├── .gitignore ├── .mvn └── wrapper │ └── maven-wrapper.properties ├── CHANGELOG.md ├── LICENSE ├── README.md ├── docs ├── Makefile ├── command.rst ├── conf.py ├── excel.rst ├── img │ ├── GitHubNewAnnotation.png │ ├── GitHubNewIssue.png │ ├── HPOworkbench.png │ ├── HPOworkbenchDiseaseView.png │ ├── excel1.png │ ├── excel2.png │ ├── excel3.png │ └── importLocalHpObo.png ├── index.rst ├── installation.rst ├── latest.rst └── release.rst ├── hpoworkbench-cli ├── pom.xml └── src │ ├── assembly │ └── dep.xml │ └── main │ ├── java │ └── org │ │ └── monarchinitiative │ │ └── hpoworkbench │ │ ├── HpoWorkbench.java │ │ ├── analysis │ │ ├── HpoStats.java │ │ └── SmallFileQc.java │ │ └── cmd │ │ ├── BatchGitPostCommand.java │ │ ├── CommandLineParsingException.java │ │ ├── CountFrequencyCommand.java │ │ ├── CountGenes.java │ │ ├── CountHpoIdRanges.java │ │ ├── DownloadCommand.java │ │ ├── EncodingCheckCommand.java │ │ ├── GitCommand.java │ │ ├── HPO2CSVCommand.java │ │ ├── HPOCommand.java │ │ ├── Hpo2HpoCommand.java │ │ ├── HpoBestMatchCommand.java │ │ ├── HpoListDescendentsCommand.java │ │ ├── HpoStatsCommand.java │ │ ├── MapToPtools.java │ │ ├── MatchTermsCommand.java │ │ ├── OnsetCommand.java │ │ ├── PhenopacketCompareCommand.java │ │ ├── PhenopacketConvertCommand.java │ │ └── WordCommand.java │ └── resources │ ├── default_sources.ini │ ├── log4j2.xml │ └── term2onset.txt ├── hpoworkbench-core ├── pom.xml └── src │ └── main │ └── java │ └── org │ └── monarchinitiative │ └── hpoworkbench │ ├── analysis │ ├── AnnotationTlc.java │ ├── HpoStats.java │ └── MondoStats.java │ ├── annotation │ └── SubClassTermPair.java │ ├── excel │ ├── HierarchicalExcelExporter.java │ ├── Hpo2ExcelExporter.java │ └── TermRow.java │ ├── exception │ ├── HPOException.java │ └── UncheckedException.java │ ├── github │ ├── GitHubIssue.java │ ├── GitHubIssueRetriever.java │ ├── GitHubLabelRetriever.java │ └── GitHubPoster.java │ ├── io │ └── HPOParser.java │ └── word │ ├── GitIssue2Doc4J.java │ ├── Hpo2Word.java │ ├── HpoRtfTableRow.java │ ├── Pair.java │ └── RtfTable.java ├── hpoworkbench-gui ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── monarchinitiative │ │ │ └── hpoworkbench │ │ │ ├── HpoWorkbenchApplication.java │ │ │ ├── StageInitializer.java │ │ │ ├── StartupTask.java │ │ │ ├── StockUiApplication.java │ │ │ ├── config │ │ │ ├── ApplicationProperties.java │ │ │ └── HpoWorkbenchConfig.java │ │ │ ├── controller │ │ │ ├── GenericTermWrapper.java │ │ │ ├── HpoHtmlPageGenerator.java │ │ │ ├── MainController.java │ │ │ ├── MessageType.java │ │ │ └── OntologyTermWrapper.java │ │ │ ├── exception │ │ │ ├── BadResponseException.java │ │ │ ├── HPOWorkbenchException.java │ │ │ └── HpoWorkbenchRuntimeException.java │ │ │ ├── gui │ │ │ ├── GitHubPopup.java │ │ │ ├── HelpViewFactory.java │ │ │ ├── PasswordPopup.java │ │ │ ├── Platform.java │ │ │ ├── PlatformUtil.java │ │ │ ├── PopUps.java │ │ │ ├── WidthAwareTextFields.java │ │ │ ├── webpopup │ │ │ │ ├── SettingsPopup.java │ │ │ │ └── WebViewerPopup.java │ │ │ └── webviewerutil │ │ │ │ ├── HelpViewFactory.java │ │ │ │ ├── InfoViewerFactory.java │ │ │ │ ├── SimpleWebViewerPopup.java │ │ │ │ ├── WebViewerFactory.java │ │ │ │ └── WebViewerPopup.java │ │ │ ├── html │ │ │ ├── AnnotationTlcHtmlGenerator.java │ │ │ ├── Css.java │ │ │ ├── HpoStatsHtmlGenerator.java │ │ │ ├── MondoStatsHtmlGenerator.java │ │ │ ├── MondoTermHtmlGenerator.java │ │ │ ├── SingleDiseaseHTMLGenerator.java │ │ │ └── package-info.java │ │ │ ├── io │ │ │ ├── DirectIndirectHpoAnnotationParser.java │ │ │ ├── Downloader.java │ │ │ ├── DownloaderFactory.java │ │ │ └── FileDownloader.java │ │ │ └── resources │ │ │ ├── HostServicesWrapper.java │ │ │ ├── OptionalHpoResource.java │ │ │ ├── OptionalHpoaResource.java │ │ │ ├── OptionalOntologyResource.java │ │ │ ├── ResourceValidator.java │ │ │ ├── ResourceValidators.java │ │ │ └── package-info.java │ └── resources │ │ ├── application.properties │ │ ├── banner.txt │ │ ├── css │ │ 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