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Project: chipster (GitHub Link)
  • chipster-master
    • .github
      • workflows
        • ant.yml
    • src
      • main
        • resources
          • forward.gif
          • circle.gif
          • version.number
          • chipster-config-specification.xml
          • help
            • microarray-manual
              • info.txt
          • image.gif
          • gbrowserLegend
          • double_forward.gif
          • build.number
          • types
            • folder.gif
          • fonts
          • gc.gif
          • running.gif
          • square.gif
          • listicons
            • crystal
            • pca.xcf
            • crystal-LGPL
              • modified
                • profile.xcf
                • scatterplot.xcf
                • volcano.xcf
                • axes.xcf
            • scatter3d_2.xcf
        • web
          • tool-editor
            • src
              • fi
                • csc
                  • chipster
                    • web
                      • tooledit
                        • TextEditor.java
                        • ConfirmClearAll.java
                        • Icon.java
                        • TreeToolEditor.java
                        • ToolEditor.java
                        • ToolEditorUI.java
                      • model
                        • BasicModel.java
                        • Input.java
                        • Parameter.java
                        • Tool.java
                        • InputOutputUI.java
                        • Output.java
                      • listener
                        • CSCToolToTextClickListener.java
                        • CSCTextToToolClickListener.java
                        • CSCTextChangeListener.java
                        • CSCTypeValueChangeListener.java
            • examples
              • simple-list.txt
              • newDesignQuestions.PNG
              • tool-editor-table.xlsx
            • download-libs.xml
            • .settings
              • org.apache.ivyde.eclipse.prefs
              • org.eclipse.wst.jsdt.ui.superType.container
              • org.eclipse.wst.jsdt.ui.superType.name
              • org.eclipse.wst.common.project.facet.core.xml
              • com.vaadin.integration.eclipse.prefs
              • org.eclipse.wst.common.component
              • .jsdtscope
              • org.eclipse.jdt.core.prefs
            • WebContent
              • VAADIN
                • themes
                  • tool_editor
                    • styles.scss
                    • tool_editor.scss
                    • images
                    • styles.css
              • META-INF
                • MANIFEST.MF
              • WEB-INF
                • lib-ivy
                  • commons-cli-jar-1.2.jar
                  • commons-logging-jar-1.1.1.jar
                  • sac-jar-1.3.jar
                  • validation-api-jar-1.0.0.GA.jar
                • lib-ext
                • web.xml
            • ivy.xml
            • ivysettings.xml
            • .gitignore
            • .project
            • .classpath
          • admin-web
            • src
              • fi
                • csc
                  • chipster
                    • web
                      • adminweb
                        • ui
                          • StorageAggregateTable.java
                          • StatView.java
                          • JobsTable.java
                          • JobLogTable.java
                          • JobLogFilter.java
                          • AfterUpdateCallBack.java
                          • StorageView.java
                          • ServicesView.java
                          • StorageEntryTable.java
                          • JobsView.java
                          • DateColumnGenerator.java
                          • AsynchronousView.java
                          • ReportView.java
                          • ServicesTable.java
                          • JobLogView.java
                          • HumanReadableLongColumnGenerator.java
                        • NavigationMenu.java
                        • util
                          • Notificationutil.java
                          • RandomUtil.java
                          • StringUtils.java
                        • data
                          • JobsContainer.java
                          • ServiceContainer.java
                          • StorageAggregateContainer.java
                          • JobLogContainer.java
                          • DateContainerFilter.java
                          • ServiceEntry.java
                          • StatDataSource.java
                          • ReportDataSource.java
                          • JobLogEntry.java
                          • StorageEntryContainer.java
                          • AccountEntry.java
                          • TestAccountFilter.java
                        • ChipsterAdminUI.java
                        • hbncontainer
                          • HibernateUtil.java
                          • HibernateServletFilter.java
            • download-libs.xml
            • .settings
              • org.eclipse.wst.jsdt.ui.superType.container
              • org.eclipse.wst.jsdt.ui.superType.name
              • org.eclipse.wst.common.project.facet.core.xml
              • com.vaadin.integration.eclipse.prefs
              • org.eclipse.wst.common.component
              • .jsdtscope
              • org.eclipse.jdt.core.prefs
            • WebContent
              • VAADIN
                • themes
                  • admin
                    • crystal
                    • images
                    • styles.css
              • META-INF
                • MANIFEST.MF
              • WEB-INF
                • lib-ivy
                  • log4j-api-jar-2.2.jar
                  • hibernate-commons-annotations-jar-4.0.5.Final.jar
                  • vaadin-slf4j-jdk14-jar-1.6.1.jar
                  • jandex-jar-1.1.0.Final.jar
                  • jboss-logging-jar-3.1.3.GA.jar
                  • streamhtmlparser-jsilver-jar-0.0.10.vaadin1.jar
