Index (MethodAtlas)

A B C D E F G H I J K L M N O P R S T U V W
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

Access conventions - Section in package org.egothor.methodatlas.command
accuracy() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Counts: Returns the accuracy.
AccuracyEvaluator - Class in org.egothor.methodatlas.eval: Joins AI predictions with human-reviewed labels and scores them with AccuracyMetrics.
AccuracyEvaluator.Evaluation - Record Class in org.egothor.methodatlas.eval: Metrics together with the coverage bookkeeping of the join.
AccuracyMetrics - Class in org.egothor.methodatlas.eval: Pure, deterministic computation of AI-classification quality metrics from (prediction, truth) pairs.
AccuracyMetrics.Counts - Record Class in org.egothor.methodatlas.eval: Confusion counts for one binary decision.
AccuracyMetrics.Result - Record Class in org.egothor.methodatlas.eval: The complete metric set.
AccuracyMetrics.Sample - Record Class in org.egothor.methodatlas.eval: One method for which a prediction is compared with a human label.
AccuracyMetrics.TagResult - Record Class in org.egothor.methodatlas.eval: Metrics of a single taxonomy tag.
AccuracyReportRenderer - Class in org.egothor.methodatlas.eval: Renders an AccuracyEvaluator.Evaluation as Markdown or JSON.
Activation - Section in class org.egothor.methodatlas.JsonLineFormatter
AI-Based Security Tagging - Section in package org.egothor.methodatlas
AiCacheEntry - Record Class in org.egothor.methodatlas: One entry of the unified AI result cache: the complete AI answer for a single test class, keyed by the class content hash and tagged with the prompt-catalogue signature that produced it.
AiCacheEntry(String, String, AiClassSuggestion) - Constructor for record class org.egothor.methodatlas.AiCacheEntry: Creates an instance of a AiCacheEntry record class.
aiCacheFile() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the aiCacheFile record component.
aiCacheOut() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the aiCacheOut record component.
AiCacheStore - Class in org.egothor.methodatlas: Reads and writes the unified AI result cache as a JSON Lines file: one AiCacheEntry per line.
AI-column promotion (risky, opt-in) - Section in class org.egothor.methodatlas.ApplyTagsFromCsvEngine
aiCwe() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the aiCwe record component.
AI Enrichment - Section in class org.egothor.methodatlas.MethodAtlasApp
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 results loaded from a previous MethodAtlas run, keyed by the per-class content_hash fingerprint.
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 - Section in class org.egothor.methodatlas.command.ScanOrchestrator
apply(Path, List, int, List, PrintWriter, boolean, boolean) - 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.
asSink() - Method in class org.egothor.methodatlas.attest.AttestFacade.Handle: Returns the TestMethodSink that the orchestrator must receive every per-method record on.
asSink() - Method in class org.egothor.methodatlas.coverage.CoverageFacade.Handle: Returns the TestMethodSink that the orchestrator must receive every per-method record on.
asSink() - Method in class org.egothor.methodatlas.evidencereport.EvidenceReportFacade.Handle: Returns the TestMethodSink that the orchestrator must receive every per-method record on.
asSink() - Method in class org.egothor.methodatlas.gap.GapFacade.Handle: Returns the TestMethodSink that the orchestrator must receive every per-method record on.
ASVS - Enum constant in enum class org.egothor.methodatlas.evidence.EvidenceFramework: OWASP Application Security Verification Standard.
attest() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the attest record component.
AttestFacade - Class in org.egothor.methodatlas.attest: Single public entry point used by MethodAtlasApp to drive -attest.
AttestFacade.Handle - Class in org.egothor.methodatlas.attest: Opaque handle returned by AttestFacade.prepare(double, List).
attestFile() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the attestFile record component.

