Index

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

A

Access conventions - Search tag in package org.egothor.methodatlas.command

Section

Activation - Search tag in class org.egothor.methodatlas.JsonLineFormatter

Section

AI-Based Security Tagging - Search tag in package org.egothor.methodatlas

Section

aiCacheFile() - Method in record class org.egothor.methodatlas.CliConfig

Returns the value of the aiCacheFile record component.

AI Enrichment - Search tag in class org.egothor.methodatlas.MethodAtlasApp

Section

aiOptions() - Method in record class org.egothor.methodatlas.CliConfig

Returns the value of the aiOptions record component.

AiResultCache - Class in org.egothor.methodatlas

In-memory cache of AI classification results loaded from a previous MethodAtlas scan output.

AiRuntime - Record Class in org.egothor.methodatlas.command

Bundle of AI infrastructure that is constant for the duration of a scan run.

AiRuntime(AiOptions, AiSuggestionEngine, ClassificationOverride, AiResultCache) - Constructor for record class org.egothor.methodatlas.command.AiRuntime

Creates an instance of a AiRuntime record class.

AiRuntimeBuilder - Class in org.egothor.methodatlas.command

Constructs the per-run AI infrastructure: the suggestion engine, the result cache, and the human-readable taxonomy descriptor.

AiRuntimeBuilder() - Constructor for class org.egothor.methodatlas.command.AiRuntimeBuilder

Creates a new builder.

API shape - Search tag in class org.egothor.methodatlas.command.ScanOrchestrator

Section

apply(Path, List<Path>, int, List<SourcePatcher>, PrintWriter) - Static method in class org.egothor.methodatlas.ApplyTagsFromCsvEngine

Applies annotation changes from a reviewed CSV to source files.

applyTags() - Method in record class org.egothor.methodatlas.CliConfig

Returns the value of the applyTags record component.

ApplyTagsCommand - Class in org.egothor.methodatlas.command

CLI command handler for the -apply-tags mode.

ApplyTagsCommand(CliConfig, TestDiscoveryConfig, AiSuggestionEngine, ClassificationOverride, AiResultCache, PluginLoader, ScanOrchestrator) - Constructor for class org.egothor.methodatlas.command.ApplyTagsCommand

Creates a new apply-tags command.

ApplyTagsFromCsvCommand - Class in org.egothor.methodatlas.command

CLI command handler for the -apply-tags-from-csv mode.

ApplyTagsFromCsvCommand(CliConfig, TestDiscoveryConfig, PluginLoader) - Constructor for class org.egothor.methodatlas.command.ApplyTagsFromCsvCommand

Creates a new apply-tags-from-csv command.

ApplyTagsFromCsvEngine - Class in org.egothor.methodatlas

Engine that applies annotation changes to source files driven by a reviewed MethodAtlas CSV export.

applyTagsFromCsvFile() - Method in record class org.egothor.methodatlas.CliConfig

Returns the value of the applyTagsFromCsvFile record component.

B

buildCache(Path) - Method in class org.egothor.methodatlas.command.AiRuntimeBuilder

Loads the AI result cache from a previous MethodAtlas CSV output, or returns the empty no-op cache when no cache file was configured.

buildEngine(AiOptions) - Method in class org.egothor.methodatlas.command.AiRuntimeBuilder

Creates the AI suggestion engine for the current run, or returns null when AI support is disabled.

C

cache() - Method in record class org.egothor.methodatlas.command.AiRuntime

Returns the value of the cache record component.

Cleanup - Search tag in class org.egothor.methodatlas.ScanRunContext

Section

clear() - Static method in class org.egothor.methodatlas.ScanRunContext

Removes the current scan run from the calling thread.

CliConfig - Record Class in org.egothor.methodatlas

Parsed command-line configuration used to drive a single application run.

CliConfig(OutputMode, AiOptions, List<Path>, List<String>, Set<String>, Map<String, List<String>>, boolean, ManualMode, boolean, boolean, Path, boolean, Path, boolean, Path, int, boolean, boolean, double) - Constructor for record class org.egothor.methodatlas.CliConfig

Creates an instance of a CliConfig record class.

closeAll(List<TestDiscovery>) - Method in class org.egothor.methodatlas.command.PluginLoader

Closes every provider in the list, logging any IOException at Level.FINE and continuing so that all providers are attempted.

collectMethodsByFile(List<Path>, List<TestDiscovery>) - Method in class org.egothor.methodatlas.command.ScanOrchestrator

Collects all discovered methods from every configured root, keyed by source-file path.

