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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Common.Identifiable
org.biomage.BioSequence.BioSequence
public class BioSequence
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 |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasSequenceDatabases |
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HasSequenceDatabases.SequenceDatabases_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasOntologyEntries |
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HasOntologyEntries.OntologyEntries_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasSeqFeatures |
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HasSeqFeatures.SeqFeatures_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail |
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HasAuditTrail.AuditTrail_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions |
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HasDescriptions.Descriptions_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets |
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HasPropertySets.PropertySets_list |
Field Summary | |
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protected OntologyEntry |
polymerType
A choice of protein, RNA, or DNA. |
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 |
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security |
Fields inherited from class org.biomage.Common.Extendable |
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editable, id, securedElementId |
Constructor Summary | |
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BioSequence()
Default constructor. |
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BioSequence(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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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 |
boolean |
emptyMAGEobject()
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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 |
java.lang.Boolean |
getIsApproximateLength()
Get method for isApproximateLength |
java.lang.Boolean |
getIsCircular()
Get method for isCircular |
java.lang.Integer |
getLength()
Get method for length |
java.lang.String |
getModelClassName()
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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 |
setAttributes(org.xml.sax.Attributes atts)
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void |
setIsApproximateLength(java.lang.Boolean isApproximateLength)
Set method for isApproximateLength |
void |
setIsCircular(java.lang.Boolean isCircular)
Set method for isCircular |
void |
setLength(java.lang.Integer 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 |
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getIdentifier, getName, setIdentifier, setName, toString |
Methods inherited from class org.biomage.Common.Describable |
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addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAuditTrail, setDescriptions, setSecurity |
Methods inherited from class org.biomage.Common.Extendable |
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addToPropertySets, addToPropertySets, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId |
Methods inherited from class java.lang.Object |
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clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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protected OntologyEntry polymerType
protected OntologyEntry type
protected OntologyEntry species
Constructor Detail |
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public BioSequence()
public BioSequence(org.xml.sax.Attributes atts)
atts:
- the attribute list.Method Detail |
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public void setAttributes(org.xml.sax.Attributes atts)
setAttributes
in class Identifiable
public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class Identifiable
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class Identifiable
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class Identifiable
java.io.IOException
public void setLength(java.lang.Integer length)
value
- to setpublic java.lang.Integer getLength()
public void setIsApproximateLength(java.lang.Boolean isApproximateLength)
value
- to setpublic java.lang.Boolean getIsApproximateLength()
public void setIsCircular(java.lang.Boolean isCircular)
value
- to setpublic java.lang.Boolean getIsCircular()
public void setSequence(java.lang.String sequence)
value
- to setpublic java.lang.String getSequence()
public java.lang.String getModelClassName()
getModelClassName
in class Identifiable
public void setSequenceDatabases(HasSequenceDatabases.SequenceDatabases_list sequenceDatabases)
setSequenceDatabases
in interface HasSequenceDatabases
value
- to setpublic HasSequenceDatabases.SequenceDatabases_list getSequenceDatabases()
getSequenceDatabases
in interface HasSequenceDatabases
public void addToSequenceDatabases(DatabaseEntry databaseEntry)
addToSequenceDatabases
in interface HasSequenceDatabases
public void addToSequenceDatabases(int position, DatabaseEntry databaseEntry)
addToSequenceDatabases
in interface HasSequenceDatabases
public DatabaseEntry getFromSequenceDatabases(int position)
getFromSequenceDatabases
in interface HasSequenceDatabases
public void removeElementAtFromSequenceDatabases(int position)
removeElementAtFromSequenceDatabases
in interface HasSequenceDatabases
public void removeFromSequenceDatabases(DatabaseEntry databaseEntry)
removeFromSequenceDatabases
in interface HasSequenceDatabases
public void setOntologyEntries(HasOntologyEntries.OntologyEntries_list ontologyEntries)
setOntologyEntries
in interface HasOntologyEntries
value
- to setpublic HasOntologyEntries.OntologyEntries_list getOntologyEntries()
getOntologyEntries
in interface HasOntologyEntries
public void addToOntologyEntries(OntologyEntry ontologyEntry)
addToOntologyEntries
in interface HasOntologyEntries
public void addToOntologyEntries(int position, OntologyEntry ontologyEntry)
addToOntologyEntries
in interface HasOntologyEntries
public OntologyEntry getFromOntologyEntries(int position)
getFromOntologyEntries
in interface HasOntologyEntries
public void removeElementAtFromOntologyEntries(int position)
removeElementAtFromOntologyEntries
in interface HasOntologyEntries
public void removeFromOntologyEntries(OntologyEntry ontologyEntry)
removeFromOntologyEntries
in interface HasOntologyEntries
public void setPolymerType(OntologyEntry polymerType)
setPolymerType
in interface HasPolymerType
value
- to setpublic OntologyEntry getPolymerType()
getPolymerType
in interface HasPolymerType
public void setType(OntologyEntry type)
setType
in interface HasType
value
- to setpublic OntologyEntry getType()
getType
in interface HasType
public void setSpecies(OntologyEntry species)
setSpecies
in interface HasSpecies
value
- to setpublic OntologyEntry getSpecies()
getSpecies
in interface HasSpecies
public void setSeqFeatures(HasSeqFeatures.SeqFeatures_list seqFeatures)
setSeqFeatures
in interface HasSeqFeatures
value
- to setpublic HasSeqFeatures.SeqFeatures_list getSeqFeatures()
getSeqFeatures
in interface HasSeqFeatures
public void addToSeqFeatures(SeqFeature seqFeature)
addToSeqFeatures
in interface HasSeqFeatures
public void addToSeqFeatures(int position, SeqFeature seqFeature)
addToSeqFeatures
in interface HasSeqFeatures
public SeqFeature getFromSeqFeatures(int position)
getFromSeqFeatures
in interface HasSeqFeatures
public void removeElementAtFromSeqFeatures(int position)
removeElementAtFromSeqFeatures
in interface HasSeqFeatures
public void removeFromSeqFeatures(SeqFeature seqFeature)
removeFromSeqFeatures
in interface HasSeqFeatures
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