denoptim.files.FileFormat Enum Reference

File formats identified by DENOPTIM. More...

Collaboration diagram for denoptim.files.FileFormat:

Classes
enum	DataKind
	The kind of data found in a file. More...

Public Member Functions
boolean	isFolder ()
String	getSampleEndRegex ()
	In identifying a text file we read as many lines as possible until we match the "end-of-sample" string. More...
Set< String >	getDefiningRegex ()
	Returns the list of regex strings that allow identification of a file. More...
Set< String >	getNegatingRegex ()
	Returns the list of regex strings that exclude a file format. More...
String	getExtension ()

Static Public Member Functions
	[static initializer]
static FileFormat	fromString (String extension, DataKind kind)
	Gets the FileFormat from file extension and kind of data. More...
static FileFormat[]	getSDFFormats ()
	Returns the collection of file formats using SDF syntax. More...
static FileFormat[]	getParameterFormats ()
	Returns the collection of file formats with input parameters. More...
static FileFormat[]	getTXTFormats ()
	Returns the collection of file formats restricted to TXT files (excluded parameter files) More...

Public Attributes
	CANDIDATESDF
	GRAPHJSON
	GRAPHSDF
	VRTXJSON
	VRTXSDF
	MOLSDF
	FSE_RUN
	GA_RUN
	GA_PARAM
	FSE_PARAM
	FR_PARAM
	COMP_MAP
	GO_PARAM
	CLG_PARAM
	GE_PARAM
	GI_PARAM
	B3D_PARAM
	FRG_RUN
	FRG_PARAM
	CUTRULE
	TXT
	GRAPHTXT
	GENSUMMARY
	UNRECOGNIZED

Private Attributes
String	extension = ""
Set< String >	definingRegex = new HashSet<String>()
	Collection of regex that, if matched, suggests assigning the format to a specific FileFormat. More...
Set< String >	negatingRegex = new HashSet<String>()
	Collection of regex that, if matched, prevents assigning the format to a specific FileFormat. More...
String	endOfSampleRegex = null
	Regex used to identify the end of the sampled text used to determine the format of a file. More...
Boolean	isFolder = false

Detailed Description

File formats identified by DENOPTIM.

Definition at line 32 of file FileFormat.java.

Member Function Documentation

[static initializer]()

denoptim.files.FileFormat.[static initializer]

static

References denoptim.constants.DENOPTIMConstants.APSTAG, denoptim.programs.RunTimeParameters.ParametersType.CEBL_PARAMS, denoptim.constants.DENOPTIMConstants.FITNESSTAG, denoptim.programs.RunTimeParameters.ParametersType.FR_PARAMS, denoptim.programs.RunTimeParameters.ParametersType.FRG_PARAMS, denoptim.programs.RunTimeParameters.ParametersType.GA_PARAMS, denoptim.constants.DENOPTIMConstants.GAGENSUMMARYHEADER, denoptim.programs.RunTimeParameters.ParametersType.GE_PARAMS, denoptim.programs.RunTimeParameters.ParametersType.GLH_PARAMS, denoptim.programs.RunTimeParameters.ParametersType.GO_PARAMS, denoptim.constants.DENOPTIMConstants.GRAPHJSONTAG, denoptim.constants.DENOPTIMConstants.GRAPHTAG, denoptim.programs.RunTimeParameters.ParametersType.ISO_PARAMS, denoptim.programs.RunTimeParameters.ParametersType.MMB_PARAM, denoptim.constants.DENOPTIMConstants.MOLERRORTAG, denoptim.constants.DENOPTIMConstants.UNIQUEIDTAG, and denoptim.constants.DENOPTIMConstants.VERTEXJSONTAG.

fromString()

static FileFormat denoptim.files.FileFormat.fromString ( String  extension, DataKind  kind  )

static

Gets the FileFormat from file extension and kind of data.

Parameters

extension	the extension of the file (i.e., in blabla.ext the extension is ext).
kind	the kind of data contained in the file.

Returns

the file format corresponding to the given extension and kind of data.

Definition at line 246 of file FileFormat.java.

