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org.biomage.BioSequence
Class BioSequence  view BioSequence download BioSequence.java

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Common.Identifiable
              extended byorg.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

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.


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.


isApproximateLength

boolean isApproximateLength
If length not positively known will be true


isCircular

boolean isCircular
Indicates if the BioSequence is circular in nature.


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.


sequenceDatabases

private org.biomage.Interface.HasSequenceDatabases.SequenceDatabases_list sequenceDatabases
References an entry in a species database, like GenBank, UniGene, etc.


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.


polymerType

private org.biomage.Description.OntologyEntry polymerType
A choice of protein, RNA, or DNA.


type

private org.biomage.Description.OntologyEntry type
The type of biosequence, i.e. gene, exon, UniGene cluster, fragment, BAC, EST, etc.


species

private org.biomage.Description.OntologyEntry species
The organism from which this sequence was obtained.


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.


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.


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.


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.


setLength

public void setLength(int length)
Set method for length


getLength

public int getLength()
Get method for length


setIsApproximateLength

public void setIsApproximateLength(boolean isApproximateLength)
Set method for isApproximateLength


getIsApproximateLength

public boolean getIsApproximateLength()
Get method for isApproximateLength


setIsCircular

public void setIsCircular(boolean isCircular)
Set method for isCircular


getIsCircular

public boolean getIsCircular()
Get method for isCircular


setSequence

public void setSequence(java.lang.String sequence)
Set method for sequence


getSequence

public java.lang.String getSequence()
Get method for sequence


setSequenceDatabases

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

Specified by:
setSequenceDatabases in interface org.biomage.Interface.HasSequenceDatabases

getSequenceDatabases

public org.biomage.Interface.HasSequenceDatabases.SequenceDatabases_list getSequenceDatabases()
Get method for sequenceDatabases

Specified by:
getSequenceDatabases in interface org.biomage.Interface.HasSequenceDatabases

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

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

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

removeElementAtFromSequenceDatabases

public void removeElementAtFromSequenceDatabases(int position)
Method to remove by position from SequenceDatabases_list

Specified by:
removeElementAtFromSequenceDatabases in interface org.biomage.Interface.HasSequenceDatabases

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

setOntologyEntries

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

Specified by:
setOntologyEntries in interface org.biomage.Interface.HasOntologyEntries

getOntologyEntries

public org.biomage.Interface.HasOntologyEntries.OntologyEntries_list getOntologyEntries()
Get method for ontologyEntries

Specified by:
getOntologyEntries in interface org.biomage.Interface.HasOntologyEntries

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

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

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

removeElementAtFromOntologyEntries

public void removeElementAtFromOntologyEntries(int position)
Method to remove by position from OntologyEntries_list

Specified by:
removeElementAtFromOntologyEntries in interface org.biomage.Interface.HasOntologyEntries

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

setPolymerType

public void setPolymerType(org.biomage.Description.OntologyEntry polymerType)
Set method for polymerType

Specified by:
setPolymerType in interface org.biomage.Interface.HasPolymerType

getPolymerType

public org.biomage.Description.OntologyEntry getPolymerType()
Get method for polymerType

Specified by:
getPolymerType in interface org.biomage.Interface.HasPolymerType

setType

public void setType(org.biomage.Description.OntologyEntry type)
Set method for type

Specified by:
setType in interface org.biomage.Interface.HasType

getType

public org.biomage.Description.OntologyEntry getType()
Get method for type

Specified by:
getType in interface org.biomage.Interface.HasType

setSpecies

public void setSpecies(org.biomage.Description.OntologyEntry species)
Set method for species

Specified by:
setSpecies in interface org.biomage.Interface.HasSpecies

getSpecies

public org.biomage.Description.OntologyEntry getSpecies()
Get method for species

Specified by:
getSpecies in interface org.biomage.Interface.HasSpecies

setSeqFeatures

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

Specified by:
setSeqFeatures in interface org.biomage.Interface.HasSeqFeatures

getSeqFeatures

public org.biomage.Interface.HasSeqFeatures.SeqFeatures_list getSeqFeatures()
Get method for seqFeatures

Specified by:
getSeqFeatures in interface org.biomage.Interface.HasSeqFeatures

addToSeqFeatures

public void addToSeqFeatures(SeqFeature seqFeature)
Method to add SeqFeature to SeqFeatures_list

Specified by:
addToSeqFeatures in interface org.biomage.Interface.HasSeqFeatures

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

getFromSeqFeatures

public SeqFeature getFromSeqFeatures(int position)
Method to get SeqFeature from SeqFeatures_list

Specified by:
getFromSeqFeatures in interface org.biomage.Interface.HasSeqFeatures

removeElementAtFromSeqFeatures

public void removeElementAtFromSeqFeatures(int position)
Method to remove by position from SeqFeatures_list

Specified by:
removeElementAtFromSeqFeatures in interface org.biomage.Interface.HasSeqFeatures

removeFromSeqFeatures

public void removeFromSeqFeatures(SeqFeature seqFeature)
Method to remove first SeqFeature from SeqFeatures_list

Specified by:
removeFromSeqFeatures in interface org.biomage.Interface.HasSeqFeatures