Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> biomage >> [ BioMaterial overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

---

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:

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

---

Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> biomage >> [ BioMaterial overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

---