Referenced by denoptim.gui.GUIFileSaver.pickFileForSavingGraphs(), and denoptim.gui.GUIFileSaver.pickFileForSavingVertexes().

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getDefiningRegex()

Set< String > denoptim.files.FileFormat.getDefiningRegex

(

)

Returns the list of regex strings that allow identification of a file.

Returns

Definition at line 427 of file FileFormat.java.

getExtension()

String denoptim.files.FileFormat.getExtension

(

)

Definition at line 445 of file FileFormat.java.

Referenced by denoptim.files.FileUtils.detectFileFormat(), denoptim.programs.fragmenter.FragmenterParameters.getMWSlotFileNameAllFrags(), and denoptim.programs.fragmenter.FragmenterParameters.getMWSlotFileNameUnqFrags().

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getNegatingRegex()

Set< String > denoptim.files.FileFormat.getNegatingRegex

(

)

Returns the list of regex strings that exclude a file format.

Returns

Definition at line 438 of file FileFormat.java.

getParameterFormats()

static FileFormat[] denoptim.files.FileFormat.getParameterFormats ( )

static

Returns the collection of file formats with input parameters.

Returns

the collection of file formats with input parameters.

Definition at line 362 of file FileFormat.java.

References denoptim.files.FileFormat.B3D_PARAM, denoptim.files.FileFormat.CLG_PARAM, denoptim.files.FileFormat.COMP_MAP, denoptim.files.FileFormat.FR_PARAM, denoptim.files.FileFormat.FRG_PARAM, denoptim.files.FileFormat.FSE_PARAM, denoptim.files.FileFormat.GA_PARAM, denoptim.files.FileFormat.GE_PARAM, denoptim.files.FileFormat.GI_PARAM, and denoptim.files.FileFormat.GO_PARAM.

Referenced by denoptim.files.FileUtils.detectKindOfParameterFile().

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getSampleEndRegex()

String denoptim.files.FileFormat.getSampleEndRegex

(

)

In identifying a text file we read as many lines as possible until we match the "end-of-sample" string.

This method returns the regex that defines the "end-of-sample" string.

Returns

the regex identifying the end of the sample text.

Definition at line 416 of file FileFormat.java.

getSDFFormats()

static FileFormat[] denoptim.files.FileFormat.getSDFFormats ( )

static

Returns the collection of file formats using SDF syntax.

Returns

the collection of file formats using SDF syntax.

Definition at line 345 of file FileFormat.java.

References denoptim.files.FileFormat.CANDIDATESDF, denoptim.files.FileFormat.GRAPHSDF, denoptim.files.FileFormat.MOLSDF, and denoptim.files.FileFormat.VRTXSDF.

Referenced by denoptim.files.FileUtils.detectKindOfSDFFile().

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getTXTFormats()

static FileFormat[] denoptim.files.FileFormat.getTXTFormats ( )

static

Returns the collection of file formats restricted to TXT files (excluded parameter files)

Returns

the collection of file formats restricted to TXT files.

Definition at line 387 of file FileFormat.java.

References denoptim.files.FileFormat.CUTRULE, denoptim.files.FileFormat.GENSUMMARY, and denoptim.files.FileFormat.GRAPHTXT.

Referenced by denoptim.files.FileUtils.detectKindOfTXTFile().

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isFolder()

boolean denoptim.files.FileFormat.isFolder

(

)

Returns

true if the file is supposed to be a folder

Definition at line 403 of file FileFormat.java.

Member Data Documentation

B3D_PARAM

denoptim.files.FileFormat.B3D_PARAM

Definition at line 39 of file FileFormat.java.

Referenced by denoptim.files.FileFormat.getParameterFormats().

CANDIDATESDF

denoptim.files.FileFormat.CANDIDATESDF

Definition at line 34 of file FileFormat.java.

Referenced by denoptim.files.FileFormat.getSDFFormats(), denoptim.io.DenoptimIO.writeCandidatesToFile(), and denoptim.io.DenoptimIO.writeCandidateToFile().

CLG_PARAM

denoptim.files.FileFormat.CLG_PARAM

Definition at line 38 of file FileFormat.java.

