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

Quick Search    Search Deep

org.biomage.BioMaterial
Class Compound  view Compound download Compound.java

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Common.Identifiable
              extended byorg.biomage.BioMaterial.Compound
All Implemented Interfaces:
org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasComponentCompounds, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasMerckIndex, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasSecurity, java.io.Serializable

public class Compound
extends org.biomage.Common.Identifiable
implements java.io.Serializable, org.biomage.Interface.HasComponentCompounds, org.biomage.Interface.HasMerckIndex

A Compound can be a simple compound such as SDS (sodium dodecyl sulfate). It may also be made of other Compounds in proportions using CompoundMeasurements to enumerate the Compounds and their amounts such as LB (Luria Broth) Media.


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasComponentCompounds
org.biomage.Interface.HasComponentCompounds.ComponentCompounds_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.Interface.HasComponentCompounds.ComponentCompounds_list componentCompounds
          The Compounds and their amounts used to create this Compound.
(package private)  boolean isSolvent
          A Compound may be a special case Solvent.
private  org.biomage.Description.OntologyEntry merckIndex
          The Merck Index of this Compound.
 
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
Compound()
          Default constructor.
Compound(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToComponentCompounds(CompoundMeasurement compoundMeasurement)
          Method to add CompoundMeasurement to ComponentCompounds_list
 void addToComponentCompounds(int position, CompoundMeasurement compoundMeasurement)
          Method to add CompoundMeasurement at position to ComponentCompounds_list
 org.biomage.Interface.HasComponentCompounds.ComponentCompounds_list getComponentCompounds()
          Get method for componentCompounds
 CompoundMeasurement getFromComponentCompounds(int position)
          Method to get CompoundMeasurement from ComponentCompounds_list
 boolean getIsSolvent()
          Get method for isSolvent
 org.biomage.Description.OntologyEntry getMerckIndex()
          Get method for merckIndex
 void removeElementAtFromComponentCompounds(int position)
          Method to remove by position from ComponentCompounds_list
 void removeFromComponentCompounds(CompoundMeasurement compoundMeasurement)
          Method to remove first CompoundMeasurement from ComponentCompounds_list
 void setComponentCompounds(org.biomage.Interface.HasComponentCompounds.ComponentCompounds_list componentCompounds)
          Set method for componentCompounds
 void setIsSolvent(boolean isSolvent)
          Set method for isSolvent
 void setMerckIndex(org.biomage.Description.OntologyEntry merckIndex)
          Set method for merckIndex
 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.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

isSolvent

boolean isSolvent
A Compound may be a special case Solvent.


componentCompounds

private org.biomage.Interface.HasComponentCompounds.ComponentCompounds_list componentCompounds
The Compounds and their amounts used to create this Compound.


merckIndex

private org.biomage.Description.OntologyEntry merckIndex
The Merck Index of this Compound.

Constructor Detail

Compound

public Compound()
Default constructor.


Compound

public Compound(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.


setIsSolvent

public void setIsSolvent(boolean isSolvent)
Set method for isSolvent


getIsSolvent

public boolean getIsSolvent()
Get method for isSolvent


setComponentCompounds

public void setComponentCompounds(org.biomage.Interface.HasComponentCompounds.ComponentCompounds_list componentCompounds)
Set method for componentCompounds

Specified by:
setComponentCompounds in interface org.biomage.Interface.HasComponentCompounds

getComponentCompounds

public org.biomage.Interface.HasComponentCompounds.ComponentCompounds_list getComponentCompounds()
Get method for componentCompounds

Specified by:
getComponentCompounds in interface org.biomage.Interface.HasComponentCompounds

addToComponentCompounds

public void addToComponentCompounds(CompoundMeasurement compoundMeasurement)
Method to add CompoundMeasurement to ComponentCompounds_list

Specified by:
addToComponentCompounds in interface org.biomage.Interface.HasComponentCompounds

addToComponentCompounds

public void addToComponentCompounds(int position,
                                    CompoundMeasurement compoundMeasurement)
Method to add CompoundMeasurement at position to ComponentCompounds_list

Specified by:
addToComponentCompounds in interface org.biomage.Interface.HasComponentCompounds

getFromComponentCompounds

public CompoundMeasurement getFromComponentCompounds(int position)
Method to get CompoundMeasurement from ComponentCompounds_list

Specified by:
getFromComponentCompounds in interface org.biomage.Interface.HasComponentCompounds

removeElementAtFromComponentCompounds

public void removeElementAtFromComponentCompounds(int position)
Method to remove by position from ComponentCompounds_list

Specified by:
removeElementAtFromComponentCompounds in interface org.biomage.Interface.HasComponentCompounds

removeFromComponentCompounds

public void removeFromComponentCompounds(CompoundMeasurement compoundMeasurement)
Method to remove first CompoundMeasurement from ComponentCompounds_list

Specified by:
removeFromComponentCompounds in interface org.biomage.Interface.HasComponentCompounds

setMerckIndex

public void setMerckIndex(org.biomage.Description.OntologyEntry merckIndex)
Set method for merckIndex

Specified by:
setMerckIndex in interface org.biomage.Interface.HasMerckIndex

getMerckIndex

public org.biomage.Description.OntologyEntry getMerckIndex()
Get method for merckIndex

Specified by:
getMerckIndex in interface org.biomage.Interface.HasMerckIndex