Class BioSequence
- java.lang.Object
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- ubic.gemma.model.common.AbstractDescribable
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- ubic.gemma.model.genome.biosequence.BioSequence
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- All Implemented Interfaces:
Serializable
,Describable
,Identifiable
@Indexed public class BioSequence extends AbstractDescribable implements Serializable
The sequence of a biological polymer such as a protein or DNA. BioSequences may be artificial, such as Affymetrix reporter oligonucleotide chains, or they may be the sequence
of nucleotides associated with a gene product. This class only represents the sequence itself ("ATCGCCG..."), not the physical item, and not the database entry for the sequence.
- See Also:
- Serialized Form
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
BioSequence.Factory
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Constructor Summary
Constructors Constructor Description BioSequence()
No-arg constructor added to satisfy javabean contract
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
equals(Object object)
Returnstrue
if the argument is an Describable instance and all identifiers for this entity equal the identifiers of the argument entity.Set<BioSequence2GeneProduct>
getBioSequence2GeneProduct()
Double
getFractionRepeats()
Long
getId()
Boolean
getIsApproximateLength()
Boolean
getIsCircular()
Long
getLength()
String
getName()
Obtain the name of an object is a possibly ambiguous human-readable identifier that need not be an external database reference.PolymerType
getPolymerType()
String
getSequence()
DatabaseEntry
getSequenceDatabaseEntry()
Taxon
getTaxon()
SequenceType
getType()
int
hashCode()
Returns a hash code based on this entity's identifiers.void
setBioSequence2GeneProduct(Set<BioSequence2GeneProduct> bioSequence2GeneProduct)
void
setFractionRepeats(Double fractionRepeats)
void
setIsApproximateLength(Boolean isApproximateLength)
void
setIsCircular(Boolean isCircular)
void
setLength(Long length)
void
setPolymerType(PolymerType polymerType)
void
setSequence(String sequence)
void
setSequenceDatabaseEntry(DatabaseEntry sequenceDatabaseEntry)
void
setTaxon(Taxon taxon)
void
setType(SequenceType type)
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Methods inherited from class ubic.gemma.model.common.AbstractDescribable
getDescription, setDescription, setId, setName, toString
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Method Detail
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getId
@DocumentId public Long getId()
- Specified by:
getId
in interfaceIdentifiable
- Overrides:
getId
in classAbstractDescribable
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getName
@Field public String getName()
Description copied from interface:Describable
Obtain the name of an object is a possibly ambiguous human-readable identifier that need not be an external database reference.- Specified by:
getName
in interfaceDescribable
- Overrides:
getName
in classAbstractDescribable
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getBioSequence2GeneProduct
public Set<BioSequence2GeneProduct> getBioSequence2GeneProduct()
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setBioSequence2GeneProduct
public void setBioSequence2GeneProduct(Set<BioSequence2GeneProduct> bioSequence2GeneProduct)
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getFractionRepeats
public Double getFractionRepeats()
- Returns:
- The fraction of the sequences determined to be made up of repeats (e.g., via repeat masker)
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setFractionRepeats
public void setFractionRepeats(Double fractionRepeats)
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getIsApproximateLength
public Boolean getIsApproximateLength()
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setIsApproximateLength
public void setIsApproximateLength(Boolean isApproximateLength)
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getIsCircular
public Boolean getIsCircular()
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setIsCircular
public void setIsCircular(Boolean isCircular)
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getLength
public Long getLength()
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setLength
public void setLength(Long length)
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getPolymerType
@Nullable public PolymerType getPolymerType()
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setPolymerType
public void setPolymerType(@Nullable PolymerType polymerType)
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getSequence
public String getSequence()
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setSequence
public void setSequence(String sequence)
- Parameters:
sequence
- The actual nucleotic sequence as in ATGC
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getSequenceDatabaseEntry
@IndexedEmbedded public DatabaseEntry getSequenceDatabaseEntry()
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setSequenceDatabaseEntry
public void setSequenceDatabaseEntry(DatabaseEntry sequenceDatabaseEntry)
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getTaxon
public Taxon getTaxon()
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setTaxon
public void setTaxon(Taxon taxon)
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getType
@Nullable public SequenceType getType()
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setType
public void setType(@Nullable SequenceType type)
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hashCode
public int hashCode()
Description copied from class:AbstractDescribable
Returns a hash code based on this entity's identifiers.- Overrides:
hashCode
in classAbstractDescribable
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equals
public boolean equals(Object object)
Description copied from class:AbstractDescribable
Returnstrue
if the argument is an Describable instance and all identifiers for this entity equal the identifiers of the argument entity. Returnsfalse
otherwise.- Overrides:
equals
in classAbstractDescribable
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