Static Public Member Functions
static void	addToRecentFiles (String fileName, FileFormat ff)
	Appends an entry to the list of recent files. More...

static void	addToRecentFiles (File file, FileFormat ff)
	Appends an entry to the list of recent files. More...

static boolean	isLineInTxtFile (String query, File file, boolean add) throws IOException
	Search in a file for a line matching the given string query. More...

static boolean	canWriteAndReadTo (String pathName)
	Check whether we can write and read to a given pathname. More...

static String	getTempFolder ()
	Looks for a writable location where to put temporary files and returns an absolute pathname to the folder where tmp files can be created. More...

static boolean	createDirectory (String fileName)
	Creates a directory. More...

static boolean	checkExists (String fileName)

static void	deleteFile (String fileName) throws DENOPTIMException
	Delete the file. More...

static void	deleteFilesContaining (String path, String pattern) throws DENOPTIMException
	Delete all files with pathname containing a given string. More...

static int	countLinesInFile (String fileName) throws DENOPTIMException
	Count the number of lines in the file. More...

static void	createZipFile (String zipOutputFileName, String[] filesToZip) throws Exception
	Creates a zip file. More...

static FileFormat	detectFileFormat (File inFile) throws UndetectedFileFormatException, IOException
	Inspects a file/folder and tries to detect if there is one of the data sources that is recognized by DENOPTIM. More...

static FileFormat	detectKindOfJSONFile (String fileName) throws IOException
	Detect the content of a json file. More...

static FileFormat	detectKindOfSDFFile (String fileName) throws IOException
	Looks into a text file and tries to understand if the file is a collection of parameters for any specific DENOPTIM module. More...

static FileFormat	detectKindOfParameterFile (String fileName) throws IOException
	Looks into a text file and tries to understand if the file is a collection of parameters for any specific DENOPTIM module. More...

static FileFormat	detectKindOfTXTFile (String fileName) throws IOException
	Looks into a text file and tries to understand if the file is a known text file. More...

static FileFormat	detectKindFile (String fileName, FileFormat[] ffs) throws IOException
	Looks into a text file and tries to understand what format it is among the given formats. More...

static File	getAvailableFileName (File parent, String baseName) throws DENOPTIMException
	Define a filename that can be used, i.e., is still available, because no other file with the same pathname exists. More...

static void	mergeIntoOneFile (String destinationPathname, List< String > sourcePathnames) throws IOException
	Copies the content of all the files specified in the list of sources and places it into the destination file. More...

Detailed Description

Definition at line 57 of file FileUtils.java.

Member Function Documentation

◆ addToRecentFiles() [1/2]

static void denoptim.files.FileUtils.addToRecentFiles	(	File	file,
		FileFormat	ff
	)

static

Appends an entry to the list of recent files.

If the current list is reaching the max length, then this method will append the new entry and remove the oldest one.

Parameters

file	the file to record.
ff	the declared format of file.

Definition at line 81 of file FileUtils.java.

References denoptim.logging.StaticLogger.appLogger, denoptim.constants.DENOPTIMConstants.EOL, denoptim.io.DenoptimIO.readRecentFilesMap(), denoptim.constants.DENOPTIMConstants.RECENTFILESLIST, and denoptim.io.DenoptimIO.writeData().

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◆ addToRecentFiles() [2/2]

static void denoptim.files.FileUtils.addToRecentFiles	(	String	fileName,
		FileFormat	ff
	)

static

Appends an entry to the list of recent files.

Parameters

fileName	the file to record.
ff	the declared format of file.

Definition at line 67 of file FileUtils.java.

References denoptim.files.FileUtils.addToRecentFiles().

Referenced by denoptim.files.FileUtils.addToRecentFiles(), denoptim.programs.combinatorial.CEBLParameters.createWorkingDirectory(), denoptim.programs.fragmenter.FragmenterParameters.createWorkingDirectory(), denoptim.gui.CuttingRulesSelectionDialog.CuttingRulesSelectionDialog(), denoptim.gui.GUICompatibilityMatrixTab.initialize(), denoptim.gui.GUIGraphHandler.initialize(), denoptim.gui.GUIPrepare.initialize(), denoptim.gui.GUIVertexInspector.initialize(), denoptim.task.ProgramTask.printErrorToFile(), and denoptim.programs.fitnessevaluator.FRParameters.processParameters().