                  • jboss-transaction-api_1.2_spec-jar-1.0.0.Final.jar
                  • sac-jar-1.3.jar
                  • jboss-logging-annotations-jar-1.2.0.Beta1.jar
                  • xml-apis-jar-1.0.b2.jar
                  • hibernate-jpa-2.1-api-jar-1.0.0.Final.jar
                  • flute-jar-1.3.0.gg2.jar
                  • hibernate-c3p0-jar-4.3.8.Final.jar
                • lib
                  • hbncontainer-2.0.1-pull-request.jar
                • ngs-module-copy.xml
                • lib-ext
                • microarray-module-copy.xml
                • misc-module-copy.xml
                • web.xml
            • ivy.xml
            • ivysettings.xml
            • .gitignore
            • .project
            • .classpath
        • admin
          • admin-web
            • .gitignore
          • vm
            • install-chipster-before-3.0.sh
            • update-exec-3.6.2.sh
            • update.sh
            • install-chipster.sh
            • list.sh
            • update-exec3.sh
            • module-list.bash
            • install-module.sh
            • update-exec.sh
            • update-exec-3.11.0.sh
            • docs
              • VirusDetect-compile.bash
            • config.bash
            • installation_files
              • generate_installation_file.bash
              • functions.bash
            • modules
              • start
                • create_dirs.bash
              • external_tools
                • conda.bash
                • bcftools.bash
                • Weeder.bash
                • QDNAseq.bash
                • sym_link_to_admin_scripts.bash
                • phylipnew.bash
                • zifa.bash
                • Express.bash
                • vienna.bash
                • Cufflinks_2.bash
                • Picard_tools.bash
                • vcftools.bash
                • SAM_tools1.bash
                • Trimmomatic.bash
                • Tophat.bash
                • edirect.bash
                • tools-bin_python.bash
                • seqtk.bash
                • Tophat_2.bash
                • BEDTools.bash
                • tagcleaner.bash
                • GATK.bash
                • BaseSpace.bash
                • fseq.bash
                • gtf2bed.bash
                • Fastx_links.bash
                • HISAT2.bash
                • drop-seq_tools.bash
                • BLAST.bash
                • enaBrowserTools.bash
                • STAR.bash
                • VirusDetect.bash
                • A5.bash
                • dimont.bash
                • cd-hit.bash
                • mothur.bash
                • Bowtie_2.bash
                • BWA.bash
                • mview.bash
                • EMBOSS.bash
                • stringtie.bash
                • primer3.bash
                • fseq_bff.bash
                • DEXSeq.bash
                • sratoolkit.bash
                • rtg-tools.bash
                • SAM_tools.bash
                • tabix.bash
                • FastQC.bash
                • miRNA_mapping_data.bash
                • prinseq.bash
                • seurat.bash
                • Bowtie.bash
                • Mafft.bash
                • data_for_tools.bash
              • finish
                • fix_rights.bash
                • cleaner.bash
              • R
                • R-3.2.3.bash
                • R-3.3.2.bash
                • R-3.4.3.bash
                • R-3.6.1.bash
                • R-3.6.1-plain.bash
          • bundle
            • gbrowser-annotation-conversion.sh
            • setup-genome-browser-sheep.sh
            • bundles.yaml
            • to_bundle.py
            • create-bundle.sh
            • contentsToYaml.sh
            • bundle.py
            • installed.yaml
            • create-bundles.sh
            • setup-genome-browser-chicken.sh
            • gbrowser-annotation-package.sh
            • gbrowser-annotation-check.sh
            • bundles-template.yaml
            • edit_bundle.py
          • fedcloud
            • add_tools_to _path.sh
            • FedCloud_chipster_manager
        • applications
          • wrapper
            • comp
              • security
                • dir_not_empty.txt
              • chipster-comp-generic
              • chipster-comp
              • logs
                • dir_not_empty.txt
              • conf
                • runtimes.xml
                • chipster-config.xml
                • wrapper.conf
            • comp-admin.sh
            • jobmanager
              • security
                • dir_not_empty.txt
              • chipster-jobmanager-generic
              • chipster-jobmanager
              • logs
                • dir_not_empty.txt
              • conf
                • chipster-config.xml
                • wrapper.conf
            • configure.sh
            • download-tools.sh
            • chipster-client-config.xml
            • readme.txt
            • toolbox
              • security
                • dir_not_empty.txt
              • chipster-toolbox-generic
              • reload-tools.sh
              • logs
                • dir_not_empty.txt
              • chipster-toolbox
              • conf
                • chipster-config.xml
                • wrapper.conf
            • webstart
              • security
                • dir_not_empty.txt
              • web-root
                • images
                • styles.css
                • chipster.jnlp
                • index.html
                • chipster-cli.bash
              • chipster-webstart
              • chipster-webstart-generic
              • logs
                • dir_not_empty.txt
              • conf
                • chipster-config.xml
                • wrapper.conf
            • fileserver
              • security
                • dir_not_empty.txt
              • chipster-fileserver-generic
              • chipster-fileserver
              • logs
                • dir_not_empty.txt
              • conf
                • chipster-config.xml
                • wrapper.conf
                • shared-directory-mappings.xml
            • genpasswd.sh
            • auth
              • security
                • dir_not_empty.txt
                • users
