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DENOPTIM
denoptim.fitness.DescriptorUtils Class Reference
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Static Public Member Functions

static List< String > getAllClassNamesInPackage (String packageName, String jarFileWildQuery)
 Search for packages in the class path and in the appended archives. More...
 
static List< String > getClassNamesToDenoptimDescriptors ()
 
static List< String > getClassNamesToCDKDescriptors ()
 
static DescriptorEngine getCDKDescriptorEngine ()
 Makes an engine using CDK descriptors. More...
 
static List< DescriptorForFitnessfindAllCDKDescriptors (Set< String > requiredDescriptors) throws DENOPTIMException
 Searches for descriptor implementations in the CDK packages. More...
 
static List< DescriptorForFitnessfindAllDENOPTIMDescriptors (Set< String > requiredDescriptors) throws DENOPTIMException
 Searches for descriptor implementations in the DENOPTIM packages. More...
 
static List< DescriptorForFitnessfindAllDescriptorImplementations (Set< String > requiredDescriptors) throws DENOPTIMException
 Searches for descriptor implementations. More...
 
static List< DescriptorForFitnessfindDescriptorImplementations (Set< String > requiredDescriptors, List< String > classNames) throws DENOPTIMException
 Searches for descriptor implementations. More...
 

Static Private Attributes

static final String FS = System.getProperty("file.separator")
 
static List< String > rejectedDescriptors
 List of descriptor names that are excluded from default import because they have been shown to contain bugs. More...
 

Detailed Description

Definition at line 43 of file DescriptorUtils.java.

Member Function Documentation

◆ findAllCDKDescriptors()

static List< DescriptorForFitness > denoptim.fitness.DescriptorUtils.findAllCDKDescriptors ( Set< String >  requiredDescriptors) throws DENOPTIMException
static

Searches for descriptor implementations in the CDK packages.

This method excludes descriptors that have been listed in rejectedDescriptors.

Parameters
requiredDescriptorslist of descriptor short names that we want to obtain. All the rest will be ignored. This parameter can be null, in which case we'll return all the descriptors.
Returns
the list of descriptor information bundles.
Exceptions
DENOPTIMException

Definition at line 179 of file DescriptorUtils.java.

References denoptim.fitness.DescriptorUtils.findDescriptorImplementations(), and denoptim.fitness.DescriptorUtils.getClassNamesToCDKDescriptors().

Referenced by denoptim.gui.FitnessParametersForm.FitnessParametersForm().

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◆ findAllDENOPTIMDescriptors()

static List< DescriptorForFitness > denoptim.fitness.DescriptorUtils.findAllDENOPTIMDescriptors ( Set< String >  requiredDescriptors) throws DENOPTIMException
static

Searches for descriptor implementations in the DENOPTIM packages.

This method excludes descriptors that have been listed in rejectedDescriptors.

Parameters
requiredDescriptorslist of descriptor short names that we want to obtain. All the rest will be ignored. This parameter can be null, in which case we'll return all the descriptors.
Returns
the list of descriptor information bundles.
Exceptions
DENOPTIMException

Definition at line 199 of file DescriptorUtils.java.

References denoptim.fitness.DescriptorUtils.findDescriptorImplementations(), and denoptim.fitness.DescriptorUtils.getClassNamesToDenoptimDescriptors().

Referenced by denoptim.gui.FitnessParametersForm.FitnessParametersForm().

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◆ findAllDescriptorImplementations()

static List< DescriptorForFitness > denoptim.fitness.DescriptorUtils.findAllDescriptorImplementations ( Set< String >  requiredDescriptors) throws DENOPTIMException
static

Searches for descriptor implementations.

Searches in both CDK and DENOPTIM packages. This method excludes descriptors that have been listed in rejectedDescriptors.

Parameters
requiredDescriptorslist of descriptor short names that we want to obtain. All the rest will be ignored. This parameter can be null, in which case we'll return all the descriptors.
Returns
the list of descriptor information bundles.
Exceptions
DENOPTIMException

Definition at line 219 of file DescriptorUtils.java.

References denoptim.fitness.DescriptorUtils.findDescriptorImplementations(), denoptim.fitness.DescriptorUtils.getClassNamesToCDKDescriptors(), and denoptim.fitness.DescriptorUtils.getClassNamesToDenoptimDescriptors().

