org.biomage.BioSequence
Class BioSequence

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.Common.Identifiable
                    |
                    +--org.biomage.BioSequence.BioSequence

All Implemented Interfaces:

HasAuditTrail, HasDescriptions, HasOntologyEntries, HasPolymerType, HasPropertySets, HasSecurity, HasSeqFeatures, HasSequenceDatabases, HasSpecies, HasType, java.io.Serializable

public class BioSequence

extends Identifiable

implements java.io.Serializable, HasSequenceDatabases, HasOntologyEntries, HasPolymerType, HasType, HasSpecies, HasSeqFeatures

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

See Also:

Serialized Form

Nested Class Summary

Nested classes inherited from class org.biomage.Interface.HasSequenceDatabases

HasSequenceDatabases.SequenceDatabases_list

Nested classes inherited from class org.biomage.Interface.HasOntologyEntries

HasOntologyEntries.OntologyEntries_list

Nested classes inherited from class org.biomage.Interface.HasSeqFeatures

HasSeqFeatures.SeqFeatures_list

Nested classes inherited from class org.biomage.Interface.HasAuditTrail

HasAuditTrail.AuditTrail_list

Nested classes inherited from class org.biomage.Interface.HasDescriptions

HasDescriptions.Descriptions_list

Nested classes inherited from class org.biomage.Interface.HasPropertySets

HasPropertySets.PropertySets_list

Field Summary

protected HasOntologyEntries.OntologyEntries_list	ontologyEntries Ontology entries referring to common values associated with BioSequences, such as gene names, go ids, etc.
protected OntologyEntry	polymerType A choice of protein, RNA, or DNA.
protected HasSeqFeatures.SeqFeatures_list	seqFeatures Association to annotations for subsequences.
protected HasSequenceDatabases.SequenceDatabases_list	sequenceDatabases References an entry in a species database, like GenBank, UniGene, etc.
protected OntologyEntry	species The organism from which this sequence was obtained.
protected OntologyEntry	type The type of biosequence, i.e.

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

BioSequence()
Default constructor.

BioSequence(org.xml.sax.Attributes atts)
Attribute constructor.

Method Summary

void	addToOntologyEntries(int position, OntologyEntry ontologyEntry) Method to add OntologyEntry at position to OntologyEntries_list
void	addToOntologyEntries(OntologyEntry ontologyEntry) Method to add OntologyEntry to OntologyEntries_list
void	addToSeqFeatures(int position, SeqFeature seqFeature) Method to add SeqFeature at position to SeqFeatures_list
void	addToSeqFeatures(SeqFeature seqFeature) Method to add SeqFeature to SeqFeatures_list
void	addToSequenceDatabases(DatabaseEntry databaseEntry) Method to add DatabaseEntry to SequenceDatabases_list
void	addToSequenceDatabases(int position, DatabaseEntry databaseEntry) Method to add DatabaseEntry at position to SequenceDatabases_list
OntologyEntry	getFromOntologyEntries(int position) Method to get OntologyEntry from OntologyEntries_list
SeqFeature	getFromSeqFeatures(int position) Method to get SeqFeature from SeqFeatures_list
DatabaseEntry	getFromSequenceDatabases(int position) Method to get DatabaseEntry from SequenceDatabases_list
boolean	getIsApproximateLength() Get method for isApproximateLength
boolean	getIsCircular() Get method for isCircular
int	getLength() Get method for length
HasOntologyEntries.OntologyEntries_list	getOntologyEntries() Get method for ontologyEntries
OntologyEntry	getPolymerType() Get method for polymerType
HasSeqFeatures.SeqFeatures_list	getSeqFeatures() Get method for seqFeatures
java.lang.String	getSequence() Get method for sequence
HasSequenceDatabases.SequenceDatabases_list	getSequenceDatabases() Get method for sequenceDatabases
OntologyEntry	getSpecies() Get method for species
OntologyEntry	getType() Get method for type
void	removeElementAtFromOntologyEntries(int position) Method to remove by position from OntologyEntries_list
void	removeElementAtFromSeqFeatures(int position) Method to remove by position from SeqFeatures_list
void	removeElementAtFromSequenceDatabases(int position) Method to remove by position from SequenceDatabases_list
void	removeFromOntologyEntries(OntologyEntry ontologyEntry) Method to remove first OntologyEntry from OntologyEntries_list
void	removeFromSeqFeatures(SeqFeature seqFeature) Method to remove first SeqFeature from SeqFeatures_list
void	removeFromSequenceDatabases(DatabaseEntry databaseEntry) Method to remove first DatabaseEntry from SequenceDatabases_list
void	setIsApproximateLength(boolean isApproximateLength) Set method for isApproximateLength
void	setIsCircular(boolean isCircular) Set method for isCircular
void	setLength(int length) Set method for length
void	setOntologyEntries(HasOntologyEntries.OntologyEntries_list ontologyEntries) Set method for ontologyEntries
void	setPolymerType(OntologyEntry polymerType) Set method for polymerType
void	setSeqFeatures(HasSeqFeatures.SeqFeatures_list seqFeatures) Set method for seqFeatures
void	setSequence(java.lang.String sequence) Set method for sequence
void	setSequenceDatabases(HasSequenceDatabases.SequenceDatabases_list sequenceDatabases) Set method for sequenceDatabases
void	setSpecies(OntologyEntry species) Set method for species
void	setType(OntologyEntry type) Set method for type
void	writeAssociations(java.io.Writer out) writeAssociations This method is responsible for assembling the association data into XML.
void	writeAttributes(java.io.Writer out) writeAttributes This method is responsible for assembling the attribute data into XML.
void	writeMAGEML(java.io.Writer out) writeMAGEML This method is responsible for assembling the attribute and association data into XML.

