@PublicAPI public final class ExpandAction extends AbstractStandardizerAction
Modifier and Type | Field and Description |
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static java.lang.String |
STOICHIOMETRY_KEY
Key of type for parsing and property changes
|
CONFIG_PATH_KEY, FORMAT_KEY, ID_KEY, support
Constructor and Description |
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ExpandAction(java.util.Map<java.lang.String,java.lang.String> params)
Initializes the action with parameters
|
Modifier and Type | Method and Description |
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ExpandAction |
clone() |
protected java.util.List<Molecule> |
getComponents(Molecule molecule)
A recursive algorithm getting all components (reactants, agents and
products of reaction molecules, R-group definitions of Rg-Molecules) of
the molecule.
|
java.lang.String |
getStoichiometry()
Gets the stoichiometry value of the action
|
void |
setStoichiometry(java.lang.String stoichiometryData)
Sets the stoichiometry value of the action
|
protected Changes |
standardize1(Molecule molecule)
This method contains the current standardization mechanism.
|
java.lang.String |
toString() |
addPropertyChangeListener, addPropertyChangeListener, cloneItem, getDescriptor, getID, isActive, isAvailable, isLicensed, isValid, propertyChange, removePropertyChangeListener, removePropertyChangeListener, setActive, setID, setLicenseEnvironment, setValid, standardize
public static final java.lang.String STOICHIOMETRY_KEY
public ExpandAction(java.util.Map<java.lang.String,java.lang.String> params)
params
- the parameters of the actionpublic void setStoichiometry(java.lang.String stoichiometryData)
stoichiometryData
- the stoichiometry value of the actionpublic java.lang.String getStoichiometry()
protected Changes standardize1(Molecule molecule)
AbstractStandardizerAction
RgMolecule
,
RxnMolecule
) are decomponented by the method
AbstractStandardizerAction.getComponents(Molecule)
, and AbstractStandardizerAction.standardize1(Molecule)
method is called on each component, before applied on the original
molecule. If a descendant does not want this to occur, this method must
be overridden.Logger
, that can
be collected by using StandardizerLogger.getLogger()
method.standardize1
in class AbstractStandardizerAction
molecule
- the Molecule
instance to be standardizedprotected java.util.List<Molecule> getComponents(Molecule molecule)
AbstractStandardizerAction
getComponents
in class AbstractStandardizerAction
molecule
- the target moleculepublic ExpandAction clone() throws java.lang.CloneNotSupportedException
clone
in class AbstractStandardizerAction
java.lang.CloneNotSupportedException
public java.lang.String toString()
toString
in class AbstractStandardizerAction