Referenced by denoptim.fitness.FitnessExpressionParser.parse().

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◆ findDescriptorImplementations()

static List< DescriptorForFitness > denoptim.fitness.DescriptorUtils.findDescriptorImplementations ( Set< String >  requiredDescriptors,
List< String >  classNames 
) throws DENOPTIMException
static

Searches for descriptor implementations.

This method excludes descriptors that have been listed in rejectedDescriptors.

Parameters
requiredDescriptorslist of descriptor short names that we want to obtain. All the rest will be ignored. This parameter can be null, in which case we'll return all the descriptors.
classNamesthe classnames of the implementations.
Returns
the list of descriptor information bundles.
Exceptions
DENOPTIMException

Definition at line 240 of file DescriptorUtils.java.

References denoptim.fitness.IDenoptimDescriptor.getDictionaryClass(), denoptim.fitness.IDenoptimDescriptor.getDictionaryDefinition(), denoptim.fitness.IDenoptimDescriptor.getDictionaryTitle(), and denoptim.fitness.DescriptorUtils.rejectedDescriptors.

Referenced by denoptim.fitness.DescriptorUtils.findAllCDKDescriptors(), denoptim.fitness.DescriptorUtils.findAllDENOPTIMDescriptors(), and denoptim.fitness.DescriptorUtils.findAllDescriptorImplementations().

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◆ getAllClassNamesInPackage()

static List< String > denoptim.fitness.DescriptorUtils.getAllClassNamesInPackage ( String  packageName,
String  jarFileWildQuery 
)
static

Search for packages in the class path and in the appended archives.

Parameters
packageNamepackage name that uses '.' as separator.
jarFileWildQuerya query to identify the jar file that should contain the wanter package.
Returns
the list of class names reported in Java format (e.g., 'org.openscience.cdk.qsar.descriptors....'.

Definition at line 64 of file DescriptorUtils.java.

References denoptim.fitness.DescriptorUtils.FS.

Referenced by denoptim.fitness.DescriptorUtils.getClassNamesToCDKDescriptors(), and denoptim.fitness.DescriptorUtils.getClassNamesToDenoptimDescriptors().

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◆ getCDKDescriptorEngine()

static DescriptorEngine denoptim.fitness.DescriptorUtils.getCDKDescriptorEngine ( )
static

Makes an engine using CDK descriptors.

Returns
an engine using CDK descriptors.

Definition at line 162 of file DescriptorUtils.java.

References denoptim.fitness.DescriptorUtils.getClassNamesToCDKDescriptors().

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◆ getClassNamesToCDKDescriptors()

static List< String > denoptim.fitness.DescriptorUtils.getClassNamesToCDKDescriptors ( )
static

Definition at line 150 of file DescriptorUtils.java.

References denoptim.fitness.DescriptorUtils.getAllClassNamesInPackage().

Referenced by denoptim.fitness.DescriptorUtils.findAllCDKDescriptors(), denoptim.fitness.DescriptorUtils.findAllDescriptorImplementations(), denoptim.fitness.DescriptorUtils.getCDKDescriptorEngine(), and denoptim.fitness.DescriptorUtilsTest.testFindCDKDescriptors().

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◆ getClassNamesToDenoptimDescriptors()

static List< String > denoptim.fitness.DescriptorUtils.getClassNamesToDenoptimDescriptors ( )
static

Definition at line 142 of file DescriptorUtils.java.

References denoptim.fitness.DescriptorUtils.getAllClassNamesInPackage().

Referenced by denoptim.fitness.DescriptorUtils.findAllDENOPTIMDescriptors(), denoptim.fitness.DescriptorUtils.findAllDescriptorImplementations(), and denoptim.fitness.DescriptorUtilsTest.testFindDemoptimDescriptors().

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Member Data Documentation

◆ FS

final String denoptim.fitness.DescriptorUtils.FS = System.getProperty("file.separator")
staticprivate

◆ rejectedDescriptors

List<String> denoptim.fitness.DescriptorUtils.rejectedDescriptors
staticprivate
Initial value:
= Arrays.asList(
new String[]{"JPLogP"})

List of descriptor names that are excluded from default import because they have been shown to contain bugs.

Definition at line 51 of file DescriptorUtils.java.

Referenced by denoptim.fitness.DescriptorUtils.findDescriptorImplementations().


The documentation for this class was generated from the following file: