Index (anchor-io-input 0.2.1 API)

A C D E F G H I L M N O P R S T W
All Classes All Packages

A

allAssociatedPaths() - Method in interface org.anchoranalysis.io.input.InputFromManager: A path to all files associated with the input, including InputFromManager.pathForBinding().
asFile() - Method in interface org.anchoranalysis.io.input.InputFromManager: Expresses the input as a file with a name (the unique identifier).
assignFilterGlob(String) - Method in class org.anchoranalysis.io.input.InputContextParameters: Assigns a glob that can be used by beans to filter input.
assignFixedLimit(int) - Method in class org.anchoranalysis.io.input.InputContextParameters: Assigns a fixed upper limit of number of inputs.
assignIdentifierSubrange(IndexRangeNegative) - Method in class org.anchoranalysis.io.input.InputContextParameters: If defined, this indicates and specifies only a subset of the elements of the identifier to use.
assignInputDirectory(Optional<Path>) - Method in class org.anchoranalysis.io.input.InputContextParameters: Sets an input-directory.
assignInputFilterExtensions(StringSetTrie) - Method in class org.anchoranalysis.io.input.InputContextParameters: Assigns extensions that can be used filter inputs, but irrespective of whether extensions have already been set.
assignInputFilterExtensionsIfMissing(Supplier<Optional<StringSetTrie>>) - Method in class org.anchoranalysis.io.input.InputContextParameters: Assigns extensions that can be used filter inputs, but only when no extensions have already been set.
assignPaths(List<Path>) - Method in class org.anchoranalysis.io.input.InputContextParameters: Assigns a specific list of paths that are used for the inputs.
assignRatioLimit(double) - Method in class org.anchoranalysis.io.input.InputContextParameters: Assigns a fixed upper limit that is a ratio of the number of inputs allowed.
assignRelativeForIdentifier() - Method in class org.anchoranalysis.io.input.InputContextParameters: Specify that the entire filename or relative path (excluding extension) is used to determine a unique identifier.
assignShuffle() - Method in class org.anchoranalysis.io.input.InputContextParameters: Indicates that the order of the inputs should be shuffled (randomized).

C

canMatchSubdirectories() - Method in class org.anchoranalysis.io.input.bean.path.matcher.FilePathMatcher: Determines if it possible to match a file in a subdirectory.
canMatchSubdirectories() - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchExtensions
canMatchSubdirectories() - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchGlob
canMatchSubdirectories() - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchRegularExpression
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchRegularExpression
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.io.input.bean.path.NameElementRange
close() - Method in class org.anchoranalysis.io.input.csv.CSVReader.OpenedCSVFile
close() - Method in class org.anchoranalysis.io.input.csv.ReadByLine: Closes any opened-files
close(ErrorReporter) - Method in interface org.anchoranalysis.io.input.InputFromManager: Performs all tidying up, file-closing etc.
close(ErrorReporter) - Method in class org.anchoranalysis.io.input.InputFromManagerDelegate
consumeMatchingFiles(List<Path>, Consumer<File>) - Method in class org.anchoranalysis.io.input.path.matcher.DualPathPredicates: Calls a Consumer on any path that matches the predicate file.
containsOrEmpty() - Method in class org.anchoranalysis.io.input.bean.DebugModeParameters
create(InputManagerParameters) - Method in class org.anchoranalysis.io.input.bean.files.FilesProvider: Creates or provides a list of files.
create(InputManagerParameters) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderUnary
create(InputManagerParameters) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectory
create(InputManagerParameters) - Method in class org.anchoranalysis.io.input.bean.files.SpecificPathList
createInputGrouper(Optional<IndexRangeNegative>) - Method in class org.anchoranalysis.io.input.bean.grouper.FromDerivePath: Creates an InputGrouper that can be used to derive a group-key from a particular input.
createInputGrouper(Optional<IndexRangeNegative>) - Method in class org.anchoranalysis.io.input.bean.grouper.Grouper: Creates an InputGrouper that can be used to derive a group-key from a particular input.
createInputGrouper(Optional<IndexRangeNegative>) - Method in class org.anchoranalysis.io.input.bean.grouper.WithoutGrouping
createMatcherFile(Path, Optional<InputContextParameters>) - Method in class org.anchoranalysis.io.input.bean.path.matcher.FilePathMatcher: Create a predicate to be used for matching against path.
createMatcherFile(Path, Optional<InputContextParameters>) - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchExtensions
createMatcherFile(Path, Optional<InputContextParameters>) - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchGlob
createMatcherFile(Path, Optional<InputContextParameters>) - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchRegularExpression
createWithEmptyList() - Static method in class org.anchoranalysis.io.input.bean.files.SpecificPathList: Factory method for creating the class with an empty list of paths.
CSVReader - Class in org.anchoranalysis.io.input.csv: Reads a CSV File from the file-system.
CSVReader(String, boolean) - Constructor for class org.anchoranalysis.io.input.csv.CSVReader: Create, expecting unquoted strings.
CSVReader(String, boolean, boolean) - Constructor for class org.anchoranalysis.io.input.csv.CSVReader
CSVReader.OpenedCSVFile - Class in org.anchoranalysis.io.input.csv: A CSV file that has been opened for reading from the file-system.
CSVReaderByLine - Class in org.anchoranalysis.io.input.csv: Reads a CSV file line-by-line.
CSVReaderException - Exception in org.anchoranalysis.io.input.csv: When an error occurs reading a CSV file.
CSVReaderException(String) - Constructor for exception org.anchoranalysis.io.input.csv.CSVReaderException: Create with a message only.
CSVReaderException(Throwable) - Constructor for exception org.anchoranalysis.io.input.csv.CSVReaderException: Create with a cause only.