              • chipster-auth-generic
              • chipster-auth
              • chipster-auth.sh
              • logs
                • dir_not_empty.txt
              • conf
                • chipster-config.xml
                • jaas.config
                • wrapper.conf
            • manager
              • security
                • dir_not_empty.txt
              • testrunner
                • sessions
                • tool-tests.sh
              • chipster-manager
              • logs
                • dir_not_empty.txt
              • conf
                • chipster-config.xml
                • wrapper.conf
              • chipster-manager-generic
            • chipster
            • shared
              • bin
                • chipster-generic.sh
          • activemq
            • wrapper
              • linux-x86-64
                • wrapper.conf
              • linux-x86-32
                • wrapper.conf
            • activemq
            • activemq.xml
        • java
          • log4j.properties
          • htsjdk
            • samtools
              • reference
                • PicardIndexedFastaSequenceFile.java
                • ChipsterIndexedFastaSequenceFile.java
                • ChipsterFastaSequenceIndex.java
          • fi
            • csc
              • microarray
                • security
                  • CryptoKey.java
                  • SecureSessionPool.java
                • description
                  • SADLParser.java
                  • SADLTokeniser.java
                  • SADLSyntax.java
                  • SADLGenerator.java
                  • SADLDescription.java
                  • package.html
                  • GenericInputTypes.java
                • comp
                  • OnDiskCompJobBase.java
                  • InterpreterJobFactory.java
                  • ResourceMonitor.java
                  • ProcessPool.java
                  • JobCancelledException.java
                  • JobFactory.java
                  • CompJob.java
                  • ResultCallback.java
                  • RuntimeRepository.java
                  • ProcessUtils.java
                  • CompServer.java
                  • RetryException.java
                  • python
                    • PythonCompJob.java
                    • PythonJobFactory.java
                    • package.html
                  • ToolDescriptionGenerator.java
                  • java
                    • FailingCompJob.java
                    • JavaJobFactory.java
                    • JavaCompJobBase.java
                    • package.html
                  • r
                    • RJobFactory.java
                    • RCompJob.java
                    • package.html
                  • ToolDescription.java
                  • ProcessMonitor.java
                  • CompException.java
                  • package.html
                  • ToolRuntime.java
                • jobmanager
                  • HibernateUtil.java
                  • JobManager.java
                  • model
                    • JobManagerDB.java
                    • Job.java
                • client
                  • dialog
                    • FeedbackDialog.java
                    • URLImportDialog.java
                    • ErrorDialogUtils.java
                    • CreateFromTextDialog.java
                    • ClipboardImportDialog.java
                    • SessionRestoreDialog.java
                    • DialogInfo.java
                    • TaskImportDialog.java
                    • LoginDialog.java
                    • ImportSettingsAccessory.java
                    • ChipsterDialog.java
                    • package.html
                    • SequenceImportDialog.java
                  • ClientConstants.java
                  • dataimport
                    • Delimiter.java
                    • ActionChooserScreen.java
                    • ConversionModel.java
                    • ColumnType.java
                    • ImportItem.java
                    • trimmer
                      • DataTrimmer.java
                      • NormalStringReplace.java
                      • DataTrimmingOperation.java
                      • ReqularExpressionStringReplace.java
                      • package.html
                    • ImportSession.java
                    • ImportScreen.java
                    • table
                      • ImportPreviewTable.java
                      • EditableHeaderTableColumn.java
                      • TableInternalFrame.java
                      • PanelTableHeaderEditor.java
                      • EditableHeaderUI.java
                      • package.html
                      • PanelTableHeaderRenderer.java
                      • EditableHeader.java
                      • InformationDialog.java
                    • FileAnalyser.java
                    • RunnableImportProcess.java
                    • ImportUtils.java
                    • ImportScreenModel.java
                    • tools
                      • ToolsInternalFrame.java
                      • ChipCountPanel.java
                      • package.html
                      • DataTrimmingPanel.java
                    • ProgressInformator.java
                    • DataColumn.java
                    • package.html
                    • ColumnTypeManager.java
                    • ColumnTypePattern.java
                    • events
                      • ColumnTypeChangedEvent.java
                      • DecimalSeparatorChangedEvent.java
                      • DelimiterChangedEvent.java
                      • ColumnTypeChangeSupport.java
                      • ConversionModelChangeListener.java
                      • TableRowChangeEvent.java
                      • ColumnTitlesChangedEvent.java
                      • ConversionModelChangeSupport.java
                      • ImportChangeEvent.java
                      • ChipNumberChangedEvent.java
                      • ColumnTypeChangeListener.java
                      • HeaderChangedEvent.java
                      • ChipCountChangeEvent.java
                      • FooterChangedEvent.java
                      • package.html
                      • InputFileChangedEvent.java
                      • TitleRowChangedEvent.java
                  • Authenticator.java
                  • dataview
                    • GraphPanel.java
                    • PositionChangeAnimator.java
                    • ScrollAnimator.java
                    • TreePanel.java
                    • package.html
                    • MicroarrayGraph.java
                    • AnimatorScrollable.java
                    • LayoutManager.java
                  • waiting
                    • WaitGlassPane.java
                  • HelpMapping.java
                  • screen
                    • ShowSourceScreen.java
                    • Screen.java
                    • ChildScreenPool.java
                    • ScreenBase.java
                    • TaskManagerScreen.java
                    • HistoryScreen.java
                    • package.html
                  • StatusBar.java
                  • cli
                    • CliClient.java
                    • UserErrorException.java
                    • CliClientApplication.java
                  • ToolBarComponentFactory.java
                  • workflow
                    • api
                      • WfDataBean.java
                      • WfSelectionManager.java
                      • WfOperation.java
                      • WfOperationDefinition.java
                      • WfResultBlocker.java
                      • package.html
                      • WfApplication.java
                    • WorkflowManager.java
                    • WorkflowWriter.java
                    • package.html
                  • ClientListener.java
                  • visualisation
                    • VisualisationMethodRepository.java
                    • VisualisationFrameManager.java
                    • TableAnnotationProvider.java
                    • VisualisationToolBar.java
                    • Visualisation.java
                    • ExternalVisualisationFrame.java
                    • VisualisationMethodChangedEvent.java
                    • VisualisationMethod.java
                    • ComboBoxItemRenderer.java
                    • NonScalableChartPanel.java
                    • VisualisationFrame.java
                    • VisualisationTaskManager.java
                    • SelectionList.java
                    • methods
                      • SelectableChartPanel.java
                      • EmptyVisualisation.java
                      • RowSelection.java
                      • ChipVisualisation.java
                      • SessionDetails.java
                      • Empty.java
                      • SOM.java
                      • HtmlViewer.java
                      • Scatterplot.java
                      • ArrayLayout.java
                      • VennDiagram.java
                      • threed
                        • RoundGradientContext.java
                        • Line.java
                        • Scatterplot3D.java
                        • CoordinateArea.java
                        • DataPoint.java
                        • DataModel.java
                        • Matrix.java
                        • ColorScalePanel.java
                        • Projection.java
                        • Text.java
                        • RoundGradientPaint.java
                        • Drawable.java
                        • package.html
                        • AutomatedMovement.java
                      • ImageViewer.java
                      • TextViewer.java
                      • Volcanoplot.java
                      • Scatterplot3DPCA.java
                      • Heatmap.java
                      • Histogram.java
                      • DataRowSelection.java
                      • ModifiedPlot.java
                      • hc
                        • OrderSuperviser.java
                      • ExternalBrowserViewer.java
                      • HierarchicalClustering.java
                      • PDFViewer.java
                      • DataDetails.java
                      • PhenodataEditor.java
                      • ClusteredProfiles.java
                      • Spreadsheet.java
                      • SamBamViewer.java
                      • ExpressionProfile.java
                      • package.html
                      • ChipsterGBrowserVisualisation.java
                      • VenndiPlot.java
                      • gbrowser
                        • GBrowserStarter.java
                        • fileIndex
                          • IndexedFastaConversion.java
                          • IndexedFastaDataSource.java
                          • BamDataSource.java
                          • ConcisedValueCache.java
                          • BamToCoverageEstimateConversion.java
                          • GtfToFeatureConversion.java
                          • BamToDetailsConversion.java
                          • TabixDataSource.java
                          • package.html
                          • CoverageTool.java
                          • BamToCoverageConversion.java
                        • track
                          • PassiveItem.java
                          • BedTrackGroup.java
                          • CoverageAverageTrack.java
                          • GeneTrack.java
                          • TrackGroup.java
                          • QualityCoverageTrack.java
                          • ScatterplotTrack.java
                          • ReadPileTrack.java
                          • LayoutParent.java
                          • CoverageTrack.java
                          • AnnotationTrackGroup.java
                          • CnaFrequenciesTrackGroup.java
                          • LayoutChild.java
                          • CnaCallsTrackGroup.java
                          • StatusAnimation.java
                          • SeparatorTrack3D.java
                          • RepeatMaskerTrack.java
                          • CnaTrackGroup.java
                          • RulerTrack.java
                          • CoverageEstimateTrack.java
                          • TitleTrack.java
                          • TrackFactory.java