B

beginLine() - Method in record class org.egothor.methodatlas.command.DetectCredentialsStage.MethodRange: Returns the value of the beginLine record component.
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.
canonicalToken() - Method in enum class org.egothor.methodatlas.evidence.EvidenceFramework: Returns the canonical, case-sensitive token used to identify this framework in pack metadata and on disk.
CheckPromptsCommand - Class in org.egothor.methodatlas.command: Utility CLI mode (-check-prompts) that validates prompt templates and prints their SHA-256 checksums without running a scan.
classification(String, String) - Method in class org.egothor.methodatlas.AiResultCache: Returns the cached classification for a class when the content hash matches and the cached answer is compatible with the current prompt catalogue.
Cleanup - Section in class org.egothor.methodatlas.ScanRunContext
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, List, Set, Map, boolean, ManualMode, boolean, boolean, Path, boolean, Path, boolean, Path, int, boolean, boolean, double, boolean, Path, boolean, Path, Path, String, Path, boolean, Path, String, Path, String, String, String, boolean, boolean, boolean, String, Path, Path, boolean, boolean, double, double, double, Path, boolean, boolean, boolean, Path, boolean, Path, boolean, Path) - Constructor for record class org.egothor.methodatlas.CliConfig: Creates an instance of a CliConfig record class.
closeAll(List) - Method in class org.egothor.methodatlas.command.PluginLoader: Closes every provider in the list, logging any IOException at Level.WARNING and continuing so that all providers are attempted.
closeAllCredentialDetectors(List) - Method in class org.egothor.methodatlas.command.PluginLoader: Closes every detector in the list, logging any IOException at Level.WARNING and continuing so that all detectors are attempted.
collect(List) - Method in class org.egothor.methodatlas.command.CredentialScanUnitSource: Walks roots and returns one unit per matching, readable file, in deterministic sorted order.
collectMethodsByFile(List, List) - 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 - Section in package org.egothor.methodatlas.command
CommentRedaction - Class in org.egothor.methodatlas.command: Applies the loaded CommentRedactors to source text on its way to an AI provider, failing closed.
CommentRedaction(List) - Constructor for class org.egothor.methodatlas.command.CommentRedaction: Creates a service over the given redactors.
compute(Collection) - Static method in class org.egothor.methodatlas.eval.AccuracyMetrics: Computes all metrics for the given samples.
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.AiCacheEntry: Returns the value of the contentHash record component.
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.
counts() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.TagResult: Returns the value of the counts record component.
Counts(int, int, int, int) - Constructor for record class org.egothor.methodatlas.eval.AccuracyMetrics.Counts: Creates an instance of a Counts record class.
Coverage bookkeeping - Section in class org.egothor.methodatlas.eval.AccuracyEvaluator
CoverageFacade - Class in org.egothor.methodatlas.coverage: Single public entry point used by MethodAtlasApp to drive -emit-coverage.
CoverageFacade.Handle - Class in org.egothor.methodatlas.coverage: Opaque handle returned by CoverageFacade.prepare(Path, double).
coverageFile() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the coverageFile record component.
coverageMappingFile() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the coverageMappingFile record component.
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.
CredentialScanUnitSource - Class in org.egothor.methodatlas.command: Selects files to scan for credentials by mask and reads each into a CredentialScanUnit.
CredentialScanUnitSource(List, String) - Constructor for class org.egothor.methodatlas.command.CredentialScanUnitSource: Creates a source.
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

DEFAULT_ATTEST_FILENAME - Static variable in class org.egothor.methodatlas.attest.AttestFacade: Default filename used when -attest-file is not supplied.
DEFAULT_COVERAGE_FILENAME - Static variable in class org.egothor.methodatlas.coverage.CoverageFacade: Default filename used when -coverage-file is not supplied.
DEFAULT_GAP_REPORT_FILENAME - Static variable in class org.egothor.methodatlas.gap.GapFacade: Default filename used when -gap-report-file is not supplied.
DEFAULT_REPORT_FILENAME - Static variable in class org.egothor.methodatlas.evidencereport.EvidenceReportFacade: Default filename used when -evidence-report-file is not supplied.
DetectCredentialsStage - Class in org.egothor.methodatlas.command: Runs the deterministic detectors over the scan units, attaches best-effort enclosing-method attribution, and produces CredentialFindings.
DetectCredentialsStage(List, Map) - Constructor for class org.egothor.methodatlas.command.DetectCredentialsStage: Creates a stage.
DetectCredentialsStage.MethodRange - Record Class in org.egothor.methodatlas.command: A method's line span, used for attribution.
detectSecrets() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the detectSecrets record component.
Determinism - Section in class org.egothor.methodatlas.eval.AccuracyReportRenderer
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 without the removal gate.
DiffCommand(Path, Path, boolean, Path) - Constructor for class org.egothor.methodatlas.command.DiffCommand: Creates a new diff command with optional removal-gate enforcement.
driftDetect() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the driftDetect record component.

