Index (anchor-feature-io 1.0.0 API)

A C E F G H I L M N O R S T W
All Classes and Interfaces|All Packages|Constant Field Values

A

add(LabelledResultsVector) - Method in class org.anchoranalysis.feature.io.csv.results.LabelledResultsCSVWriter: Adds a results-element to be written.
add(LabelledResultsVector) - Method in interface org.anchoranalysis.feature.io.results.LabelledResultsCollector: Adds a results-element to be written.
addResultsFor(LabelledResultsVector) - Method in class org.anchoranalysis.feature.io.results.group.GroupedResults: Adds a result to the group-writer, but doesn't write yet.
addRow(List<TypedValue>) - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVWriter: Directly adds a row in the form of typed-values.
addRow(LabelledResultsVector) - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVWriter: Directly adds a row of feature-values.
addToRow(List<TypedValue>) - Method in class org.anchoranalysis.feature.io.csv.metadata.RowLabels: Adds the identifiers to a row to be outputted in a features CSV.
allHeaders() - Method in class org.anchoranalysis.feature.io.csv.metadata.LabelHeaders: The non-group and group headers combined (in this order respectively)

C

calculationResultsNeeded(MultiLevelOutputEnabled) - Method in class org.anchoranalysis.feature.io.results.FeatureOutputNames: If any output is enabled that requires calculation of feature results?
canEqual(Object) - Method in class org.anchoranalysis.feature.io.name.SimpleName
close() - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVWriter: Closes any open file-handles.
CombinedName - Class in org.anchoranalysis.feature.io.name: A name which is unique when a primaryName is combined with a secondaryName
CombinedName(String, String) - Constructor for class org.anchoranalysis.feature.io.name.CombinedName: Creates with explicit strings for both parts.
compareTo(MultiName) - Method in class org.anchoranalysis.feature.io.name.CombinedName
compareTo(MultiName) - Method in class org.anchoranalysis.feature.io.name.SimpleName
create(Optional<String>, String) - Static method in class org.anchoranalysis.feature.io.name.MultiNameFactory: Creates either a multi-name that is either has a single part or a double part.
create(FeatureCSVMetadata) - Method in interface org.anchoranalysis.feature.io.csv.results.FeatureCSVWriterFactory: Maybe creates a FeatureCSVWriter corresponding to particular metadata.
create(FeatureCSVMetadataForOutput, FeatureCSVWriterFactory, Optional<Consumer<LabelledResultsVector>>, boolean) - Static method in class org.anchoranalysis.feature.io.csv.results.LabelledResultsCSVWriterFactory: Creates with appropriate support classes for outputting.
create(FeatureCSVMetadata, Outputter, boolean) - Static method in class org.anchoranalysis.feature.io.csv.FeatureCSVWriter: Maybe creates a FeatureCSVWriter depending if the output is allowed.
create(FeatureNameList, boolean) - Static method in class org.anchoranalysis.feature.io.csv.table.FeatureTableCSVGeneratorFactory: Creates either a FeatureTableCSVGenerator in either horizontal or vertical style.
createWriter(FeatureCSVMetadata) - Method in class org.anchoranalysis.feature.io.csv.results.LabelledResultsCSVWriter: Creates a CSVWriter.
csvAggregated(FeatureNameList) - Method in class org.anchoranalysis.feature.io.results.FeatureOutputMetadata: Specific metadata for writing an aggregated CSV file.
csvNonAggregated() - Method in class org.anchoranalysis.feature.io.results.FeatureOutputMetadata: Specific metadata for writing a non-aggregated CSV file.

E

end() - Method in class org.anchoranalysis.feature.io.csv.results.LabelledResultsCSVWriter: Stops writing the CSV file.
equals(Object) - Method in class org.anchoranalysis.feature.io.csv.metadata.FeatureCSVMetadata
equals(Object) - Method in class org.anchoranalysis.feature.io.name.CombinedName
equals(Object) - Method in interface org.anchoranalysis.feature.io.name.MultiName: If another name is equal to the current name.
equals(Object) - Method in class org.anchoranalysis.feature.io.name.SimpleName
equals(Object) - Method in class org.anchoranalysis.feature.io.results.LabelledResultsVector