Methods inherited from class org.biomage.Common.Identifiable

getIdentifier, getName, setIdentifier, setName

Methods inherited from class org.biomage.Common.Describable

addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAuditTrail, setDescriptions, setSecurity

Methods inherited from class org.biomage.Common.Extendable

addToPropertySets, addToPropertySets, getFromPropertySets, getPropertySets, removeElementAtFromPropertySets, removeFromPropertySets, setPropertySets

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

sequenceDatabases

protected HasSequenceDatabases.SequenceDatabases_list sequenceDatabases

References an entry in a species database, like GenBank, UniGene, etc.

ontologyEntries

protected HasOntologyEntries.OntologyEntries_list ontologyEntries

Ontology entries referring to common values associated with BioSequences, such as gene names, go ids, etc.

polymerType

protected OntologyEntry polymerType

A choice of protein, RNA, or DNA.

type

protected OntologyEntry type

The type of biosequence, i.e. gene, exon, UniGene cluster, fragment, BAC, EST, etc.

species

protected OntologyEntry species

The organism from which this sequence was obtained.

seqFeatures

protected HasSeqFeatures.SeqFeatures_list seqFeatures

Association to annotations for subsequences. Corresponds to the GenBank Frame Table.

Constructor Detail

BioSequence

public BioSequence()

Default constructor.

BioSequence

public BioSequence(org.xml.sax.Attributes atts)

Attribute constructor. Looks up the attributes in the parameter and casts them from strings appropriately

Method Detail

writeMAGEML

public void writeMAGEML(java.io.Writer out)
                 throws java.io.IOException

writeMAGEML This method is responsible for assembling the attribute and association data into XML. It creates the object tag and then calls the writeAttributes and writeAssociation methods.

Overrides:

writeMAGEML in class Identifiable

java.io.IOException

writeAttributes

public void writeAttributes(java.io.Writer out)
                     throws java.io.IOException

writeAttributes This method is responsible for assembling the attribute data into XML. It calls the super method to write out all attributes of this class and it's ancestors.

Overrides:

writeAttributes in class Identifiable

java.io.IOException

writeAssociations

public void writeAssociations(java.io.Writer out)
                       throws java.io.IOException

writeAssociations This method is responsible for assembling the association data into XML. It calls the super method to write out all associations of this class's ancestors.

Overrides:

writeAssociations in class Identifiable

java.io.IOException

setLength

public void setLength(int length)

Set method for length

getLength

public int getLength()

Get method for length

Returns:

value of the attribute

setIsApproximateLength

public void setIsApproximateLength(boolean isApproximateLength)

Set method for isApproximateLength

getIsApproximateLength

public boolean getIsApproximateLength()

Get method for isApproximateLength

Returns:

value of the attribute

setIsCircular

public void setIsCircular(boolean isCircular)

Set method for isCircular

getIsCircular

public boolean getIsCircular()

Get method for isCircular

Returns:

value of the attribute

setSequence

public void setSequence(java.lang.String sequence)

Set method for sequence

getSequence

public java.lang.String getSequence()

Get method for sequence

Returns:

value of the attribute

setSequenceDatabases

public void setSequenceDatabases(HasSequenceDatabases.SequenceDatabases_list sequenceDatabases)

Set method for sequenceDatabases

Specified by:

setSequenceDatabases in interface HasSequenceDatabases

getSequenceDatabases

public HasSequenceDatabases.SequenceDatabases_list getSequenceDatabases()

Get method for sequenceDatabases

Specified by:

getSequenceDatabases in interface HasSequenceDatabases

Returns:

value of the attribute

addToSequenceDatabases

public void addToSequenceDatabases(DatabaseEntry databaseEntry)

Method to add DatabaseEntry to SequenceDatabases_list

Specified by:

addToSequenceDatabases in interface HasSequenceDatabases

addToSequenceDatabases

public void addToSequenceDatabases(int position,
                                   DatabaseEntry databaseEntry)