E

emit(CliConfig, String, String) - Static method in class org.egothor.methodatlas.receipt.ReceiptFacade: Builds and writes a reproducibility receipt for the supplied scan configuration.
emitCoverage() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the emitCoverage record component.
emitMetadata() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the emitMetadata record component.
emitReceipt() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the emitReceipt 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.
endLine() - Method in record class org.egothor.methodatlas.command.DetectCredentialsStage.MethodRange: Returns the value of the endLine record component.
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.AiCacheEntry: Indicates whether some other object is "equal to" this one.
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.command.DetectCredentialsStage.MethodRange: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.egothor.methodatlas.eval.AccuracyEvaluator.Evaluation: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Counts: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Result: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Sample: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.TagResult: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.egothor.methodatlas.evidence.EvidencePackOptions: 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.
EvalAccuracyCommand - Class in org.egothor.methodatlas.command: Utility CLI mode (-eval-accuracy) that measures how accurate the AI classification is against a human-reviewed labelled set.
EvalAccuracyCommand(Path, Path, boolean, OptionalDouble) - Constructor for class org.egothor.methodatlas.command.EvalAccuracyCommand: Creates a command.
evaluate(Path, Path) - Static method in class org.egothor.methodatlas.eval.AccuracyEvaluator: Loads the label file and the predictions CSV and evaluates them.
evaluate(ClassificationOverride, List) - Static method in class org.egothor.methodatlas.eval.AccuracyEvaluator: Evaluates already-loaded labels against already-loaded predictions.
evaluated() - Method in record class org.egothor.methodatlas.eval.AccuracyEvaluator.Evaluation: Returns the value of the evaluated record component.
Evaluation(AccuracyMetrics.Result, int, int, int, int, int) - Constructor for record class org.egothor.methodatlas.eval.AccuracyEvaluator.Evaluation: Creates an instance of a Evaluation record class.
EvidenceFramework - Enum Class in org.egothor.methodatlas.evidence: Compliance frameworks that the -evidence-pack CLI mode can target.
EvidencePackCommand - Class in org.egothor.methodatlas.evidence: Materialises a tamper-evident evidence pack on disk by running one scan and bundling every artefact an auditor needs to verify it later.
EvidencePackCommand(CliConfig, EvidencePackOptions, TestDiscoveryConfig, AiSuggestionEngine, ClassificationOverride, AiResultCache, ScanOrchestrator) - Constructor for class org.egothor.methodatlas.evidence.EvidencePackCommand: Creates a new evidence-pack command.
evidencePackDir() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the evidencePackDir record component.
evidencePackFramework() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the evidencePackFramework record component.
evidencePackKeyAlias() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the evidencePackKeyAlias record component.
evidencePackKeyringEnv() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the evidencePackKeyringEnv record component.
evidencePackKeyringFile() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the evidencePackKeyringFile record component.
EvidencePackOptions - Record Class in org.egothor.methodatlas.evidence: Immutable bag of evidence-pack options collected from the command line.
EvidencePackOptions(EvidenceFramework, Path, boolean, Path, String, Path, String, String, String) - Constructor for record class org.egothor.methodatlas.evidence.EvidencePackOptions: Creates an instance of a EvidencePackOptions record class.
evidencePackOverwrite() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the evidencePackOverwrite record component.
evidencePackPasswordEnv() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the evidencePackPasswordEnv record component.
evidencePackPasswordFile() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the evidencePackPasswordFile record component.
evidencePackSignAlgo() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the evidencePackSignAlgo record component.
evidenceReport() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the evidenceReport record component.
EvidenceReportFacade - Class in org.egothor.methodatlas.evidencereport: Single public entry point used by MethodAtlasApp to drive -evidence-report.
EvidenceReportFacade.Handle - Class in org.egothor.methodatlas.evidencereport: Opaque handle returned by EvidenceReportFacade.prepare(double, List).
evidenceReportFile() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the evidenceReportFile record component.
execute() - Method in class org.egothor.methodatlas.evidence.EvidencePackCommand: Executes the command: runs the scan, writes every pack artefact, and — when a keyring is configured — signs the manifest.
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 class org.egothor.methodatlas.command.CheckPromptsCommand: Validates each template kind and prints a report.
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, and optionally enforces the removal-justification gate.
execute(PrintWriter) - Method in class org.egothor.methodatlas.command.EvalAccuracyCommand: Evaluates the predictions against the labels and writes the report.
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.
ExportKeyringSecretCommand - Class in org.egothor.methodatlas.evidence: CLI command handler for the -export-keyring-secret mode, which prints an encrypted keyring as a single text value for a CI/CD platform secret.