F

FeatureCSVMetadata - Class in org.anchoranalysis.feature.io.csv.metadata: Needed non-result information to output a feature-values CSV file.
FeatureCSVMetadata(String, String[], FeatureNameList) - Constructor for class org.anchoranalysis.feature.io.csv.metadata.FeatureCSVMetadata: Create for a particular output-name.
FeatureCSVMetadata(String, List<String>) - Constructor for class org.anchoranalysis.feature.io.csv.metadata.FeatureCSVMetadata: Creates a new FeatureCSVMetadata instance.
FeatureCSVMetadataForOutput - Class in org.anchoranalysis.feature.io.csv.metadata: Like a FeatureCSVMetadata but additionally associates an output-name.
FeatureCSVMetadataForOutput(String[], FeatureNameList, String) - Constructor for class org.anchoranalysis.feature.io.csv.metadata.FeatureCSVMetadataForOutput: Creates a new FeatureCSVMetadataForOutput instance.
FeatureCSVWriter - Class in org.anchoranalysis.feature.io.csv: Writes the results of feature-calculations as a CSV file.
FeatureCSVWriter(CSVWriter, boolean) - Constructor for class org.anchoranalysis.feature.io.csv.FeatureCSVWriter: Creates for a CSVWriter.
FeatureCSVWriterFactory - Interface in org.anchoranalysis.feature.io.csv.results: To facilitate creation of a FeatureCSVWriter from corresponding FeatureCSVMetadata.
featureNames() - Method in class org.anchoranalysis.feature.io.csv.metadata.FeatureCSVMetadataForOutput: Names of each feature in the feature columns.
featureNamesNonAggregated() - Method in class org.anchoranalysis.feature.io.results.FeatureOutputMetadata: Names of each feature in the feature columns, for non-aggregated features.
FeatureOutputMetadata - Class in org.anchoranalysis.feature.io.results: Information needed for the outputting differnt types of feature-table CSV files.
FeatureOutputMetadata(LabelHeaders, FeatureNameList, FeatureOutputNames) - Constructor for class org.anchoranalysis.feature.io.results.FeatureOutputMetadata: Creates a new FeatureOutputMetadata instance.
FeatureOutputNames - Class in org.anchoranalysis.feature.io.results: The customizable output names used by LabelledResultsCollector, which all follow a pattern based on a prefix.
FeatureOutputNames() - Constructor for class org.anchoranalysis.feature.io.results.FeatureOutputNames: Creates using default names, equivalent to a prefix of features.
FeatureOutputNames(String, boolean, boolean) - Constructor for class org.anchoranalysis.feature.io.results.FeatureOutputNames: Creates output-names based upon a prefix.
FeatureTableCSVGenerator<T> - Class in org.anchoranalysis.feature.io.csv.table: Base class for a Generator that outputs a feature-table in CSV format.
FeatureTableCSVGenerator(List<String>) - Constructor for class org.anchoranalysis.feature.io.csv.table.FeatureTableCSVGenerator: Creates a new FeatureTableCSVGenerator instance.
FeatureTableCSVGeneratorFactory - Class in org.anchoranalysis.feature.io.csv.table: Creates a FeatureTableCSVGenerator.
firstPart() - Method in class org.anchoranalysis.feature.io.name.CombinedName
firstPart() - Method in interface org.anchoranalysis.feature.io.name.MultiName: The first part, and grouping key.
firstPart() - Method in class org.anchoranalysis.feature.io.name.SimpleName
flushAndClose(Optional<NamedFeatureStore<FeatureInputResults>>, boolean, Function<InputOutputContext, FeatureCSVWriterFactory>, FeatureOutputMetadata, InputOutputContext) - Method in interface org.anchoranalysis.feature.io.results.LabelledResultsCollector: Writes any queued (but not yet written elements to the file-system), and closes open file-handles.

G

get(int) - Method in class org.anchoranalysis.feature.io.results.LabelledResultsVector: The result of a feature-calculation stored at a particular index.
getCsvFeaturesAggregated() - Method in class org.anchoranalysis.feature.io.results.FeatureOutputNames: The CSV of aggregated feature-results, if enabled.
getCsvFeaturesGroup() - Method in class org.anchoranalysis.feature.io.results.FeatureOutputNames: The CSV individually written for each group, if enabled.
getCsvFeaturesNonAggregated() - Method in class org.anchoranalysis.feature.io.results.FeatureOutputNames: The CSV of non-aggregated feature-results.
getGroup() - Method in class org.anchoranalysis.feature.io.csv.metadata.RowLabels: An identifier for a higher-level group which the row belongs to (foreign key)
getGroupHeaders() - Method in class org.anchoranalysis.feature.io.csv.metadata.LabelHeaders: Headers describing the non-feature columns outputted in the CSV related to identifying the group of a row
getHeaders() - Method in class org.anchoranalysis.feature.io.csv.metadata.FeatureCSVMetadata: Headers for the CSV file.
getLabels() - Method in class org.anchoranalysis.feature.io.results.LabelledResultsVector: The labels.
getOutputName() - Method in class org.anchoranalysis.feature.io.csv.metadata.FeatureCSVMetadata: The output name for the features CSV.
getResults() - Method in class org.anchoranalysis.feature.io.results.LabelledResultsVector: The results.
getXmlAggregatedGroup() - Method in class org.anchoranalysis.feature.io.results.FeatureOutputNames: The name of the XML file outputted with aggregated values for each group, if enabled.
GroupedResults - Class in org.anchoranalysis.feature.io.results.group: Stores feature-calculation results, indexing by their group.
GroupedResults() - Constructor for class org.anchoranalysis.feature.io.results.group.GroupedResults

