gov.nih.nci.mageom.domain.BioSequence
Interface BioSequence

All Superinterfaces:
Describable, Extendable, Identifiable
All Known Implementing Classes:
BioSequenceImpl

public interface BioSequence
extends Identifiable

A BioSequence is a representation of a DNA, RNA, or protein sequence. It can be represented by a Clone, Gene, or the sequence.

Version:
%I%, %G%

Method Summary
 java.lang.Boolean getIsApproximateLength()
          Returns the value of this BioSequence object's isApproximateLength attribute.
 java.lang.Boolean getIsCircular()
          Returns the value of this BioSequence object's isCircular attribute.
 java.lang.Integer getLength()
          Returns the value of this BioSequence object's length attribute.
 OntologyEntry[] getOntologyEntries()
          Returns the value of this BioSequence object's ontologyEntries attribute.
 OntologyEntry getPolymerType()
          Returns the value of this BioSequence object's polymerType attribute.
 SeqFeature[] getSeqFeatures()
          Returns the value of this BioSequence object's seqFeatures attribute.
 java.lang.String getSequence()
          Returns the value of this BioSequence object's sequence attribute.
 DatabaseEntry[] getSequenceDatabases()
          Returns the value of this BioSequence object's sequenceDatabases attribute.
 OntologyEntry getSpecies()
          Returns the value of this BioSequence object's species attribute.
 OntologyEntry getType()
          Returns the value of this BioSequence object's type attribute.
 void setIsApproximateLength(java.lang.Boolean p_isApproximateLength)
          Sets the isApproximateLength attribute.
 void setIsCircular(java.lang.Boolean p_isCircular)
          Sets the isCircular attribute.
 void setLength(java.lang.Integer p_length)
          Sets the length attribute.
 void setOntologyEntries(OntologyEntry[] p_ontologyEntries)
          Sets the ontologyEntries attribute.
 void setPolymerType(OntologyEntry p_polymerType)
          Sets the polymerType attribute.
 void setSeqFeatures(SeqFeature[] p_seqFeatures)
          Sets the seqFeatures attribute.
 void setSequence(java.lang.String p_sequence)
          Sets the sequence attribute.
 void setSequenceDatabases(DatabaseEntry[] p_sequenceDatabases)
          Sets the sequenceDatabases attribute.
 void setSpecies(OntologyEntry p_species)
          Sets the species attribute.
 void setType(OntologyEntry p_type)
          Sets the type attribute.
 
Methods inherited from interface gov.nih.nci.mageom.domain.Identifiable
getIdentifier, getName, setIdentifier, setName
 
Methods inherited from interface gov.nih.nci.mageom.domain.Describable
getAuditTrail, getDescriptions, getSecurity, setAuditTrail, setDescriptions, setSecurity
 
Methods inherited from interface gov.nih.nci.mageom.domain.Extendable
getPropertySets, setPropertySets
 

Method Detail

setLength

void setLength(java.lang.Integer p_length)
Sets the length attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a BioSequence object.

Parameters:
p_length - The new value for length.
See Also:
getLength()

getLength

java.lang.Integer getLength()
Returns the value of this BioSequence object's length attribute. Description of length: The number of residues in the biosequence.

Returns:
int The value of length.

setIsApproximateLength

void setIsApproximateLength(java.lang.Boolean p_isApproximateLength)
Sets the isApproximateLength attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a BioSequence object.

Parameters:
p_isApproximateLength - The new value for isApproximateLength.
See Also:
getIsApproximateLength()

getIsApproximateLength

java.lang.Boolean getIsApproximateLength()
Returns the value of this BioSequence object's isApproximateLength attribute. Description of isApproximateLength: If length not positively known will be true

Returns:
boolean The value of isApproximateLength.

setIsCircular

void setIsCircular(java.lang.Boolean p_isCircular)
Sets the isCircular attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a BioSequence object.

Parameters:
p_isCircular - The new value for isCircular.
See Also:
getIsCircular()

getIsCircular

java.lang.Boolean getIsCircular()
Returns the value of this BioSequence object's isCircular attribute. Description of isCircular: Indicates if the BioSequence is circular in nature.

Returns:
boolean The value of isCircular.

setSequence

void setSequence(java.lang.String p_sequence)
Sets the sequence attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a BioSequence object.

Parameters:
p_sequence - The new value for sequence.
See Also:
getSequence()

getSequence

java.lang.String getSequence()
Returns the value of this BioSequence object's sequence attribute. Description of sequence: The actual components of the sequence, for instance, for DNA a string consisting of A,T,C and G. The attribute is optional and instead of specified here, can be found through the DatabaseEntry.

Returns:
String The value of sequence.

setSeqFeatures

void setSeqFeatures(SeqFeature[] p_seqFeatures)
Sets the seqFeatures attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a BioSequence object.

Parameters:
p_seqFeatures - The new value for seqFeatures.
See Also:
getSeqFeatures()

getSeqFeatures

SeqFeature[] getSeqFeatures()
Returns the value of this BioSequence object's seqFeatures attribute.

Returns:
gov.nih.nci.mageom.bean.BioSequence.SeqFeature[] The value of seqFeatures.
See Also:
SeqFeature

setOntologyEntries

void setOntologyEntries(OntologyEntry[] p_ontologyEntries)
Sets the ontologyEntries attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a BioSequence object.

Parameters:
p_ontologyEntries - The new value for ontologyEntries.
See Also:
getOntologyEntries()

getOntologyEntries

OntologyEntry[] getOntologyEntries()
Returns the value of this BioSequence object's ontologyEntries attribute.

Returns:
gov.nih.nci.mageom.bean.Description.OntologyEntry[] The value of ontologyEntries.
See Also:
OntologyEntry

setPolymerType

void setPolymerType(OntologyEntry p_polymerType)
Sets the polymerType attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a BioSequence object.

Parameters:
p_polymerType - The new value for polymerType.
See Also:
getPolymerType()

getPolymerType

OntologyEntry getPolymerType()
Returns the value of this BioSequence object's polymerType attribute.

Returns:
gov.nih.nci.mageom.bean.Description.OntologyEntry The value of polymerType.
See Also:
OntologyEntry

setSequenceDatabases

void setSequenceDatabases(DatabaseEntry[] p_sequenceDatabases)
Sets the sequenceDatabases attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a BioSequence object.

Parameters:
p_sequenceDatabases - The new value for sequenceDatabases.
See Also:
getSequenceDatabases()

getSequenceDatabases

DatabaseEntry[] getSequenceDatabases()
Returns the value of this BioSequence object's sequenceDatabases attribute.

Returns:
gov.nih.nci.mageom.bean.Description.DatabaseEntry[] The value of sequenceDatabases.
See Also:
DatabaseEntry

setType

void setType(OntologyEntry p_type)
Sets the type attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a BioSequence object.

Parameters:
p_type - The new value for type.
See Also:
getType()

getType

OntologyEntry getType()
Returns the value of this BioSequence object's type attribute.

Returns:
gov.nih.nci.mageom.bean.Description.OntologyEntry The value of type.
See Also:
OntologyEntry

setSpecies

void setSpecies(OntologyEntry p_species)
Sets the species attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a BioSequence object.

Parameters:
p_species - The new value for species.
See Also:
getSpecies()

getSpecies

OntologyEntry getSpecies()
Returns the value of this BioSequence object's species attribute.

Returns:
gov.nih.nci.mageom.bean.Description.OntologyEntry The value of species.
See Also:
OntologyEntry