                          • ScaleTrack.java
                          • SampleTrackGroup.java
                          • Track.java
                          • CnaLogRatiosTrackGroup.java
                          • RegionTrackGroup.java
                          • CnaFlagTrack.java
                          • PeakSelectable.java
                          • ReferenceSequenceTrack.java
                          • EmptyTrack.java
                          • DensityGraphTrack.java
                          • SeparatorTrack.java
                          • Selectable.java
                          • package.html
                          • LayoutUpdater.java
                          • CytobandTrack.java
                          • ScatterplotPoint.java
                          • RegionTrack.java
                          • TranscriptTrack.java
                        • util
                          • ChromosomeNormaliser.java
                          • NcbiGff3ToGtf.java
                          • ChromosomeNameUnnormaliser.java
                          • ArtemisGffToGtf.java
                          • GtfUtil.java
                          • GenbankToGtf.java
                          • TsvSorter.java
                          • SamBamUtils.java
                          • GBrowserException.java
                          • RegionOperations.java
                          • UnsortedDataException.java
                          • GtfSort.java
                          • package.html
                          • CoverageStorage.java
                          • BaseStorage.java
                        • gui
                          • Interpretation.java
                          • AnnotationManager.java
                          • HorizontalView.java
                          • BrowserSelectionListener.java
                          • GBrowserConstants.java
                          • RectDrawable.java
                          • GBrowserLegend.java
                          • GBrowserView.java
                          • SelectionManager.java
                          • DataUrl.java
                          • QueueManager.java
                          • OverviewHorizontalView.java
                          • TextDrawable.java
                          • ScrollGroup.java
                          • SelectionPanel.java
                          • LineDrawable.java
                          • ViewLimiter.java
                          • GBrowserSettings.java
                          • GenomeInfo.java
                          • GBrowserPlot.java
                          • GeneIndexActions.java
                          • Drawable.java
                          • package.html
                          • LayoutTool.java
                          • RegionListener.java
                        • runtimeIndex
                          • LineParser.java
                          • TsvLineParser.java
                          • GtfLineParser.java
                          • CnaLineParser.java
                          • VcfLine.java
                          • LineDataSource.java
                          • SearchIndexConversion.java
                          • Index.java
                          • VcfLineParser.java
                          • BedLine.java
                          • FileLine.java
                          • AbstractTsvLineParser.java
                          • CnaConversion.java
                          • RandomAccessLineReader.java
                          • CytobandLineParser.java
                          • ScatterplotFileLineConversion.java
                          • FileLineConversion.java
                          • BinarySearchIndex.java
                          • RandomAccessLineDataSource.java
                          • BedTabixToRegionConversion.java
                          • InMemoryIndex.java
                          • ByteDataSource.java
                          • TsvLine.java
                          • CytobandConversion.java
                          • DataThread.java
                          • DataSource.java
                          • SelectionText.java
                          • ChromosomeBinarySearch.java
                          • ScatterplotValue.java
                          • BedLineParser.java
                          • package.html
                        • message
                          • Sequence.java
                          • ConfigurableRegionRequest.java
                          • DataType.java
                          • ReadPart.java
                          • DataResultListener.java
                          • PositionAndStringKey.java
                          • Strand.java
                          • DataRequest.java
                          • RegionDouble.java
                          • Region.java
                          • SearchRequest.java
                          • IndexKey.java
                          • CigarItem.java
                          • Cytoband.java
                          • SynonymReplace.java
                          • Cigar.java
                          • GeneResult.java
                          • Chromosome.java
                          • BpCoordDouble.java
                          • DataResult.java
                          • BpCoord.java
                          • DataStatus.java
                          • GeneSet.java
                          • Transcript.java
                          • CnaRow.java
                          • Feature.java
                          • Exon.java
                          • Gene.java
                          • package.html
                        • ChipsterAnnotationsScreen.java
                        • GBrowser.java
                        • package.html
                    • InternalVisualisationFrame.java
                    • VisualisationUtilities.java
                    • package.html
                    • ExtendedJXTable.java
                  • SwingClientApplication.java
                  • selection
                    • PointSelectionEvent.java
                    • IntegratedEntity.java
                    • DataSelectionManager.java