Command - Interface in org.egothor.methodatlas.command

A self-contained CLI command handler.

Command handlers - Search tag in package org.egothor.methodatlas.command

Section

configFingerprint() - Method in record class org.egothor.methodatlas.ScanRun

Returns the value of the configFingerprint record component.

Consume(Path, Path) - Constructor for record class org.egothor.methodatlas.ManualMode.Consume

Creates an instance of a Consume record class.

contentHash() - Method in record class org.egothor.methodatlas.CliConfig

Returns the value of the contentHash record component.

ContentHasher - Class in org.egothor.methodatlas.command

Pure utility helpers for content fingerprints and scan-root path prefixes.

create(String, String) - Static method in record class org.egothor.methodatlas.ScanRun

Creates a new ScanRun with a freshly generated correlation id and the current wall-clock timestamp.

current() - Static method in class org.egothor.methodatlas.ScanRunContext

Returns the current scan run for the calling thread, or Optional.empty() when no run is currently set (the standard case before MethodAtlasApp.main(String[]) runs or after ScanRunContext.clear()).

D

DiffCommand - Class in org.egothor.methodatlas.command

CLI command handler for the -diff mode.

DiffCommand(Path, Path) - Constructor for class org.egothor.methodatlas.command.DiffCommand

Creates a new diff command.

driftDetect() - Method in record class org.egothor.methodatlas.CliConfig

Returns the value of the driftDetect record component.

E

emitMetadata() - Method in record class org.egothor.methodatlas.CliConfig

Returns the value of the emitMetadata record component.

emitSourceRoot() - Method in record class org.egothor.methodatlas.CliConfig

Returns the value of the emitSourceRoot record component.

empty() - Static method in class org.egothor.methodatlas.AiResultCache

Returns an empty cache that always produces misses.

engine() - Method in record class org.egothor.methodatlas.command.AiRuntime

Returns the value of the engine record component.

equals(Object) - Method in record class org.egothor.methodatlas.CliConfig

Indicates whether some other object is "equal to" this one.

equals(Object) - Method in record class org.egothor.methodatlas.command.AiRuntime

Indicates whether some other object is "equal to" this one.

equals(Object) - Method in record class org.egothor.methodatlas.ManualMode.Consume

Indicates whether some other object is "equal to" this one.

equals(Object) - Method in record class org.egothor.methodatlas.ManualMode.Prepare

Indicates whether some other object is "equal to" this one.

equals(Object) - Method in record class org.egothor.methodatlas.ScanRun

Indicates whether some other object is "equal to" this one.

execute(PrintWriter) - Method in class org.egothor.methodatlas.command.ApplyTagsCommand

Discovers test methods, gathers AI suggestions, and patches source files.

execute(PrintWriter) - Method in class org.egothor.methodatlas.command.ApplyTagsFromCsvCommand

Applies annotation decisions from the reviewed CSV to source files.

execute(PrintWriter) - Method in interface org.egothor.methodatlas.command.Command

Executes this command and returns an exit code.

execute(PrintWriter) - Method in class org.egothor.methodatlas.command.DiffCommand

Computes and emits the delta between the two scan CSV outputs.

execute(PrintWriter) - Method in class org.egothor.methodatlas.command.GitHubAnnotationsCommand

Scans all roots and emits GitHub Actions workflow commands.

execute(PrintWriter) - Method in class org.egothor.methodatlas.command.JsonCommand

Scans all roots and emits the buffered result as a JSON array.

execute(PrintWriter) - Method in class org.egothor.methodatlas.command.ManualPrepareCommand

Discovers test classes, writes work files, and reports progress.

execute(PrintWriter) - Method in class org.egothor.methodatlas.command.SarifCommand

Scans all roots and emits the buffered result as SARIF JSON.

execute(PrintWriter) - Method in class org.egothor.methodatlas.command.ScanCommand

Runs the scan and emits output incrementally.

F

Failure handling - Search tag in class org.egothor.methodatlas.command.AiRuntimeBuilder

Section

Fields - Search tag in record class org.egothor.methodatlas.ScanRun

Section

filePrefix(List<Path>) - Static method in class org.egothor.methodatlas.command.ContentHasher

Derives the forward-slashed path prefix used in GitHub Actions workflow annotations and SARIF location URIs.

fileSuffixes() - Method in record class org.egothor.methodatlas.CliConfig

Returns the value of the fileSuffixes record component.

filterSink(TestMethodSink, boolean, double, boolean) - Method in class org.egothor.methodatlas.command.ScanOrchestrator

Wraps a TestMethodSink so that only records that pass all active filters are forwarded to delegate.

format(LogRecord) - Method in class org.egothor.methodatlas.JsonLineFormatter

Renders record as a single line of JSON terminated by \n.