Method to add DatabaseEntry at position to SequenceDatabases_list

Specified by:

addToSequenceDatabases in interface HasSequenceDatabases

getFromSequenceDatabases

public DatabaseEntry getFromSequenceDatabases(int position)

Method to get DatabaseEntry from SequenceDatabases_list

Specified by:

getFromSequenceDatabases in interface HasSequenceDatabases

removeElementAtFromSequenceDatabases

public void removeElementAtFromSequenceDatabases(int position)

Method to remove by position from SequenceDatabases_list

Specified by:

removeElementAtFromSequenceDatabases in interface HasSequenceDatabases

removeFromSequenceDatabases

public void removeFromSequenceDatabases(DatabaseEntry databaseEntry)

Method to remove first DatabaseEntry from SequenceDatabases_list

Specified by:

removeFromSequenceDatabases in interface HasSequenceDatabases

setOntologyEntries

public void setOntologyEntries(HasOntologyEntries.OntologyEntries_list ontologyEntries)

Set method for ontologyEntries

Specified by:

setOntologyEntries in interface HasOntologyEntries

getOntologyEntries

public HasOntologyEntries.OntologyEntries_list getOntologyEntries()

Get method for ontologyEntries

Specified by:

getOntologyEntries in interface HasOntologyEntries

Returns:

value of the attribute

addToOntologyEntries

public void addToOntologyEntries(OntologyEntry ontologyEntry)

Method to add OntologyEntry to OntologyEntries_list

Specified by:

addToOntologyEntries in interface HasOntologyEntries

addToOntologyEntries

public void addToOntologyEntries(int position,
                                 OntologyEntry ontologyEntry)

Method to add OntologyEntry at position to OntologyEntries_list

Specified by:

addToOntologyEntries in interface HasOntologyEntries

getFromOntologyEntries

public OntologyEntry getFromOntologyEntries(int position)

Method to get OntologyEntry from OntologyEntries_list

Specified by:

getFromOntologyEntries in interface HasOntologyEntries

removeElementAtFromOntologyEntries

public void removeElementAtFromOntologyEntries(int position)

Method to remove by position from OntologyEntries_list

Specified by:

removeElementAtFromOntologyEntries in interface HasOntologyEntries

removeFromOntologyEntries

public void removeFromOntologyEntries(OntologyEntry ontologyEntry)

Method to remove first OntologyEntry from OntologyEntries_list

Specified by:

removeFromOntologyEntries in interface HasOntologyEntries

setPolymerType

public void setPolymerType(OntologyEntry polymerType)

Set method for polymerType

Specified by:

setPolymerType in interface HasPolymerType

getPolymerType

public OntologyEntry getPolymerType()

Get method for polymerType

Specified by:

getPolymerType in interface HasPolymerType

Returns:

value of the attribute

setType

public void setType(OntologyEntry type)

Set method for type

Specified by:

setType in interface HasType

getType

public OntologyEntry getType()

Get method for type

Specified by:

getType in interface HasType

Returns:

value of the attribute

setSpecies

public void setSpecies(OntologyEntry species)

Set method for species

Specified by:

setSpecies in interface HasSpecies

getSpecies

public OntologyEntry getSpecies()

Get method for species

Specified by:

getSpecies in interface HasSpecies

Returns:

value of the attribute

setSeqFeatures

public void setSeqFeatures(HasSeqFeatures.SeqFeatures_list seqFeatures)

Set method for seqFeatures

Specified by:

setSeqFeatures in interface HasSeqFeatures

getSeqFeatures

public HasSeqFeatures.SeqFeatures_list getSeqFeatures()

Get method for seqFeatures

Specified by:

getSeqFeatures in interface HasSeqFeatures

Returns:

value of the attribute

addToSeqFeatures

public void addToSeqFeatures(SeqFeature seqFeature)

Method to add SeqFeature to SeqFeatures_list

Specified by:

addToSeqFeatures in interface HasSeqFeatures

addToSeqFeatures

public void addToSeqFeatures(int position,
                             SeqFeature seqFeature)

Method to add SeqFeature at position to SeqFeatures_list

Specified by:

addToSeqFeatures in interface HasSeqFeatures

getFromSeqFeatures

public SeqFeature getFromSeqFeatures(int position)

Method to get SeqFeature from SeqFeatures_list

Specified by:

getFromSeqFeatures in interface HasSeqFeatures

removeElementAtFromSeqFeatures

public void removeElementAtFromSeqFeatures(int position)

Method to remove by position from SeqFeatures_list

Specified by:

removeElementAtFromSeqFeatures in interface HasSeqFeatures

removeFromSeqFeatures

public void removeFromSeqFeatures(SeqFeature seqFeature)

Method to remove first SeqFeature from SeqFeatures_list

Specified by:

removeFromSeqFeatures in interface HasSeqFeatures