                    • DatasetChoiceEvent.java
                    • IntegratedSelectionManager.java
                    • SelectionEvent.java
                    • package.html
                  • serverfiles
                    • ServerFile.java
                    • ServerFileSystemView.java
                    • ServerFileUtils.java
                  • Session.java
                  • Frames.java
                  • ClientContextMenu.java
                  • QuickLinkPanel.java
                  • ServiceAccessor.java
                  • tasks
                    • ResultBlocker.java
                    • Task.java
                    • TaskException.java
                    • TaskEventListener.java
                    • package.html
                    • TaskExecutor.java
                    • LocalTaskExecutor.java
                  • operation
                    • OperationDefinition.java
                    • ToolModule.java
                    • Operation.java
                    • parameter
                      • DecimalParameter.java
                      • SteppedComboBox.java
                      • ToolParameterPanel.java
                      • PercentageParameter.java
                      • EnumParameter.java
                      • DecimalInputComponent.java
                      • SingleSelectionInputComponent.java
                      • Parameter.java
                      • IntegerInputComponent.java
                      • MultipleSelectionInputComponent.java
                      • DataSelectionParameter.java
                      • MetaColnameParameter.java
                      • ColnameParameter.java
                      • ParameterInputComponent.java
                      • StringInputComponent.java
                      • InputParameters.java
                      • ImportParameterPanel.java
                      • StringParameter.java
                      • IntegerParameter.java
                      • ParameterPanel.java
                      • InputSelectParameter.java
                      • package.html
                      • PercentageInputComponent.java
                      • InputFileComponent.java
                    • OperationRecord.java
                    • ToolCategory.java
                    • ToolPanel.java
                    • ExecutionItem.java
                    • ColoredCircleIcon.java
                    • ToolSelectorPanel.java
                    • ToolFilterPanel.java
                    • package.html
                  • RemoteServiceAccessor.java
                  • LocalServiceAccessor.java
                  • ClientApplication.java
                  • AtEndListener.java
                  • dataviews
                    • vertexes
                      • GraphVertex.java
                      • PhenodataVertex.java
                      • AbstractGraphVertex.java
                      • GraphRenderer.java
                      • GroupVertex.java
                  • MicroarrayMenuBar.java
                  • package.html
                  • ClientFocusTraversalPolicy.java
                  • session
                    • RemoteSessionAccessory.java
                    • session.xsd
                    • SessionManager.java
                    • UserSession.java
                    • RemoteSessionChooserFactory.java
                    • NonStoppingValidationEventHandler.java
                    • SessionLoader.java
                    • session2.xsd
                    • SessionLoaderImpl2.java
                    • SessionLoaderImpl1.java
                    • schema2
                      • SessionType.java
                      • DataType.java
                      • ObjectFactory.java
                      • InputType.java
                      • NameType.java
                      • OperationType.java
                      • LinkType.java
                      • LocationType.java
                      • FolderType.java
                      • ParameterType.java
                    • schema
                      • SessionType.java
                      • DataType.java
                      • ObjectFactory.java
                      • InputType.java
                      • NameType.java
                      • OperationType.java
                      • LinkType.java
                      • FolderType.java
                      • ParameterType.java
                    • SessionSaver.java
                  • NameID.java
                • databeans
                  • DataChangeListener.java
                  • HistoryText.java
                  • LinkUtils.java
                  • LinksChangedEvent.java
                  • DataChangeEvent.java
                  • DataItem.java
                  • ContentType.java
                  • DataManager.java
                  • handlers
                    • ZipContentHandler.java
                    • LocalFileContentHandler.java
                    • ContentHandler.java
                    • RemoteContentHandler.java
                  • DataItemBase.java
                  • ContentChangedEvent.java
                  • DataBeanSelector.java
                  • DataItemCreatedEvent.java
                  • DataFolder.java
                  • features
                    • FeatureProviderBase.java
                    • FeatureBase.java
                    • bio
                      • IdentifierProvider.java
                      • NormalisedExpressionProvider.java
                      • PhenodataProvider.java
                      • package.html
                    • BoolTrueFeature.java
                    • BasicFeature.java
                    • FeatureProvider.java
                    • ConstantFloatFeature.java
                    • table
                      • EditableTable.java
                      • HeaderProvider.java
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                      • TableBeanEditor.java
                      • DynamicallyParsedTable.java
                      • package.html
                    • ConstantStringFeature.java
                    • NonexistingFeature.java
                    • BoolFalseFeature.java
                    • ModifiedFeature.java
