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org.biomage.BioSequence
Class SeqFeature  

java.lang.Object
  org.biomage.Common.Extendable
      org.biomage.Common.Describable
          org.biomage.BioSequence.SeqFeature

All Implemented Interfaces:

org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasRegions, org.biomage.Interface.HasSecurity, java.io.Serializable

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public class SeqFeature

extends org.biomage.Common.Describable

implements java.io.Serializable, org.biomage.Interface.HasRegions

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

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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

org.biomage.Interface.HasRegions.Regions_list

 

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

org.biomage.Interface.HasAuditTrail.AuditTrail_list

 

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

org.biomage.Interface.HasDescriptions.Descriptions_list

 

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

org.biomage.Interface.HasPropertySets.PropertySets_list

 

Field Summary
(package private)  SeqFeature.Basis	basis           How the evidence for a SeqFeature was determined.
private  org.biomage.Interface.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

 

Fields inherited from class org.biomage.Common.Extendable

 

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
org.biomage.Interface.HasRegions.Regions_list	getRegions()           Get method for regions
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
void	setRegions(org.biomage.Interface.HasRegions.Regions_list regions)           Set method for regions
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.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

basis

SeqFeature.Basis basis

How the evidence for a SeqFeature was determined.

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regions

private org.biomage.Interface.HasRegions.Regions_list regions

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

Constructor Detail

SeqFeature

public SeqFeature()

Default constructor.

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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.

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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.

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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.

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setBasis

public void setBasis(SeqFeature.Basis basis)

Set method for basis

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getBasis

public SeqFeature.Basis getBasis()

Get method for basis

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setRegions

public void setRegions(org.biomage.Interface.HasRegions.Regions_list regions)

Set method for regions

Specified by:

setRegions in interface org.biomage.Interface.HasRegions

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getRegions

public org.biomage.Interface.HasRegions.Regions_list getRegions()

Get method for regions

Specified by:

getRegions in interface org.biomage.Interface.HasRegions

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addToRegions

public void addToRegions(SeqFeatureLocation seqFeatureLocation)

Method to add SeqFeatureLocation to Regions_list

Specified by:

addToRegions in interface org.biomage.Interface.HasRegions

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addToRegions

public void addToRegions(int position,
                         SeqFeatureLocation seqFeatureLocation)

Method to add SeqFeatureLocation at position to Regions_list

Specified by:

addToRegions in interface org.biomage.Interface.HasRegions

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getFromRegions

public SeqFeatureLocation getFromRegions(int position)

Method to get SeqFeatureLocation from Regions_list

Specified by:

getFromRegions in interface org.biomage.Interface.HasRegions

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removeElementAtFromRegions

public void removeElementAtFromRegions(int position)

Method to remove by position from Regions_list

Specified by:

removeElementAtFromRegions in interface org.biomage.Interface.HasRegions

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removeFromRegions

public void removeFromRegions(SeqFeatureLocation seqFeatureLocation)

Method to remove first SeqFeatureLocation from Regions_list

Specified by:

removeFromRegions in interface org.biomage.Interface.HasRegions

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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

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