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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:

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

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public class BioSequence

extends org.biomage.Common.Identifiable

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

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

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Nested Class Summary

 

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

org.biomage.Interface.HasSequenceDatabases.SequenceDatabases_list

 

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

org.biomage.Interface.HasOntologyEntries.OntologyEntries_list

 

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

org.biomage.Interface.HasSeqFeatures.SeqFeatures_list

 

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

org.biomage.Interface.HasAuditTrail.AuditTrail_list

 

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

org.biomage.Interface.HasDescriptions.Descriptions_list

 

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

org.biomage.Interface.HasPropertySets.PropertySets_list

 

Field Summary
(package private)  boolean	isApproximateLength           If length not positively known will be true
(package private)  boolean	isCircular           Indicates if the BioSequence is circular in nature.
(package private)  int	length           The number of residues in the biosequence.
private  org.biomage.Interface.HasOntologyEntries.OntologyEntries_list	ontologyEntries           Ontology entries referring to common values associated with BioSequences, such as gene names, go ids, etc.
private  org.biomage.Description.OntologyEntry	polymerType           A choice of protein, RNA, or DNA.
private  org.biomage.Interface.HasSeqFeatures.SeqFeatures_list	seqFeatures           Association to annotations for subsequences.
(package private)  java.lang.String	sequence           The actual components of the sequence, for instance, for DNA a string consisting of A,T,C and G.
private  org.biomage.Interface.HasSequenceDatabases.SequenceDatabases_list	sequenceDatabases           References an entry in a species database, like GenBank, UniGene, etc.
private  org.biomage.Description.OntologyEntry	species           The organism from which this sequence was obtained.
private  org.biomage.Description.OntologyEntry	type           The type of biosequence, i.e.

 

Fields inherited from class org.biomage.Common.Identifiable

 

Fields inherited from class org.biomage.Common.Describable

 

Fields inherited from class org.biomage.Common.Extendable

 

Constructor Summary

BioSequence()           Default constructor.

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

 

Method Summary
void	addToOntologyEntries(int position, org.biomage.Description.OntologyEntry ontologyEntry)           Method to add OntologyEntry at position to OntologyEntries_list
void	addToOntologyEntries(org.biomage.Description.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(org.biomage.Description.DatabaseEntry databaseEntry)           Method to add DatabaseEntry to SequenceDatabases_list
void	addToSequenceDatabases(int position, org.biomage.Description.DatabaseEntry databaseEntry)           Method to add DatabaseEntry at position to SequenceDatabases_list
org.biomage.Description.OntologyEntry	getFromOntologyEntries(int position)           Method to get OntologyEntry from OntologyEntries_list
SeqFeature	getFromSeqFeatures(int position)           Method to get SeqFeature from SeqFeatures_list
org.biomage.Description.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
org.biomage.Interface.HasOntologyEntries.OntologyEntries_list	getOntologyEntries()           Get method for ontologyEntries
org.biomage.Description.OntologyEntry	getPolymerType()           Get method for polymerType
org.biomage.Interface.HasSeqFeatures.SeqFeatures_list	getSeqFeatures()           Get method for seqFeatures
java.lang.String	getSequence()           Get method for sequence
org.biomage.Interface.HasSequenceDatabases.SequenceDatabases_list	getSequenceDatabases()           Get method for sequenceDatabases
org.biomage.Description.OntologyEntry	getSpecies()           Get method for species
org.biomage.Description.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(org.biomage.Description.OntologyEntry ontologyEntry)           Method to remove first OntologyEntry from OntologyEntries_list
void	removeFromSeqFeatures(SeqFeature seqFeature)           Method to remove first SeqFeature from SeqFeatures_list
void	removeFromSequenceDatabases(org.biomage.Description.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(org.biomage.Interface.HasOntologyEntries.OntologyEntries_list ontologyEntries)           Set method for ontologyEntries
void	setPolymerType(org.biomage.Description.OntologyEntry polymerType)           Set method for polymerType
void	setSeqFeatures(org.biomage.Interface.HasSeqFeatures.SeqFeatures_list seqFeatures)           Set method for seqFeatures
void	setSequence(java.lang.String sequence)           Set method for sequence
void	setSequenceDatabases(org.biomage.Interface.HasSequenceDatabases.SequenceDatabases_list sequenceDatabases)           Set method for sequenceDatabases
void	setSpecies(org.biomage.Description.OntologyEntry species)           Set method for species
void	setType(org.biomage.Description.OntologyEntry type)           Set method for type
void	writeAssociations(java.io.Writer out)           writeAssociations
void	writeAttributes(java.io.Writer out)           writeAttributes
void	writeMAGEML(java.io.Writer out)           writeMAGEML

 

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

length

int length

The number of residues in the biosequence.

