Index (anchor-io-output 1.0.0 API)

A B C D E F G H I L M N O P R S T W X
All Classes and Interfaces|All Packages|Serialized Form

A

add(String, boolean) - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: Adds a new output-name to the set of recorded names.
addEnabledOutputFirst(String...) - Method in class org.anchoranalysis.io.output.enabled.OutputEnabledMutable: Adds enabled first-level outputs.
addEnabledOutputs(OutputEnabledMutable) - Method in class org.anchoranalysis.io.output.enabled.OutputEnabledMutable: Adds enabled outputs from another OutputEnabledMutable.
addEnabledOutputSecond(String, String...) - Method in class org.anchoranalysis.io.output.enabled.OutputEnabledMutable: Adds enabled second-level outputs.
AddToDefaults - Class in org.anchoranalysis.io.output.bean.rules: Adds additional outputs-names to be enabled to the defaults.
AddToDefaults() - Constructor for class org.anchoranalysis.io.output.bean.rules.AddToDefaults
All - Class in org.anchoranalysis.io.output.bean.enabled: All outputs are allowed irrespective of outputName.
AlwaysAllowed - Class in org.anchoranalysis.io.output.writer: Allows every output, irrespective of whether the OutputterChecked allows the output-name.
AlwaysAllowed(ElementOutputter, Optional<WriterExecuteBeforeEveryOperation>) - Constructor for class org.anchoranalysis.io.output.writer.AlwaysAllowed: Creates a new AlwaysAllowed instance.
applyDelta(MultiLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.recorded.OutputEnabledDelta: Applies the changes to enable or disable additional outputs, if they are defined.
asPath(boolean) - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix: A path that combines the directory and fileNamePrefix and delimiter.
assignLogger(Logger) - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: Assigns a logger to the outputter, which is used to output warnings or messages when outputting.
assignOutputDirectory(Path) - Method in class org.anchoranalysis.io.output.path.prefixer.OutputPrefixerSettings: Assigns a directory indicating where inputs can be located.
assignSuggestedImageOutputFormat(ImageFileFormat) - Method in class org.anchoranalysis.io.output.path.prefixer.OutputPrefixerSettings: Assigns a suggestion for a preferred image-output format.

B

BindFailedException - Exception Class in org.anchoranalysis.io.output.outputter: When an outputter cannot be successfully bound to an output directory.
BindFailedException(String) - Constructor for exception class org.anchoranalysis.io.output.outputter.BindFailedException: Create from message.
BindFailedException(Throwable) - Constructor for exception class org.anchoranalysis.io.output.outputter.BindFailedException: Create from cause.

C

changePrefix(DirectoryWithPrefix) - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget: Creates a new OutputterTarget with a changed prefix.
changePrefix(DirectoryWithPrefix) - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: Creates a OutputterChecked with a changed prefix.
checkAbsolutePath() - Method in class org.anchoranalysis.io.output.path.prefixer.OutputPrefixerSettings: Checks that if a path is defined as the output-directory then it must be absolute.
CheckIfAllowed - Class in org.anchoranalysis.io.output.writer: Only allows outputs, if the output-name is allowed in the OutputterChecked.
CheckIfAllowed(SingleLevelOutputEnabled, Optional<WriterExecuteBeforeEveryOperation>, Writer) - Constructor for class org.anchoranalysis.io.output.writer.CheckIfAllowed: Creates a new CheckIfAllowed instance.
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelAnd
combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelBinary: Determines whether an output is enabled via a combination of the two MultiLevelOutputEnabled.
combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelOr
combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelAnd
combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelBinary: Determines whether an output is enabled via a combination of the two MultiLevelOutputEnabled.
combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelOr
combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelAnd
combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelBinary: Builds a second-level output by combining enabled1 and enabled2.
combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelOr
common() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: Creates a CommonContext a context that contains a subset of this context.
create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.io.output.bean.rules.AddToDefaults
create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.io.output.bean.rules.IgnoreUnderscorePrefixUnless
create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.io.output.bean.rules.NoneExcept
create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnabledRules: Creates rules for determining whether an output is enabled or disabled.
create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.io.output.bean.rules.Permissive
create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.io.output.bean.rules.PermissiveExcept
createContextForWriting(Optional<ImageFileFormat>, ExecutionTimeRecorder) - Method in class org.anchoranalysis.io.output.bean.OutputManager: Creates the OutputWriteContext needed for writing files.
createExperimentOutputter(Optional<String>, MultiLevelOutputEnabled, Optional<MultiLevelRecordedOutputs>, OutputWriteContext, PathPrefixerContext, Optional<Consumer<Path>>, Optional<Logger>) - Method in class org.anchoranalysis.io.output.bean.OutputManager: Creates an outputter for the experiment in general.
createFilenameForWriting(String, String) - Method in class org.anchoranalysis.io.output.writer.AlwaysAllowed
createFilenameForWriting(String, String) - Method in class org.anchoranalysis.io.output.writer.CheckIfAllowed
createFilenameForWriting(String, String) - Method in interface org.anchoranalysis.io.output.writer.Writer: The path to write a particular output to.
createFilenameForWriting(String, String) - Method in class org.anchoranalysis.io.output.writer.WriterRouterErrors: The path to write a particular output to.
createForDirectoryPermissive(Path, DirectoryCreationParameters, Optional<Logger>) - Static method in class org.anchoranalysis.io.output.outputter.OutputterChecked: Creates, defaulting to a permissive output-manager in a particular directory.
createSecondLevelFromSet(StringSet) - Method in class org.anchoranalysis.io.output.bean.rules.AddToDefaults
createSecondLevelFromSet(StringSet) - Method in class org.anchoranalysis.io.output.bean.rules.IgnoreUnderscorePrefixUnless
createSecondLevelFromSet(StringSet) - Method in class org.anchoranalysis.io.output.bean.rules.NoneExcept
createSecondLevelFromSet(StringSet) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify: Creates a new second-level SingleLevelOutputEnabled from the relevant set of strings.
createSecondLevelFromSet(StringSet) - Method in class org.anchoranalysis.io.output.bean.rules.PermissiveExcept
createSubdirectory(String, boolean) - Method in class org.anchoranalysis.io.output.writer.AlwaysAllowed
createSubdirectory(String, boolean) - Method in class org.anchoranalysis.io.output.writer.CheckIfAllowed
createSubdirectory(String, boolean) - Method in interface org.anchoranalysis.io.output.writer.Writer: Maybe creates a subdirectory for writing to.
createSubdirectory(String, boolean) - Method in class org.anchoranalysis.io.output.writer.WriterRouterErrors: Maybe creates a subdirectory for writing to.
createWithPrefix(DirectoryWithPrefix, MultiLevelOutputEnabled, OutputWriteContext, Optional<MultiLevelRecordedOutputs>, DirectoryCreationParameters, Optional<Logger>) - Static method in class org.anchoranalysis.io.output.outputter.OutputterChecked: Creates a bound output-manager from an existing OutputManager with a prefix.

