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public interface BioSequence
A BioSequence is a representation of a DNA, RNA, or protein sequence. It can be represented by a Clone, Gene, or the sequence.
| 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 |
|---|
void setLength(java.lang.Integer p_length)
BioSequence object.
p_length - The new value for length.getLength()java.lang.Integer getLength()
BioSequence object's length attribute.
Description of length:
The number of residues in the biosequence.
int The value of length.void setIsApproximateLength(java.lang.Boolean p_isApproximateLength)
BioSequence object.
p_isApproximateLength - The new value for isApproximateLength.getIsApproximateLength()java.lang.Boolean getIsApproximateLength()
BioSequence object's isApproximateLength attribute.
Description of isApproximateLength:
If length not positively known will be true
boolean The value of isApproximateLength.void setIsCircular(java.lang.Boolean p_isCircular)
BioSequence object.
p_isCircular - The new value for isCircular.getIsCircular()java.lang.Boolean getIsCircular()
BioSequence object's isCircular attribute.
Description of isCircular:
Indicates if the BioSequence is circular in nature.
boolean The value of isCircular.void setSequence(java.lang.String p_sequence)
BioSequence object.
p_sequence - The new value for sequence.getSequence()java.lang.String getSequence()
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.
String The value of sequence.void setSeqFeatures(SeqFeature[] p_seqFeatures)
BioSequence object.
p_seqFeatures - The new value for seqFeatures.getSeqFeatures()SeqFeature[] getSeqFeatures()
BioSequence object's seqFeatures attribute.
gov.nih.nci.mageom.bean.BioSequence.SeqFeature[] The value of seqFeatures.SeqFeaturevoid setOntologyEntries(OntologyEntry[] p_ontologyEntries)
BioSequence object.
p_ontologyEntries - The new value for ontologyEntries.getOntologyEntries()OntologyEntry[] getOntologyEntries()
BioSequence object's ontologyEntries attribute.
gov.nih.nci.mageom.bean.Description.OntologyEntry[] The value of ontologyEntries.OntologyEntryvoid setPolymerType(OntologyEntry p_polymerType)
BioSequence object.
p_polymerType - The new value for polymerType.getPolymerType()OntologyEntry getPolymerType()
BioSequence object's polymerType attribute.
gov.nih.nci.mageom.bean.Description.OntologyEntry The value of polymerType.OntologyEntryvoid setSequenceDatabases(DatabaseEntry[] p_sequenceDatabases)
BioSequence object.
p_sequenceDatabases - The new value for sequenceDatabases.getSequenceDatabases()DatabaseEntry[] getSequenceDatabases()
BioSequence object's sequenceDatabases attribute.
gov.nih.nci.mageom.bean.Description.DatabaseEntry[] The value of sequenceDatabases.DatabaseEntryvoid setType(OntologyEntry p_type)
BioSequence object.
p_type - The new value for type.getType()OntologyEntry getType()
BioSequence object's type attribute.
gov.nih.nci.mageom.bean.Description.OntologyEntry The value of type.OntologyEntryvoid setSpecies(OntologyEntry p_species)
BioSequence object.
p_species - The new value for species.getSpecies()OntologyEntry getSpecies()
BioSequence object's species attribute.
gov.nih.nci.mageom.bean.Description.OntologyEntry The value of species.OntologyEntry
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