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

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