gov.nih.nci.mageom.domain.BioSequence.impl
Class BioSequenceImpl

java.lang.Object
  extended by gov.nih.nci.mageom.domain.impl.MAGEOMObject
      extended by gov.nih.nci.mageom.domain.impl.ExtendableImpl
          extended by gov.nih.nci.mageom.domain.impl.DescribableImpl
              extended by gov.nih.nci.mageom.domain.impl.IdentifiableImpl
                  extended by gov.nih.nci.mageom.domain.BioSequence.impl.BioSequenceImpl
All Implemented Interfaces:
BioSequence, Describable, Extendable, Identifiable, java.io.Serializable

public class BioSequenceImpl
extends IdentifiableImpl
implements BioSequence

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%
See Also:
Serialized Form

Field Summary
protected static java.util.ArrayList allAssociationMethods
           
protected static java.util.Hashtable associationMethods
           
protected  java.lang.Boolean isApproximateLength
          If length not positively known will be true
protected  java.lang.Boolean isCircular
          Indicates if the BioSequence is circular in nature.
protected  java.lang.Integer length
          The number of residues in the biosequence.
protected  OntologyEntry[] ontologyEntries
          DOCUMENT ME
protected  int ontologyEntriesCount
          The count of OntologyEntry objects.
protected  OntologyEntry polymerType
          DOCUMENT ME
protected  java.lang.Long polymerTypeId
          The internal ID of the associated polymerType object.
protected  SeqFeature[] seqFeatures
          DOCUMENT ME
protected  int seqFeaturesCount
          The count of SeqFeature objects.
protected  java.lang.String sequence
          The actual components of the sequence, for instance, for DNA a string consisting of A,T,C and G.
protected  DatabaseEntry[] sequenceDatabases
          DOCUMENT ME
protected  int sequenceDatabasesCount
          The count of DatabaseEntry objects.
protected  OntologyEntry species
          DOCUMENT ME
protected  java.lang.Long speciesId
          The internal ID of the associated species object.
protected  OntologyEntry type
          DOCUMENT ME
protected  java.lang.Long typeId
          The internal ID of the associated type object.
 
Fields inherited from class gov.nih.nci.mageom.domain.impl.IdentifiableImpl
identifier, name
 
Fields inherited from class gov.nih.nci.mageom.domain.impl.DescribableImpl
auditTrail, auditTrailCount, descriptions, descriptionsCount, security, securityId
 
Fields inherited from class gov.nih.nci.mageom.domain.impl.ExtendableImpl
propertySets, propertySetsCount, securedElementId
 
Constructor Summary
BioSequenceImpl()
          Default constructor
 
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.
 int getOntologyEntriesCount()
          Returns the count of all OntologyEntry associated with this BioSequence object.
 OntologyEntry getPolymerType()
          Returns the value of this BioSequence object's polymerType attribute.
 SeqFeature[] getSeqFeatures()
          Returns the value of this BioSequence object's seqFeatures attribute.
 int getSeqFeaturesCount()
          Returns the count of all SeqFeature associated with this BioSequence object.
 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.
 int getSequenceDatabasesCount()
          Returns the count of all DatabaseEntry associated with this BioSequence object.
 OntologyEntry getSpecies()
          Returns the value of this BioSequence object's species attribute.
 OntologyEntry getType()
          Returns the value of this BioSequence object's type attribute.
 java.util.Hashtable getXMLMethodDescriptors()
          Returns a Hashtable containing XMLMethodDescriptors descriptors of the association methods of this object.
protected  void init()
           
 BioSequence[] searchBioSequences(BioSequenceSearchCriteria criteria)
          Returns an array of BioSequence objects that satisfy the given BioSequenceSearchCriteria.
 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.
 java.lang.String toString()
          Returns a String representation of this object suitable for console display.
 org.w3c.dom.Element toXML(org.w3c.dom.Document doc)
           
 org.w3c.dom.Element toXMLDoc(org.w3c.dom.Document doc)
           
 org.w3c.dom.Element toXMLProcessor(org.w3c.dom.Document doc, java.util.ArrayList fillOutValues)
          Returns an XML representation of the object.
 