D

DebugModeParameters - Class in org.anchoranalysis.io.input.bean: An alternative mode of option where behaviours change.
DebugModeParameters(Optional<String>) - Constructor for class org.anchoranalysis.io.input.bean.DebugModeParameters
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.io.input.bean.path.DerivePath: Derives a new path from an existing path.
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.io.input.bean.path.Identity
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.io.input.bean.path.NameElementRange
deriveFrom(Supplier<Optional<Path>>, boolean) - Method in class org.anchoranalysis.io.input.bean.path.DerivePath: Derives a new path from an existing path.
deriveGroupKeyOptional(Path) - Method in interface org.anchoranalysis.io.input.grouper.InputGrouper: Derives a key for the group from identifier.
deriveName(File, Optional<Path>, int) - Method in class org.anchoranalysis.io.input.bean.namer.FileNamerIndependent: Derives a unique name for this file.
deriveName(File, FileNamerContext) - Method in class org.anchoranalysis.io.input.bean.namer.FileNamer: A name for a file.
deriveName(List<File>, FileNamerContext) - Method in class org.anchoranalysis.io.input.bean.namer.FileNamer: Derives a list of names (associated with each file) for some files.
deriveName(List<File>, FileNamerContext) - Method in class org.anchoranalysis.io.input.bean.namer.FileNamerIndependent
deriveNameUnique(List<File>, FileNamerContext) - Method in class org.anchoranalysis.io.input.bean.namer.FileNamer: Like FileNamer.deriveName(List, FileNamerContext) but checks that the final list of named-files all have unique names.
DerivePath - Class in org.anchoranalysis.io.input.bean.path: Derives a path from an existing path.
DerivePath() - Constructor for class org.anchoranalysis.io.input.bean.path.DerivePath
DerivePathException - Exception in org.anchoranalysis.io.input.path: When an error occurs deriving a path from another path.
DerivePathException(String) - Constructor for exception org.anchoranalysis.io.input.path.DerivePathException: Create with a message only.
DerivePathException(String, Throwable) - Constructor for exception org.anchoranalysis.io.input.path.DerivePathException: Create with a message and cause.
DerivePathException(Throwable) - Constructor for exception org.anchoranalysis.io.input.path.DerivePathException: Create with a cause only.
directory() - Method in class org.anchoranalysis.io.input.InputsWithDirectory: The directory associated with the inputs.
DualPathPredicates - Class in org.anchoranalysis.io.input.path.matcher: A Predicate<Path for both a file and a directory.
DualPathPredicates(CheckedPredicate<Path, IOException>, CheckedPredicate<Path, IOException>) - Constructor for class org.anchoranalysis.io.input.path.matcher.DualPathPredicates

E

equals(Object) - Method in class org.anchoranalysis.io.input.file.FileNamerContext
equals(Object) - Method in class org.anchoranalysis.io.input.file.NamedFile
equals(Object) - Method in class org.anchoranalysis.io.input.InputsWithDirectory
equals(Object) - Method in class org.anchoranalysis.io.input.path.GlobExtractor.GlobWithDirectory
extract(String) - Static method in class org.anchoranalysis.io.input.path.GlobExtractor: Extracts a glob, and a directory portion if it exists from a string with a wildcard.
extract(Path, IndexRangeNegative) - Static method in class org.anchoranalysis.io.input.path.ExtractPathElementRange: Extracts a sub-path from a Path by only retaining a range of elements.
ExtractPathElementRange - Class in org.anchoranalysis.io.input.path: Extracts a range of elements from a Path.