Referenced by denoptim.files.FileFormat.getParameterFormats().

COMP_MAP

denoptim.files.FileFormat.COMP_MAP

Definition at line 38 of file FileFormat.java.

Referenced by denoptim.files.FileFormat.getParameterFormats(), denoptim.gui.GUICompatibilityMatrixTab.initialize(), denoptim.gui.MainToolBar.initialize(), and denoptim.io.DenoptimIOTest.testDetectFileFormat().

CUTRULE

denoptim.files.FileFormat.CUTRULE

Definition at line 39 of file FileFormat.java.

Referenced by denoptim.gui.CuttingRulesSelectionDialog.CuttingRulesSelectionDialog(), denoptim.files.FileFormat.getTXTFormats(), and denoptim.gui.GUIFileSaver.pickFileForSavingCuttingRules().

definingRegex

Set<String> denoptim.files.FileFormat.definingRegex = new HashSet<String>()

private

Collection of regex that, if matched, suggests assigning the format to a specific FileFormat.

Consider a logical OR operator, i.e., any match will suggest among the set of regex will lead to format interpretation. Regex are matches against toUpperCase strings, so they behave as case-insensitive.

Definition at line 53 of file FileFormat.java.

endOfSampleRegex

String denoptim.files.FileFormat.endOfSampleRegex = null

private

Regex used to identify the end of the sampled text used to determine the format of a file.

Regex are matches against toUpperCase strings, so they behave as case-insensitive.

Definition at line 67 of file FileFormat.java.

extension

String denoptim.files.FileFormat.extension = ""

private

Definition at line 44 of file FileFormat.java.

FR_PARAM

denoptim.files.FileFormat.FR_PARAM

Definition at line 38 of file FileFormat.java.

Referenced by denoptim.files.FileFormat.getParameterFormats(), and denoptim.gui.MainToolBar.initialize().

FRG_PARAM

denoptim.files.FileFormat.FRG_PARAM

Definition at line 39 of file FileFormat.java.

Referenced by denoptim.files.FileFormat.getParameterFormats().

FRG_RUN

denoptim.files.FileFormat.FRG_RUN

Definition at line 39 of file FileFormat.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.createWorkingDirectory().

FSE_PARAM

denoptim.files.FileFormat.FSE_PARAM

Definition at line 38 of file FileFormat.java.

Referenced by denoptim.gui.GUIPrepare.getFileFormat(), denoptim.files.FileFormat.getParameterFormats(), denoptim.gui.MainToolBar.initialize(), and denoptim.io.DenoptimIOTest.testDetectFileFormat().

FSE_RUN

denoptim.files.FileFormat.FSE_RUN

Definition at line 36 of file FileFormat.java.

Referenced by denoptim.programs.combinatorial.CEBLParameters.createWorkingDirectory(), denoptim.files.FileUtils.detectFileFormat(), denoptim.gui.MainToolBar.initialize(), and denoptim.io.DenoptimIOTest.testDetectFileFormat().

GA_PARAM

denoptim.files.FileFormat.GA_PARAM

Definition at line 38 of file FileFormat.java.

Referenced by denoptim.gui.GUIPrepare.getFileFormat(), denoptim.files.FileFormat.getParameterFormats(), denoptim.gui.MainToolBar.initialize(), and denoptim.io.DenoptimIOTest.testDetectFileFormat().

GA_RUN

denoptim.files.FileFormat.GA_RUN

Definition at line 36 of file FileFormat.java.

Referenced by denoptim.programs.denovo.GAParameters.createWorkingDirectory(), denoptim.files.FileUtils.detectFileFormat(), denoptim.gui.GUIPrepare.getFileFormat(), denoptim.gui.MainToolBar.initialize(), and denoptim.io.DenoptimIOTest.testDetectFileFormat().

GE_PARAM

denoptim.files.FileFormat.GE_PARAM

Definition at line 38 of file FileFormat.java.

Referenced by denoptim.files.FileFormat.getParameterFormats().

