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DENOPTIM
Public Member Functions | Package Attributes | Private Member Functions | Private Attributes | Static Private Attributes | List of all members
denoptim.io.DenoptimIOTest Class Reference

Unit test for input/output. More...

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Public Member Functions

void testReadAllAtomContainersFromCIF () throws Exception
 
void testIOEmptyVertex () throws Exception
 
void testIOMolFragment () throws Exception
 
void testIOTemplate () throws Exception
 
void testReadGenerationFromSummary () throws Exception
 
void testReadLightWeightCandidate () throws Exception
 
void testSerializeDeserializeDENOPTIMGraphs () throws Exception
 
void testReadAllAPClasses () throws Exception
 
void testAppendToJSON () throws Exception
 
void testDetectFileFormat () throws Exception
 
void testReadCuttingRulsedDefault () throws Exception
 
void testIOCuttingRules () throws Exception
 
void testReadCSDFormulae () throws Exception
 

Package Attributes

File tempDir
 

Private Member Functions

void buildVertexAndConnectToGraph (EmptyVertex v, int apCount, DGraph graph) throws DENOPTIMException
 

Private Attributes

final String SEP = System.getProperty("file.separator")
 
final String NL = System.getProperty("line.separator")
 

Static Private Attributes

static final BondType BT = BondType.SINGLE
 

Detailed Description

Unit test for input/output.

Author
Marco Foscato

Definition at line 80 of file DenoptimIOTest.java.

Member Function Documentation

◆ buildVertexAndConnectToGraph()

void denoptim.io.DenoptimIOTest.buildVertexAndConnectToGraph ( EmptyVertex  v,
int  apCount,
DGraph  graph 
) throws DENOPTIMException
private

Definition at line 524 of file DenoptimIOTest.java.

Referenced by denoptim.io.DenoptimIOTest.testSerializeDeserializeDENOPTIMGraphs().

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◆ testAppendToJSON()

void denoptim.io.DenoptimIOTest.testAppendToJSON ( ) throws Exception

Definition at line 474 of file DenoptimIOTest.java.

References denoptim.graph.Fragment.addAPOnAtom(), denoptim.graph.Fragment.addAtom(), denoptim.graph.Fragment.getAtom(), denoptim.graph.APClass.make(), denoptim.graph.Fragment.projectAPsToProperties(), denoptim.io.DenoptimIO.readDENOPTIMVertexesFromJSONFile(), denoptim.io.DenoptimIOTest.SEP, denoptim.io.DenoptimIOTest.tempDir, denoptim.files.FileFormat.VRTXJSON, and denoptim.io.DenoptimIO.writeVertexesToFile().

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◆ testDetectFileFormat()

void denoptim.io.DenoptimIOTest.testDetectFileFormat ( ) throws Exception

Definition at line 536 of file DenoptimIOTest.java.

References denoptim.constants.DENOPTIMConstants.APSTAG, denoptim.programs.RunTimeParameters.ParametersType.CEBL_PARAMS, denoptim.files.FileFormat.COMP_MAP, denoptim.files.FileUtils.createDirectory(), denoptim.files.FileUtils.detectFileFormat(), denoptim.files.FileFormat.FSE_PARAM, denoptim.files.FileFormat.FSE_RUN, denoptim.constants.DENOPTIMConstants.FSEIDXNAMEROOT, denoptim.files.FileFormat.GA_PARAM, denoptim.programs.RunTimeParameters.ParametersType.GA_PARAMS, denoptim.files.FileFormat.GA_RUN, denoptim.constants.DENOPTIMConstants.GAGENDIRNAMEROOT, denoptim.constants.DENOPTIMConstants.GAGENSUMMARYHEADER, denoptim.files.FileFormat.GENSUMMARY, denoptim.constants.DENOPTIMConstants.GRAPHJSONTAG, denoptim.files.FileFormat.GRAPHSDF, denoptim.io.DenoptimIOTest.NL, denoptim.io.DenoptimIOTest.SEP, denoptim.io.DenoptimIOTest.tempDir, denoptim.constants.DENOPTIMConstants.VERTEXJSONTAG, denoptim.files.FileFormat.VRTXSDF, and denoptim.io.DenoptimIO.writeData().

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◆ testIOCuttingRules()

void denoptim.io.DenoptimIOTest.testIOCuttingRules ( ) throws Exception

Definition at line 629 of file DenoptimIOTest.java.

References denoptim.io.DenoptimIO.readCuttingRules(), denoptim.io.DenoptimIOTest.SEP, denoptim.io.DenoptimIOTest.tempDir, and denoptim.io.DenoptimIO.writeCuttingRules().

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◆ testIOEmptyVertex()

void denoptim.io.DenoptimIOTest.testIOEmptyVertex ( ) throws Exception

Definition at line 137 of file DenoptimIOTest.java.