F

FileInput - Class in org.anchoranalysis.io.input.file: An input pertaining to a single file on the file-system.
FileInput(NamedFile) - Constructor for class org.anchoranalysis.io.input.file.FileInput: Creates for a single file.
FileNamer - Class in org.anchoranalysis.io.input.bean.namer: Associates a name (a compact unique identifier) with a file.
FileNamer() - Constructor for class org.anchoranalysis.io.input.bean.namer.FileNamer
FileNamerContext - Class in org.anchoranalysis.io.input.file: Provides useful additional objects when assigning a name to a file.
FileNamerContext(String, Logger) - Constructor for class org.anchoranalysis.io.input.file.FileNamerContext: Creates with a fallback-name and a logger, but otherwise using sensible defaults.
FileNamerContext(Optional<Path>, boolean, String, Optional<IndexRangeNegative>, Logger) - Constructor for class org.anchoranalysis.io.input.file.FileNamerContext
FileNamerContext(Optional<Path>, boolean, Optional<IndexRangeNegative>, Logger) - Constructor for class org.anchoranalysis.io.input.file.FileNamerContext: Creates with specific parameters.
FileNamerContext(Logger) - Constructor for class org.anchoranalysis.io.input.file.FileNamerContext: Creates with a logger, and otherwise uses sensible defaults.
FileNamerIndependent - Class in org.anchoranalysis.io.input.bean.namer: Base class for methods that derive the name independently for each file.
FileNamerIndependent() - Constructor for class org.anchoranalysis.io.input.bean.namer.FileNamerIndependent
FilePathMatcher - Class in org.anchoranalysis.io.input.bean.path.matcher: Matches file-paths against some kind of pattern.
FilePathMatcher() - Constructor for class org.anchoranalysis.io.input.bean.path.matcher.FilePathMatcher
FilePathProvider - Class in org.anchoranalysis.io.input.bean.path.provider: Base class for beans that implement Provider to provide a Path.
FilePathProvider() - Constructor for class org.anchoranalysis.io.input.bean.path.provider.FilePathProvider
FilePathProviderReference - Class in org.anchoranalysis.io.input.bean.path.provider: Calls an existing FilePathProvider indirectly to provide an identical result.
FilePathProviderReference() - Constructor for class org.anchoranalysis.io.input.bean.path.provider.FilePathProviderReference
FilesProvider - Class in org.anchoranalysis.io.input.bean.files: Base class for providing a list of Files.
FilesProvider() - Constructor for class org.anchoranalysis.io.input.bean.files.FilesProvider
FilesProviderException - Exception in org.anchoranalysis.io.input.file: When an error occurs providing a set of files.
FilesProviderException(String) - Constructor for exception org.anchoranalysis.io.input.file.FilesProviderException: Create with a message only.
FilesProviderException(Throwable) - Constructor for exception org.anchoranalysis.io.input.file.FilesProviderException: Create with a cause only.
FilesProviderUnary - Class in org.anchoranalysis.io.input.bean.files: Like FilesProvider but employs a unary operator on a call to an existing FilesProvider.
FilesProviderUnary() - Constructor for class org.anchoranalysis.io.input.bean.files.FilesProviderUnary
FilesProviderWithDirectory - Class in org.anchoranalysis.io.input.bean.files: Base class for implementations of FilesProvider which do have an associated directory.
FilesProviderWithDirectory() - Constructor for class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectory
FilesProviderWithDirectoryString - Class in org.anchoranalysis.io.input.bean.files: A FilesProviderWithDirectory where the directory is optionally specified as a string constant
FilesProviderWithDirectoryString() - Constructor for class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectoryString
FilesProviderWithDirectoryUnary - Class in org.anchoranalysis.io.input.bean.files: Like FilesProviderWithDirectory but employs a unary operator on a call to an existing FilesProviderWithDirectory.
FilesProviderWithDirectoryUnary() - Constructor for class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectoryUnary
FilesProviderWithoutDirectory - Class in org.anchoranalysis.io.input.bean.files: Base class for implementations of FilesProvider which do not have an associated directory.
FilesProviderWithoutDirectory() - Constructor for class org.anchoranalysis.io.input.bean.files.FilesProviderWithoutDirectory
FileWithDirectoryInput - Class in org.anchoranalysis.io.input.file: An input pertaining to a single file on the file-system - and a directory in which it resides.
FileWithDirectoryInput(NamedFile, Path) - Constructor for class org.anchoranalysis.io.input.file.FileWithDirectoryInput: Create for a particular file and directory.
findAllNonInputFiles() - Method in class org.anchoranalysis.io.input.InputsWithDirectory: Find all files in the input directory are not used as inputs.
FindFilesException - Exception in org.anchoranalysis.io.input.path.matcher: When an error occurs finding files.
FindFilesException(String) - Constructor for exception org.anchoranalysis.io.input.path.matcher.FindFilesException: Create with a message only.
FindFilesException(String, Throwable) - Constructor for exception org.anchoranalysis.io.input.path.matcher.FindFilesException: Create with a message and cause.
FromDerivePath - Class in org.anchoranalysis.io.input.bean.grouper: Derives the grouping-key via a call to DerivePath.
FromDerivePath() - Constructor for class org.anchoranalysis.io.input.bean.grouper.FromDerivePath
FromFiles - Class in org.anchoranalysis.io.input.bean.path.provider: Extracts a path from a FilesProvider.
FromFiles() - Constructor for class org.anchoranalysis.io.input.bean.path.provider.FromFiles

