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java.lang.Objectgov.nih.nci.mageom.domain.impl.MAGEOMObject
gov.nih.nci.mageom.domain.impl.ExtendableImpl
gov.nih.nci.mageom.domain.impl.DescribableImpl
gov.nih.nci.mageom.domain.impl.IdentifiableImpl
gov.nih.nci.mageom.domain.BioSequence.impl.BioSequenceImpl
public class BioSequenceImpl
A BioSequence is a representation of a DNA, RNA, or protein sequence. It can be represented by a Clone, Gene, or the sequence.
| 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 |
|---|
protected static java.util.ArrayList allAssociationMethods
protected static java.util.Hashtable associationMethods
protected java.lang.Integer length
protected java.lang.Boolean isApproximateLength
protected java.lang.Boolean isCircular
protected java.lang.String sequence
protected int seqFeaturesCount
protected SeqFeature[] seqFeatures
protected int ontologyEntriesCount
protected OntologyEntry[] ontologyEntries
protected OntologyEntry polymerType
protected java.lang.Long polymerTypeId
protected int sequenceDatabasesCount
protected DatabaseEntry[] sequenceDatabases
protected OntologyEntry type
protected java.lang.Long typeId
protected OntologyEntry species
protected java.lang.Long speciesId
| Constructor Detail |
|---|
public BioSequenceImpl()
| Method Detail |
|---|
protected void init()
init in class IdentifiableImpl
public BioSequence[] searchBioSequences(BioSequenceSearchCriteria criteria)
throws gov.nih.nci.common.search.SearchException
BioSequence objects that
satisfy the given BioSequenceSearchCriteria.
criteria - The BioSequenceSearchCriteria
which represents a query for BioSequence objects.
BioSequence objects.
A - gov.nih.nci.common.search.SearchException if there is a problem searching.
gov.nih.nci.common.search.SearchExceptionpublic void setLength(java.lang.Integer p_length)
BioSequence object.
setLength in interface BioSequencep_length - The new value for length.BioSequence.getLength()public java.lang.Integer getLength()
BioSequenceBioSequence object's length attribute.
Description of length:
The number of residues in the biosequence.
getLength in interface BioSequenceint The value of length.BioSequence.getLength()public void setIsApproximateLength(java.lang.Boolean p_isApproximateLength)
BioSequence object.
setIsApproximateLength in interface BioSequencep_isApproximateLength - The new value for isApproximateLength.BioSequence.getIsApproximateLength()public java.lang.Boolean getIsApproximateLength()
BioSequenceBioSequence object's isApproximateLength attribute.
Description of isApproximateLength:
If length not positively known will be true
getIsApproximateLength in interface BioSequenceboolean The value of isApproximateLength.BioSequence.getIsApproximateLength()public void setIsCircular(java.lang.Boolean p_isCircular)
BioSequence object.
setIsCircular in interface BioSequencep_isCircular - The new value for isCircular.BioSequence.getIsCircular()public java.lang.Boolean getIsCircular()
BioSequenceBioSequence object's isCircular attribute.
Description of isCircular:
Indicates if the BioSequence is circular in nature.
getIsCircular in interface BioSequenceboolean The value of isCircular.BioSequence.getIsCircular()public void setSequence(java.lang.String p_sequence)
BioSequence object.
setSequence in interface BioSequencep_sequence - The new value for sequence.BioSequence.getSequence()public java.lang.String getSequence()
BioSequenceBioSequence 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.
getSequence in interface BioSequenceString The value of sequence.BioSequence.getSequence()public void setSeqFeatures(SeqFeature[] p_seqFeatures)
BioSequence object.
setSeqFeatures in interface BioSequencep_seqFeatures - The new value for seqFeatures.BioSequence.getSeqFeatures()public SeqFeature[] getSeqFeatures()
BioSequenceBioSequence object's seqFeatures attribute.
getSeqFeatures in interface BioSequencegov.nih.nci.mageom.bean.BioSequence.SeqFeature[] The value of seqFeatures.BioSequence.getSeqFeatures()public void setOntologyEntries(OntologyEntry[] p_ontologyEntries)
BioSequence object.
setOntologyEntries in interface BioSequencep_ontologyEntries - The new value for ontologyEntries.BioSequence.getOntologyEntries()public OntologyEntry[] getOntologyEntries()
BioSequenceBioSequence object's ontologyEntries attribute.
getOntologyEntries in interface BioSequencegov.nih.nci.mageom.bean.Description.OntologyEntry[] The value of ontologyEntries.BioSequence.getOntologyEntries()public void setPolymerType(OntologyEntry p_polymerType)
BioSequence object.
setPolymerType in interface BioSequencep_polymerType - The new value for polymerType.BioSequence.getPolymerType()public OntologyEntry getPolymerType()
BioSequenceBioSequence object's polymerType attribute.
getPolymerType in interface BioSequencegov.nih.nci.mageom.bean.Description.OntologyEntry The value of polymerType.BioSequence.getPolymerType()public void setSequenceDatabases(DatabaseEntry[] p_sequenceDatabases)
BioSequence object.
setSequenceDatabases in interface BioSequencep_sequenceDatabases - The new value for sequenceDatabases.BioSequence.getSequenceDatabases()public DatabaseEntry[] getSequenceDatabases()
BioSequenceBioSequence object's sequenceDatabases attribute.
getSequenceDatabases in interface BioSequencegov.nih.nci.mageom.bean.Description.DatabaseEntry[] The value of sequenceDatabases.BioSequence.getSequenceDatabases()public void setType(OntologyEntry p_type)
BioSequence object.
setType in interface BioSequencep_type - The new value for type.BioSequence.getType()public OntologyEntry getType()
BioSequenceBioSequence object's type attribute.
getType in interface BioSequencegov.nih.nci.mageom.bean.Description.OntologyEntry The value of type.BioSequence.getType()public void setSpecies(OntologyEntry p_species)
BioSequence object.
setSpecies in interface BioSequencep_species - The new value for species.BioSequence.getSpecies()public OntologyEntry getSpecies()
BioSequenceBioSequence object's species attribute.
getSpecies in interface BioSequencegov.nih.nci.mageom.bean.Description.OntologyEntry The value of species.BioSequence.getSpecies()public int getSeqFeaturesCount()
SeqFeature
associated with this BioSequence object.
BioSequence.getSeqFeatures()public int getOntologyEntriesCount()
OntologyEntry
associated with this BioSequence object.
BioSequence.getOntologyEntries()public int getSequenceDatabasesCount()
DatabaseEntry
associated with this BioSequence object.
BioSequence.getSequenceDatabases()public org.w3c.dom.Element toXML(org.w3c.dom.Document doc)
toXML in class IdentifiableImplpublic org.w3c.dom.Element toXMLDoc(org.w3c.dom.Document doc)
toXMLDoc in class IdentifiableImpl
public org.w3c.dom.Element toXMLProcessor(org.w3c.dom.Document doc,
java.util.ArrayList fillOutValues)
toXMLProcessor in class IdentifiableImpldoc - the working documentfillOutValues - a list of attribute names that should have
full XML for their values.
public java.util.Hashtable getXMLMethodDescriptors()
XMLMethodDescriptors descriptors of
the association methods of this object.
getXMLMethodDescriptors in class IdentifiableImplpublic java.lang.String toString()
toString in class IdentifiableImpl
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