D

deriveSubdirectory(String, boolean) - Method in class org.anchoranalysis.io.output.outputter.Outputter: Creates a new Outputter by appending a relative folder-path to the current Outputter
deriveSubdirectory(String, boolean) - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: Derives a bound-output-manager for a (possibly newly created) subdirectory of the existing manager
deriveSubdirectory(String, boolean) - Method in class org.anchoranalysis.io.output.writer.ElementOutputter: Derives a bound-output-manager for a (possibly newly created) subdirectory of the existing manager.
determineEnabledOutputs(RecordedOutputsWithRules) - Method in class org.anchoranalysis.io.output.bean.OutputManager: Determines which outputs are enabled or not.
DirectoryCreationParameters - Class in org.anchoranalysis.io.output.outputter: Options that influence how an output directory is created.
DirectoryCreationParameters() - Constructor for class org.anchoranalysis.io.output.outputter.DirectoryCreationParameters: Creates to not delete directories, and with no consumer called upon directory creation.
DirectoryCreationParameters(boolean, Optional<Consumer<Path>>) - Constructor for class org.anchoranalysis.io.output.outputter.DirectoryCreationParameters: Creates a new DirectoryCreationParameters instance.
DirectoryWithPrefix - Class in org.anchoranalysis.io.output.path.prefixer: A directory into which files can be written, and a prefix for the name of each written file.
DirectoryWithPrefix(Path) - Constructor for class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix: Creates for a directory, with no prefix.
DirectoryWithPrefix(Path, String, String) - Constructor for class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix: Creates a new DirectoryWithPrefix instance.
disableAdditionalOutputs(MultiLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.recorded.OutputEnabledDelta: Assigns additional outputs to disable.
duplicate() - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
duplicate() - Method in class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle
duplicate() - Method in class org.anchoranalysis.io.output.namestyle.OutputNameStyle: Deep copy the current object.
duplicate() - Method in class org.anchoranalysis.io.output.namestyle.SimpleOutputNameStyle
duplicate() - Method in class org.anchoranalysis.io.output.namestyle.StringSuffixOutputNameStyle
duplicate() - Method in class org.anchoranalysis.io.output.namestyle.WithoutOutputNameStyle

E

ElementOutputter - Class in org.anchoranalysis.io.output.writer: Outputs an element to the file-system.
ElementOutputter(OutputterChecked, ExecutionTimeRecorder, Supplier<Optional<Logger>>) - Constructor for class org.anchoranalysis.io.output.writer.ElementOutputter: Creates a new ElementOutputter instance.
ElementSupplier<T> - Interface in org.anchoranalysis.io.output.writer: Creates or gets a element to output files together with a ElementWriter.
ElementWriter<T> - Interface in org.anchoranalysis.io.output.writer: Writes an element (with or without an index) to the file system.
ElementWriterSupplier<T> - Interface in org.anchoranalysis.io.output.writer: Creates or gets a element-writer to output files.
enableAdditionalOutputs(MultiLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.recorded.OutputEnabledDelta: Assigns additional outputs to enable.
equals(Object) - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
equals(Object) - Method in class org.anchoranalysis.io.output.outputter.DirectoryCreationParameters
equals(Object) - Method in class org.anchoranalysis.io.output.outputter.Outputter
equals(Object) - Method in class org.anchoranalysis.io.output.path.prefixer.NamedPath
execute() - Method in interface org.anchoranalysis.io.output.writer.WriterExecuteBeforeEveryOperation: To be called before every operation.

F

filenameFromOutputFormatString(String, String) - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle: Constructs a file name from the output format string and an index.
filenameFromOutputFormatString(String, String) - Method in class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle
filenameFromOutputFormatString(String, String) - Method in class org.anchoranalysis.io.output.namestyle.StringSuffixOutputNameStyle
filenameWithoutExtension() - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
filenameWithoutExtension() - Method in class org.anchoranalysis.io.output.namestyle.OutputNameStyle: The filename to be written, including prefix, suffix, etc.
filenameWithoutExtension() - Method in class org.anchoranalysis.io.output.namestyle.SimpleOutputNameStyle
filenameWithoutExtension() - Method in class org.anchoranalysis.io.output.namestyle.WithoutOutputNameStyle
filenameWithoutExtension(int) - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle: Like IndexableOutputNameStyle.filenameWithoutExtension() but incorporates an integer index.
filenameWithoutExtension(String) - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle: Like IndexableOutputNameStyle.filenameWithoutExtension() but incorporates an string index.
first() - Method in class org.anchoranalysis.io.output.recorded.MultiLevelRecordedOutputs: For recording first-level outputs.
firstLevelContains(String) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify: Whether the first-level names contain a particular output (if defined)?