G

gatherAiSuggestionsForFile(Map<String, List<DiscoveredMethod>>, AiRuntime, AiResultCache, Map<String, List<String>>, Map<String, String>) - Method in class org.egothor.methodatlas.command.ScanOrchestrator

Resolves AI security-classification suggestions for every class in byClass and populates tagsToApply and displayNames with the results for methods that are security-relevant.

GitHubAnnotationsCommand - Class in org.egothor.methodatlas.command

CLI command handler for the -github-annotations output mode.

GitHubAnnotationsCommand(CliConfig, TestDiscoveryConfig, AiSuggestionEngine, ClassificationOverride, AiResultCache, ScanOrchestrator) - Constructor for class org.egothor.methodatlas.command.GitHubAnnotationsCommand

Creates a new GitHub Annotations command.

H

hashClass(String) - Static method in class org.egothor.methodatlas.command.ContentHasher

Computes a SHA-256 content fingerprint of a class source string.

hashCode() - Method in record class org.egothor.methodatlas.CliConfig

Returns a hash code value for this object.

hashCode() - Method in record class org.egothor.methodatlas.command.AiRuntime

Returns a hash code value for this object.

hashCode() - Method in record class org.egothor.methodatlas.ManualMode.Consume

Returns a hash code value for this object.

hashCode() - Method in record class org.egothor.methodatlas.ManualMode.Prepare

Returns a hash code value for this object.

hashCode() - Method in record class org.egothor.methodatlas.ScanRun

Returns a hash code value for this object.

hits() - Method in class org.egothor.methodatlas.AiResultCache

Returns the number of successful cache lookups so far.

I

Implementation Notes - Search tag in package org.egothor.methodatlas

Section

Invariant - Search tag in class org.egothor.methodatlas.ApplyTagsFromCsvEngine

Section

isActive() - Method in class org.egothor.methodatlas.AiResultCache

Returns true when this cache contains at least one entry.

J

JsonCommand - Class in org.egothor.methodatlas.command

CLI command handler for the -json output mode.

JsonCommand(CliConfig, TestDiscoveryConfig, AiSuggestionEngine, ClassificationOverride, AiResultCache, PluginLoader, ScanOrchestrator) - Constructor for class org.egothor.methodatlas.command.JsonCommand

Creates a new JSON command.

JsonLineFormatter - Class in org.egothor.methodatlas

Formatter that emits one JSON object per log record, on a single line, suitable for ingestion by log-aggregation pipelines (Elastic, Splunk, Loki) and for reproducible audit-trail archives.

JsonLineFormatter() - Constructor for class org.egothor.methodatlas.JsonLineFormatter

Creates a new formatter.

K

Key Capabilities - Search tag in Overview

Section

L

Languages supported for write-back - Search tag in class org.egothor.methodatlas.ApplyTagsFromCsvEngine

Section

Languages supported for write-back - Search tag in class org.egothor.methodatlas.command.ApplyTagsCommand

Section

License - Search tag in Overview

Section

Lifecycle - Search tag in class org.egothor.methodatlas.command.PluginLoader

Section

load(Path) - Static method in class org.egothor.methodatlas.AiResultCache

Loads a cache from a MethodAtlas CSV output file.

load(Path) - Method in class org.egothor.methodatlas.command.OverrideLoader

Loads the classification override file at the given path, or returns the empty no-op singleton when no override file was configured.

loadPatchers(TestDiscoveryConfig) - Method in class org.egothor.methodatlas.command.PluginLoader

Loads all SourcePatcher providers registered via ServiceLoader, configures each one with config, and returns them in registration order.

loadProviders(TestDiscoveryConfig) - Method in class org.egothor.methodatlas.command.PluginLoader

Loads all TestDiscovery providers registered via ServiceLoader, configures each one with config, and returns them in registration order.

lookup(String) - Method in class org.egothor.methodatlas.AiResultCache

Returns the cached classification for the class with the given content hash, or empty when the hash is absent from the cache.

M

main(String[]) - Static method in class org.egothor.methodatlas.MethodAtlasApp

Program entry point.

Manual AI Workflow - Search tag in class org.egothor.methodatlas.MethodAtlasApp

Section

manualMode() - Method in record class org.egothor.methodatlas.CliConfig

Returns the value of the manualMode record component.

ManualMode - Interface in org.egothor.methodatlas

Selects between the two phases of the manual AI workflow.

