Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> biomage >> [ BioSequence overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

---

org.biomage.BioSequence
Class SeqFeatureLocation  

java.lang.Object
  org.biomage.Common.Extendable
      org.biomage.BioSequence.SeqFeatureLocation

All Implemented Interfaces:

org.biomage.Interface.HasCoordinate, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasSubregions, java.io.Serializable

---

public class SeqFeatureLocation

extends org.biomage.Common.Extendable

implements java.io.Serializable, org.biomage.Interface.HasSubregions, org.biomage.Interface.HasCoordinate

The location of the SeqFeature annotation.

---

Nested Class Summary

 

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

org.biomage.Interface.HasSubregions.Subregions_list

 

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

org.biomage.Interface.HasPropertySets.PropertySets_list

 

Field Summary
private  SequencePosition	coordinate           At which base pairs or amino acid this SeqFeature begins and ends.
(package private)  java.lang.String	strandType           Indicates the direction and/or type of the SeqFeature, i.e.
private  org.biomage.Interface.HasSubregions.Subregions_list	subregions           Regions within the SeqFeature.

 

Fields inherited from class org.biomage.Common.Extendable

 

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
org.biomage.Interface.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(org.biomage.Interface.HasSubregions.Subregions_list subregions)           Set method for subregions
void	writeAssociations(java.io.Writer out)           writeAssociations
void	writeAttributes(java.io.Writer out)           writeAttributes
void	writeMAGEML(java.io.Writer out)           writeMAGEML

 

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

strandType

java.lang.String strandType

Indicates the direction and/or type of the SeqFeature, i.e. whether it is in the 5' or 3' direction, is double stranded, etc.

---

subregions

private org.biomage.Interface.HasSubregions.Subregions_list subregions

Regions within the SeqFeature.

---

coordinate

private 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.

---

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.

---

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.

---

setStrandType

public void setStrandType(java.lang.String strandType)

Set method for strandType

---

getStrandType

public java.lang.String getStrandType()

Get method for strandType

---

setSubregions

public void setSubregions(org.biomage.Interface.HasSubregions.Subregions_list subregions)

Set method for subregions

Specified by:

setSubregions in interface org.biomage.Interface.HasSubregions

---

getSubregions

public org.biomage.Interface.HasSubregions.Subregions_list getSubregions()

Get method for subregions

Specified by:

getSubregions in interface org.biomage.Interface.HasSubregions

---

addToSubregions

public void addToSubregions(SeqFeatureLocation seqFeatureLocation)

Method to add SeqFeatureLocation to Subregions_list

Specified by:

addToSubregions in interface org.biomage.Interface.HasSubregions

---

addToSubregions

public void addToSubregions(int position,
                            SeqFeatureLocation seqFeatureLocation)

Method to add SeqFeatureLocation at position to Subregions_list

Specified by:

addToSubregions in interface org.biomage.Interface.HasSubregions

---

getFromSubregions

public SeqFeatureLocation getFromSubregions(int position)

Method to get SeqFeatureLocation from Subregions_list

Specified by:

getFromSubregions in interface org.biomage.Interface.HasSubregions

---

removeElementAtFromSubregions

public void removeElementAtFromSubregions(int position)

Method to remove by position from Subregions_list

Specified by:

removeElementAtFromSubregions in interface org.biomage.Interface.HasSubregions

---

removeFromSubregions

public void removeFromSubregions(SeqFeatureLocation seqFeatureLocation)

Method to remove first SeqFeatureLocation from Subregions_list

Specified by:

removeFromSubregions in interface org.biomage.Interface.HasSubregions

---

setCoordinate

public void setCoordinate(SequencePosition coordinate)

Set method for coordinate

Specified by:

setCoordinate in interface org.biomage.Interface.HasCoordinate

---

getCoordinate

public SequencePosition getCoordinate()

Get method for coordinate

Specified by:

getCoordinate in interface org.biomage.Interface.HasCoordinate

---

Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> biomage >> [ BioSequence overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

---