F

f1() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Counts: Returns the F1 score, the harmonic mean of precision and recall.
Failure handling - Section in class org.egothor.methodatlas.command.AiRuntimeBuilder
Fields - Section in record class org.egothor.methodatlas.ScanRun
filePrefix(List) - 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.
FLAG_CHECK_PROMPTS - Static variable in class org.egothor.methodatlas.command.CheckPromptsCommand: Flag that selects this utility mode.
FLAG_CLASSIFICATION_PROMPT - Static variable in class org.egothor.methodatlas.command.CheckPromptsCommand: Flag supplying a custom method-classification template file.
FLAG_DEDICATED_TRIAGE_PROMPT - Static variable in class org.egothor.methodatlas.command.CheckPromptsCommand: Flag supplying a custom standalone credential-triage template file.
FLAG_EVAL_ACCURACY - Static variable in class org.egothor.methodatlas.command.EvalAccuracyCommand: Flag that selects this utility mode; takes two path arguments.
FLAG_EVAL_FORMAT - Static variable in class org.egothor.methodatlas.command.EvalAccuracyCommand: Flag selecting the report format.
FLAG_EVAL_MIN_F1 - Static variable in class org.egothor.methodatlas.command.EvalAccuracyCommand: Flag setting the minimum acceptable F1.
FLAG_EXPORT_KEYRING_SECRET - Static variable in class org.egothor.methodatlas.evidence.ExportKeyringSecretCommand: Mode flag that selects this command.
FLAG_GEN_SIGNING_KEY - Static variable in class org.egothor.methodatlas.evidence.GenSigningKeyCommand: Mode flag that selects this command.
FLAG_TRIAGE_PROMPT - Static variable in class org.egothor.methodatlas.command.CheckPromptsCommand: Flag supplying a custom folded credential-triage appendix template file.
fn() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Counts: Returns the value of the fn record component.
format(LogRecord) - Method in class org.egothor.methodatlas.JsonLineFormatter: Renders record as a single line of JSON terminated by \n.
fp() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Counts: Returns the value of the fp record component.
framework() - Method in class org.egothor.methodatlas.evidence.EvidencePackCommand: Returns the resolved framework name (canonical token).
framework() - Method in record class org.egothor.methodatlas.evidence.EvidencePackOptions: Returns the value of the framework record component.
fromArgs(String...) - Static method in class org.egothor.methodatlas.command.CheckPromptsCommand: Builds a command by scanning raw command-line arguments for the three prompt-override flags.
fromArgs(String...) - Static method in class org.egothor.methodatlas.command.EvalAccuracyCommand: Builds the command from raw command-line arguments.

G

GapFacade - Class in org.egothor.methodatlas.gap: Single public entry point used by MethodAtlasApp to drive -gap-report.
GapFacade.Handle - Class in org.egothor.methodatlas.gap: Opaque handle returned by GapFacade.prepare(double).
gapReport() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the gapReport record component.
gapReportFile() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the gapReportFile record component.
gatherAiSuggestionsForFile(Map, AiRuntime, AiResultCache, Map, Map) - 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.
GenSigningKeyCommand - Class in org.egothor.methodatlas.evidence: CLI command handler for the -gen-signing-key mode, which creates (or extends) an encrypted ZeroEcho keyring containing a fresh signing key pair for evidence-pack signing.
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.
Ground truth - Section in class org.egothor.methodatlas.eval.AccuracyEvaluator

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.AiCacheEntry: Returns a hash code value for this object.
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.command.DetectCredentialsStage.MethodRange: Returns a hash code value for this object.
hashCode() - Method in record class org.egothor.methodatlas.eval.AccuracyEvaluator.Evaluation: Returns a hash code value for this object.
hashCode() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Counts: Returns a hash code value for this object.
hashCode() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Result: Returns a hash code value for this object.
hashCode() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Sample: Returns a hash code value for this object.
hashCode() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.TagResult: Returns a hash code value for this object.
hashCode() - Method in record class org.egothor.methodatlas.evidence.EvidencePackOptions: 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.
hashFile(Path) - Static method in class org.egothor.methodatlas.command.ContentHasher: Computes a SHA-256 content fingerprint of the raw bytes of a file.
hits() - Method in class org.egothor.methodatlas.AiResultCache: Returns the number of successful cache lookups so far.

I

id() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Sample: Returns the value of the id record component.
Implementation Notes - Section in package org.egothor.methodatlas
Invariant - Section in class org.egothor.methodatlas.ApplyTagsFromCsvEngine
isActive() - Method in class org.egothor.methodatlas.AiResultCache: Returns true when this cache contains at least one entry.
ISO_27001_8_29 - Enum constant in enum class org.egothor.methodatlas.evidence.EvidenceFramework: ISO/IEC 27001:2022 control 8.29 (secure development lifecycle).