G

get() - Method in class org.anchoranalysis.io.input.bean.dictionary.ReadFromFile
get() - Method in class org.anchoranalysis.io.input.bean.path.provider.FilePathProviderReference
get() - Method in class org.anchoranalysis.io.input.bean.path.provider.FromFiles
get() - Method in interface org.anchoranalysis.io.input.path.PathSupplier: Supplies a Path.
getDebugModeParameters() - Method in class org.anchoranalysis.io.input.bean.InputManagerParameters: Parameters for debug-mode (only defined if we are in debug mode).
getDebugModeParameters() - Method in class org.anchoranalysis.io.input.InputContextParameters: Parameters for debug-mode (only defined if we are in debug mode).
getDelegate() - Method in class org.anchoranalysis.io.input.InputFromManagerDelegate: The delegate.
getDirectory() - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectoryString: A directory in which to look for files.
getDirectory() - Method in class org.anchoranalysis.io.input.file.FileWithDirectoryInput: A directory that must be a containing directory (at some hierarchical level) of file associated with this input.
getDirectory() - Method in class org.anchoranalysis.io.input.path.GlobExtractor.GlobWithDirectory: The directory part of the string, or null if it doesn't exist
getDirectory() - Method in class org.anchoranalysis.io.input.path.matcher.DualPathPredicates: Only accepts any containing directories where the predicate returns true
getDirectoryAsPath(InputContextParameters) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectory: The associated directory with the list of files.
getDirectoryAsPath(InputContextParameters) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectoryString
getDirectoryAsPath(InputContextParameters) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectoryUnary
getDirectoryAsPath(InputContextParameters) - Method in class org.anchoranalysis.io.input.bean.files.SingleFile
getDirectoryAsPathEnsureAbsolute(InputContextParameters) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectory: Like FilesProviderWithDirectory.getDirectoryAsPath(org.anchoranalysis.io.input.InputContextParameters) but converts any relative path to absolute one.
getElseName() - Method in class org.anchoranalysis.io.input.file.FileNamerContext: A fallback name, if a failure occurs when naming.
getExecutionTimeRecorder() - Method in class org.anchoranalysis.io.input.bean.InputManagerParameters: Allows for the execution time of certain operations to be recorded.
getExpression() - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchRegularExpression: The regular-expression, Java-style as described in Pattern.
getExtensions() - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchExtensions: A set of file-extensions (without the period), one of which must match the end of a path.
getFallback() - Method in class org.anchoranalysis.io.input.bean.files.SpecificPathList: If no paths can be found either from listPaths or the input-context, then the fallback is called if exists, otherwise an error is thrown
getFile() - Method in class org.anchoranalysis.io.input.file.NamedFile: The file.
getFile() - Method in class org.anchoranalysis.io.input.file.SingleFileInputBase: The associated single file.
getFiles() - Method in class org.anchoranalysis.io.input.bean.dictionary.ReadFromFile: Provides a single file containing a dictionary.
getFiles() - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderUnary
getFiles() - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectoryUnary
getFiles() - Method in class org.anchoranalysis.io.input.bean.path.provider.FromFiles: A provider that should return exactly one File whose path is employed.
getGlob() - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchGlob: The string describing a glob e.g.
getGlob() - Method in class org.anchoranalysis.io.input.path.GlobExtractor.GlobWithDirectory: A glob with Java's getPathMatcher syntax.
getHeaders() - Method in class org.anchoranalysis.io.input.csv.CSVReader.OpenedCSVFile: The header-names of the CSV file if available.
getId() - Method in class org.anchoranalysis.io.input.bean.path.provider.FilePathProviderReference: A unique identifer for another FilePathProvider that is referenced.
getIdentifier() - Method in class org.anchoranalysis.io.input.file.NamedFile: Unique identifier associated with the file.
getIdentifierSubrange() - Method in class org.anchoranalysis.io.input.InputContextParameters: If defined, this indicates and specifies only a subset of the naming-elements to use.
getIndexEnd() - Method in class org.anchoranalysis.io.input.bean.path.NameElementRange: The index of the last element (inclusive) for the range.
getIndexStart() - Method in class org.anchoranalysis.io.input.bean.path.NameElementRange: The index of the first element (inclusive) for the range.
getInput() - Method in class org.anchoranalysis.io.input.bean.InputManagerUnary: The delegate input-manager which will be circumstantially called by the current input-manager.
getInputContext() - Method in class org.anchoranalysis.io.input.bean.InputManagerParameters: Additional parameters that offer context for many beans that provide input-functions.
getInputDirectory() - Method in class org.anchoranalysis.io.input.file.FileNamerContext: A directory associated with the inputs, which if defined, is guaranteed to be a parent of them all.
getInputDirectory() - Method in class org.anchoranalysis.io.input.InputContextParameters: If defined, a directory which can be used by beans to find input.
getInputFilterExtensions() - Method in class org.anchoranalysis.io.input.InputContextParameters: A trie of extensions that can be used filter inputs.
getInputFilterGlob() - Method in class org.anchoranalysis.io.input.InputContextParameters: A glob that can be used by beans to filter input.
getInputPaths() - Method in class org.anchoranalysis.io.input.InputContextParameters: A list of paths referring to specific inputs.
getLimitUpper() - Method in class org.anchoranalysis.io.input.InputContextParameters: If defined, an upper limit that is imposed on the number of inputs.
getListPaths() - Method in class org.anchoranalysis.io.input.bean.files.SpecificPathList: If specified, this forms the list of paths which is provided as input.
getLogger() - Method in class org.anchoranalysis.io.input.bean.InputManagerParameters: Where to write informative messages to, and and any non-fatal errors (fatal errors are throw as exceptions).
getLogger() - Method in class org.anchoranalysis.io.input.file.FileNamerContext: Logs information messages.
getMatcher() - Method in class org.anchoranalysis.io.input.bean.files.SearchDirectory
getMatcher() - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchExtensions: A secondary matcher, which is required additionally match (as well as the extension).
getMaxDirectoryDepth() - Method in class org.anchoranalysis.io.input.bean.files.SearchDirectory: If non-negative the max depth of directories.
getNameSubrange() - Method in class org.anchoranalysis.io.input.file.FileNamerContext: If defined, this indicates and specifies only a subset of the naming-elements to use.
getOperationContext() - Method in class org.anchoranalysis.io.input.bean.InputManagerParameters: Allows for logging and recording the execution-time of particular operations.
getPath() - Method in class org.anchoranalysis.io.input.bean.files.SingleFile: The path of the single-file.
getPath() - Method in class org.anchoranalysis.io.input.file.NamedFile: The path of NamedFile.getFile().
GlobExtractor - Class in org.anchoranalysis.io.input.path: Extracts a glob from a string describing it, and a direcory which gives it context.
GlobExtractor.GlobWithDirectory - Class in org.anchoranalysis.io.input.path: A string describing a glob, associated with a directory onto which it will be applied.
GlobWithDirectory(Optional<String>, String) - Constructor for class org.anchoranalysis.io.input.path.GlobExtractor.GlobWithDirectory
Grouper - Class in org.anchoranalysis.io.input.bean.grouper: Determines how partition inputs into groups.
Grouper() - Constructor for class org.anchoranalysis.io.input.bean.grouper.Grouper

H

hashCode() - Method in class org.anchoranalysis.io.input.file.FileNamerContext
hashCode() - Method in class org.anchoranalysis.io.input.file.NamedFile
hashCode() - Method in class org.anchoranalysis.io.input.InputsWithDirectory
hashCode() - Method in class org.anchoranalysis.io.input.path.GlobExtractor.GlobWithDirectory
hasHeaders() - Method in class org.anchoranalysis.io.input.csv.CSVReader.OpenedCSVFile: Does the first line of the CSV file specify headers rather than values?
headers() - Method in class org.anchoranalysis.io.input.csv.ReadByLine: The headers of the CSV file.