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◆ canWriteAndReadTo()

static boolean denoptim.files.FileUtils.canWriteAndReadTo ( String pathName )

static

Check whether we can write and read to a given pathname.

Parameters

pathName

Returns: true if we can write and read in that pathname

Definition at line 185 of file FileUtils.java.

References denoptim.io.DenoptimIO.readList(), and denoptim.io.DenoptimIO.writeData().

Referenced by denoptim.gui.Utils.getTempFile(), denoptim.files.FileUtils.getTempFolder(), and denoptim.gui.GUIPreferencesDialog.pathMustBeReadableWritable().

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◆ checkExists()

static boolean denoptim.files.FileUtils.checkExists ( String fileName )

static

Parameters

fileName

Returns: true if file exists

Definition at line 241 of file FileUtils.java.

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◆ countLinesInFile()

static int denoptim.files.FileUtils.countLinesInFile ( String fileName ) throws DENOPTIMException

static

Count the number of lines in the file.

Parameters

fileName

Returns: number of lines in the file

Exceptions

DENOPTIMException

Definition at line 312 of file FileUtils.java.

◆ createDirectory()

static boolean denoptim.files.FileUtils.createDirectory ( String fileName )

static

Creates a directory.

Parameters

fileName

Returns: true if directory is successfully created

Definition at line 231 of file FileUtils.java.

Referenced by denoptim.programs.combinatorial.CEBLParameters.createWorkingDirectory(), denoptim.programs.fragmenter.FragmenterParameters.createWorkingDirectory(), denoptim.constants.DENOPTIMConstants.ensureConfigFolderExists(), denoptim.files.FileUtils.getAvailableFileName(), denoptim.gui.GUIPrepare.prepareWorkSpace(), denoptim.io.DenoptimIOTest.testDetectFileFormat(), denoptim.programs.denovo.GAParametersTest.testLogging(), and denoptim.io.DenoptimIOTest.testReadGenerationFromSummary().

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◆ createZipFile()

static void denoptim.files.FileUtils.createZipFile	(	String	zipOutputFileName,
		String[]	filesToZip
	)		throws Exception

static

Creates a zip file.

Parameters

zipOutputFileName
filesToZip

Exceptions

Exception

Definition at line 349 of file FileUtils.java.

◆ deleteFile()

static void denoptim.files.FileUtils.deleteFile ( String fileName ) throws DENOPTIMException

static

Delete the file.

Parameters

fileName

Exceptions

DENOPTIMException

Definition at line 256 of file FileUtils.java.

Referenced by denoptim.files.FileUtils.deleteFilesContaining(), denoptim.gui.GUIPreferencesDialog.pathMustBeReadableWritable(), denoptim.fragspace.FragmentSpaceTest.testFusedRingAddedToFragmentLibrary(), denoptim.fragspace.FragmentSpaceTest.testFusedRingAddedToScaffoldLibrary(), denoptim.fragspace.FragmentSpaceTest.testFusedRingOnlyAddedOnce(), and denoptim.fragspace.FragmentSpaceTest.testUseWholeMolGeometryForExtractedTemplates().

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◆ deleteFilesContaining()

static void denoptim.files.FileUtils.deleteFilesContaining	(	String	path,
		String	pattern
	)		throws DENOPTIMException

static

Delete all files with pathname containing a given string.

Parameters

path
pattern

Exceptions

DENOPTIMException

Definition at line 289 of file FileUtils.java.

References denoptim.files.FileUtils.deleteFile().

Referenced by denoptim.molecularmodeling.RingClosureTool.attemptRingClosure(), and denoptim.integration.tinker.ConformationalSearchPSSROT.performPSSROT().

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◆ detectFileFormat()

static FileFormat denoptim.files.FileUtils.detectFileFormat ( File inFile ) throws UndetectedFileFormatException, IOException

static

Inspects a file/folder and tries to detect if there is one of the data sources that is recognized by DENOPTIM.