GENSUMMARY

denoptim.files.FileFormat.GENSUMMARY

Definition at line 41 of file FileFormat.java.

Referenced by denoptim.files.FileFormat.getTXTFormats(), and denoptim.io.DenoptimIOTest.testDetectFileFormat().

GI_PARAM

denoptim.files.FileFormat.GI_PARAM

Definition at line 39 of file FileFormat.java.

Referenced by denoptim.files.FileFormat.getParameterFormats().

GO_PARAM

denoptim.files.FileFormat.GO_PARAM

Definition at line 38 of file FileFormat.java.

Referenced by denoptim.files.FileFormat.getParameterFormats().

GRAPHJSON

denoptim.files.FileFormat.GRAPHJSON

Definition at line 35 of file FileFormat.java.

Referenced by denoptim.files.FileUtils.detectKindOfJSONFile(), and denoptim.programs.grapheditor.GraphEdParameters.interpretKeyword().

GRAPHSDF

denoptim.files.FileFormat.GRAPHSDF

Definition at line 35 of file FileFormat.java.

Referenced by denoptim.files.FileFormat.getSDFFormats(), denoptim.programs.grapheditor.GraphEdParameters.interpretKeyword(), denoptim.programs.fitnessevaluator.FRParameters.processParameters(), and denoptim.io.DenoptimIOTest.testDetectFileFormat().

GRAPHTXT

denoptim.files.FileFormat.GRAPHTXT

Definition at line 41 of file FileFormat.java.

Referenced by denoptim.files.FileFormat.getTXTFormats().

isFolder

Boolean denoptim.files.FileFormat.isFolder = false

private

Definition at line 69 of file FileFormat.java.

MOLSDF

denoptim.files.FileFormat.MOLSDF

Definition at line 35 of file FileFormat.java.

Referenced by denoptim.fragmenter.ParallelFragmentationAlgorithm.doPostFlightOperations(), and denoptim.files.FileFormat.getSDFFormats().

negatingRegex

Set<String> denoptim.files.FileFormat.negatingRegex = new HashSet<String>()

private

Collection of regex that, if matched, prevents assigning the format to a specific FileFormat.

Regex are matches against toUpperCase strings, so they behave as case-insensitive.

Definition at line 60 of file FileFormat.java.

TXT

denoptim.files.FileFormat.TXT

Definition at line 41 of file FileFormat.java.

Referenced by denoptim.task.ProgramTask.printErrorToFile().

UNRECOGNIZED

denoptim.files.FileFormat.UNRECOGNIZED

Definition at line 42 of file FileFormat.java.

Referenced by denoptim.main.Main.ensureFileExistsAndIsReadable(), denoptim.io.DenoptimIO.readDENOPTIMData(), and denoptim.gui.GUI.run().

VRTXJSON

denoptim.files.FileFormat.VRTXJSON

Definition at line 35 of file FileFormat.java.

Referenced by denoptim.files.FileUtils.detectKindOfJSONFile(), denoptim.io.DenoptimIOTest.testAppendToJSON(), denoptim.io.DenoptimIOTest.testIOEmptyVertex(), denoptim.io.DenoptimIOTest.testIOMolFragment(), and denoptim.io.DenoptimIOTest.testIOTemplate().

VRTXSDF

denoptim.files.FileFormat.VRTXSDF

Definition at line 35 of file FileFormat.java.

Referenced by denoptim.fragmenter.ConformerExtractorTask.call(), denoptim.fragmenter.FragmenterTools.fragmentation(), denoptim.files.FileFormat.getSDFFormats(), denoptim.fragmenter.FragmenterTools.manageFragmentCollection(), denoptim.io.DenoptimIO.readDENOPTIMGraphsFromFile(), denoptim.fragmenter.FragmentClustererTest.testCluster(), denoptim.io.DenoptimIOTest.testDetectFileFormat(), denoptim.io.DenoptimIOTest.testIOEmptyVertex(), denoptim.io.DenoptimIOTest.testIOMolFragment(), and denoptim.io.DenoptimIOTest.testIOTemplate().

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

• /github/workspace/src/main/java/denoptim/files/FileFormat.java