J

json(AccuracyEvaluator.Evaluation) - Static method in class org.egothor.methodatlas.eval.AccuracyReportRenderer: Renders the evaluation as a JSON document.
JSON_SCHEMA_VERSION - Static variable in class org.egothor.methodatlas.eval.AccuracyReportRenderer: JSON report schema version; bump on any breaking field change.
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

keyAlias() - Method in record class org.egothor.methodatlas.evidence.EvidencePackOptions: Returns the value of the keyAlias record component.
Key Capabilities - Section in Overview
keyringEnv() - Method in record class org.egothor.methodatlas.evidence.EvidencePackOptions: Returns the value of the keyringEnv record component.
keyringFile() - Method in record class org.egothor.methodatlas.evidence.EvidencePackOptions: Returns the value of the keyringFile record component.

L

Languages supported for write-back - Section in class org.egothor.methodatlas.ApplyTagsFromCsvEngine
Languages supported for write-back - Section in class org.egothor.methodatlas.command.ApplyTagsCommand
License - Section in Overview
Lifecycle - Section in class org.egothor.methodatlas.command.PluginLoader
load(Path) - Static method in class org.egothor.methodatlas.AiResultCache: Loads a cache from a unified JSON-Lines cache file or a legacy scan CSV, auto-detected from the file's first non-blank character.
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.
loadCredentialDetectors(CredentialDetectorConfig) - Method in class org.egothor.methodatlas.command.PluginLoader: Loads all CredentialDetector providers registered via ServiceLoader, configures each with config, and returns them in registration order.
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 sorted by SourcePatcher.pluginId().
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 sorted by TestDiscovery.pluginId().
loadRedactors(TestDiscoveryConfig) - Method in class org.egothor.methodatlas.command.PluginLoader: Loads all CommentRedactor providers registered via ServiceLoader, configures each one with config, and returns them sorted by CommentRedactor.pluginId().
looksLikeJsonLines(Path) - Static method in class org.egothor.methodatlas.AiCacheStore: Returns true if file appears to be a unified JSON-Lines cache rather than a legacy scan CSV, by inspecting the first non-whitespace byte.
lookup(String) - Method in class org.egothor.methodatlas.AiResultCache: Returns the cached AI answer for a class by content hash, ignoring the prompt signature.

M

main(String[]) - Static method in class org.egothor.methodatlas.MethodAtlasApp: Program entry point.
Manual AI Workflow - Section in class org.egothor.methodatlas.MethodAtlasApp
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.
markdown(AccuracyEvaluator.Evaluation) - Static method in class org.egothor.methodatlas.eval.AccuracyReportRenderer: Renders the evaluation as a Markdown document.
mergeVerdicts(List, Map) - Static method in class org.egothor.methodatlas.command.DetectCredentialsStage: Merges LLM triage verdicts into a per-class finding list by candidate index.
method() - Method in record class org.egothor.methodatlas.command.DetectCredentialsStage.MethodRange: Returns the value of the method record component.
MethodAtlasApp - Class in org.egothor.methodatlas: Command-line entry point that parses the arguments and routes the invocation to the matching Command or utility mode.
MethodRange(String, int, int) - Constructor for record class org.egothor.methodatlas.command.DetectCredentialsStage.MethodRange: Creates an instance of a MethodRange record class.
metrics() - Method in record class org.egothor.methodatlas.eval.AccuracyEvaluator.Evaluation: Returns the value of the metrics record component.
minConfidence() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the minConfidence record component.
Mismatch handling - Section in class org.egothor.methodatlas.ApplyTagsFromCsvEngine
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

NIST_SSDF_PW8 - Enum constant in enum class org.egothor.methodatlas.evidence.EvidenceFramework: NIST Secure Software Development Framework, practice PW.8.
none() - Static method in class org.egothor.methodatlas.command.CommentRedaction: Returns a service with no redactors, which rejects every file.
normalise(Collection) - Static method in class org.egothor.methodatlas.eval.AccuracyMetrics: Normalises a tag collection (trim, lower-case with Locale.ROOT, drop blanks, de-duplicate).
Null handling - Section in class org.egothor.methodatlas.command.OverrideLoader