                    • RestrictModifier.java
                    • ConstantTableFeature.java
                    • RequestExecuter.java
                    • Table.java
                    • Feature.java
                    • QueryResult.java
                    • stat
                      • CalcModifier.java
                      • SomClusterProvider.java
                      • HierarchicalClusterProvider.java
                      • NegModifier.java
                      • package.html
                      • LogModifier.java
                    • package.html
                    • Modifier.java
                    • CalculatingIterable.java
                  • DataBean.java
                  • TypeTag.java
                  • package.html
                  • DataItemRemovedEvent.java
                • module
                  • Module.java
                  • sequence
                    • SequenceModule.java
                  • ModuleManager.java
                  • basic
                    • BasicModule.java
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                    • ChipsterInputTypes.java
                    • KielipankkiModule.java
                    • MicroarrayModule.java
                    • ChipsterSADLParser.java
                    • package.html
                • util
                  • SystemMonitorUtil.java
                  • StringValidator.java
                  • XmlUtil.java
                  • BrowserLauncher.java
                  • AdvancedStringTokenizer.java
                  • SwingTools.java
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                  • SslTest.java
                  • LinkUtil.java
                  • UrlTransferUtil.java
                  • LookaheadStringReader.java
                  • InputStreamSource.java
                  • LangUtil.java
                  • HttpRangeTest.java
                  • Exceptions.java
                  • Files.java
                  • SplashScreen.java
                  • ToolUtils.java
                  • FileCleanUpTimerTask.java
                  • FloatArrayList.java
                  • Emails.java
                  • SocketFactoryCache.java
                  • BitTwiddling.java
                  • Version.java
                  • ZipUtils.java
                  • ScaleUtil.java
                  • BrowsableHtmlPanel.java
                  • IOUtils.java
                  • ImageExportUtils.java
                  • ThreadUtils.java
                  • GeneralFileFilter.java
                  • CommandLineParser.java
                  • Strings.java
                  • package.html
                  • LookaheadLineReader.java
                  • KeyAndTrustManager.java
                  • FloatArrayListIterator.java
                • filebroker
                  • ChecksumInputStream.java
                  • RestServlet.java
                  • ExampleSessionUpdater.java
                  • AuthorisedUrlRepository.java
                  • SimpleFileBrokerClient.java
                  • FileServer.java
                  • JettyFileServer.java
                  • DerbyMetadataServer.java
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                  • ChecksumParseException.java
                  • WelcomePage.java
                  • JettyCheckTimerTask.java
                  • DiskCleanUp.java
                  • NotEnoughDiskSpaceException.java
                  • DbSession.java
                  • FileBrokerException.java
                  • ContentLengthException.java
                  • Md5FileUtils.java
                  • FileServerAdminTools.java
                  • ChecksumException.java
                  • FileBrokerAreas.java
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                  • package.html
                  • ServerSessionImportExportTool.java
                • config
                  • ConfigurationModule.java
                  • Configuration.java
                  • ConfigurationEntry.java
                  • DirectoryLayout.java
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                  • package.html
                • service
                  • ShutdownCallback.java
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                  • ErrorReportAsException.java
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                  • VisualConstants.java
                  • ApplicationConstants.java
                • webstart
                  • JnlpServlet.java
                  • WebstartJettyServer.java
                  • package.html
                • auth
                  • JaasAuthenticationProvider.java
                  • Authenticator.java
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                  • UnixCryptLoginModule.java
                  • AuthorisationException.java
                  • AuthenticationProvider.java
                  • package.html
                  • LoginModuleBase.java
                • manager
                  • LogParser.java
                  • ManagerClient.java
                  • LogImport.java
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                • MicroarrayMain.java
                • cluster
                  • ClusterLeafNode.java
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                  • TreeParseException.java
                  • ClusterNode.java
                  • package.html
                  • ClusterParser.java
                • messaging
                  • JsonMessageListener.java
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                  • DescriptionMessageListener.java
                  • MonitoredNode.java
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                  • TempTopicMessagingListenerBase.java
                  • MessagingListener.java
                  • NodeBase.java
                  • admin
                    • StorageAggregate.java
                    • JobmanagerAdminAPI.java
                    • StorageEntry.java
                    • AdminAPI.java
                    • JobsEntry.java
                    • ManagerConfiguration.java
                    • CompAdminAPI.java
                    • StorageAdminAPI.java