H

hashCode() - Method in class org.anchoranalysis.feature.io.csv.metadata.FeatureCSVMetadata
hashCode() - Method in class org.anchoranalysis.feature.io.name.CombinedName
hashCode() - Method in class org.anchoranalysis.feature.io.name.SimpleName
hashCode() - Method in class org.anchoranalysis.feature.io.results.LabelledResultsVector

I

iterator() - Method in class org.anchoranalysis.feature.io.name.CombinedName
iterator() - Method in class org.anchoranalysis.feature.io.name.SimpleName

L

labelHeaders() - Method in class org.anchoranalysis.feature.io.results.FeatureOutputMetadata: Headers for the CSV File.
LabelHeaders - Class in org.anchoranalysis.feature.io.csv.metadata: Headers in a CSV file for the non-results (i.e.
LabelHeaders(String[]) - Constructor for class org.anchoranalysis.feature.io.csv.metadata.LabelHeaders: Creates with only non-group headers
LabelHeaders(String[], String[]) - Constructor for class org.anchoranalysis.feature.io.csv.metadata.LabelHeaders: Creates a new LabelHeaders instance.
LabelledResultsCollector - Interface in org.anchoranalysis.feature.io.results: Stores LabelledResultsVector as they are calculated, and writes to the file-system.
LabelledResultsCSVWriter - Class in org.anchoranalysis.feature.io.csv.results: Allows results to be written to a FeatureCSVWriter, possibly adding further processing.
LabelledResultsCSVWriter(FeatureCSVMetadataForOutput, FeatureCSVWriterFactory, Optional<Consumer<LabelledResultsVector>>) - Constructor for class org.anchoranalysis.feature.io.csv.results.LabelledResultsCSVWriter: Creates a new LabelledResultsCSVWriter instance.
LabelledResultsCSVWriterFactory - Class in org.anchoranalysis.feature.io.csv.results: Creates a new instance of LabelledResultsCSVWriter.
LabelledResultsVector - Class in org.anchoranalysis.feature.io.results: Like a ResultsVector but additionally contains labels to describe the calculated results.
LabelledResultsVector(Optional<MultiName>, ResultsVector) - Constructor for class org.anchoranalysis.feature.io.results.LabelledResultsVector: Creates with no additional labels other than a group.
LabelledResultsVector(RowLabels, ResultsVector) - Constructor for class org.anchoranalysis.feature.io.results.LabelledResultsVector: Creates a new LabelledResultsVector instance.
LabelledResultsVector(ResultsVector) - Constructor for class org.anchoranalysis.feature.io.results.LabelledResultsVector: Creates with no additional labels, and no group.

M

maybeConsumeResults(LabelledResultsVector) - Method in class org.anchoranalysis.feature.io.csv.results.LabelledResultsCSVWriter: Consumes the LabelledResultsVector if consumeAfterAdding is present.
metadata() - Method in class org.anchoranalysis.feature.io.csv.metadata.FeatureCSVMetadataForOutput: Derives metadata for writing to a CSV file
MultiName - Interface in org.anchoranalysis.feature.io.name: A name that that uniquely identifies an entity, and is composed of two parts.
MultiNameFactory - Class in org.anchoranalysis.feature.io.name: Creates MultiName.

N

nonFeatureHeaders() - Method in class org.anchoranalysis.feature.io.csv.metadata.FeatureCSVMetadataForOutput: Headers for the CSV File
NUMBER_DECIMAL_PLACES - Static variable in class org.anchoranalysis.feature.io.csv.FeatureCSVWriter: The number of decimal places to use for double values, unless visuallyShortened==true.

