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org.biomage.BioAssayData
Class BioAssayMapping  view BioAssayMapping download BioAssayMapping.java

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.BioAssayData.BioAssayMapping
All Implemented Interfaces:
org.biomage.Interface.HasBioAssayMaps, org.biomage.Interface.HasPropertySets, java.io.Serializable

public class BioAssayMapping
extends org.biomage.Common.Extendable
implements java.io.Serializable, org.biomage.Interface.HasBioAssayMaps

Container of the mappings of the input BioAssay dimensions to the output BioAssay dimension.


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasBioAssayMaps
org.biomage.Interface.HasBioAssayMaps.BioAssayMaps_list
 
Nested classes inherited from class org.biomage.Interface.HasPropertySets
org.biomage.Interface.HasPropertySets.PropertySets_list
 
Field Summary
private  org.biomage.Interface.HasBioAssayMaps.BioAssayMaps_list bioAssayMaps
          The maps for the BioAssays.
 
Fields inherited from class org.biomage.Common.Extendable
 
Constructor Summary
BioAssayMapping()
          Default constructor.
BioAssayMapping(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToBioAssayMaps(BioAssayMap bioAssayMap)
          Method to add BioAssayMap to BioAssayMaps_list
 void addToBioAssayMaps(int position, BioAssayMap bioAssayMap)
          Method to add BioAssayMap at position to BioAssayMaps_list
 org.biomage.Interface.HasBioAssayMaps.BioAssayMaps_list getBioAssayMaps()
          Get method for bioAssayMaps
 BioAssayMap getFromBioAssayMaps(int position)
          Method to get BioAssayMap from BioAssayMaps_list
 void removeElementAtFromBioAssayMaps(int position)
          Method to remove by position from BioAssayMaps_list
 void removeFromBioAssayMaps(BioAssayMap bioAssayMap)
          Method to remove first BioAssayMap from BioAssayMaps_list
 void setBioAssayMaps(org.biomage.Interface.HasBioAssayMaps.BioAssayMaps_list bioAssayMaps)
          Set method for bioAssayMaps
 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

bioAssayMaps

private org.biomage.Interface.HasBioAssayMaps.BioAssayMaps_list bioAssayMaps
The maps for the BioAssays.

Constructor Detail

BioAssayMapping

public BioAssayMapping()
Default constructor.


BioAssayMapping

public BioAssayMapping(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.


setBioAssayMaps

public void setBioAssayMaps(org.biomage.Interface.HasBioAssayMaps.BioAssayMaps_list bioAssayMaps)
Set method for bioAssayMaps

Specified by:
setBioAssayMaps in interface org.biomage.Interface.HasBioAssayMaps

getBioAssayMaps

public org.biomage.Interface.HasBioAssayMaps.BioAssayMaps_list getBioAssayMaps()
Get method for bioAssayMaps

Specified by:
getBioAssayMaps in interface org.biomage.Interface.HasBioAssayMaps

addToBioAssayMaps

public void addToBioAssayMaps(BioAssayMap bioAssayMap)
Method to add BioAssayMap to BioAssayMaps_list

Specified by:
addToBioAssayMaps in interface org.biomage.Interface.HasBioAssayMaps

addToBioAssayMaps

public void addToBioAssayMaps(int position,
                              BioAssayMap bioAssayMap)
Method to add BioAssayMap at position to BioAssayMaps_list

Specified by:
addToBioAssayMaps in interface org.biomage.Interface.HasBioAssayMaps

getFromBioAssayMaps

public BioAssayMap getFromBioAssayMaps(int position)
Method to get BioAssayMap from BioAssayMaps_list

Specified by:
getFromBioAssayMaps in interface org.biomage.Interface.HasBioAssayMaps

removeElementAtFromBioAssayMaps

public void removeElementAtFromBioAssayMaps(int position)
Method to remove by position from BioAssayMaps_list

Specified by:
removeElementAtFromBioAssayMaps in interface org.biomage.Interface.HasBioAssayMaps

removeFromBioAssayMaps

public void removeFromBioAssayMaps(BioAssayMap bioAssayMap)
Method to remove first BioAssayMap from BioAssayMaps_list

Specified by:
removeFromBioAssayMaps in interface org.biomage.Interface.HasBioAssayMaps