I

identifier() - Method in class org.anchoranalysis.io.input.file.SingleFileInputBase
identifier() - Method in interface org.anchoranalysis.io.input.InputFromManager: A unique name associated with the input.
identifier() - Method in class org.anchoranalysis.io.input.InputFromManagerDelegate
identifierAsPath() - Method in interface org.anchoranalysis.io.input.InputFromManager: Like InputFromManager.identifier() but converts the identifier to a path.
Identity - Class in org.anchoranalysis.io.input.bean.path: Returns the same Path as the argument passed in.
Identity() - Constructor for class org.anchoranalysis.io.input.bean.path.Identity
InputContextParameters - Class in org.anchoranalysis.io.input: Additional parameters that offer context for many beans that provide input-functions.
InputContextParameters() - Constructor for class org.anchoranalysis.io.input.InputContextParameters
InputFromManager - Interface in org.anchoranalysis.io.input: One particular input for processing.
InputFromManagerDelegate<T extends InputFromManager> - Class in org.anchoranalysis.io.input: A base class for InputFromManager-implementing classes that delegate to another.
InputFromManagerDelegate(T) - Constructor for class org.anchoranalysis.io.input.InputFromManagerDelegate
InputGrouper - Interface in org.anchoranalysis.io.input.grouper: Derives a grouping key from an input.
InputManager<T extends InputFromManager> - Class in org.anchoranalysis.io.input.bean: Base class for describing the inputs.
InputManager() - Constructor for class org.anchoranalysis.io.input.bean.InputManager
InputManagerParameters - Class in org.anchoranalysis.io.input.bean: Parameters passed to an InputManager to generate input-objects.
InputManagerParameters(Logger) - Constructor for class org.anchoranalysis.io.input.bean.InputManagerParameters: Create with only a logger, and using sensible default values for the other fields.
InputManagerParameters(OperationContext) - Constructor for class org.anchoranalysis.io.input.bean.InputManagerParameters: Create with only a OperationContext, and using sensible default values for the other fields.
InputManagerParameters(InputContextParameters, OperationContext) - Constructor for class org.anchoranalysis.io.input.bean.InputManagerParameters
InputManagerUnary<T extends InputFromManager> - Class in org.anchoranalysis.io.input.bean: Base class for an InputManager that delegates to another InputManager with the same input-type.
InputManagerUnary() - Constructor for class org.anchoranalysis.io.input.bean.InputManagerUnary
InputReadFailedException - Exception in org.anchoranalysis.io.input: When an error occurs reading an input.
InputReadFailedException(String) - Constructor for exception org.anchoranalysis.io.input.InputReadFailedException: Create with a message only.
InputReadFailedException(String, Throwable) - Constructor for exception org.anchoranalysis.io.input.InputReadFailedException: Create with a message and cause.
InputReadFailedException(Throwable) - Constructor for exception org.anchoranalysis.io.input.InputReadFailedException: Create with a cause only.
inputs() - Method in class org.anchoranalysis.io.input.InputsWithDirectory: The inputs.
inputs(InputManagerParameters) - Method in class org.anchoranalysis.io.input.bean.InputManager: Creates a list of inputs given particular parameters.
inputs(InputManagerParameters) - Method in class org.anchoranalysis.io.input.bean.InputManagerUnary
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class org.anchoranalysis.io.input.bean.InputManagerUnary: Calculates the inputs to return given the inputs from the delegate.
InputsWithDirectory<T extends InputFromManager> - Class in org.anchoranalysis.io.input: All inputs for an experiment, together with any parent directory which is specified as a parent for these inputs.
InputsWithDirectory(List<T>) - Constructor for class org.anchoranalysis.io.input.InputsWithDirectory: Creates without any parent directory.
InputsWithDirectory(List<T>, Optional<Path>) - Constructor for class org.anchoranalysis.io.input.InputsWithDirectory
isAcceptDirectoryErrors() - Method in class org.anchoranalysis.io.input.bean.files.SearchDirectory: If true, continues when a directory-access-error occurs (logging it), otherwise throws an exception.
isApplyToPath() - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchRegularExpression: If true, the filter is applied to the path, not just the filename (using forward slashes as directory separators)
isDebugModeActivated() - Method in class org.anchoranalysis.io.input.bean.InputManagerParameters: Whether debug-mode has been activated.
isEmpty() - Method in class org.anchoranalysis.io.input.InputsWithDirectory: Whether no inputs exist.
isIgnoreHidden() - Method in class org.anchoranalysis.io.input.bean.files.SearchDirectory: If true, case is ignored in the pattern matching.
isLocalized() - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectoryString: When true paths are resolved against the location of the associated BeanXML file.
isPrioritizeInputContext() - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchExtensions: When true, any extensions available in the input-context are prioritized ahead of extensions.
isRecursive() - Method in class org.anchoranalysis.io.input.bean.files.SearchDirectory: If true the search is applied recursively over sub-directories.
isRelativeForIdentifier() - Method in class org.anchoranalysis.io.input.InputContextParameters: If true, the entire filename or relative path (excluding extension) is used to determine a unique identifier.
isRelativeToDirectory() - Method in class org.anchoranalysis.io.input.file.FileNamerContext: If true, the namer should prefer to derive file-names relative to the directory, rather than only the varying elements in the file-names.
isShuffle() - Method in class org.anchoranalysis.io.input.InputContextParameters: If true, the order of the inputs are shuffled (randomized).
iterator() - Method in class org.anchoranalysis.io.input.InputsWithDirectory: Returns an iterator over the elements in this list in proper sequence.