G

get() - Method in interface org.anchoranalysis.io.output.writer.ElementSupplier: Gets/creates the element to be written.
get() - Method in interface org.anchoranalysis.io.output.writer.ElementWriterSupplier: Gets/creates the ElementWriter to be used for an output.
get(Optional<String>) - Method in class org.anchoranalysis.io.output.outputter.InputOutputContextSubdirectoryCache: Gets (from the cache if it's already there) a context for a subdirectory of given-name
getCallUponDirectoryCreation() - Method in class org.anchoranalysis.io.output.outputter.DirectoryCreationParameters: When defined, this consumer is called when the directory is first created, as it is created lazily only when first needed.
getChecked() - Method in class org.anchoranalysis.io.output.outputter.Outputter: Gets the underlying delegate of Outputter that throws checked-exceptions instead of using a ErrorReporter.
getContext() - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: General settings for writing outputs.
getDefaultColors() - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings: The default color-scheme used for outputs, if no other scheme is specified.
getDirectory() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget: The directory into which outputting occurs.
getDirectory() - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix: The directory in which files can be written to.
getErrorReporter() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: The associated error reporter.
getErrorReporter() - Method in class org.anchoranalysis.io.output.outputter.Outputter
getExecutionTimeRecorder() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: Allows execution-times to be recorded for particular operations.
getExecutionTimeRecorder() - Method in class org.anchoranalysis.io.output.outputter.OutputWriteContext: Records the execution time of particular operations.
getExecutionTimeRecorder() - Method in class org.anchoranalysis.io.output.writer.ElementOutputter: Records the execution time of particular operations.
getFirst() - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify: Output-names in the first-level.
getLogger() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: The associated logger.
getMessageReporter() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: The associated message reporter.
getModelDirectory() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: An input-directory in which models are stored.
getName() - Method in class org.anchoranalysis.io.output.path.prefixer.NamedPath: A unique name associated with the path
getNumberDigits() - Method in class org.anchoranalysis.io.output.bean.path.prefixer.IncrementingNumber: Number of digits in the number, with leading zeros as necessary.
getOutputDirectory() - Method in class org.anchoranalysis.io.output.outputter.Outputter: The directory into which outputting occurs.
getOutputDirectory() - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: The directory into which outputting occurs.
getOutputDirectory() - Method in class org.anchoranalysis.io.output.path.prefixer.OutputPrefixerSettings: A directory indicating where inputs can be located.
getOutputName() - Method in class org.anchoranalysis.io.output.namestyle.OutputNameStyle: An identifier used in rules to determine if an output is enabled or not.
getOutputsDisabled() - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificDisabled: The names of the outputs that are disbled.
getOutputsEnabled() - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificEnabled: The names of the outputs that are enabled.
getOutputsEnabled() - Method in class org.anchoranalysis.io.output.bean.OutputManager: Which outputs are enabled or not enabled.
getOutputsEnabled() - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: Which outputs are enabled or not enabled.
getOutputsEnabled() - Method in class org.anchoranalysis.io.output.writer.ElementOutputter: Which outputs are enabled or not enabled.
getOutputter() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: An outputter that writes to the particular output-directory.
getOutputter() - Method in class org.anchoranalysis.io.output.writer.ElementOutputter: The outputter for writing the element.
getOutputWriteSettings() - Method in class org.anchoranalysis.io.output.bean.OutputManager: General settings (default file extensions, colors etc.) for outputting files.
getParentDirectoryCreator() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget: Parent directory creator to be executed before any derived sub-directories.
getPath() - Method in class org.anchoranalysis.io.output.path.prefixer.NamedPath: The path
getPrefix() - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve: A string prefixed to each output-path.
getPrefix() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget: The directory and prefix into which outputting occurs.
getPrefix() - Method in class org.anchoranalysis.io.output.outputter.Outputter: The directory and prefix into which outputting occurs.
getPrefix() - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: The directory and prefix into which outputting occurs.
getPrefixer() - Method in class org.anchoranalysis.io.output.bean.OutputManager: Determines a prefix to use when outputting a file based upon an input-path.
getPrefixer() - Method in class org.anchoranalysis.io.output.path.prefixer.PathPrefixerContext: Settings for where and how outputs should be prefixed.
getRecordedOutputs() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputsWithRules: If defined, records output-names that are written / not-written during the experiment.
getSecond() - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify: Output-names in the second-level (for all first level output-names).
getSettings() - Method in class org.anchoranalysis.io.output.outputter.Outputter: General settings for outputting.
getSettings() - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: General settings for outputting.
getSettings() - Method in class org.anchoranalysis.io.output.outputter.OutputWriteContext: User-define settings for outputting in output-manager.
getSettings() - Method in class org.anchoranalysis.io.output.writer.ElementOutputter: General settings for outputting.
getSuggestedFormatToWrite() - Method in class org.anchoranalysis.io.output.outputter.OutputWriteContext: A suggestion on what file-format to write.
getSuggestedFormatToWrite() - Method in class org.anchoranalysis.io.output.writer.ElementOutputter: A suggestion on what file-format to write.
getSuggestedImageOutputFormat() - Method in class org.anchoranalysis.io.output.path.prefixer.OutputPrefixerSettings: A file format suggested for writing images to the file system.
getWriterInstance(Class<? extends T>) - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings: Gets a writer-instance for a particular writerParentClass.
getWriters() - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings: Specifies a writer bean instance for a particular type of writer (identified by the writer bean class)
getWriters() - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: The writers associated with this output-manager.

H

hasAtLeastOneDisabled() - Method in class org.anchoranalysis.io.output.recorded.MultiLevelRecordedOutputs: If there is at least one disabled output.
hasAtLeastOneDisabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: If there is at least one disabled output.
hasAtLeastOneEnabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: If there is at least one enabled output.
hasAtLeastOneMultiplex(boolean) - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: Multiplex between RecordedOutputs.hasAtLeastOneEnabled() and RecordedOutputs.hasAtLeastOneDisabled().
hasBeenInitialized() - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings: Whether the method OutputWriteSettings.initialize(org.anchoranalysis.bean.BeanInstanceMap) has been called yet?
hashCode() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
hashCode() - Method in class org.anchoranalysis.io.output.outputter.DirectoryCreationParameters
hashCode() - Method in class org.anchoranalysis.io.output.outputter.Outputter
hashCode() - Method in class org.anchoranalysis.io.output.path.prefixer.NamedPath

