org.biomage.BioSequence
Class SeqFeatureLocation

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.BioSequence.SeqFeatureLocation
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasCoordinate, HasPropertySets, HasSubregions

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/interfaces inherited from interface org.biomage.Interface.HasSubregions
HasSubregions.Subregions_list
 
Nested classes/interfaces inherited from interface 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  java.util.List subregions
          Regions within the SeqFeature.
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
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
 boolean emptyMAGEobject()
           
 SequencePosition getCoordinate()
          Get method for coordinate
 SeqFeatureLocation getFromSubregions(int position)
          Method to get SeqFeatureLocation from Subregions_list
 java.lang.String getModelClassName()
           
 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, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setAttributes, setId, setIsEditable, setPropertySets, setSecuredElementId, toString
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

subregions

protected java.util.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

Parameters:
atts: - the attribute list.
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
Throws:
java.io.IOException

emptyMAGEobject

public boolean emptyMAGEobject()

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
Throws:
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
Throws:
java.io.IOException

setStrandType

public void setStrandType(java.lang.String strandType)
Set method for strandType

Parameters:
value - to set

getStrandType

public java.lang.String getStrandType()
Get method for strandType

Returns:
value of the attribute

getModelClassName

public java.lang.String getModelClassName()
Overrides:
getModelClassName in class Extendable

setSubregions

public void setSubregions(HasSubregions.Subregions_list subregions)
Set method for subregions

Specified by:
setSubregions in interface HasSubregions
Parameters:
value - to set

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
Parameters:
value - to set

getCoordinate

public SequencePosition getCoordinate()
Get method for coordinate

Specified by:
getCoordinate in interface HasCoordinate
Returns:
value of the attribute