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isApproximateLength

boolean isApproximateLength

If length not positively known will be true

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isCircular

boolean isCircular

Indicates if the BioSequence is circular in nature.

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sequence

java.lang.String 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.

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sequenceDatabases

private org.biomage.Interface.HasSequenceDatabases.SequenceDatabases_list sequenceDatabases

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

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ontologyEntries

private org.biomage.Interface.HasOntologyEntries.OntologyEntries_list ontologyEntries

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

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polymerType

private org.biomage.Description.OntologyEntry polymerType

A choice of protein, RNA, or DNA.

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type

private org.biomage.Description.OntologyEntry type

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

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species

private org.biomage.Description.OntologyEntry species

The organism from which this sequence was obtained.

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seqFeatures

private org.biomage.Interface.HasSeqFeatures.SeqFeatures_list seqFeatures

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

Constructor Detail

BioSequence

public BioSequence()

Default constructor.

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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.

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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.

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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.

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setLength

public void setLength(int length)

Set method for length

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getLength

public int getLength()

Get method for length

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setIsApproximateLength

public void setIsApproximateLength(boolean isApproximateLength)

Set method for isApproximateLength

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getIsApproximateLength

public boolean getIsApproximateLength()

Get method for isApproximateLength

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setIsCircular

public void setIsCircular(boolean isCircular)

Set method for isCircular

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getIsCircular

public boolean getIsCircular()

Get method for isCircular

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setSequence

public void setSequence(java.lang.String sequence)

Set method for sequence

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getSequence

public java.lang.String getSequence()

Get method for sequence

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setSequenceDatabases

public void setSequenceDatabases(org.biomage.Interface.HasSequenceDatabases.SequenceDatabases_list sequenceDatabases)

Set method for sequenceDatabases

Specified by:

setSequenceDatabases in interface org.biomage.Interface.HasSequenceDatabases

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getSequenceDatabases

public org.biomage.Interface.HasSequenceDatabases.SequenceDatabases_list getSequenceDatabases()

Get method for sequenceDatabases

Specified by:

getSequenceDatabases in interface org.biomage.Interface.HasSequenceDatabases

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addToSequenceDatabases

public void addToSequenceDatabases(org.biomage.Description.DatabaseEntry databaseEntry)

Method to add DatabaseEntry to SequenceDatabases_list

Specified by:

addToSequenceDatabases in interface org.biomage.Interface.HasSequenceDatabases

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addToSequenceDatabases

public void addToSequenceDatabases(int position,
                                   org.biomage.Description.DatabaseEntry databaseEntry)

Method to add DatabaseEntry at position to SequenceDatabases_list

Specified by:

addToSequenceDatabases in interface org.biomage.Interface.HasSequenceDatabases

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getFromSequenceDatabases

public org.biomage.Description.DatabaseEntry getFromSequenceDatabases(int position)

Method to get DatabaseEntry from SequenceDatabases_list

Specified by:

getFromSequenceDatabases in interface org.biomage.Interface.HasSequenceDatabases

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removeElementAtFromSequenceDatabases

public void removeElementAtFromSequenceDatabases(int position)

Method to remove by position from SequenceDatabases_list

Specified by:

removeElementAtFromSequenceDatabases in interface org.biomage.Interface.HasSequenceDatabases

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removeFromSequenceDatabases

public void removeFromSequenceDatabases(org.biomage.Description.DatabaseEntry databaseEntry)

Method to remove first DatabaseEntry from SequenceDatabases_list

Specified by:

removeFromSequenceDatabases in interface org.biomage.Interface.HasSequenceDatabases

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setOntologyEntries

public void setOntologyEntries(org.biomage.Interface.HasOntologyEntries.OntologyEntries_list ontologyEntries)

Set method for ontologyEntries

Specified by:

setOntologyEntries in interface org.biomage.Interface.HasOntologyEntries

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getOntologyEntries

public org.biomage.Interface.HasOntologyEntries.OntologyEntries_list getOntologyEntries()