O

org.anchoranalysis.feature.io.csv - package org.anchoranalysis.feature.io.csv: Metadata for writing feature calculation-results in CSV format.
org.anchoranalysis.feature.io.csv.metadata - package org.anchoranalysis.feature.io.csv.metadata: Writing the results of feature calculations to the file-system.
org.anchoranalysis.feature.io.csv.results - package org.anchoranalysis.feature.io.csv.results: Writing the results from feature-calculation to a CSV file.
org.anchoranalysis.feature.io.csv.table - package org.anchoranalysis.feature.io.csv.table: A Generator for writing a table of feature values as a CSV.
org.anchoranalysis.feature.io.name - package org.anchoranalysis.feature.io.name: Naming items in a weay that breaks down into multiple elements.
org.anchoranalysis.feature.io.results - package org.anchoranalysis.feature.io.results: Writes feature-calculation results in different formats, also grouped results.
org.anchoranalysis.feature.io.results.group - package org.anchoranalysis.feature.io.results.group: Various different outputs that can be written for the a grouped version of the results in LabelledResultsCollector.
OUTPUT_DEFAULT_NON_AGGREGATED - Static variable in class org.anchoranalysis.feature.io.results.FeatureOutputNames: If not otherwise specified, the output name for a non-aggregated CSV of the results.
OUTPUT_SUFFIX_AGGREGATED - Static variable in class org.anchoranalysis.feature.io.results.FeatureOutputNames: Suffix appended to FeatureOutputNames.csvFeaturesNonAggregated to form an output-name for aggregated features.
OUTPUT_SUFFIX_AGGREGATED_GROUP - Static variable in class org.anchoranalysis.feature.io.results.FeatureOutputNames: Suffix appended to FeatureOutputNames.csvFeaturesNonAggregated to form an output-name for aggregated grouped features.
OUTPUT_SUFFIX_GROUP - Static variable in class org.anchoranalysis.feature.io.results.FeatureOutputNames: Suffix appended to FeatureOutputNames.csvFeaturesNonAggregated to form an output-name for grouped features.
outputMetadata - Variable in class org.anchoranalysis.feature.io.csv.results.LabelledResultsCSVWriter: Metadata defining which CSV file to write to, and which headers.
outputName() - Method in class org.anchoranalysis.feature.io.csv.metadata.FeatureCSVMetadataForOutput: Names for the produced output.
outputNames() - Method in class org.anchoranalysis.feature.io.results.FeatureOutputMetadata: Names for any outputs produced by LabelledResultsCollector.

R

RowLabels - Class in org.anchoranalysis.feature.io.csv.metadata: Labels for each row of feature-results in the outputted CSV row.
RowLabels(String) - Constructor for class org.anchoranalysis.feature.io.csv.metadata.RowLabels: Creates with a single string as an identifier.
RowLabels(Optional<String[]>, Optional<MultiName>) - Constructor for class org.anchoranalysis.feature.io.csv.metadata.RowLabels: Creates a new RowLabels instance.

S

secondPart() - Method in class org.anchoranalysis.feature.io.name.CombinedName
secondPart() - Method in interface org.anchoranalysis.feature.io.name.MultiName: The second part of the name.
secondPart() - Method in class org.anchoranalysis.feature.io.name.SimpleName
SimpleName - Class in org.anchoranalysis.feature.io.name: A name with only one part, and is always unique.
SimpleName(String) - Constructor for class org.anchoranalysis.feature.io.name.SimpleName
size() - Method in class org.anchoranalysis.feature.io.results.LabelledResultsVector: The number of calculations stored in the vector.
start() - Method in class org.anchoranalysis.feature.io.csv.results.LabelledResultsCSVWriter: Starts writing the CSV file.

T

toString() - Method in class org.anchoranalysis.feature.io.csv.metadata.FeatureCSVMetadata
toString() - Method in class org.anchoranalysis.feature.io.name.CombinedName
toString() - Method in interface org.anchoranalysis.feature.io.name.MultiName: The full name, including both directory and file part, as a string.
toString() - Method in class org.anchoranalysis.feature.io.name.SimpleName
toString() - Method in class org.anchoranalysis.feature.io.results.LabelledResultsVector

W

writeFeaturesToCSV(CSVWriter, T, List<String>) - Method in class org.anchoranalysis.feature.io.csv.table.FeatureTableCSVGenerator: Writes the features to the CSV-file.
writeGroupResults(Optional<NamedFeatureStore<FeatureInputResults>>, boolean, FeatureOutputMetadata, FeatureCSVWriterFactory, InputOutputContextSubdirectoryCache) - Method in class org.anchoranalysis.feature.io.results.group.GroupedResults: Writes outputs for groups that have been previously added with GroupedResults.addResultsFor(org.anchoranalysis.feature.io.results.LabelledResultsVector).
writeToFile(T, OutputWriteSettings, Path) - Method in class org.anchoranalysis.feature.io.csv.table.FeatureTableCSVGenerator

A C E F G H I L M N O R S T W
All Classes and Interfaces|All Packages|Constant Field Values