Methods inherited from class gov.nih.nci.mageom.domain.impl.IdentifiableImpl
getIdentifier, getName, searchIdentifiables, setIdentifier, setName
 
Methods inherited from class gov.nih.nci.mageom.domain.impl.DescribableImpl
getAuditTrail, getAuditTrailCount, getDescriptions, getDescriptionsCount, getSecurity, searchDescribables, setAuditTrail, setDescriptions, setSecurity
 
Methods inherited from class gov.nih.nci.mageom.domain.impl.ExtendableImpl
getPropertySets, getPropertySetsCount, getSecuredElementId, searchExtendables, setPropertySets, setSecuredElementId
 
Methods inherited from class gov.nih.nci.mageom.domain.impl.MAGEOMObject
getId, getIsEditable, setId
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 
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
 

Field Detail

allAssociationMethods

protected static java.util.ArrayList allAssociationMethods

associationMethods

protected static java.util.Hashtable associationMethods

length

protected java.lang.Integer length
The number of residues in the biosequence.


isApproximateLength

protected java.lang.Boolean isApproximateLength
If length not positively known will be true


isCircular

protected java.lang.Boolean isCircular
Indicates if the BioSequence is circular in nature.


sequence

protected java.lang.String sequence
The actual components of the sequence, for instance, for DNA a string consisting of A,T,C and G. attribute is optional and instead of specified here, can be found through the DatabaseEntry.


seqFeaturesCount

protected int seqFeaturesCount
The count of SeqFeature objects.


seqFeatures

protected SeqFeature[] seqFeatures
DOCUMENT ME


ontologyEntriesCount

protected int ontologyEntriesCount
The count of OntologyEntry objects.


ontologyEntries

protected OntologyEntry[] ontologyEntries
DOCUMENT ME


polymerType

protected OntologyEntry polymerType
DOCUMENT ME


polymerTypeId

protected java.lang.Long polymerTypeId
The internal ID of the associated polymerType object.


sequenceDatabasesCount

protected int sequenceDatabasesCount
The count of DatabaseEntry objects.


sequenceDatabases

protected DatabaseEntry[] sequenceDatabases
DOCUMENT ME


type

protected OntologyEntry type
DOCUMENT ME


typeId

protected java.lang.Long typeId
The internal ID of the associated type object.


species

protected OntologyEntry species
DOCUMENT ME


speciesId

protected java.lang.Long speciesId
The internal ID of the associated species object.

Constructor Detail

BioSequenceImpl

public BioSequenceImpl()
Default constructor

Method Detail

init

protected void init()
Overrides:
init in class IdentifiableImpl

searchBioSequences

public BioSequence[] searchBioSequences(BioSequenceSearchCriteria criteria)
                                 throws gov.nih.nci.common.search.SearchException
Returns an array of BioSequence objects that satisfy the given BioSequenceSearchCriteria.

Parameters:
criteria - The BioSequenceSearchCriteria which represents a query for BioSequence objects.
Returns:
An array of BioSequence objects.
Throws:
A - gov.nih.nci.common.search.SearchException if there is a problem searching.
gov.nih.nci.common.search.SearchException

setLength

public 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.

Specified by:
setLength in interface BioSequence
Parameters:
p_length - The new value for length.
See Also:
BioSequence.getLength()

getLength

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

Specified by:
getLength in interface BioSequence
Returns:
int The value of length.
See Also:
BioSequence.getLength()

setIsApproximateLength

public 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.

Specified by:
setIsApproximateLength in interface BioSequence
Parameters:
p_isApproximateLength - The new value for isApproximateLength.
See Also:
BioSequence.getIsApproximateLength()

getIsApproximateLength

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

Specified by:
getIsApproximateLength in interface BioSequence
Returns:
boolean The value of isApproximateLength.
See Also:
BioSequence.getIsApproximateLength()

setIsCircular

public 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.

Specified by:
setIsCircular in interface BioSequence
Parameters:
p_isCircular - The new value for isCircular.
See Also:
BioSequence.getIsCircular()

getIsCircular

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

Specified by:
getIsCircular in interface BioSequence
Returns:
boolean The value of isCircular.
See Also:
BioSequence.getIsCircular()

setSequence

public 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.

Specified by:
setSequence in interface BioSequence
Parameters:
p_sequence - The new value for sequence.
See Also:
BioSequence.getSequence()

getSequence

public java.lang.String getSequence()
Description copied from interface: BioSequence
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.

Specified by:
getSequence in interface BioSequence
Returns:
String The value of sequence.
See Also:
BioSequence.getSequence()

setSeqFeatures

public 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.

Specified by:
setSeqFeatures in interface BioSequence
Parameters:
p_seqFeatures - The new value for seqFeatures.
See Also:
BioSequence.getSeqFeatures()

getSeqFeatures

public SeqFeature[] getSeqFeatures()
Description copied from interface: BioSequence
Returns the value of this BioSequence object's seqFeatures attribute.

Specified by:
getSeqFeatures in interface BioSequence
Returns:
gov.nih.nci.mageom.bean.BioSequence.SeqFeature[] The value of seqFeatures.
See Also:
BioSequence.getSeqFeatures()

setOntologyEntries

public 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.

