org.biomage.BioMaterial
Class Compound

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.Common.Identifiable
                    |
                    +--org.biomage.BioMaterial.Compound

All Implemented Interfaces:

HasAuditTrail, HasComponentCompounds, HasDescriptions, HasMerckIndex, HasPropertySets, HasSecurity, java.io.Serializable

public class Compound

extends Identifiable

implements java.io.Serializable, HasComponentCompounds, 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.

See Also:

Serialized Form

Nested Class Summary

Nested classes inherited from class org.biomage.Interface.HasComponentCompounds

HasComponentCompounds.ComponentCompounds_list

Nested classes inherited from class org.biomage.Interface.HasAuditTrail

HasAuditTrail.AuditTrail_list

Nested classes inherited from class org.biomage.Interface.HasDescriptions

HasDescriptions.Descriptions_list

Nested classes inherited from class org.biomage.Interface.HasPropertySets

HasPropertySets.PropertySets_list

Field Summary

protected HasComponentCompounds.ComponentCompounds_list	componentCompounds The Compounds and their amounts used to create this Compound.
protected OntologyEntry	merckIndex The Merck Index of this Compound.

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

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
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
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(HasComponentCompounds.ComponentCompounds_list componentCompounds) Set method for componentCompounds
void	setIsSolvent(boolean isSolvent) Set method for isSolvent
void	setMerckIndex(OntologyEntry merckIndex) Set method for merckIndex
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.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

merckIndex

protected OntologyEntry merckIndex

The Merck Index of this Compound.

componentCompounds

protected HasComponentCompounds.ComponentCompounds_list componentCompounds

The Compounds and their amounts used to create 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.

Overrides:

writeMAGEML in class Identifiable

java.io.IOException

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 Identifiable

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 Identifiable

java.io.IOException

setIsSolvent

public void setIsSolvent(boolean isSolvent)

Set method for isSolvent

getIsSolvent

public boolean getIsSolvent()

Get method for isSolvent

Returns:

value of the attribute

setMerckIndex

public void setMerckIndex(OntologyEntry merckIndex)

Set method for merckIndex

Specified by:

setMerckIndex in interface HasMerckIndex

getMerckIndex

public OntologyEntry getMerckIndex()

Get method for merckIndex

Specified by:

getMerckIndex in interface HasMerckIndex

Returns:

value of the attribute

setComponentCompounds

public void setComponentCompounds(HasComponentCompounds.ComponentCompounds_list componentCompounds)

Set method for componentCompounds

Specified by:

setComponentCompounds in interface HasComponentCompounds

getComponentCompounds

public HasComponentCompounds.ComponentCompounds_list getComponentCompounds()

Get method for componentCompounds

Specified by:

getComponentCompounds in interface HasComponentCompounds

Returns:

value of the attribute

addToComponentCompounds

public void addToComponentCompounds(CompoundMeasurement compoundMeasurement)

Method to add CompoundMeasurement to ComponentCompounds_list

Specified by:

addToComponentCompounds in interface HasComponentCompounds

addToComponentCompounds

public void addToComponentCompounds(int position,
                                    CompoundMeasurement compoundMeasurement)

Method to add CompoundMeasurement at position to ComponentCompounds_list

Specified by:

addToComponentCompounds in interface HasComponentCompounds

getFromComponentCompounds

public CompoundMeasurement getFromComponentCompounds(int position)

Method to get CompoundMeasurement from ComponentCompounds_list

Specified by:

getFromComponentCompounds in interface HasComponentCompounds

removeElementAtFromComponentCompounds

public void removeElementAtFromComponentCompounds(int position)

Method to remove by position from ComponentCompounds_list

Specified by:

removeElementAtFromComponentCompounds in interface HasComponentCompounds

removeFromComponentCompounds

public void removeFromComponentCompounds(CompoundMeasurement compoundMeasurement)

Method to remove first CompoundMeasurement from ComponentCompounds_list

Specified by:

removeFromComponentCompounds in interface HasComponentCompounds