ManualMode.Consume - Record Class in org.egothor.methodatlas

Consume phase: read operator-saved response files and emit enriched CSV.

ManualMode.Prepare - Record Class in org.egothor.methodatlas

Prepare phase: scan source files and write AI prompt work files and empty response stubs.

ManualPrepareCommand - Class in org.egothor.methodatlas.command

CLI command handler for the -manual-prepare mode.

ManualPrepareCommand(ManualMode.Prepare, CliConfig, TestDiscoveryConfig, PluginLoader) - Constructor for class org.egothor.methodatlas.command.ManualPrepareCommand

Creates a new manual-prepare command.

MethodAtlasApp - Class in org.egothor.methodatlas

Command-line application for scanning Java test sources, extracting JUnit test metadata, and optionally enriching the emitted results with AI-generated security tagging suggestions.

minConfidence() - Method in record class org.egothor.methodatlas.CliConfig

Returns the value of the minConfidence record component.

Mismatch handling - Search tag in class org.egothor.methodatlas.ApplyTagsFromCsvEngine

Section

mismatchLimit() - Method in record class org.egothor.methodatlas.CliConfig

Returns the value of the mismatchLimit record component.

misses() - Method in class org.egothor.methodatlas.AiResultCache

Returns the number of unsuccessful cache lookups so far.

N

Null handling - Search tag in class org.egothor.methodatlas.command.OverrideLoader

Section

O

options() - Method in record class org.egothor.methodatlas.command.AiRuntime

Returns the value of the options record component.

org.egothor.methodatlas - package org.egothor.methodatlas

Provides the core command-line utility for analyzing Java test sources and producing structured metadata about JUnit test methods.

org.egothor.methodatlas.command - package org.egothor.methodatlas.command

CLI command handler implementations for MethodAtlas.

Output Formats - Search tag in package org.egothor.methodatlas

Section

outputMode() - Method in record class org.egothor.methodatlas.CliConfig

Returns the value of the outputMode record component.

Output schema - Search tag in class org.egothor.methodatlas.JsonLineFormatter

Section

override() - Method in record class org.egothor.methodatlas.command.AiRuntime

Returns the value of the override record component.

overrideFile() - Method in record class org.egothor.methodatlas.CliConfig

Returns the value of the overrideFile record component.

OverrideLoader - Class in org.egothor.methodatlas.command

Loads classification override files into ClassificationOverride instances.

OverrideLoader() - Constructor for class org.egothor.methodatlas.command.OverrideLoader

Creates a new override loader.

Overview - Search tag in package org.egothor.methodatlas

Section

P

Package Structure - Search tag in Overview

Section

paths() - Method in record class org.egothor.methodatlas.CliConfig

Returns the value of the paths record component.

PluginLoader - Class in org.egothor.methodatlas.command

Resolves and configures discovery plugins via ServiceLoader.

PluginLoader() - Constructor for class org.egothor.methodatlas.command.PluginLoader

Creates a new plugin loader.

Prepare(Path, Path) - Constructor for record class org.egothor.methodatlas.ManualMode.Prepare

Creates an instance of a Prepare record class.

properties() - Method in record class org.egothor.methodatlas.CliConfig

Returns the value of the properties record component.

R

requireUniqueDiscoveryIds(List<TestDiscovery>) - Static method in class org.egothor.methodatlas.command.PluginLoader

Verifies that every TestDiscovery provider in the list has a unique TestDiscovery.pluginId().

requireUniquePatcherIds(List<SourcePatcher>) - Static method in class org.egothor.methodatlas.command.PluginLoader

Verifies that every SourcePatcher in the list has a unique SourcePatcher.pluginId().

resolveTaxonomyInfo(AiOptions, boolean) - Method in class org.egothor.methodatlas.command.AiRuntimeBuilder

Produces a human-readable string identifying which taxonomy configuration is in effect, for inclusion in scan-metadata output.

responseDir() - Method in record class org.egothor.methodatlas.ManualMode.Consume

Returns the value of the responseDir record component.

responseDir() - Method in record class org.egothor.methodatlas.ManualMode.Prepare

Returns the value of the responseDir record component.

runDiscovery(Path, List<TestDiscovery>, AiOptions, AiSuggestionEngine, TestMethodSink, boolean, ClassificationOverride, AiResultCache) - Method in class org.egothor.methodatlas.command.ScanOrchestrator

Runs all configured TestDiscovery providers on root, merges their results, orchestrates AI analysis per class, and forwards each method record to sink.

runId() - Method in record class org.egothor.methodatlas.ScanRun

Returns the value of the runId record component.