Specified by:
setOntologyEntries in interface BioSequence
Parameters:
p_ontologyEntries - The new value for ontologyEntries.
See Also:
BioSequence.getOntologyEntries()

getOntologyEntries

public OntologyEntry[] getOntologyEntries()
Description copied from interface: BioSequence
Returns the value of this BioSequence object's ontologyEntries attribute.

Specified by:
getOntologyEntries in interface BioSequence
Returns:
gov.nih.nci.mageom.bean.Description.OntologyEntry[] The value of ontologyEntries.
See Also:
BioSequence.getOntologyEntries()

setPolymerType

public 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.

Specified by:
setPolymerType in interface BioSequence
Parameters:
p_polymerType - The new value for polymerType.
See Also:
BioSequence.getPolymerType()

getPolymerType

public OntologyEntry getPolymerType()
Description copied from interface: BioSequence
Returns the value of this BioSequence object's polymerType attribute.

Specified by:
getPolymerType in interface BioSequence
Returns:
gov.nih.nci.mageom.bean.Description.OntologyEntry The value of polymerType.
See Also:
BioSequence.getPolymerType()

setSequenceDatabases

public 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.

Specified by:
setSequenceDatabases in interface BioSequence
Parameters:
p_sequenceDatabases - The new value for sequenceDatabases.
See Also:
BioSequence.getSequenceDatabases()

getSequenceDatabases

public DatabaseEntry[] getSequenceDatabases()
Description copied from interface: BioSequence
Returns the value of this BioSequence object's sequenceDatabases attribute.

Specified by:
getSequenceDatabases in interface BioSequence
Returns:
gov.nih.nci.mageom.bean.Description.DatabaseEntry[] The value of sequenceDatabases.
See Also:
BioSequence.getSequenceDatabases()

setType

public 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.

Specified by:
setType in interface BioSequence
Parameters:
p_type - The new value for type.
See Also:
BioSequence.getType()

getType

public OntologyEntry getType()
Description copied from interface: BioSequence
Returns the value of this BioSequence object's type attribute.

Specified by:
getType in interface BioSequence
Returns:
gov.nih.nci.mageom.bean.Description.OntologyEntry The value of type.
See Also:
BioSequence.getType()

setSpecies

public 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.

Specified by:
setSpecies in interface BioSequence
Parameters:
p_species - The new value for species.
See Also:
BioSequence.getSpecies()

getSpecies

public OntologyEntry getSpecies()
Description copied from interface: BioSequence
Returns the value of this BioSequence object's species attribute.

Specified by:
getSpecies in interface BioSequence
Returns:
gov.nih.nci.mageom.bean.Description.OntologyEntry The value of species.
See Also:
BioSequence.getSpecies()

getSeqFeaturesCount

public int getSeqFeaturesCount()
Returns the count of all SeqFeature associated with this BioSequence object.

Returns:
the count
See Also:
BioSequence.getSeqFeatures()

getOntologyEntriesCount

public int getOntologyEntriesCount()
Returns the count of all OntologyEntry associated with this BioSequence object.

Returns:
the count
See Also:
BioSequence.getOntologyEntries()

getSequenceDatabasesCount

public int getSequenceDatabasesCount()
Returns the count of all DatabaseEntry associated with this BioSequence object.

Returns:
the count
See Also:
BioSequence.getSequenceDatabases()

toXML

public org.w3c.dom.Element toXML(org.w3c.dom.Document doc)
Overrides:
toXML in class IdentifiableImpl

toXMLDoc

public org.w3c.dom.Element toXMLDoc(org.w3c.dom.Document doc)
Overrides:
toXMLDoc in class IdentifiableImpl

toXMLProcessor

public org.w3c.dom.Element toXMLProcessor(org.w3c.dom.Document doc,
                                          java.util.ArrayList fillOutValues)
Returns an XML representation of the object. The document is not modified.

Overrides:
toXMLProcessor in class IdentifiableImpl
Parameters:
doc - the working document
fillOutValues - a list of attribute names that should have full XML for their values.
Returns:
org.w3c.dom.Element an XML representation

getXMLMethodDescriptors

public java.util.Hashtable getXMLMethodDescriptors()
Returns a Hashtable containing XMLMethodDescriptors descriptors of the association methods of this object.

Overrides:
getXMLMethodDescriptors in class IdentifiableImpl
Returns:
Hashtable The Hashtable of descriptors.

toString

public java.lang.String toString()
Returns a String representation of this object suitable for console display.

Overrides:
toString in class IdentifiableImpl
Returns:
the String representation.