I

IgnoreUnderscorePrefix - Class in org.anchoranalysis.io.output.bean.enabled: All outputs are allowed unless the name's first character is an underscore.
IgnoreUnderscorePrefix() - Constructor for class org.anchoranalysis.io.output.bean.enabled.IgnoreUnderscorePrefix
IgnoreUnderscorePrefixUnless - Class in org.anchoranalysis.io.output.bean.rules: Like IgnoreUnderscorePrefix for all first and level-outputs unless a particular outputs are explicitly specified.
IgnoreUnderscorePrefixUnless() - Constructor for class org.anchoranalysis.io.output.bean.rules.IgnoreUnderscorePrefixUnless
IgnoreUnderscorePrefixUnless(StringSet) - Constructor for class org.anchoranalysis.io.output.bean.rules.IgnoreUnderscorePrefixUnless: Create with first-level output names
IncrementingNumber - Class in org.anchoranalysis.io.output.bean.path.prefixer: Outputs an incrementing number for each output that occurs.
IncrementingNumber() - Constructor for class org.anchoranalysis.io.output.bean.path.prefixer.IncrementingNumber
IncrementingNumber(String) - Constructor for class org.anchoranalysis.io.output.bean.path.prefixer.IncrementingNumber: Creates with a prefix.
IndexableOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle: An output-name with an index somehow appended or prepended in a particular style.
IndexableOutputNameStyle() - Constructor for class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle: Empty constructor, as needed for deserialization.
IndexableOutputNameStyle(String) - Constructor for class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle: Creates with an output-name.
IndexableOutputNameStyle(IndexableOutputNameStyle) - Constructor for class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle: Copy constructor.
initialize(BeanInstanceMap) - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings: This method should be called once on this object before further calling OutputWriteSettings.getWriterInstance(java.lang.Class<? extends T>).
InputOutputContext - Interface in org.anchoranalysis.io.output.outputter: A context for performing input generally and outputting to a particular output-directory.
InputOutputContextSubdirectoryCache - Class in org.anchoranalysis.io.output.outputter: Caches a InputOutputContext for each subdirectory as they are created.
InputOutputContextSubdirectoryCache(InputOutputContext, boolean) - Constructor for class org.anchoranalysis.io.output.outputter.InputOutputContextSubdirectoryCache: Creates a new InputOutputContextSubdirectoryCache instance.
INSTANCE - Static variable in class org.anchoranalysis.io.output.bean.enabled.All: A singleton instance of All.
INSTANCE - Static variable in class org.anchoranalysis.io.output.bean.enabled.IgnoreUnderscorePrefix: A singleton instance of IgnoreUnderscorePrefix.
INSTANCE - Static variable in class org.anchoranalysis.io.output.bean.enabled.None: A singleton instance of None.
INSTANCE - Static variable in class org.anchoranalysis.io.output.bean.rules.Permissive: A singleton instance of Permissive.
IntegerSuffixOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle: Outputs a file-name involving an integer suffix of length numberDigits with leading zeros.
IntegerSuffixOutputNameStyle() - Constructor for class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle: Empty constructor, as needed for deserialization.
IntegerSuffixOutputNameStyle(String, int) - Constructor for class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle: Creates with an output-name and a number of digits.
IntegerSuffixOutputNameStyle(String, String, int) - Constructor for class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle: Creates with an output-name, a prefix, and a number of digits.
isDebugEnabled() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: Is debug-mode enabled?
isDebugMode() - Method in class org.anchoranalysis.io.output.path.prefixer.PathPrefixerContext: Whether debug-mode is activated.
isDeleteExistingDirectory() - Method in class org.anchoranalysis.io.output.outputter.DirectoryCreationParameters: When true, this will delete any existing directory with the same path, and then create it anew.
isEmpty() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: If no output-names exist.
isFirstDefined() - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify: Are output-names in the first-level defined?
isOmitExperimentIdentifier() - Method in class org.anchoranalysis.io.output.path.prefixer.OutputPrefixerSettings: When true, Requests that the experiment-identifier (name and index) is not included in the output-directory path.
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.bean.enabled.All
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.bean.enabled.IgnoreUnderscorePrefix
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.bean.enabled.None
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificDisabled
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificEnabled
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelBinary
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelNot
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.OutputEnabledMutable
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelBinary
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelInSet
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelNot
isOutputEnabled(String) - Method in interface org.anchoranalysis.io.output.enabled.single.SingleLevelOutputEnabled: Is a particular a particular output-enabled?
isOutputIncrementingNumberSequence() - Method in class org.anchoranalysis.io.output.path.prefixer.OutputPrefixerSettings: When true, requests outputting with an incrementing number sequence, rather than the usual outputter (normally based upon input filenames).
isRecordedAsEnabled(String) - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: Is a particular output-name recorded as enabled?
isSilentlyDeleteExisting() - Method in class org.anchoranalysis.io.output.bean.OutputManager: Whether to silently first delete any existing output at the intended path, or rather throw an error.

L

logger() - Method in class org.anchoranalysis.io.output.writer.ElementOutputter: The associated logger.

M

makeOutputPath(String) - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: Creates a full absolute path that completes the part of the path present in the outputter with an additional suffix.
makeOutputPath(Optional<String>, String, String) - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: Like OutputterChecked.makeOutputPath(String) but additionally adds an extension.
makeOutputPath(Optional<String>, String, String) - Method in class org.anchoranalysis.io.output.writer.ElementOutputter: Creates a full absolute path that completes the part of the path present in the outputter with an additional suffix.
makePathAbsolute(Optional<String>, Optional<String>, String) - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
makePathAbsolute(Optional<String>, Optional<String>, String) - Method in interface org.anchoranalysis.io.output.path.prefixer.PathCreator: Generates a full path, given the final part (suffix) of a path.
makePathRelative(Path) - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
makePathRelative(Path) - Method in interface org.anchoranalysis.io.output.path.prefixer.PathCreator: Extracts a relative-file path, given the final part (suffix) of a path.
maybeSubdirectory(Optional<String>, boolean) - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: Optionally creates a new context like with InputOutputContext.subdirectory(java.lang.String, boolean) but only if a directory-name is defined
maybeSuppressDirectories(String, boolean) - Method in class org.anchoranalysis.io.output.path.prefixer.OutputPrefixerSettings: Derives an identifier that maybe has its directories suppressed.
MultiLevelAnd - Class in org.anchoranalysis.io.output.enabled.multi: Outputs are enabled if they are contained in both of two MultiLevelOutputEnableds.
MultiLevelAnd(MultiLevelOutputEnabled, MultiLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.multi.MultiLevelAnd: Creates using two MultiLevelOutputEnableds.
MultiLevelBinary - Class in org.anchoranalysis.io.output.enabled.multi: Base class for operations that combines two MultiLevelOutputEnableds.
MultiLevelBinary(MultiLevelOutputEnabled, MultiLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.multi.MultiLevelBinary: Creates a new MultiLevelBinary instance.
MultiLevelNot - Class in org.anchoranalysis.io.output.enabled.multi: The complement of an existing MultiLevelOutputEnabled where disabled outputs are enabled, and vice-versa.
MultiLevelNot(MultiLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.multi.MultiLevelNot: Creates a new MultiLevelNot instance.
MultiLevelOr - Class in org.anchoranalysis.io.output.enabled.multi: Outputs are enabled if they are contained in either of two MultiLevelOutputEnableds.
MultiLevelOr(MultiLevelOutputEnabled, MultiLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.multi.MultiLevelOr: Creates using two MultiLevelOutputEnableds.
MultiLevelOutputEnabled - Interface in org.anchoranalysis.io.output.enabled.multi: Whether an output is enabled or not in a context of hierarchy of different rules for outputting.
MultiLevelRecordedOutputs - Class in org.anchoranalysis.io.output.recorded: Like RecordedOutputs but accepts two levels, first and second, like in a MultiLevelRecordedOutputs.
MultiLevelRecordedOutputs() - Constructor for class org.anchoranalysis.io.output.recorded.MultiLevelRecordedOutputs
multiplex(boolean) - Method in class org.anchoranalysis.io.output.recorded.RecordingWriters: Multiplexes between the selective and permissive writers based on a flag.

