Docjar: A Java Source and Docuemnt Enginecom.*    java.*    javax.*    org.*    all    new    plug-in

Quick Search    Search Deep

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

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Common.Identifiable
              extended byorg.biomage.BioEvent.BioEvent
                  extended byorg.biomage.BioEvent.Map
                      extended byorg.biomage.BioAssayData.BioAssayMap
All Implemented Interfaces:
org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasBioAssayMapTarget, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasProtocolApplications, org.biomage.Interface.HasSecurity, org.biomage.Interface.HasSourceBioAssays, java.io.Serializable

public class BioAssayMap
extends org.biomage.BioEvent.Map
implements java.io.Serializable, org.biomage.Interface.HasBioAssayMapTarget, org.biomage.Interface.HasSourceBioAssays

The BioAssayMap is the description of how source MeasuredBioAssays and/or DerivedBioAssays are manipulated (mathematically) to produce DerivedBioAssays.


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasSourceBioAssays
org.biomage.Interface.HasSourceBioAssays.SourceBioAssays_list
 
Nested classes inherited from class org.biomage.Interface.HasProtocolApplications
org.biomage.Interface.HasProtocolApplications.ProtocolApplications_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
private  org.biomage.BioAssay.DerivedBioAssay bioAssayMapTarget
          The DerivedBioAssay that is produced by the sources of the BioAssayMap.
private  org.biomage.Interface.HasSourceBioAssays.SourceBioAssays_list sourceBioAssays
          The sources of the BioAssayMap that are used to produce a target DerivedBioAssay.
 
Fields inherited from class org.biomage.BioEvent.BioEvent
 
Fields inherited from class org.biomage.Common.Identifiable
 
Fields inherited from class org.biomage.Common.Describable
 
Fields inherited from class org.biomage.Common.Extendable
 
Constructor Summary
BioAssayMap()
          Default constructor.
BioAssayMap(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToSourceBioAssays(org.biomage.BioAssay.BioAssay bioAssay)
          Method to add BioAssay to SourceBioAssays_list
 void addToSourceBioAssays(int position, org.biomage.BioAssay.BioAssay bioAssay)
          Method to add BioAssay at position to SourceBioAssays_list
 org.biomage.BioAssay.DerivedBioAssay getBioAssayMapTarget()
          Get method for bioAssayMapTarget
 org.biomage.BioAssay.BioAssay getFromSourceBioAssays(int position)
          Method to get BioAssay from SourceBioAssays_list
 org.biomage.Interface.HasSourceBioAssays.SourceBioAssays_list getSourceBioAssays()
          Get method for sourceBioAssays
 void removeElementAtFromSourceBioAssays(int position)
          Method to remove by position from SourceBioAssays_list
 void removeFromSourceBioAssays(org.biomage.BioAssay.BioAssay bioAssay)
          Method to remove first BioAssay from SourceBioAssays_list
 void setBioAssayMapTarget(org.biomage.BioAssay.DerivedBioAssay bioAssayMapTarget)
          Set method for bioAssayMapTarget
 void setSourceBioAssays(org.biomage.Interface.HasSourceBioAssays.SourceBioAssays_list sourceBioAssays)
          Set method for sourceBioAssays
 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.BioEvent.BioEvent
addToProtocolApplications, addToProtocolApplications, getFromProtocolApplications, getProtocolApplications, removeElementAtFromProtocolApplications, removeFromProtocolApplications, setProtocolApplications
 
Methods inherited from class org.biomage.Common.Identifiable
getIdentifier, getName, setIdentifier, setName
 
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

bioAssayMapTarget

private org.biomage.BioAssay.DerivedBioAssay bioAssayMapTarget
The DerivedBioAssay that is produced by the sources of the BioAssayMap.


sourceBioAssays

private org.biomage.Interface.HasSourceBioAssays.SourceBioAssays_list sourceBioAssays
The sources of the BioAssayMap that are used to produce a target DerivedBioAssay.

Constructor Detail

BioAssayMap

public BioAssayMap()
Default constructor.


BioAssayMap

public BioAssayMap(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.


setBioAssayMapTarget

public void setBioAssayMapTarget(org.biomage.BioAssay.DerivedBioAssay bioAssayMapTarget)
Set method for bioAssayMapTarget

Specified by:
setBioAssayMapTarget in interface org.biomage.Interface.HasBioAssayMapTarget

getBioAssayMapTarget

public org.biomage.BioAssay.DerivedBioAssay getBioAssayMapTarget()
Get method for bioAssayMapTarget

Specified by:
getBioAssayMapTarget in interface org.biomage.Interface.HasBioAssayMapTarget

setSourceBioAssays

public void setSourceBioAssays(org.biomage.Interface.HasSourceBioAssays.SourceBioAssays_list sourceBioAssays)
Set method for sourceBioAssays

Specified by:
setSourceBioAssays in interface org.biomage.Interface.HasSourceBioAssays

getSourceBioAssays

public org.biomage.Interface.HasSourceBioAssays.SourceBioAssays_list getSourceBioAssays()
Get method for sourceBioAssays

Specified by:
getSourceBioAssays in interface org.biomage.Interface.HasSourceBioAssays

addToSourceBioAssays

public void addToSourceBioAssays(org.biomage.BioAssay.BioAssay bioAssay)
Method to add BioAssay to SourceBioAssays_list

Specified by:
addToSourceBioAssays in interface org.biomage.Interface.HasSourceBioAssays

addToSourceBioAssays

public void addToSourceBioAssays(int position,
                                 org.biomage.BioAssay.BioAssay bioAssay)
Method to add BioAssay at position to SourceBioAssays_list

Specified by:
addToSourceBioAssays in interface org.biomage.Interface.HasSourceBioAssays

getFromSourceBioAssays

public org.biomage.BioAssay.BioAssay getFromSourceBioAssays(int position)
Method to get BioAssay from SourceBioAssays_list

Specified by:
getFromSourceBioAssays in interface org.biomage.Interface.HasSourceBioAssays

removeElementAtFromSourceBioAssays

public void removeElementAtFromSourceBioAssays(int position)
Method to remove by position from SourceBioAssays_list

Specified by:
removeElementAtFromSourceBioAssays in interface org.biomage.Interface.HasSourceBioAssays

removeFromSourceBioAssays

public void removeFromSourceBioAssays(org.biomage.BioAssay.BioAssay bioAssay)
Method to remove first BioAssay from SourceBioAssays_list

Specified by:
removeFromSourceBioAssays in interface org.biomage.Interface.HasSourceBioAssays