References denoptim.graph.EmptyVertex.addAP(), denoptim.graph.APClass.make(), denoptim.io.DenoptimIO.readVertexes(), denoptim.graph.EmptyVertex.sameAs(), denoptim.io.DenoptimIOTest.SEP, denoptim.io.DenoptimIOTest.tempDir, denoptim.graph.Vertex.BBType.UNDEFINED, denoptim.files.FileFormat.VRTXJSON, denoptim.files.FileFormat.VRTXSDF, and denoptim.io.DenoptimIO.writeVertexesToFile().

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◆ testIOMolFragment()

void denoptim.io.DenoptimIOTest.testIOMolFragment ( ) throws Exception

Definition at line 171 of file DenoptimIOTest.java.

References denoptim.graph.FragmentTest.makeFragment(), denoptim.io.DenoptimIO.readVertexes(), denoptim.graph.Fragment.sameAs(), denoptim.graph.Vertex.BBType.SCAFFOLD, denoptim.io.DenoptimIOTest.SEP, denoptim.io.DenoptimIOTest.tempDir, denoptim.files.FileFormat.VRTXJSON, denoptim.files.FileFormat.VRTXSDF, and denoptim.io.DenoptimIO.writeVertexesToFile().

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◆ testIOTemplate()

void denoptim.io.DenoptimIOTest.testIOTemplate ( ) throws Exception

Definition at line 201 of file DenoptimIOTest.java.

References denoptim.graph.TemplateTest.getTestAmideTemplate(), denoptim.io.DenoptimIO.readVertexes(), denoptim.graph.Template.sameAs(), denoptim.graph.Vertex.BBType.SCAFFOLD, denoptim.io.DenoptimIOTest.SEP, denoptim.io.DenoptimIOTest.tempDir, denoptim.graph.Vertex.BBType.UNDEFINED, denoptim.files.FileFormat.VRTXJSON, denoptim.files.FileFormat.VRTXSDF, and denoptim.io.DenoptimIO.writeVertexesToFile().

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◆ testReadAllAPClasses()

void denoptim.io.DenoptimIOTest.testReadAllAPClasses ( ) throws Exception

Definition at line 419 of file DenoptimIOTest.java.

References denoptim.graph.Fragment.addAPOnAtom(), denoptim.graph.Fragment.addAtom(), denoptim.files.FileUtils.getTempFolder(), denoptim.graph.APClass.make(), denoptim.graph.Fragment.projectAPsToProperties(), denoptim.io.DenoptimIO.readAllAPClasses(), and denoptim.io.DenoptimIO.writeVertexesToSDF().

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◆ testReadAllAtomContainersFromCIF()

void denoptim.io.DenoptimIOTest.testReadAllAtomContainersFromCIF ( ) throws Exception

Definition at line 94 of file DenoptimIOTest.java.

References denoptim.io.DenoptimIOTest.NL, denoptim.io.DenoptimIO.readAllAtomContainers(), denoptim.io.DenoptimIOTest.SEP, denoptim.io.DenoptimIOTest.tempDir, and denoptim.io.DenoptimIO.writeData().

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◆ testReadCSDFormulae()

void denoptim.io.DenoptimIOTest.testReadCSDFormulae ( ) throws Exception

Definition at line 653 of file DenoptimIOTest.java.

References denoptim.io.DenoptimIOTest.NL, denoptim.io.DenoptimIO.readCSDFormulae(), denoptim.io.DenoptimIOTest.SEP, denoptim.io.DenoptimIOTest.tempDir, and denoptim.io.DenoptimIO.writeData().

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◆ testReadCuttingRulsedDefault()

void denoptim.io.DenoptimIOTest.testReadCuttingRulsedDefault ( ) throws Exception

Definition at line 609 of file DenoptimIOTest.java.

References denoptim.io.DenoptimIO.readCuttingRules().

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◆ testReadGenerationFromSummary()

void denoptim.io.DenoptimIOTest.testReadGenerationFromSummary ( ) throws Exception

Definition at line 231 of file DenoptimIOTest.java.

References denoptim.ga.Population.add(), denoptim.files.FileUtils.createDirectory(), denoptim.graph.Candidate.getGraph(), denoptim.ga.EAUtils.getPathNameToGenerationDetailsFile(), denoptim.ga.EAUtils.getPathNameToGenerationFolder(), denoptim.ga.EAUtils.outputPopulationDetails(), denoptim.io.DenoptimIO.readGenerationFromSummary(), denoptim.io.DenoptimIOTest.SEP, denoptim.graph.Candidate.setFitness(), denoptim.graph.DGraph.setGraphId(), denoptim.programs.RunTimeParameters.setParameters(), denoptim.programs.denovo.GAParameters.setPopulationSize(), denoptim.graph.Candidate.setSDFFile(), denoptim.graph.Candidate.setUID(), denoptim.programs.denovo.GAParameters.setWorkingDirectory(), denoptim.io.DenoptimIOTest.tempDir, and denoptim.io.DenoptimIO.writeCandidateToFile().