N

NamedPath - Class in org.anchoranalysis.io.output.path.prefixer: A path and associated name.
NamedPath(String, Path) - Constructor for class org.anchoranalysis.io.output.path.prefixer.NamedPath: Creates a new NamedPath instance.
None - Class in org.anchoranalysis.io.output.bean.enabled: No outputs are enabled.
None() - Constructor for class org.anchoranalysis.io.output.bean.enabled.None
NoneExcept - Class in org.anchoranalysis.io.output.bean.rules: All outputs are disabled except particular ones.
NoneExcept() - Constructor for class org.anchoranalysis.io.output.bean.rules.NoneExcept
NoneExcept(String) - Constructor for class org.anchoranalysis.io.output.bean.rules.NoneExcept: Create with a single first-level output-name.
NoneExcept(StringSet) - Constructor for class org.anchoranalysis.io.output.bean.rules.NoneExcept: Create with first-level output names
numberDisabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: Number of output-names that were not enabled.
numberEnabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: Number of output-names that were enabled.

O

operationContext() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: Creates a OperationContext based upon the state in this class.
org.anchoranalysis.io.output.bean - package org.anchoranalysis.io.output.bean: Beans for the framework around writing files to the file-system.
org.anchoranalysis.io.output.bean.enabled - package org.anchoranalysis.io.output.bean.enabled: Beans indicating whether a particular output is enabled or not.
org.anchoranalysis.io.output.bean.path.prefixer - package org.anchoranalysis.io.output.bean.path.prefixer: Beans for generating paths for outputting files by adding a prefix, suffix etc.
org.anchoranalysis.io.output.bean.rules - package org.anchoranalysis.io.output.bean.rules: Rules for determining if a particular output is enabled or not in a context of a hierarchy.
org.anchoranalysis.io.output.enabled - package org.anchoranalysis.io.output.enabled: Non-beans pertaining to whether a particular output is enabled or not.
org.anchoranalysis.io.output.enabled.multi - package org.anchoranalysis.io.output.enabled.multi: Non-beans that pertain to whether multiple-levels have outputs that are enabled or not.
org.anchoranalysis.io.output.enabled.single - package org.anchoranalysis.io.output.enabled.single: Non-beans that pertain to whether a single level has outputs that are enabled or not.
org.anchoranalysis.io.output.error - package org.anchoranalysis.io.output.error: Exceptions that may be thrown when writing files to the file-system.
org.anchoranalysis.io.output.namestyle - package org.anchoranalysis.io.output.namestyle: Methods of naming a file with an index in the file-name.
org.anchoranalysis.io.output.outputter - package org.anchoranalysis.io.output.outputter: Classes for outputting to particular directories.
org.anchoranalysis.io.output.outputter.directory - package org.anchoranalysis.io.output.outputter.directory: BoundDirectory and related classes.
org.anchoranalysis.io.output.path.prefixer - package org.anchoranalysis.io.output.path.prefixer: Non-beans for generating paths for outputting files by adding a prefix, suffix etc.
org.anchoranalysis.io.output.recorded - package org.anchoranalysis.io.output.recorded: Classes for recording the output-names used as they are written / queried.
org.anchoranalysis.io.output.writer - package org.anchoranalysis.io.output.writer: Allows a generators to write element(s) to the filesystem.
org.anchoranalysis.io.output.xml - package org.anchoranalysis.io.output.xml: Outputting XML to the file-system.
outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixer: Provides a prefix which can be prepended to all output files.
outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve
outFilePrefixAvoidResolve(NamedPath, Optional<String>, PathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve: Provides a prefix which can be prepended to all output files.
outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.IncrementingNumber
outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve: Determines the out-file prefix from a path.
OutputDirectoryAlreadyExistsException - Exception Class in org.anchoranalysis.io.output.error: When an output-directory already exists.
OutputDirectoryAlreadyExistsException(String) - Constructor for exception class org.anchoranalysis.io.output.error.OutputDirectoryAlreadyExistsException: Create with a message only.
OutputEnabled - Class in org.anchoranalysis.io.output.bean.enabled: Whether a particular output, identified by a textual name, is enabled or not.
OutputEnabled() - Constructor for class org.anchoranalysis.io.output.bean.enabled.OutputEnabled
OutputEnabledDelta - Class in org.anchoranalysis.io.output.recorded: Additional output-names to enable or disable from an existing set of output-enabled rules.
OutputEnabledDelta() - Constructor for class org.anchoranalysis.io.output.recorded.OutputEnabledDelta
OutputEnabledMutable - Class in org.anchoranalysis.io.output.enabled: A specific set of first-level outputs are enabled, to which more can be added.
OutputEnabledMutable(String...) - Constructor for class org.anchoranalysis.io.output.enabled.OutputEnabledMutable: Creates with one or more enabled outputs.
OutputEnabledMutable(SingleLevelOutputEnabled, String...) - Constructor for class org.anchoranalysis.io.output.enabled.OutputEnabledMutable: Creates with one or more enabled outputs.
OutputEnabledRules - Class in org.anchoranalysis.io.output.bean.rules: Bean that specifies an implementation of MultiLevelOutputEnabled.
OutputEnabledRules() - Constructor for class org.anchoranalysis.io.output.bean.rules.OutputEnabledRules
OutputEnableRulesSpecify - Class in org.anchoranalysis.io.output.bean.rules: Base class for an OutputEnabledRules that specifies particular output-names for first and second levels.
OutputEnableRulesSpecify() - Constructor for class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify
OutputEnableRulesSpecify(StringSet) - Constructor for class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify: Create with a specific set of first-level output names.
outputFormatString() - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle: A format-string as recognized by String.format(java.lang.String, java.lang.Object...) that expects a single string element.
outputFormatString() - Method in class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle
outputFormatString() - Method in class org.anchoranalysis.io.output.namestyle.StringSuffixOutputNameStyle
OutputManager - Class in org.anchoranalysis.io.output.bean: Responsible for making decisions on where output goes and what form it takes.
OutputManager() - Constructor for class org.anchoranalysis.io.output.bean.OutputManager
OutputNameStyle - Class in org.anchoranalysis.io.output.namestyle: Base class for an approach to generate a filename for an output.
OutputNameStyle() - Constructor for class org.anchoranalysis.io.output.namestyle.OutputNameStyle
OutputNameStyle(String) - Constructor for class org.anchoranalysis.io.output.namestyle.OutputNameStyle: Creates a new OutputNameStyle instance.
OutputPrefixerSettings - Class in org.anchoranalysis.io.output.path.prefixer: Arguments influencing into which directory outputs are written, and how identifiers are expressed.
OutputPrefixerSettings() - Constructor for class org.anchoranalysis.io.output.path.prefixer.OutputPrefixerSettings
outputsEnabled() - Method in class org.anchoranalysis.io.output.outputter.Outputter: Which outputs are enabled or not enabled.
Outputter - Class in org.anchoranalysis.io.output.outputter: Like OutputterChecked but exceptions are reported in a ErrorReporter.
Outputter(OutputterChecked, ErrorReporter) - Constructor for class org.anchoranalysis.io.output.outputter.Outputter
OutputterChecked - Class in org.anchoranalysis.io.output.outputter: A particular directory on the filesystem in which outputting can occur.
OutputterTarget - Class in org.anchoranalysis.io.output.outputter.directory: The directory and prefix an outputter writes to.
OutputterTarget(DirectoryWithPrefix, DirectoryCreationParameters) - Constructor for class org.anchoranalysis.io.output.outputter.directory.OutputterTarget: Creates for a particular directory, with optionally an associated prefix.
OutputWriteContext - Class in org.anchoranalysis.io.output.outputter: Settings and user-arguments for writing files.
OutputWriteContext() - Constructor for class org.anchoranalysis.io.output.outputter.OutputWriteContext: Create with default state, including no default beans assigned.
OutputWriteContext(OutputWriteSettings) - Constructor for class org.anchoranalysis.io.output.outputter.OutputWriteContext: Create from OutputWriteSettings and otherwise with defaults.
OutputWriteContext(OutputWriteSettings, Optional<ImageFileFormat>, ExecutionTimeRecorder) - Constructor for class org.anchoranalysis.io.output.outputter.OutputWriteContext: Creates a new OutputWriteContext instance.
OutputWriteFailedException - Exception Class in org.anchoranalysis.io.output.error: When an output could not be successfully written to the file-system.
OutputWriteFailedException(String) - Constructor for exception class org.anchoranalysis.io.output.error.OutputWriteFailedException: Creates with a message only.
OutputWriteFailedException(String, AnchorCombinableException) - Constructor for exception class org.anchoranalysis.io.output.error.OutputWriteFailedException: Creates with a message and a cause that can be combined with others in summary form.
OutputWriteFailedException(String, HasFriendlyErrorMessage) - Constructor for exception class org.anchoranalysis.io.output.error.OutputWriteFailedException: Creates with a message and a cause that provides a friendly error message.
OutputWriteFailedException(Throwable) - Constructor for exception class org.anchoranalysis.io.output.error.OutputWriteFailedException: Creates with a cause only.
OutputWriteSettings - Class in org.anchoranalysis.io.output.bean: Settings for how to write output, including default writers.
OutputWriteSettings() - Constructor for class org.anchoranalysis.io.output.bean.OutputWriteSettings

