org.biomage.BioSequence
Class SeqFeatureLocation

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

All Implemented Interfaces:

HasCoordinate, HasPropertySets, HasSubregions, java.io.Serializable

public class SeqFeatureLocation

extends Extendable

implements java.io.Serializable, HasSubregions, HasCoordinate

The location of the SeqFeature annotation.

See Also:

Serialized Form

Nested Class Summary

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

HasSubregions.Subregions_list

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

HasPropertySets.PropertySets_list

Field Summary

protected SequencePosition	coordinate At which base pairs or amino acid this SeqFeature begins and ends.
protected HasSubregions.Subregions_list	subregions Regions within the SeqFeature.

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

SeqFeatureLocation()
Default constructor.

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

Method Summary

void	addToSubregions(int position, SeqFeatureLocation seqFeatureLocation) Method to add SeqFeatureLocation at position to Subregions_list
void	addToSubregions(SeqFeatureLocation seqFeatureLocation) Method to add SeqFeatureLocation to Subregions_list
SequencePosition	getCoordinate() Get method for coordinate
SeqFeatureLocation	getFromSubregions(int position) Method to get SeqFeatureLocation from Subregions_list
java.lang.String	getStrandType() Get method for strandType
HasSubregions.Subregions_list	getSubregions() Get method for subregions
void	removeElementAtFromSubregions(int position) Method to remove by position from Subregions_list
void	removeFromSubregions(SeqFeatureLocation seqFeatureLocation) Method to remove first SeqFeatureLocation from Subregions_list
void	setCoordinate(SequencePosition coordinate) Set method for coordinate
void	setStrandType(java.lang.String strandType) Set method for strandType
void	setSubregions(HasSubregions.Subregions_list subregions) Set method for subregions
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.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

subregions

protected HasSubregions.Subregions_list subregions

Regions within the SeqFeature.

coordinate

protected SequencePosition coordinate

At which base pairs or amino acid this SeqFeature begins and ends.

Constructor Detail

SeqFeatureLocation

public SeqFeatureLocation()

Default constructor.

SeqFeatureLocation

public SeqFeatureLocation(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 Extendable

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 Extendable

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 Extendable

java.io.IOException

setStrandType

public void setStrandType(java.lang.String strandType)

Set method for strandType

getStrandType

public java.lang.String getStrandType()

Get method for strandType

Returns:

value of the attribute

setSubregions

public void setSubregions(HasSubregions.Subregions_list subregions)

Set method for subregions

Specified by:

setSubregions in interface HasSubregions

getSubregions

public HasSubregions.Subregions_list getSubregions()

Get method for subregions

Specified by:

getSubregions in interface HasSubregions

Returns:

value of the attribute

addToSubregions

public void addToSubregions(SeqFeatureLocation seqFeatureLocation)

Method to add SeqFeatureLocation to Subregions_list

Specified by:

addToSubregions in interface HasSubregions

addToSubregions

public void addToSubregions(int position,
                            SeqFeatureLocation seqFeatureLocation)

Method to add SeqFeatureLocation at position to Subregions_list

Specified by:

addToSubregions in interface HasSubregions

getFromSubregions

public SeqFeatureLocation getFromSubregions(int position)

Method to get SeqFeatureLocation from Subregions_list

Specified by:

getFromSubregions in interface HasSubregions

removeElementAtFromSubregions

public void removeElementAtFromSubregions(int position)

Method to remove by position from Subregions_list

Specified by:

removeElementAtFromSubregions in interface HasSubregions

removeFromSubregions

public void removeFromSubregions(SeqFeatureLocation seqFeatureLocation)

Method to remove first SeqFeatureLocation from Subregions_list

Specified by:

removeFromSubregions in interface HasSubregions

setCoordinate

public void setCoordinate(SequencePosition coordinate)

Set method for coordinate

Specified by:

setCoordinate in interface HasCoordinate

getCoordinate

public SequencePosition getCoordinate()

Get method for coordinate

Specified by:

getCoordinate in interface HasCoordinate

Returns:

value of the attribute