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◆ testReadLightWeightCandidate()

void denoptim.io.DenoptimIOTest.testReadLightWeightCandidate ( ) throws Exception

Definition at line 296 of file DenoptimIOTest.java.

References denoptim.constants.DENOPTIMConstants.FITNESSTAG, denoptim.constants.DENOPTIMConstants.GRAPHLEVELTAG, denoptim.constants.DENOPTIMConstants.MOLERRORTAG, denoptim.constants.DENOPTIMConstants.PROVENANCE, denoptim.io.DenoptimIO.readLightWeightCandidate(), denoptim.io.DenoptimIOTest.SEP, denoptim.io.DenoptimIOTest.tempDir, denoptim.constants.DENOPTIMConstants.UNIQUEIDTAG, and denoptim.io.DenoptimIO.writeSDFFile().

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◆ testSerializeDeserializeDENOPTIMGraphs()

void denoptim.io.DenoptimIOTest.testSerializeDeserializeDENOPTIMGraphs ( ) throws Exception

Definition at line 353 of file DenoptimIOTest.java.

References denoptim.graph.SymmetricSet< T >.add(), denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addRing(), denoptim.graph.DGraph.addSymmetricSetOfVertices(), denoptim.io.DenoptimIOTest.BT, denoptim.io.DenoptimIOTest.buildVertexAndConnectToGraph(), denoptim.graph.Vertex.getAP(), denoptim.io.DenoptimIO.readDENOPTIMGraphsFromJSONFile(), denoptim.graph.DGraph.sameAs(), denoptim.io.DenoptimIOTest.SEP, denoptim.io.DenoptimIOTest.tempDir, denoptim.graph.DGraph.toJson(), and denoptim.io.DenoptimIO.writeData().

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Member Data Documentation

◆ BT

final BondType denoptim.io.DenoptimIOTest.BT = BondType.SINGLE
staticprivate

Definition at line 83 of file DenoptimIOTest.java.

Referenced by denoptim.io.DenoptimIOTest.testSerializeDeserializeDENOPTIMGraphs().

◆ NL

final String denoptim.io.DenoptimIOTest.NL = System.getProperty("line.separator")
private

Definition at line 86 of file DenoptimIOTest.java.

Referenced by denoptim.io.DenoptimIOTest.testDetectFileFormat(), denoptim.io.DenoptimIOTest.testReadAllAtomContainersFromCIF(), and denoptim.io.DenoptimIOTest.testReadCSDFormulae().

◆ SEP

final String denoptim.io.DenoptimIOTest.SEP = System.getProperty("file.separator")
private

Definition at line 85 of file DenoptimIOTest.java.

Referenced by denoptim.io.DenoptimIOTest.testAppendToJSON(), denoptim.io.DenoptimIOTest.testDetectFileFormat(), denoptim.io.DenoptimIOTest.testIOCuttingRules(), denoptim.io.DenoptimIOTest.testIOEmptyVertex(), denoptim.io.DenoptimIOTest.testIOMolFragment(), denoptim.io.DenoptimIOTest.testIOTemplate(), denoptim.io.DenoptimIOTest.testReadAllAtomContainersFromCIF(), denoptim.io.DenoptimIOTest.testReadCSDFormulae(), denoptim.io.DenoptimIOTest.testReadGenerationFromSummary(), denoptim.io.DenoptimIOTest.testReadLightWeightCandidate(), and denoptim.io.DenoptimIOTest.testSerializeDeserializeDENOPTIMGraphs().

◆ tempDir

File denoptim.io.DenoptimIOTest.tempDir
package

Definition at line 89 of file DenoptimIOTest.java.

Referenced by denoptim.io.DenoptimIOTest.testAppendToJSON(), denoptim.io.DenoptimIOTest.testDetectFileFormat(), denoptim.io.DenoptimIOTest.testIOCuttingRules(), denoptim.io.DenoptimIOTest.testIOEmptyVertex(), denoptim.io.DenoptimIOTest.testIOMolFragment(), denoptim.io.DenoptimIOTest.testIOTemplate(), denoptim.io.DenoptimIOTest.testReadAllAtomContainersFromCIF(), denoptim.io.DenoptimIOTest.testReadCSDFormulae(), denoptim.io.DenoptimIOTest.testReadGenerationFromSummary(), denoptim.io.DenoptimIOTest.testReadLightWeightCandidate(), and denoptim.io.DenoptimIOTest.testSerializeDeserializeDENOPTIMGraphs().

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