P

pathCreator() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget: Creates the path into which output is written.
PathCreator - Interface in org.anchoranalysis.io.output.path.prefixer: Converts file-paths between relative and absolute.
PathPrefixer - Class in org.anchoranalysis.io.output.bean.path.prefixer: Base classes for methods to determine an output directory and associated file prefix.
PathPrefixer() - Constructor for class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixer
PathPrefixerAvoidResolve - Class in org.anchoranalysis.io.output.bean.path.prefixer: A file-path-resolver that adds additional methods that perform the same function but output a relative-path rather than an absolute path after fully resolving paths
PathPrefixerAvoidResolve() - Constructor for class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve
PathPrefixerAvoidResolve(String) - Constructor for class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve: Creates with a prefix.
PathPrefixerContext - Class in org.anchoranalysis.io.output.path.prefixer: Context parameters provided to a link PathPrefixer.
PathPrefixerContext() - Constructor for class org.anchoranalysis.io.output.path.prefixer.PathPrefixerContext: Create with default parameters.
PathPrefixerContext(boolean, OutputPrefixerSettings) - Constructor for class org.anchoranalysis.io.output.path.prefixer.PathPrefixerContext: Create with specific parameters.
PathPrefixerException - Exception Class in org.anchoranalysis.io.output.path.prefixer: Thrown when unable to successfully determine a prefix for a path.
PathPrefixerException(String) - Constructor for exception class org.anchoranalysis.io.output.path.prefixer.PathPrefixerException: Creates from a message only.
PathPrefixerException(Throwable) - Constructor for exception class org.anchoranalysis.io.output.path.prefixer.PathPrefixerException: Creates from a cause only.
permissive() - Method in class org.anchoranalysis.io.output.recorded.RecordingWriters: A writer that allows all output-names, and records the written output-names.
Permissive - Class in org.anchoranalysis.io.output.bean.rules: Allows all output-names to be outputted in both first and second level.
Permissive() - Constructor for class org.anchoranalysis.io.output.bean.rules.Permissive
PermissiveExcept - Class in org.anchoranalysis.io.output.bean.rules: All outputs are enabled except particular ones.
PermissiveExcept() - Constructor for class org.anchoranalysis.io.output.bean.rules.PermissiveExcept
PermissiveExcept(StringSet) - Constructor for class org.anchoranalysis.io.output.bean.rules.PermissiveExcept: Create with first-level output names
prefixWithDelimeter() - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix: The prefix concatenated with the delimeter.