L

listIterator() - Method in class org.anchoranalysis.io.input.InputsWithDirectory: Returns a list iterator over the elements in this list (in proper sequence).

M

map(Function<T, S>) - Method in class org.anchoranalysis.io.input.InputsWithDirectory: Creates a new InputsWithDirectory which is the result of mapping the existing inputs.
map(CheckedFunction<T, S, E>, Class<? extends E>) - Method in class org.anchoranalysis.io.input.InputsWithDirectory: Creates a new InputsWithDirectory which is the result of mapping the existing inputs.
mapIdentifier(BiFunction<String, File, String>) - Method in class org.anchoranalysis.io.input.file.NamedFile: Immutably renames the file, by assigning it a new identifier.
MatchExtensions - Class in org.anchoranalysis.io.input.bean.path.matcher: Maybe imposes a file-extension condition, optionally on top of an existing matcher.
MatchExtensions() - Constructor for class org.anchoranalysis.io.input.bean.path.matcher.MatchExtensions
MatchExtensions(String...) - Constructor for class org.anchoranalysis.io.input.bean.path.matcher.MatchExtensions: Create for specific extensions.
matchFile(Path) - Method in class org.anchoranalysis.io.input.path.matcher.DualPathPredicates: Whether the path to a particular file matches the predicate file?
MatchGlob - Class in org.anchoranalysis.io.input.bean.path.matcher: Matches paths using a Java-style glob.
MatchGlob() - Constructor for class org.anchoranalysis.io.input.bean.path.matcher.MatchGlob
MatchGlob(String) - Constructor for class org.anchoranalysis.io.input.bean.path.matcher.MatchGlob
matchingFiles(Path, boolean) - Method in class org.anchoranalysis.io.input.bean.path.matcher.FilePathMatcher: Like FilePathMatcher.matchingFiles(Path, boolean, boolean, boolean, Optional, Optional) but uses sensible defaults.
matchingFiles(Path, boolean, boolean, boolean, Optional<Integer>, Optional<InputManagerParameters>) - Method in class org.anchoranalysis.io.input.bean.path.matcher.FilePathMatcher: Finds a collection of files that match particular conditions on their paths.
matchingFilesForDirectory(Path, InputManagerParameters) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectory: The matching files for this provider that exist in a particular directory.
matchingFilesForDirectory(Path, InputManagerParameters) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectoryUnary
matchingFilesForDirectory(Path, InputManagerParameters) - Method in class org.anchoranalysis.io.input.bean.files.SearchDirectory
matchingFilesForDirectory(Path, InputManagerParameters) - Method in class org.anchoranalysis.io.input.bean.files.SingleFile
matchingLeafDirectories(List<Path>) - Method in class org.anchoranalysis.io.input.path.matcher.DualPathPredicates: Creates a new list of paths to leaf-directories that match the predicate directory.
MatchRegularExpression - Class in org.anchoranalysis.io.input.bean.path.matcher: Predicates that matches a file-path against a regular expression.
MatchRegularExpression() - Constructor for class org.anchoranalysis.io.input.bean.path.matcher.MatchRegularExpression

N

NamedFile - Class in org.anchoranalysis.io.input.file: A file with an associated unique name.
NamedFile(String, File) - Constructor for class org.anchoranalysis.io.input.file.NamedFile: Create with an identifier and a file.
NameElementRange - Class in org.anchoranalysis.io.input.bean.path: Constructs a Path from a sub-range of the name-elements of the Path.
NameElementRange() - Constructor for class org.anchoranalysis.io.input.bean.path.NameElementRange

O

open(Path) - Static method in class org.anchoranalysis.io.input.csv.CSVReaderByLine: Opens a CSV file for reading.
open(Path, String, boolean) - Static method in class org.anchoranalysis.io.input.csv.CSVReaderByLine: Opens a CSV file for reading.
open(Path, String, boolean, boolean) - Static method in class org.anchoranalysis.io.input.csv.CSVReaderByLine: Opens a CSV file for reading.
OpenedCSVFile() - Constructor for class org.anchoranalysis.io.input.csv.CSVReader.OpenedCSVFile
org.anchoranalysis.io.input - package org.anchoranalysis.io.input: Classes relating to creating inputs for an experiment / task.
org.anchoranalysis.io.input.bean - package org.anchoranalysis.io.input.bean: Beans related to collecting inputs from the file-system for an experiment.
org.anchoranalysis.io.input.bean.dictionary - package org.anchoranalysis.io.input.bean.dictionary: Methods to provide a Dictionary.
org.anchoranalysis.io.input.bean.files - package org.anchoranalysis.io.input.bean.files: Methods to provide a collection of Files.
org.anchoranalysis.io.input.bean.grouper - package org.anchoranalysis.io.input.bean.grouper: Determines how inputs are aggregated into groups, if at all.
org.anchoranalysis.io.input.bean.namer - package org.anchoranalysis.io.input.bean.namer: Beans to derive names (compact unique identifiers) from files.
org.anchoranalysis.io.input.bean.path - package org.anchoranalysis.io.input.bean.path: Beans pertaining to manipulating and matching against file-paths.
org.anchoranalysis.io.input.bean.path.matcher - package org.anchoranalysis.io.input.bean.path.matcher: Beans to find a subset of files that match a particular conditions on their paths.
org.anchoranalysis.io.input.bean.path.provider - package org.anchoranalysis.io.input.bean.path.provider: Methods to provide a single file-path.
org.anchoranalysis.io.input.csv - package org.anchoranalysis.io.input.csv: Classes for reading comma-separated-values (CSV) files.
org.anchoranalysis.io.input.file - package org.anchoranalysis.io.input.file: Non-bean classes that relate to using files during inputting.
org.anchoranalysis.io.input.grouper - package org.anchoranalysis.io.input.grouper: Non-bean classes pertaining grouping inputs.
org.anchoranalysis.io.input.path - package org.anchoranalysis.io.input.path: Non-bean classes pertaining to getting/extracting/manipulating paths as used in inputting.
org.anchoranalysis.io.input.path.matcher - package org.anchoranalysis.io.input.path.matcher: Non-bean classes to help with org.anchoranalysis.io.input.bean.path.matcher.