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.attest - package org.egothor.methodatlas.attest
org.egothor.methodatlas.command - package org.egothor.methodatlas.command: CLI command handler implementations for MethodAtlas.
org.egothor.methodatlas.coverage - package org.egothor.methodatlas.coverage
org.egothor.methodatlas.eval - package org.egothor.methodatlas.eval: AI-classification accuracy evaluation: scores AI predictions against a human-reviewed labelled set (the ClassificationOverride YAML format) and reports precision, recall, F1 and support per taxonomy tag and for the securityRelevant decision.
org.egothor.methodatlas.evidence - package org.egothor.methodatlas.evidence
org.egothor.methodatlas.evidencereport - package org.egothor.methodatlas.evidencereport
org.egothor.methodatlas.gap - package org.egothor.methodatlas.gap
org.egothor.methodatlas.receipt - package org.egothor.methodatlas.receipt
outputDir() - Method in class org.egothor.methodatlas.evidence.EvidencePackCommand: Returns the absolute path of the produced pack directory.
outputDir() - Method in record class org.egothor.methodatlas.evidence.EvidencePackOptions: Returns the value of the outputDir record component.
Output Formats - Section in package org.egothor.methodatlas
outputMode() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the outputMode record component.
Output schema - Section in class org.egothor.methodatlas.JsonLineFormatter
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 - Section in package org.egothor.methodatlas
overwrite() - Method in record class org.egothor.methodatlas.evidence.EvidencePackOptions: Returns the value of the overwrite record component.

P

Package Structure - Section in Overview
parallelAi() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the parallelAi record component.
parse(String) - Static method in enum class org.egothor.methodatlas.evidence.EvidenceFramework: Parses a framework token supplied on the command line.
passwordEnv() - Method in record class org.egothor.methodatlas.evidence.EvidencePackOptions: Returns the value of the passwordEnv record component.
passwordFile() - Method in record class org.egothor.methodatlas.evidence.EvidencePackOptions: Returns the value of the passwordFile record component.
paths() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the paths record component.
PCI_6_4_1 - Enum constant in enum class org.egothor.methodatlas.evidence.EvidenceFramework: PCI DSS requirement 6.4.1 (software security requirements).
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.
precision() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Counts: Returns the precision.
predictedRelevant() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Sample: Returns the value of the predictedRelevant record component.
predictedTags() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Sample: Returns the value of the predictedTags record component.
predictionRows() - Method in record class org.egothor.methodatlas.eval.AccuracyEvaluator.Evaluation: Returns the value of the predictionRows record component.
Predictions - Section in class org.egothor.methodatlas.eval.AccuracyEvaluator
prepare(double) - Static method in class org.egothor.methodatlas.gap.GapFacade: Prepares a gap-report collector.
prepare(double, List) - Static method in class org.egothor.methodatlas.attest.AttestFacade: Prepares an attestation collector.
prepare(double, List) - Static method in class org.egothor.methodatlas.evidencereport.EvidenceReportFacade: Prepares an evidence-report collector.
prepare(Path, double) - Static method in class org.egothor.methodatlas.coverage.CoverageFacade: Loads mappingFile and prepares a coverage collector wrapped inside a CoverageFacade.Handle that the CLI can later pass to the scan orchestrator and the writer.
Prepare(Path, Path) - Constructor for record class org.egothor.methodatlas.ManualMode.Prepare: Creates an instance of a Prepare record class.
promoteAi() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the promoteAi record component.
promptSignature() - Method in record class org.egothor.methodatlas.AiCacheEntry: Returns the value of the promptSignature record component.
properties() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the properties record component.