R

recordedOutputs() - Method in class org.anchoranalysis.io.output.recorded.RecordingWriters: If defined, all output-names that are passed as arguments to both writers are recorded here.
RecordedOutputs - Class in org.anchoranalysis.io.output.recorded: Outputs recorded from RecordOutputNamesForWriter.
RecordedOutputs() - Constructor for class org.anchoranalysis.io.output.recorded.RecordedOutputs
RecordedOutputsWithRules - Class in org.anchoranalysis.io.output.recorded: Rules to determine what outputting occurs, together with maybe an entity that records the output-names that are used when writing / querying.
RecordedOutputsWithRules() - Constructor for class org.anchoranalysis.io.output.recorded.RecordedOutputsWithRules: Creates with no rules or outputs defined.
RecordedOutputsWithRules(MultiLevelRecordedOutputs, MultiLevelOutputEnabled, OutputEnabledDelta) - Constructor for class org.anchoranalysis.io.output.recorded.RecordedOutputsWithRules: Creates with all elements defined.
RecordingWriters - Class in org.anchoranalysis.io.output.recorded: Two writers that record any output-names that are passed as arguments.
RecordingWriters(ElementOutputter, Optional<WriterExecuteBeforeEveryOperation>, Optional<MultiLevelRecordedOutputs>) - Constructor for class org.anchoranalysis.io.output.recorded.RecordingWriters: Creates the two writers.
requestOmitExperimentIdentifier() - Method in class org.anchoranalysis.io.output.path.prefixer.OutputPrefixerSettings: Requests that the experiment-identifier (name and index) is not included in the output-directory path.
requestOutputIncrementingNumberSequence() - Method in class org.anchoranalysis.io.output.path.prefixer.OutputPrefixerSettings: Requests outputting with an incrementing number sequence, rather than the usual outputter (normally based upon input filenames).
requestOutputSuppressDirectories() - Method in class org.anchoranalysis.io.output.path.prefixer.OutputPrefixerSettings: Requests suppressing directories (replacing subdirectory separators with an underscore) in the identifiers that are outputted.
resolvePath(String) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixer: Like PathPrefixer.resolvePath(Path) but accepts a String as the path.
resolvePath(Path) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixer: Converts a relative-path to an absolute-path (relative to the file-path associated with this current bean)
rootDirectoryPrefix(Optional<String>, PathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixer: Provides a prefix that becomes the root-folder.
rootDirectoryPrefix(Optional<String>, PathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve
rootDirectoryPrefixAvoidResolve(Optional<String>) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve: Provides a prefix that becomes the root-folder.

S

second(String) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelBinary
second(String) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelNot
second(String) - Method in interface org.anchoranalysis.io.output.enabled.multi.MultiLevelOutputEnabled: A second-level of OutputEnabled for a particular outputName as used in first-level.
second(String) - Method in class org.anchoranalysis.io.output.enabled.OutputEnabledMutable
second(String) - Method in class org.anchoranalysis.io.output.recorded.MultiLevelRecordedOutputs: A RecordedOutputs for recording second-level outputs for a given outputName from the first-level.
secondEntries() - Method in class org.anchoranalysis.io.output.recorded.MultiLevelRecordedOutputs: All second-level recorded output entries.
secondLevel(String) - Method in class org.anchoranalysis.io.output.recorded.RecordingWriters: A writer that performs a second-level check on which outputs occur, but writes to the top-level directory.
secondLevelOutputs(String, OutputEnabled) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify: Retrieves a second-level SingleLevelOutputEnabled corresponding to a first-level output-name.
selective() - Method in class org.anchoranalysis.io.output.recorded.RecordingWriters: A writer that allows only certain selected output-names, and records the written output-names.
selectOutputEnabled(Optional<OutputEnabledRules>) - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputsWithRules: Selects which OutputEnabledRules to employ.
setDefaultColors(ColorScheme) - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings: The default color-scheme used for outputs, if no other scheme is specified.
setDelimiter(String) - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix: Added between prefix and the filename, if the filename is defined.
setDirectory(Path) - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix: Assigns a new directory, replacing the existing directory.
setFirst(StringSet) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify: Output-names in the first-level.
setNumberDigits(int) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.IncrementingNumber: Number of digits in the number, with leading zeros as necessary.
setOutputName(String) - Method in class org.anchoranalysis.io.output.namestyle.OutputNameStyle: An identifier used in rules to determine if an output is enabled or not.
setOutputsDisabled(StringSet) - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificDisabled: The names of the outputs that are disbled.
setOutputsEnabled(StringSet) - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificEnabled: The names of the outputs that are enabled.
setOutputsEnabled(OutputEnabledRules) - Method in class org.anchoranalysis.io.output.bean.OutputManager: Which outputs are enabled or not enabled.
setOutputWriteSettings(OutputWriteSettings) - Method in class org.anchoranalysis.io.output.bean.OutputManager: General settings (default file extensions, colors etc.) for outputting files.
setPrefix(String) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve: A string prefixed to each output-path.
setPrefix(String) - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix: Always prepended to outputted filenames.
setPrefixer(PathPrefixer) - Method in class org.anchoranalysis.io.output.bean.OutputManager: Determines a prefix to use when outputting a file based upon an input-path.
setSecond(List<NamedBean<StringSet>>) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify: Output-names in the second-level (for all first level output-names).
setSilentlyDeleteExisting(boolean) - Method in class org.anchoranalysis.io.output.bean.OutputManager: Whether to silently first delete any existing output at the intended path, or rather throw an error.
setWriters(List<NamedBean<?>>) - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings: Specifies a writer bean instance for a particular type of writer (identified by the writer bean class)
SimpleOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle: A constant filename that is identical to the output-name plus extension.
SimpleOutputNameStyle(String) - Constructor for class org.anchoranalysis.io.output.namestyle.SimpleOutputNameStyle: Creates with an output-name.
SingleLevelAnd - Class in org.anchoranalysis.io.output.enabled.single: Outputs are enabled if they are contained in both of two SingleLevelOutputEnabled.
SingleLevelAnd(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.single.SingleLevelAnd: Creates using two SingleLevelOutputEnableds.
SingleLevelBinary - Class in org.anchoranalysis.io.output.enabled.single: Base class for a SingleLevelOutputEnabled that combines two existing such classes.
SingleLevelBinary(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.single.SingleLevelBinary: Creates a new SingleLevelBinary instance.
SingleLevelInSet - Class in org.anchoranalysis.io.output.enabled.single: Outputs are enabled if they are contained in a set.
SingleLevelInSet(Set<String>) - Constructor for class org.anchoranalysis.io.output.enabled.single.SingleLevelInSet: Creates a new SingleLevelInSet instance.
SingleLevelNot - Class in org.anchoranalysis.io.output.enabled.single: The complement of an existing SingleLevelOutputEnabled where disabled outputs are enabled, and vice-versa.
SingleLevelNot(SingleLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.single.SingleLevelNot: Creates a new SingleLevelNot instance.
SingleLevelOr - Class in org.anchoranalysis.io.output.enabled.single: Outputs are enabled if they are contained in either of two SingleLevelOutputEnabled.
SingleLevelOr(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.single.SingleLevelOr: Creates using two SingleLevelOutputEnableds.
SingleLevelOutputEnabled - Interface in org.anchoranalysis.io.output.enabled.single: An interface for any class that defines whether a top-level output is enabled.
SpecificDisabled - Class in org.anchoranalysis.io.output.bean.enabled: Only specific outputs, identified by a textual name, are disabled, and all others are enabled.
SpecificDisabled() - Constructor for class org.anchoranalysis.io.output.bean.enabled.SpecificDisabled
SpecificDisabled(StringSet) - Constructor for class org.anchoranalysis.io.output.bean.enabled.SpecificDisabled: Creates a new SpecificDisabled instance.
SpecificEnabled - Class in org.anchoranalysis.io.output.bean.enabled: Only specific outputs, identified by a textual name, are enabled.
SpecificEnabled() - Constructor for class org.anchoranalysis.io.output.bean.enabled.SpecificEnabled
SpecificEnabled(String) - Constructor for class org.anchoranalysis.io.output.bean.enabled.SpecificEnabled: Create with a single output-enabled.
SpecificEnabled(StringSet) - Constructor for class org.anchoranalysis.io.output.bean.enabled.SpecificEnabled: Creates a new SpecificEnabled instance.
StringSuffixOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle: Outputs a file-name involving a string suffix.
StringSuffixOutputNameStyle() - Constructor for class org.anchoranalysis.io.output.namestyle.StringSuffixOutputNameStyle: Empty constructor, as needed for deserialization.
StringSuffixOutputNameStyle(String, Optional<String>) - Constructor for class org.anchoranalysis.io.output.namestyle.StringSuffixOutputNameStyle: Creates with an output-name.
subdirectory(String, boolean) - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: Creates a new context that writes instead to a subdirectory.
summarizeDisabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: A comma-separated string of all output-names that were not enabled.
summarizeEnabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: A comma-separated string of all output-names that were enabled.
summarizeMultiplex(boolean) - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: Multiplex between RecordedOutputs.summarizeEnabled() and RecordedOutputs.summarizeDisabled().