P

pathForBinding() - Method in class org.anchoranalysis.io.input.file.SingleFileInputBase
pathForBinding() - Method in interface org.anchoranalysis.io.input.InputFromManager: A path to a file from which this input originated.
pathForBinding() - Method in class org.anchoranalysis.io.input.InputFromManagerDelegate
pathForBindingRequired() - Method in interface org.anchoranalysis.io.input.InputFromManager: Like InputFromManager.pathForBinding() but throws an exception if a path isn't present.
PathSupplier - Interface in org.anchoranalysis.io.input.path: Utility interface to supply a Path or throw a DerivePathException.
ProcessCSVLine - Interface in org.anchoranalysis.io.input.csv: Called when a single line is read by a CSV-reader to determine how the entry is further processed.
processLine(String[], boolean) - Method in interface org.anchoranalysis.io.input.csv.ProcessCSVLine: Called when a single line is read by a CSV-reader to determine how the entry is further processed.

R

read(Path) - Method in class org.anchoranalysis.io.input.csv.CSVReader: Opens a CSV for reading.
read(ProcessCSVLine) - Method in class org.anchoranalysis.io.input.csv.ReadByLine: Reads a CSV-file iterating through each row and passing it to lineProcessor
ReadByLine - Class in org.anchoranalysis.io.input.csv: An opened-CSV file that is read line-by-line and processed.
ReadByLine(Path, CSVReader) - Constructor for class org.anchoranalysis.io.input.csv.ReadByLine
ReadFromFile - Class in org.anchoranalysis.io.input.bean.dictionary: Reads a Dictionary from a file in Java properties format.
ReadFromFile() - Constructor for class org.anchoranalysis.io.input.bean.dictionary.ReadFromFile
readLine() - Method in class org.anchoranalysis.io.input.csv.CSVReader.OpenedCSVFile: Reads the next-line from the open CSV file.
rootDirectory(InputContextParameters) - Method in class org.anchoranalysis.io.input.bean.files.FilesProvider: A root directory for these files, if it exists.
rootDirectory(InputContextParameters) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderUnary
rootDirectory(InputContextParameters) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectory
rootDirectory(InputContextParameters) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithoutDirectory
rootDirectory(InputContextParameters) - Method in class org.anchoranalysis.io.input.bean.files.SpecificPathList

