.Iterable

iterator

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

getAccession

Method Detail

makeGap

public static GapSequence makeGap(Integer length)

getGapString

public static String getGapString(Integer length)

getGapString

public static String getGapString(Integer length,
                  char gap)

getSequenceAsString

public String getSequenceAsString()

Specified by:

getSequenceAsString in interface Sequence<NucleotideCompound>

Overrides:

getSequenceAsString in class AbstractSequence<NucleotideCompound>

getRNASequenceAsString

public String getRNASequenceAsString()

getReverseComplementSequenceAsString

public String getReverseComplementSequenceAsString()

Description copied from class: DADNASequence

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

Specified by:

getReverseComplementSequenceAsString in interface DNASequence

Overrides:

getReverseComplementSequenceAsString in class DADNASequence

getSequenceAsString

public String getSequenceAsString(Integer start,
                         Integer stop)
                           throws RangeException

Description copied from class: DADNASequence

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

Overrides:

getSequenceAsString in class DADNASequence

Throws:

RangeException

getPaddedSequenceAsString

public String getPaddedSequenceAsString(Integer start,
                               Integer stop)

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

getRNASequenceAsString

public String getRNASequenceAsString(Integer start,
                            Integer stop)
                              throws RangeException

Throws:

RangeException

getPaddedRNASequenceAsString

public String getPaddedRNASequenceAsString(Integer start,
                                  Integer stop)

getSequenceAsString

@Deprecated
public String getSequenceAsString(Integer start,
                                    Integer stop,
                                    Strand strand)

Deprecated.

Description copied from class: DADNASequence

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

Overrides:

getSequenceAsString in class DADNASequence

getReverseComplementSequenceAsString

public String getReverseComplementSequenceAsString(Integer start,
                                          Integer stop)
                                            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

Returns:

String

Throws:

RangeException

getPaddedReverseComplementSequenceAsString

public String getPaddedReverseComplementSequenceAsString(Integer start,
                                                Integer stop)

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

toString

public String toString()

Overrides:

toString in class DADNASequence

getLength

public int getLength()

Specified by:

getLength in interface Sequence<NucleotideCompound>

Overrides:

getLength in class DADNASequence