T

toString() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
toString() - Method in class org.anchoranalysis.io.output.outputter.DirectoryCreationParameters
toString() - Method in class org.anchoranalysis.io.output.outputter.Outputter
toString() - Method in class org.anchoranalysis.io.output.path.prefixer.NamedPath

W

WithoutOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle: Avoids including an output-name in the filename.
WithoutOutputNameStyle(String) - Constructor for class org.anchoranalysis.io.output.namestyle.WithoutOutputNameStyle: Creates with an output-name.
write(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in class org.anchoranalysis.io.output.writer.AlwaysAllowed
write(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in class org.anchoranalysis.io.output.writer.CheckIfAllowed
write(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in interface org.anchoranalysis.io.output.writer.Writer: Writes an element using an ElementWriter to the current directory.
write(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in class org.anchoranalysis.io.output.writer.WriterRouterErrors: Writes an element using an ElementWriter to the current directory.
write(T, OutputNameStyle, ElementOutputter) - Method in interface org.anchoranalysis.io.output.writer.ElementWriter: Writes a non-indexable output (an output that isn't part of a collection of other similar items).
Writer - Interface in org.anchoranalysis.io.output.writer: Write data via ElementWriters to the file system, or creates new sub-directories for writing data to.
WriterExecuteBeforeEveryOperation - Interface in org.anchoranalysis.io.output.writer: Interface for classes with a method that should be called before every outputting write operation.
writerMultiplex(boolean) - Method in class org.anchoranalysis.io.output.outputter.Outputter: Multiplexes between the selective and permissive writers based on a flag.
writerPermissive() - Method in class org.anchoranalysis.io.output.outputter.Outputter: The writer that allows all outputs.
WriterRouterErrors - Class in org.anchoranalysis.io.output.writer: Write data via ElementWriters to the file system.
WriterRouterErrors(Writer, ErrorReporter) - Constructor for class org.anchoranalysis.io.output.writer.WriterRouterErrors
writerSecondLevel(String) - Method in class org.anchoranalysis.io.output.outputter.Outputter: A writer that performs a second-level check on which outputs occur, but writes to the top-level directory.
writerSelective() - Method in class org.anchoranalysis.io.output.outputter.Outputter: The writer that allows only certain selected outputs.
writeWithIndex(IndexableOutputNameStyle, ElementWriterSupplier<T>, ElementSupplier<T>, String) - Method in class org.anchoranalysis.io.output.writer.AlwaysAllowed
writeWithIndex(IndexableOutputNameStyle, ElementWriterSupplier<T>, ElementSupplier<T>, String) - Method in class org.anchoranalysis.io.output.writer.CheckIfAllowed
writeWithIndex(IndexableOutputNameStyle, ElementWriterSupplier<T>, ElementSupplier<T>, String) - Method in interface org.anchoranalysis.io.output.writer.Writer: Writes an indexed-element using an ElementWriter in the current directory.
writeWithIndex(IndexableOutputNameStyle, ElementWriterSupplier<T>, ElementSupplier<T>, String) - Method in class org.anchoranalysis.io.output.writer.WriterRouterErrors: Writes an indexed-element using an ElementWriter in the current directory.
writeWithIndex(T, String, IndexableOutputNameStyle, ElementOutputter) - Method in interface org.anchoranalysis.io.output.writer.ElementWriter: Writes an indexable output (many outputs of the same type, uniquely identified by an index).
writeWithoutName(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in class org.anchoranalysis.io.output.writer.AlwaysAllowed
writeWithoutName(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in class org.anchoranalysis.io.output.writer.CheckIfAllowed
writeWithoutName(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in interface org.anchoranalysis.io.output.writer.Writer: Writes an element using an ElementWriter to the current directory, without including an output name in the path.
writeXMLToFile(Document, Path) - Static method in class org.anchoranalysis.io.output.xml.XMLWriter: Writes a XML-document to the file-system.

X

XMLWriter - Class in org.anchoranalysis.io.output.xml: Writes XML in the form of a Document to the file-system.

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