R

read(Path) - Static method in class org.egothor.methodatlas.AiCacheStore: Reads all cache entries from a JSON-Lines file.
recall() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Counts: Returns the recall.
ReceiptFacade - Class in org.egothor.methodatlas.receipt: Single public entry point used by MethodAtlasApp to materialise a reproducibility receipt.
receiptFile() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the receiptFile record component.
redaction() - Method in class org.egothor.methodatlas.command.ScanOrchestrator: Returns the redaction service this orchestrator applies to AI payloads, so other AI-sending components (credential triage) share the same fail-closed policy.
RedactionAbortedException - Exception Class in org.egothor.methodatlas.command: Thrown when -redact-comments is active and comment redaction cannot be guaranteed for a source file, so the run must abort before any source is sent to an AI provider (fail-closed).
RedactionAbortedException(String) - Constructor for exception class org.egothor.methodatlas.command.RedactionAbortedException: Creates the exception.
RedactionAbortedException(String, Throwable) - Constructor for exception class org.egothor.methodatlas.command.RedactionAbortedException: Creates the exception with a cause.
redactOrThrow(Path, String) - Method in class org.egothor.methodatlas.command.CommentRedaction: Returns source with comments blanked by the redactor responsible for file.
relevance() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Result: Returns the value of the relevance record component.
relevanceSamples() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Result: Returns the value of the relevanceSamples record component.
requireRedactable(Collection, AiRuntime) - Method in class org.egothor.methodatlas.command.ScanOrchestrator: Verifies up front that every class of every given file can be redacted, so an unredactable file aborts a multi-file run (apply-tags) before the first provider call.
requireUniqueCredentialDetectorIds(List) - Static method in class org.egothor.methodatlas.command.PluginLoader: Verifies that every CredentialDetector in the list has a unique CredentialDetector.detectorId().
requireUniqueDiscoveryIds(List) - Static method in class org.egothor.methodatlas.command.PluginLoader: Verifies that every TestDiscovery provider in the list has a unique TestDiscovery.pluginId().
requireUniquePatcherIds(List) - Static method in class org.egothor.methodatlas.command.PluginLoader: Verifies that every SourcePatcher in the list has a unique SourcePatcher.pluginId().
requireUniqueRedactorIds(List) - Static method in class org.egothor.methodatlas.command.PluginLoader: Verifies that every CommentRedactor in the list has a unique CommentRedactor.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.
resolveTaxonomyVersion(AiOptions, boolean) - Method in class org.egothor.methodatlas.command.AiRuntimeBuilder: Resolves the taxonomy version identifier stamped into each AI-classified record (ai_taxonomy_version).
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.
Result(AccuracyMetrics.Counts, List, AccuracyMetrics.Counts, OptionalDouble, int, int) - Constructor for record class org.egothor.methodatlas.eval.AccuracyMetrics.Result: Creates an instance of a Result record class.
run(String[], PrintWriter) - Static method in class org.egothor.methodatlas.evidence.ExportKeyringSecretCommand: Parses -export-keyring-secret arguments and prints the bundle.
run(String[], PrintWriter) - Static method in class org.egothor.methodatlas.evidence.GenSigningKeyCommand: Parses -gen-signing-key arguments and runs the command.
run(List) - Method in class org.egothor.methodatlas.command.DetectCredentialsStage: Detects and builds findings for the supplied units, in unit-then-source order.
runDiscovery(Path, List, AiOptions, AiSuggestionEngine, TestMethodSink, boolean, ClassificationOverride, AiResultCache, CredentialTriageContext) - 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

Sample(String, boolean, Boolean, Collection, Collection) - Constructor for record class org.egothor.methodatlas.eval.AccuracyMetrics.Sample: Creates an instance of a Sample record class.
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, CliConfig, TestDiscoveryConfig, AiSuggestionEngine, TestMethodSink, ClassificationOverride, AiResultCache, CredentialTriageContext) - 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 with no extra sink and parallel AI disabled.
ScanOrchestrator(PluginLoader, Optional) - Constructor for class org.egothor.methodatlas.command.ScanOrchestrator: Creates a new orchestrator that fans out every record to extraSink in addition to the command's primary sink.
ScanOrchestrator(PluginLoader, Optional, boolean) - Constructor for class org.egothor.methodatlas.command.ScanOrchestrator: Creates a new orchestrator with full configuration.
ScanOrchestrator(PluginLoader, Optional, boolean, CommentRedaction) - Constructor for class org.egothor.methodatlas.command.ScanOrchestrator: Creates a new orchestrator with full configuration and a comment-redaction service.
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.
secretsErrorThreshold() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the secretsErrorThreshold record component.
secretsInclude() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the secretsInclude record component.
secretsMinScore() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the secretsMinScore record component.
secretsOut() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the secretsOut record component.
secretsRules() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the secretsRules record component.
secretsSeparateLlm() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the secretsSeparateLlm record component.
secretsShowValues() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the secretsShowValues record component.
secretsWarningThreshold() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the secretsWarningThreshold record component.
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 - Section in package org.egothor.methodatlas.command
signatureAlgorithm() - Method in class org.egothor.methodatlas.evidence.EvidencePackCommand: Returns the algorithm the manifest was signed with, for the caller's success message.
signatureAlgorithm() - Method in record class org.egothor.methodatlas.evidence.EvidencePackOptions: Returns the value of the signatureAlgorithm record component.
Source-Derived Metadata - Section in class org.egothor.methodatlas.MethodAtlasApp
staleLabelEntries() - Method in record class org.egothor.methodatlas.eval.AccuracyEvaluator.Evaluation: Returns the value of the staleLabelEntries record component.
startedAt() - Method in record class org.egothor.methodatlas.ScanRun: Returns the value of the startedAt record component.
Sub-packages - Section in package org.egothor.methodatlas
suggestion() - Method in record class org.egothor.methodatlas.AiCacheEntry: Returns the value of the suggestion record component.
support() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Counts: Returns the number of truly positive samples.
Supported Command-Line Options - Section in class org.egothor.methodatlas.MethodAtlasApp