Get method for ontologyEntries

Specified by:

getOntologyEntries in interface org.biomage.Interface.HasOntologyEntries

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addToOntologyEntries

public void addToOntologyEntries(org.biomage.Description.OntologyEntry ontologyEntry)

Method to add OntologyEntry to OntologyEntries_list

Specified by:

addToOntologyEntries in interface org.biomage.Interface.HasOntologyEntries

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addToOntologyEntries

public void addToOntologyEntries(int position,
                                 org.biomage.Description.OntologyEntry ontologyEntry)

Method to add OntologyEntry at position to OntologyEntries_list

Specified by:

addToOntologyEntries in interface org.biomage.Interface.HasOntologyEntries

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getFromOntologyEntries

public org.biomage.Description.OntologyEntry getFromOntologyEntries(int position)

Method to get OntologyEntry from OntologyEntries_list

Specified by:

getFromOntologyEntries in interface org.biomage.Interface.HasOntologyEntries

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removeElementAtFromOntologyEntries

public void removeElementAtFromOntologyEntries(int position)

Method to remove by position from OntologyEntries_list

Specified by:

removeElementAtFromOntologyEntries in interface org.biomage.Interface.HasOntologyEntries

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removeFromOntologyEntries

public void removeFromOntologyEntries(org.biomage.Description.OntologyEntry ontologyEntry)

Method to remove first OntologyEntry from OntologyEntries_list

Specified by:

removeFromOntologyEntries in interface org.biomage.Interface.HasOntologyEntries

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setPolymerType

public void setPolymerType(org.biomage.Description.OntologyEntry polymerType)

Set method for polymerType

Specified by:

setPolymerType in interface org.biomage.Interface.HasPolymerType

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getPolymerType

public org.biomage.Description.OntologyEntry getPolymerType()

Get method for polymerType

Specified by:

getPolymerType in interface org.biomage.Interface.HasPolymerType

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setType

public void setType(org.biomage.Description.OntologyEntry type)

Set method for type

Specified by:

setType in interface org.biomage.Interface.HasType

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getType

public org.biomage.Description.OntologyEntry getType()

Get method for type

Specified by:

getType in interface org.biomage.Interface.HasType

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setSpecies

public void setSpecies(org.biomage.Description.OntologyEntry species)

Set method for species

Specified by:

setSpecies in interface org.biomage.Interface.HasSpecies

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getSpecies

public org.biomage.Description.OntologyEntry getSpecies()

Get method for species

Specified by:

getSpecies in interface org.biomage.Interface.HasSpecies

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setSeqFeatures

public void setSeqFeatures(org.biomage.Interface.HasSeqFeatures.SeqFeatures_list seqFeatures)

Set method for seqFeatures

Specified by:

setSeqFeatures in interface org.biomage.Interface.HasSeqFeatures

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getSeqFeatures

public org.biomage.Interface.HasSeqFeatures.SeqFeatures_list getSeqFeatures()

Get method for seqFeatures

Specified by:

getSeqFeatures in interface org.biomage.Interface.HasSeqFeatures

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addToSeqFeatures

public void addToSeqFeatures(SeqFeature seqFeature)

Method to add SeqFeature to SeqFeatures_list

Specified by:

addToSeqFeatures in interface org.biomage.Interface.HasSeqFeatures

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addToSeqFeatures

public void addToSeqFeatures(int position,
                             SeqFeature seqFeature)

Method to add SeqFeature at position to SeqFeatures_list

Specified by:

addToSeqFeatures in interface org.biomage.Interface.HasSeqFeatures

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getFromSeqFeatures

public SeqFeature getFromSeqFeatures(int position)

Method to get SeqFeature from SeqFeatures_list

Specified by:

getFromSeqFeatures in interface org.biomage.Interface.HasSeqFeatures

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removeElementAtFromSeqFeatures

public void removeElementAtFromSeqFeatures(int position)

Method to remove by position from SeqFeatures_list

Specified by:

removeElementAtFromSeqFeatures in interface org.biomage.Interface.HasSeqFeatures

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removeFromSeqFeatures

public void removeFromSeqFeatures(SeqFeature seqFeature)

Method to remove first SeqFeature from SeqFeatures_list

Specified by:

removeFromSeqFeatures in interface org.biomage.Interface.HasSeqFeatures

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> biomage >> [ BioSequence overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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