S

SearchDirectory - Class in org.anchoranalysis.io.input.bean.files: Searches a directory for files whose paths match a particular predicate.
SearchDirectory() - Constructor for class org.anchoranalysis.io.input.bean.files.SearchDirectory
SearchDirectory(String) - Constructor for class org.anchoranalysis.io.input.bean.files.SearchDirectory: Create for a specific directory.
selectDerivePath() - Method in class org.anchoranalysis.io.input.bean.grouper.FromDerivePath: Selects the DerivePath to use for deriving a key.
setAcceptDirectoryErrors(boolean) - Method in class org.anchoranalysis.io.input.bean.files.SearchDirectory: If true, continues when a directory-access-error occurs (logging it), otherwise throws an exception.
setApplyToPath(boolean) - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchRegularExpression: If true, the filter is applied to the path, not just the filename (using forward slashes as directory separators)
setDebugModeParameters(Optional<DebugModeParameters>) - Method in class org.anchoranalysis.io.input.InputContextParameters: Parameters for debug-mode (only defined if we are in debug mode).
setDirectory(String) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectoryString: A directory in which to look for files.
setExpression(String) - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchRegularExpression: The regular-expression, Java-style as described in Pattern.
setExtensions(StringSet) - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchExtensions: A set of file-extensions (without the period), one of which must match the end of a path.
setFallback(FilesProvider) - Method in class org.anchoranalysis.io.input.bean.files.SpecificPathList: If no paths can be found either from listPaths or the input-context, then the fallback is called if exists, otherwise an error is thrown
setFileFilterAndDirectory(Path) - Method in class org.anchoranalysis.io.input.bean.files.SearchDirectory: Sets both the directory and the glob from a string containing both.
setFiles(FilesProvider) - Method in class org.anchoranalysis.io.input.bean.dictionary.ReadFromFile: Provides a single file containing a dictionary.
setFiles(FilesProvider) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderUnary
setFiles(FilesProvider) - Method in class org.anchoranalysis.io.input.bean.path.provider.FromFiles: A provider that should return exactly one File whose path is employed.
setFiles(FilesProviderWithDirectory) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectoryUnary
setGlob(String) - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchGlob: The string describing a glob e.g.
setId(String) - Method in class org.anchoranalysis.io.input.bean.path.provider.FilePathProviderReference: A unique identifer for another FilePathProvider that is referenced.
setIdentifierSubrange(Optional<IndexRangeNegative>) - Method in class org.anchoranalysis.io.input.InputContextParameters: If defined, this indicates and specifies only a subset of the naming-elements to use.
setIgnoreHidden(boolean) - Method in class org.anchoranalysis.io.input.bean.files.SearchDirectory: If true, case is ignored in the pattern matching.
setIndexEnd(int) - Method in class org.anchoranalysis.io.input.bean.path.NameElementRange: The index of the last element (inclusive) for the range.
setIndexStart(int) - Method in class org.anchoranalysis.io.input.bean.path.NameElementRange: The index of the first element (inclusive) for the range.
setInput(InputManager<T>) - Method in class org.anchoranalysis.io.input.bean.InputManagerUnary: The delegate input-manager which will be circumstantially called by the current input-manager.
setInputDirectory(Optional<Path>) - Method in class org.anchoranalysis.io.input.InputContextParameters: If defined, a directory which can be used by beans to find input.
setInputFilterExtensions(Optional<StringSetTrie>) - Method in class org.anchoranalysis.io.input.InputContextParameters: A trie of extensions that can be used filter inputs.
setInputFilterGlob(Optional<String>) - Method in class org.anchoranalysis.io.input.InputContextParameters: A glob that can be used by beans to filter input.
setInputPaths(Optional<List<Path>>) - Method in class org.anchoranalysis.io.input.InputContextParameters: A list of paths referring to specific inputs.
setLimitUpper(Optional<Either<Integer, Double>>) - Method in class org.anchoranalysis.io.input.InputContextParameters: If defined, an upper limit that is imposed on the number of inputs.
setListPaths(StringList) - Method in class org.anchoranalysis.io.input.bean.files.SpecificPathList: If specified, this forms the list of paths which is provided as input.
setLocalized(boolean) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectoryString: When true paths are resolved against the location of the associated BeanXML file.
setMatcher(FilePathMatcher) - Method in class org.anchoranalysis.io.input.bean.files.SearchDirectory
setMatcher(FilePathMatcher) - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchExtensions: A secondary matcher, which is required additionally match (as well as the extension).
setMaxDirectoryDepth(int) - Method in class org.anchoranalysis.io.input.bean.files.SearchDirectory: If non-negative the max depth of directories.
setNumberColumns(int) - Method in class org.anchoranalysis.io.input.csv.CSVReader.OpenedCSVFile: Sets the number of columns, if it is already known from elsewhere.
setPrioritizeInputContext(boolean) - Method in class org.anchoranalysis.io.input.bean.path.matcher.MatchExtensions: When true, any extensions available in the input-context are prioritized ahead of extensions.
setRecursive(boolean) - Method in class org.anchoranalysis.io.input.bean.files.SearchDirectory: If true the search is applied recursively over sub-directories.
setRelativeForIdentifier(boolean) - Method in class org.anchoranalysis.io.input.InputContextParameters: If true, the entire filename or relative path (excluding extension) is used to determine a unique identifier.
setShuffle(boolean) - Method in class org.anchoranalysis.io.input.InputContextParameters: If true, the order of the inputs are shuffled (randomized).
SingleFile - Class in org.anchoranalysis.io.input.bean.files: Provides a single file only.
SingleFile() - Constructor for class org.anchoranalysis.io.input.bean.files.SingleFile
SingleFile(String) - Constructor for class org.anchoranalysis.io.input.bean.files.SingleFile: Creates with a path for the single-file.
SingleFileInputBase - Class in org.anchoranalysis.io.input.file: A base class for inputs that refer to a single file.
SingleFileInputBase(NamedFile) - Constructor for class org.anchoranalysis.io.input.file.SingleFileInputBase: Creates for a particular file.
SpecificPathList - Class in org.anchoranalysis.io.input.bean.files: A specific list of paths which form the input.
SpecificPathList() - Constructor for class org.anchoranalysis.io.input.bean.files.SpecificPathList
SpecificPathList(List<String>) - Constructor for class org.anchoranalysis.io.input.bean.files.SpecificPathList: Creates by reusing an existing list.
SpecificPathList(StringList) - Constructor for class org.anchoranalysis.io.input.bean.files.SpecificPathList: Creates by reusing an existing list.

T

toPath() - Method in class org.anchoranalysis.io.input.file.NamedFile: Like File.toPath().
toString() - Method in class org.anchoranalysis.io.input.file.FileNamerContext
toString() - Method in class org.anchoranalysis.io.input.file.NamedFile
toString() - Method in class org.anchoranalysis.io.input.file.SingleFileInputBase
toString() - Method in class org.anchoranalysis.io.input.InputFromManagerDelegate
toString() - Method in class org.anchoranalysis.io.input.InputsWithDirectory
toString() - Method in class org.anchoranalysis.io.input.path.GlobExtractor.GlobWithDirectory
transform(List<File>) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderWithDirectoryUnary: Transform an existing collection of files.
transform(List<File>, boolean) - Method in class org.anchoranalysis.io.input.bean.files.FilesProviderUnary: Transform an existing collection of files.

W

withInputs(List<S>) - Method in class org.anchoranalysis.io.input.InputsWithDirectory: Changes the inputs, but preserves the directory.
WithoutGrouping - Class in org.anchoranalysis.io.input.bean.grouper: Avoids grouping of inputs, effectively processing all inputs as one large group.
WithoutGrouping() - Constructor for class org.anchoranalysis.io.input.bean.grouper.WithoutGrouping

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