T

tag() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.TagResult: Returns the value of the tag record component.
Tag normalisation - Section in class org.egothor.methodatlas.eval.AccuracyMetrics
TagResult(String, AccuracyMetrics.Counts) - Constructor for record class org.egothor.methodatlas.eval.AccuracyMetrics.TagResult: Creates an instance of a TagResult record class.
tags() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Result: Returns the value of the tags record component.
tagSamples() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Result: Returns the value of the tagSamples record component.
tagsMacroF1() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Result: Returns the value of the tagsMacroF1 record component.
tagsMicro() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Result: Returns the value of the tagsMicro record component.
testMarkers() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the testMarkers record component.
Thread safety - Section in class org.egothor.methodatlas.JsonLineFormatter
Thread safety - Section in class org.egothor.methodatlas.ScanRunContext
Thread safety - Section in class org.egothor.methodatlas.command.OverrideLoader
Thread safety - Section in class org.egothor.methodatlas.command.PluginLoader
Thread safety - Section in class org.egothor.methodatlas.command.ScanOrchestrator
tn() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Counts: Returns the value of the tn record component.
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.AiCacheEntry: Returns a string representation of this record class.
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.command.DetectCredentialsStage.MethodRange: Returns a string representation of this record class.
toString() - Method in record class org.egothor.methodatlas.eval.AccuracyEvaluator.Evaluation: Returns a string representation of this record class.
toString() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Counts: Returns a string representation of this record class.
toString() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Result: Returns a string representation of this record class.
toString() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Sample: Returns a string representation of this record class.
toString() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.TagResult: Returns a string representation of this record class.
toString() - Method in record class org.egothor.methodatlas.evidence.EvidencePackOptions: 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.
total() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Counts: Returns the total number of samples counted.
toTargetMethod(DiscoveredMethod) - Static method in class org.egothor.methodatlas.command.ScanOrchestrator: Converts a single discovered test method into a prompt target descriptor.
tp() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Counts: Returns the value of the tp record component.
truthRelevant() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Sample: Returns the value of the truthRelevant record component.
truthTags() - Method in record class org.egothor.methodatlas.eval.AccuracyMetrics.Sample: Returns the value of the truthTags record component.
Two evaluated dimensions - Section in class org.egothor.methodatlas.eval.AccuracyMetrics
Typical Usage - Section in package org.egothor.methodatlas

U

Undefined values - Section in class org.egothor.methodatlas.eval.AccuracyMetrics
unlabelledPredictions() - Method in record class org.egothor.methodatlas.eval.AccuracyEvaluator.Evaluation: Returns the value of the unlabelledPredictions record component.
unpredictedLabels() - Method in record class org.egothor.methodatlas.eval.AccuracyEvaluator.Evaluation: Returns the value of the unpredictedLabels record component.
Usage - Section in class org.egothor.methodatlas.evidence.ExportKeyringSecretCommand
Usage - Section in class org.egothor.methodatlas.evidence.GenSigningKeyCommand

V

valueOf(String) - Static method in enum class org.egothor.methodatlas.evidence.EvidenceFramework: Returns the enum constant of this class with the specified name.
values() - Static method in enum class org.egothor.methodatlas.evidence.EvidenceFramework: Returns an array containing the constants of this enum class, in the order they are declared.
verbose() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the verbose record component.
verdicts(String, String) - Method in class org.egothor.methodatlas.AiResultCache: Returns cached credential-triage verdicts for a class when the content hash and the prompt signature both match and verdicts were actually recorded.

W

What is applied - Section in class org.egothor.methodatlas.ApplyTagsFromCsvEngine
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.
write(String, Path) - Method in class org.egothor.methodatlas.attest.AttestFacade.Handle: Builds the attestation manifest and writes it to outputFile.
write(String, Path) - Method in class org.egothor.methodatlas.coverage.CoverageFacade.Handle: Builds the report and writes it to outputFile.
write(String, Path) - Method in class org.egothor.methodatlas.evidencereport.EvidenceReportFacade.Handle: Builds the evidence report and writes it to outputFile as Markdown.
write(String, Path) - Method in class org.egothor.methodatlas.gap.GapFacade.Handle: Builds the report and writes it to outputFile.
write(Path, Collection) - Static method in class org.egothor.methodatlas.AiCacheStore: Writes cache entries to a JSON-Lines file, one entry per line, overwriting any existing file.

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