org.biomage.BioSequence
Class SeqFeature

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.BioSequence.SeqFeature

All Implemented Interfaces:

HasAuditTrail, HasDescriptions, HasPropertySets, HasRegions, HasSecurity, java.io.Serializable

public class SeqFeature

extends Describable

implements java.io.Serializable, HasRegions

Represents, in general, what would be a GenBank Feature Table annotation for a sequence.

See Also:

Serialized Form

Nested Class Summary

class

SeqFeature.Basis Inner class for the enumeration values that the attribute basis can assume.

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

HasRegions.Regions_list

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

HasAuditTrail.AuditTrail_list

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

HasDescriptions.Descriptions_list

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

HasPropertySets.PropertySets_list

Field Summary

protected HasRegions.Regions_list

regions Association to classes that describe the location with the sequence of the SeqFeature.

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

SeqFeature()
Default constructor.

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

Method Summary

void	addToRegions(int position, SeqFeatureLocation seqFeatureLocation) Method to add SeqFeatureLocation at position to Regions_list
void	addToRegions(SeqFeatureLocation seqFeatureLocation) Method to add SeqFeatureLocation to Regions_list
SeqFeature.Basis	getBasis() Get method for basis
SeqFeatureLocation	getFromRegions(int position) Method to get SeqFeatureLocation from Regions_list
java.lang.String	getNameBasis() Return the current name of the Enumeration type of Basis.
java.lang.String	getNameByValueBasis(int val) For Basis get the Name of the Enumeration type by passing a Value to it.
HasRegions.Regions_list	getRegions() Get method for regions
int	getValueBasis() Return the currrent value of the Enumeration type of Basis.
int	getValueByNameBasis(java.lang.String name) For Basis get the Value of the Enumeration type by passing a Name to it.
void	removeElementAtFromRegions(int position) Method to remove by position from Regions_list
void	removeFromRegions(SeqFeatureLocation seqFeatureLocation) Method to remove first SeqFeatureLocation from Regions_list
void	setBasis(SeqFeature.Basis basis) Set method for basis
java.lang.String	setNameByValueBasis(int val) For Basis set the Name of the Enumeration type by passing a value (int)
void	setRegions(HasRegions.Regions_list regions) Set method for regions
int	setValueByNameBasis(java.lang.String name) For Basis set the Value of the Enumeration type by passing a Name to it.
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.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

regions

protected HasRegions.Regions_list regions

Association to classes that describe the location with the sequence of the SeqFeature.

Constructor Detail

SeqFeature

public SeqFeature()

Default constructor.

SeqFeature

public SeqFeature(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.

Overrides:

writeMAGEML in class Describable

java.io.IOException

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.

Overrides:

writeAttributes in class Describable

java.io.IOException

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.

Overrides:

writeAssociations in class Describable

java.io.IOException

setBasis

public void setBasis(SeqFeature.Basis basis)

Set method for basis

getBasis

public SeqFeature.Basis getBasis()

Get method for basis

Returns:

value of the attribute

setNameByValueBasis

public java.lang.String setNameByValueBasis(int val)

For Basis set the Name of the Enumeration type by passing a value (int)

setValueByNameBasis

public int setValueByNameBasis(java.lang.String name)

For Basis set the Value of the Enumeration type by passing a Name to it.

getNameByValueBasis

public java.lang.String getNameByValueBasis(int val)

For Basis get the Name of the Enumeration type by passing a Value to it.

getValueByNameBasis

public int getValueByNameBasis(java.lang.String name)

For Basis get the Value of the Enumeration type by passing a Name to it.

getNameBasis

public java.lang.String getNameBasis()

Return the current name of the Enumeration type of Basis.

getValueBasis

public int getValueBasis()

Return the currrent value of the Enumeration type of Basis.

setRegions

public void setRegions(HasRegions.Regions_list regions)

Set method for regions

Specified by:

setRegions in interface HasRegions

getRegions

public HasRegions.Regions_list getRegions()

Get method for regions

Specified by:

getRegions in interface HasRegions

Returns:

value of the attribute

addToRegions

public void addToRegions(SeqFeatureLocation seqFeatureLocation)

Method to add SeqFeatureLocation to Regions_list

Specified by:

addToRegions in interface HasRegions

addToRegions

public void addToRegions(int position,
                         SeqFeatureLocation seqFeatureLocation)

Method to add SeqFeatureLocation at position to Regions_list

Specified by:

addToRegions in interface HasRegions

getFromRegions

public SeqFeatureLocation getFromRegions(int position)

Method to get SeqFeatureLocation from Regions_list

Specified by:

getFromRegions in interface HasRegions

removeElementAtFromRegions

public void removeElementAtFromRegions(int position)

Method to remove by position from Regions_list

Specified by:

removeElementAtFromRegions in interface HasRegions

removeFromRegions

public void removeFromRegions(SeqFeatureLocation seqFeatureLocation)

Method to remove first SeqFeatureLocation from Regions_list

Specified by:

removeFromRegions in interface HasRegions