Parameters

inFile the file to inspect

Returns: a string informing on the detected file format, or null.

Exceptions

UndetectedFileFormatException	when the format of the file could not be detected.
IOException	when the the file could not be read properly.

Definition at line 399 of file FileUtils.java.

References denoptim.files.FileUtils.detectKindOfJSONFile(), denoptim.files.FileUtils.detectKindOfParameterFile(), denoptim.files.FileUtils.detectKindOfSDFFile(), denoptim.files.FileUtils.detectKindOfTXTFile(), denoptim.files.FileFormat.FSE_RUN, denoptim.constants.DENOPTIMConstants.FSEIDXNAMEROOT, denoptim.files.FileFormat.GA_RUN, denoptim.constants.DENOPTIMConstants.GAGENDIRNAMEROOT, and denoptim.files.FileFormat.getExtension().

Referenced by denoptim.gui.GUIGraphHandler.appendGraphsFromFile(), denoptim.main.Main.ensureFileExistsAndIsReadable(), denoptim.gui.GUIGraphHandler.importGraphsFromFile(), denoptim.gui.MainToolBar.initialize(), denoptim.io.DenoptimIO.readDENOPTIMData(), denoptim.io.DenoptimIO.readDENOPTIMGraphsFromFile(), denoptim.io.DenoptimIO.readVertexes(), denoptim.gui.GUI.run(), and denoptim.io.DenoptimIOTest.testDetectFileFormat().

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◆ detectKindFile()

static FileFormat denoptim.files.FileUtils.detectKindFile	(	String	fileName,
		FileFormat[]	ffs
	)		throws IOException

static

Looks into a text file and tries to understand what format it is among the given formats.

Parameters

fileName	The pathname of the file to analyze.
ffs	the file formats to consider.

Returns: a format of parameters, or null.

Exceptions

Exception when something goes wrong handling the file

Definition at line 605 of file FileUtils.java.

Referenced by denoptim.files.FileUtils.detectKindOfParameterFile(), denoptim.files.FileUtils.detectKindOfSDFFile(), and denoptim.files.FileUtils.detectKindOfTXTFile().

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◆ detectKindOfJSONFile()

static FileFormat denoptim.files.FileUtils.detectKindOfJSONFile ( String fileName ) throws IOException

static

Detect the content of a json file.

Parameters

fileName file to analyze.

Returns: the format of that file or null.

Exceptions

IOException

Definition at line 488 of file FileUtils.java.

References denoptim.json.DENOPTIMgson.getReader(), denoptim.files.FileFormat.GRAPHJSON, and denoptim.files.FileFormat.VRTXJSON.

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

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◆ detectKindOfParameterFile()

static FileFormat denoptim.files.FileUtils.detectKindOfParameterFile ( String fileName ) throws IOException

static

Looks into a text file and tries to understand if the file is a collection of parameters for any specific DENOPTIM module.

Parameters

fileName The pathname of the file to analyze

Returns: a the format of the parameter file or null.

Exceptions

IOException
Exception

Definition at line 570 of file FileUtils.java.

References denoptim.files.FileUtils.detectKindFile(), and denoptim.files.FileFormat.getParameterFormats().

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

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◆ detectKindOfSDFFile()

static FileFormat denoptim.files.FileUtils.detectKindOfSDFFile ( String fileName ) throws IOException

static

Looks into a text file and tries to understand if the file is a collection of parameters for any specific DENOPTIM module.

Parameters

fileName The pathname of the file to analyze

Returns: a string that defined the kind of parameters

Exceptions

IOException
Exception

Definition at line 554 of file FileUtils.java.

References denoptim.files.FileUtils.detectKindFile(), and denoptim.files.FileFormat.getSDFFormats().

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

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◆ detectKindOfTXTFile()

static FileFormat denoptim.files.FileUtils.detectKindOfTXTFile ( String fileName ) throws IOException

static

Looks into a text file and tries to understand if the file is a known text file.

Note that parameters file, which are in fact text files, are not detected here ad they are treated by the dedicated method FileUtils#detectKindOfParameterFile(String).

