@PublicAPI public final class TransformAction extends AbstractStandardizerAction
Modifier and Type | Field and Description |
---|---|
static java.lang.String |
EXACT_KEY
Key of exact for parsing and property change
|
protected static java.lang.String |
LINE_SEP
Line separator.
|
static java.lang.String |
SEARCH_OPTIONS_KEY
Key of search options for parsing and property change
|
static java.lang.String |
STRUCTURE_KEY
Key of query molecule for parsing and property change
|
CONFIG_PATH_KEY, FORMAT_KEY, ID_KEY, support
Constructor and Description |
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TransformAction(java.util.Map<java.lang.String,java.lang.String> params)
Initializes the action with parameters
|
Modifier and Type | Method and Description |
---|---|
TransformAction |
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 |
getSearchOptions()
Gets the search options of the action
|
java.lang.String |
getStructure()
Deprecated.
|
RxnMolecule |
getTransform()
Gets the transformation molecule of the action
|
java.lang.String |
getType()
Gets the type of transformation
|
boolean |
isEditable()
Returns if this action is editable.
|
boolean |
isExact()
Gets the exact value of the action
|
void |
setEditable(boolean editable)
Sets if this action is editable.
|
void |
setExact(boolean exact)
Sets the exact value of the action
|
void |
setSearchOptions(java.lang.String optionString)
Sets the search options of the action
|
void |
setStructure(java.lang.String structure)
Deprecated.
use
setTransform(RxnMolecule) method instead |
void |
setTransform(RxnMolecule structure)
Sets the transformation
|
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 EXACT_KEY
public static final java.lang.String SEARCH_OPTIONS_KEY
public static final java.lang.String STRUCTURE_KEY
protected static final java.lang.String LINE_SEP
public TransformAction(java.util.Map<java.lang.String,java.lang.String> params)
params
- the parameters of the actionpublic void setSearchOptions(java.lang.String optionString)
optionString
- the search options of the actionpublic java.lang.String getSearchOptions()
public void setEditable(boolean editable)
editable
- the new editable flagpublic boolean isEditable()
true
if the action is editablepublic void setExact(boolean exact)
exact
- the exact value of the actionpublic boolean isExact()
@Deprecated public void setStructure(java.lang.String structure)
setTransform(RxnMolecule)
method insteadstructure
- the molecule defining the transformationpublic void setTransform(RxnMolecule structure)
structure
- the molecule defining the transformation@Deprecated public java.lang.String getStructure()
public RxnMolecule getTransform()
public java.lang.String getType()
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 TransformAction clone() throws java.lang.CloneNotSupportedException
clone
in class AbstractStandardizerAction
java.lang.CloneNotSupportedException
public java.lang.String toString()
toString
in class AbstractStandardizerAction