S

SarifCommand - Class in org.egothor.methodatlas.command

CLI command handler for the -sarif output mode.

SarifCommand(CliConfig, TestDiscoveryConfig, AiSuggestionEngine, ClassificationOverride, AiResultCache, ScanOrchestrator) - Constructor for class org.egothor.methodatlas.command.SarifCommand

Creates a new SARIF command.

sarifOmitScores() - Method in record class org.egothor.methodatlas.CliConfig

Returns the value of the sarifOmitScores record component.

scan(List<Path>, CliConfig, TestDiscoveryConfig, AiSuggestionEngine, TestMethodSink, ClassificationOverride, AiResultCache) - Method in class org.egothor.methodatlas.command.ScanOrchestrator

Scans every configured root, forwarding each discovered test method to sink.

ScanCommand - Class in org.egothor.methodatlas.command

CLI command handler for the default CSV and -plain output modes.

ScanCommand(CliConfig, TestDiscoveryConfig, AiSuggestionEngine, ClassificationOverride, AiResultCache, PluginLoader, ScanOrchestrator) - Constructor for class org.egothor.methodatlas.command.ScanCommand

Creates a new scan command.

ScanOrchestrator - Class in org.egothor.methodatlas.command

Orchestrates the scan-and-emit loop that every command mode is built around.

ScanOrchestrator(PluginLoader) - Constructor for class org.egothor.methodatlas.command.ScanOrchestrator

Creates a new orchestrator that will resolve providers through pluginLoader.

ScanRun - Record Class in org.egothor.methodatlas

Immutable record identifying one CLI invocation of MethodAtlas.

ScanRun(String, Instant, String, String) - Constructor for record class org.egothor.methodatlas.ScanRun

Compact constructor enforcing the documented invariants on the component values.

ScanRunContext - Class in org.egothor.methodatlas

Thread-local holder for the current ScanRun, the JUL-friendly equivalent of SLF4J's MDC.

securityOnly() - Method in record class org.egothor.methodatlas.CliConfig

Returns the value of the securityOnly record component.

set(ScanRun) - Static method in class org.egothor.methodatlas.ScanRunContext

Sets the current scan run for the calling thread.

Shared infrastructure - Search tag in package org.egothor.methodatlas.command

Section

Source-Derived Metadata - Search tag in class org.egothor.methodatlas.MethodAtlasApp

Section

startedAt() - Method in record class org.egothor.methodatlas.ScanRun

Returns the value of the startedAt record component.

Sub-packages - Search tag in package org.egothor.methodatlas

Section

Supported Command-Line Options - Search tag in class org.egothor.methodatlas.MethodAtlasApp

Section

T

testMarkers() - Method in record class org.egothor.methodatlas.CliConfig

Returns the value of the testMarkers record component.

Thread safety - Search tag in class org.egothor.methodatlas.JsonLineFormatter

Section

Thread safety - Search tag in class org.egothor.methodatlas.ScanRunContext

Section

Thread safety - Search tag in class org.egothor.methodatlas.command.OverrideLoader

Section

Thread safety - Search tag in class org.egothor.methodatlas.command.PluginLoader

Section

Thread safety - Search tag in class org.egothor.methodatlas.command.ScanOrchestrator

Section

toolVersion() - Method in record class org.egothor.methodatlas.ScanRun

Returns the value of the toolVersion record component.

toString() - Method in record class org.egothor.methodatlas.CliConfig

Returns a string representation of this record class.

toString() - Method in record class org.egothor.methodatlas.command.AiRuntime

Returns a string representation of this record class.

toString() - Method in record class org.egothor.methodatlas.ManualMode.Consume

Returns a string representation of this record class.

toString() - Method in record class org.egothor.methodatlas.ManualMode.Prepare

Returns a string representation of this record class.

toString() - Method in record class org.egothor.methodatlas.ScanRun

Returns a string representation of this record class.

toTargetMethod(DiscoveredMethod) - Static method in class org.egothor.methodatlas.command.ScanOrchestrator

Converts a single discovered test method into a prompt target descriptor.

Typical Usage - Search tag in package org.egothor.methodatlas

Section

W

What is applied - Search tag in class org.egothor.methodatlas.ApplyTagsFromCsvEngine

Section

workDir() - Method in record class org.egothor.methodatlas.ManualMode.Consume

Returns the value of the workDir record component.

workDir() - Method in record class org.egothor.methodatlas.ManualMode.Prepare

Returns the value of the workDir record component.

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