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org.biomage.BioSequence
Class SeqFeature  view SeqFeature download SeqFeature.java

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.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

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.


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.


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.


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.


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.


setBasis

public void setBasis(SeqFeature.Basis basis)
Set method for basis


getBasis

public SeqFeature.Basis getBasis()
Get method for basis


setRegions

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

Specified by:
setRegions in interface org.biomage.Interface.HasRegions

getRegions

public org.biomage.Interface.HasRegions.Regions_list getRegions()
Get method for regions

Specified by:
getRegions in interface org.biomage.Interface.HasRegions

addToRegions

public void addToRegions(SeqFeatureLocation seqFeatureLocation)
Method to add SeqFeatureLocation to Regions_list

Specified by:
addToRegions in interface org.biomage.Interface.HasRegions

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

getFromRegions

public SeqFeatureLocation getFromRegions(int position)
Method to get SeqFeatureLocation from Regions_list

Specified by:
getFromRegions in interface org.biomage.Interface.HasRegions

removeElementAtFromRegions

public void removeElementAtFromRegions(int position)
Method to remove by position from Regions_list

Specified by:
removeElementAtFromRegions in interface org.biomage.Interface.HasRegions

removeFromRegions

public void removeFromRegions(SeqFeatureLocation seqFeatureLocation)
Method to remove first SeqFeatureLocation from Regions_list

Specified by:
removeFromRegions in interface org.biomage.Interface.HasRegions