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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Common.Identifiable
org.biomage.BioMaterial.Compound
public class Compound
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 |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasComponentCompounds |
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HasComponentCompounds.ComponentCompounds_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasCompoundIndices |
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HasCompoundIndices.CompoundIndices_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail |
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HasAuditTrail.AuditTrail_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions |
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HasDescriptions.Descriptions_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets |
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HasPropertySets.PropertySets_list |
Field Summary | |
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protected java.util.List |
componentCompounds
The Compounds and their amounts used to create this Compound. |
protected java.util.List |
compoundIndices
Indices into common Compound Indices, such as the Merck Index, for this Compound. |
protected DatabaseEntry |
externalLIMS
Reference to an entry in an external LIMS data source. |
Fields inherited from class org.biomage.Common.Describable |
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security |
Fields inherited from class org.biomage.Common.Extendable |
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editable, id, securedElementId |
Constructor Summary | |
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Compound()
Default constructor. |
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Compound(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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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 |
void |
addToCompoundIndices(int position,
OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to CompoundIndices_list |
void |
addToCompoundIndices(OntologyEntry ontologyEntry)
Method to add OntologyEntry to CompoundIndices_list |
boolean |
emptyMAGEobject()
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HasComponentCompounds.ComponentCompounds_list |
getComponentCompounds()
Get method for componentCompounds |
HasCompoundIndices.CompoundIndices_list |
getCompoundIndices()
Get method for compoundIndices |
DatabaseEntry |
getExternalLIMS()
Get method for externalLIMS |
CompoundMeasurement |
getFromComponentCompounds(int position)
Method to get CompoundMeasurement from ComponentCompounds_list |
OntologyEntry |
getFromCompoundIndices(int position)
Method to get OntologyEntry from CompoundIndices_list |
java.lang.Boolean |
getIsSolvent()
Get method for isSolvent |
java.lang.String |
getModelClassName()
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void |
removeElementAtFromComponentCompounds(int position)
Method to remove by position from ComponentCompounds_list |
void |
removeElementAtFromCompoundIndices(int position)
Method to remove by position from CompoundIndices_list |
void |
removeFromComponentCompounds(CompoundMeasurement compoundMeasurement)
Method to remove first CompoundMeasurement from ComponentCompounds_list |
void |
removeFromCompoundIndices(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from CompoundIndices_list |
void |
setAttributes(org.xml.sax.Attributes atts)
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void |
setComponentCompounds(HasComponentCompounds.ComponentCompounds_list componentCompounds)
Set method for componentCompounds |
void |
setCompoundIndices(HasCompoundIndices.CompoundIndices_list compoundIndices)
Set method for compoundIndices |
void |
setExternalLIMS(DatabaseEntry externalLIMS)
Set method for externalLIMS |
void |
setIsSolvent(java.lang.Boolean isSolvent)
Set method for isSolvent |
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 |
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getIdentifier, getName, setIdentifier, setName, toString |
Methods inherited from class org.biomage.Common.Describable |
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addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAuditTrail, setDescriptions, setSecurity |
Methods inherited from class org.biomage.Common.Extendable |
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addToPropertySets, addToPropertySets, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId |
Methods inherited from class java.lang.Object |
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clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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protected java.util.List compoundIndices
protected java.util.List componentCompounds
protected DatabaseEntry externalLIMS
Constructor Detail |
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public Compound()
public Compound(org.xml.sax.Attributes atts)
atts:
- the attribute list.Method Detail |
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public void setAttributes(org.xml.sax.Attributes atts)
setAttributes
in class Identifiable
public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class Identifiable
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class Identifiable
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class Identifiable
java.io.IOException
public void setIsSolvent(java.lang.Boolean isSolvent)
value
- to setpublic java.lang.Boolean getIsSolvent()
public java.lang.String getModelClassName()
getModelClassName
in class Identifiable
public void setCompoundIndices(HasCompoundIndices.CompoundIndices_list compoundIndices)
setCompoundIndices
in interface HasCompoundIndices
value
- to setpublic HasCompoundIndices.CompoundIndices_list getCompoundIndices()
getCompoundIndices
in interface HasCompoundIndices
public void addToCompoundIndices(OntologyEntry ontologyEntry)
addToCompoundIndices
in interface HasCompoundIndices
public void addToCompoundIndices(int position, OntologyEntry ontologyEntry)
addToCompoundIndices
in interface HasCompoundIndices
public OntologyEntry getFromCompoundIndices(int position)
getFromCompoundIndices
in interface HasCompoundIndices
public void removeElementAtFromCompoundIndices(int position)
removeElementAtFromCompoundIndices
in interface HasCompoundIndices
public void removeFromCompoundIndices(OntologyEntry ontologyEntry)
removeFromCompoundIndices
in interface HasCompoundIndices
public void setComponentCompounds(HasComponentCompounds.ComponentCompounds_list componentCompounds)
setComponentCompounds
in interface HasComponentCompounds
value
- to setpublic HasComponentCompounds.ComponentCompounds_list getComponentCompounds()
getComponentCompounds
in interface HasComponentCompounds
public void addToComponentCompounds(CompoundMeasurement compoundMeasurement)
addToComponentCompounds
in interface HasComponentCompounds
public void addToComponentCompounds(int position, CompoundMeasurement compoundMeasurement)
addToComponentCompounds
in interface HasComponentCompounds
public CompoundMeasurement getFromComponentCompounds(int position)
getFromComponentCompounds
in interface HasComponentCompounds
public void removeElementAtFromComponentCompounds(int position)
removeElementAtFromComponentCompounds
in interface HasComponentCompounds
public void removeFromComponentCompounds(CompoundMeasurement compoundMeasurement)
removeFromComponentCompounds
in interface HasComponentCompounds
public void setExternalLIMS(DatabaseEntry externalLIMS)
setExternalLIMS
in interface HasExternalLIMS
value
- to setpublic DatabaseEntry getExternalLIMS()
getExternalLIMS
in interface HasExternalLIMS
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