Parameters

fileName The pathname of the file to analyze

Returns: a the format of the text file or null.

Exceptions

IOException
Exception

Definition at line 588 of file FileUtils.java.

References denoptim.files.FileUtils.detectKindFile(), and denoptim.files.FileFormat.getTXTFormats().

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

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◆ getAvailableFileName()

static File denoptim.files.FileUtils.getAvailableFileName	(	File	parent,
		String	baseName
	)		throws DENOPTIMException

static

Define a filename that can be used, i.e., is still available, because no other file with the same pathname exists.

This method returns a string like File_3 when files File, File_1, and File_2 exist already.

Parameters

parent	the folder where the file is meant to be.
baseName	the prefix of the filename. This string will be postponed by an integer number to identify an available filename.

Returns: the available filename.

Exceptions

DENOPTIMException

Definition at line 729 of file FileUtils.java.

References denoptim.files.FileUtils.createDirectory(), and denoptim.io.DenoptimIO.FS.

Referenced by denoptim.gui.CuttingRulesSelectionDialog.getTmpFileForCuttingRules(), and denoptim.gui.GUIPrepare.prepareWorkSpace().

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◆ getTempFolder()

static String denoptim.files.FileUtils.getTempFolder ( )

static

Looks for a writable location where to put temporary files and returns an absolute pathname to the folder where tmp files can be created.

Returns: a writable absolute path

Definition at line 204 of file FileUtils.java.

References denoptim.files.FileUtils.canWriteAndReadTo().

Referenced by denoptim.gui.Utils.getTempFile(), denoptim.io.DenoptimIO.readAllAtomContainers(), and denoptim.io.DenoptimIOTest.testReadAllAPClasses().

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◆ isLineInTxtFile()

static boolean denoptim.files.FileUtils.isLineInTxtFile	(	String	query,
		File	file,
		boolean	add
	)		throws IOException

static

Search in a file for a line matching the given string query.

If the query is not found in the file, then it is added to it. Note that the query is compared in a case insensitive manner, and ignoring heading/trailing spaces, and with the content of each line in the file, so this is rather slow.

Parameters

query	the string to search for and possibly add to the file.
file	the text file to analyze.
add	if `true` then we add the query if it was not found.

Returns: true is the query was found in the file. Note that when add is true we return false when the match is not found in the file, but the moment we return the file has been already updated by this method as to add the query. So, independently on the return value, the file will contain the query string when this method returns.

Exceptions

IOException when handling of the memory written on disk returns exception.

Definition at line 132 of file FileUtils.java.

References denoptim.io.DenoptimIO.NL.

Referenced by denoptim.utils.SizeControlledSet.addNewUniqueEntry(), and denoptim.utils.SizeControlledSet.contains().

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◆ mergeIntoOneFile()

static void denoptim.files.FileUtils.mergeIntoOneFile	(	String	destinationPathname,
		List< String >	sourcePathnames
	)		throws IOException

static

Copies the content of all the files specified in the list of sources and places it into the destination file.

Parameters

destinationPathname	the destination of all content.
sourcePathnames	the pathnames of the files to be copied into the destination file.

Exceptions

IOException

Definition at line 768 of file FileUtils.java.

Referenced by denoptim.gui.GUIInspectGARun.initialize().

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

/github/workspace/src/main/java/denoptim/files/FileUtils.java

Static Public Member Functions

Detailed Description

Member Function Documentation

◆ addToRecentFiles() [1/2]

◆ addToRecentFiles() [2/2]

◆ canWriteAndReadTo()

◆ checkExists()

◆ countLinesInFile()

◆ createDirectory()

◆ createZipFile()

◆ deleteFile()

◆ deleteFilesContaining()

◆ detectFileFormat()

◆ detectKindFile()

◆ detectKindOfJSONFile()

◆ detectKindOfParameterFile()

◆ detectKindOfSDFFile()

◆ detectKindOfTXTFile()

◆ getAvailableFileName()

◆ getTempFolder()

◆ isLineInTxtFile()

◆ mergeIntoOneFile()