                    • CompAdmin.java
                    • ServerAdminAPI.java
                  • JobState.java
                  • Topics.java
                  • MessageListenerWrapper.java
                  • Node.java
                  • DirectMessagingListener.java
                  • message
                    • ParameterMessage.java
                    • CommandMessage.java
                    • ResultMessage.java
                    • ChipsterMessage.java
                    • SourceMessage.java
                    • JobMessage.java
                    • JobLogMessage.java
                    • UrlListMessage.java
                    • FeedbackMessage.java
                    • ModuleDescriptionMessage.java
                    • JsonMessage.java
                    • JobMessageUtils.java
                    • ServerStatusMessage.java
                    • GenericJobMessage.java
                    • BooleanMessage.java
                    • PayloadMessage.java
                    • AuthenticationMessage.java
                    • SuccessMessage.java
                    • package.html
                    • UrlMessage.java
                    • GenericResultMessage.java
                  • MessagingTopic.java
                  • FirstLoginListener.java
                  • BooleanMessageListener.java
                  • SourceMessageListener.java
                  • UrlMessageListener.java
                  • MonitoredNodeBase.java
                  • DirectMessagingTopic.java
                  • JMSMessagingEndpoint.java
                  • TempTopicMessagingListener.java
                  • auth
                    • SimpleAuthenticationRequestListener.java
                    • ClientLoginListener.java
                    • AuthenticatedTopic.java
                    • AuthenticationRequestListener.java
                    • package.html
                  • ReplyMessageListener.java
                  • UrlListMessageListener.java
                  • package.html
                  • MultiplexingMessagingListener.java
                  • DirectMessagingEndpoint.java
                  • SuccessMessageListener.java
                  • AuthMessagingListener.java
                • package.html
              • chipster
                • util
                  • StringUtils.java
                • toolbox
                  • ToolboxTool.java
                  • ToolboxRestUtils.java
                  • SADLTool.java
                  • RuntimeUtils.java
                  • ToolboxClientComp.java
                • dev
                  • toolchecker
                    • ToolChecker.java
                • tools
                  • gbrowser
                    • TestJavaTool.java
                • ChipsterMain.java
          • log4j-enabled.properties
          • com
            • jgoodies
              • uif_lite
                • panel
                  • SimpleInternalFrame.java
          • MANIFEST.MF
        • workflows
          • protein-expression-analysis.bsh
          • mirna-expression-analysis.bsh
          • gene-expression-analysis.bsh
        • modules
          • ngs
            • java
              • fi
                • csc
                  • chipster
                    • tools
                      • ngs
                        • GtfGenes.java
                        • regions
                          • CombineRegionsTool.java
                          • RemoveOverlappingTool.java
                          • FindOverlappingTool.java
                          • RegionTool.java
                          • FuseRegionsTool.java
                        • SortBed.java
                        • SortTsv.java
                        • PreprocessNGSSingle.java
                        • SortGtf.java
                        • LocalNGSPreprocess.java
                        • SortVcf.java
                      • common
                        • DownloadFile.java
          • microarray
            • java
              • fi
                • csc
                  • chipster
                    • tools
                      • TestJavaTool.java
      • test
        • resources
          • illumina-hc.txt
          • filtered_4_chips.tsv
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          • water.acd
          • emma.acd
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          • phenodata_4_chips.tsv
          • som.tsv
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          • ei_visualisoidu_2.tsv
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            • funghi_adh6.fasta
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          • wig
            • variableStep.wig
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          • sam
            • variousAttributes.bam
            • variousAttributes.sam
          • resultset.tsv
        • java
          • fi
            • csc
              • microarray
                • description
                  • SADLParserTest.java
                  • SADLTokeniserTest.java
                • TestConstants.java
                • comp
                  • BasicRAnalysisTest.java
                  • ToolTestResult.java
                  • AnalysisTestBase.java
                  • ToolTestTextFile.java
                  • SADLDescriptionTest.java
                  • ParameterSecurityPolicyTest.java
                  • SessionReplayTest.java
                  • SessionReplayTestParameters.java
                  • r
                    • SADLToolTest.java
                  • ToolTestSummary.java
                  • ToolTestHtmlFile.java
                  • ToolTestBase.java
                • DemoAuthenticationRequestListener.java
                • client
                  • dataimport
                    • DataParsingTest.java
                    • DataTrimmerTest.java
                  • visualisation
                    • methods
                      • gbrowser
                        • runtimeIndex
                          • ChromosomeBinarySearchTest.java
                          • RandomAccessLineDataSourceHttpTest.java
                          • RandomAccessLineDataSourceTest.java
                          • RandomAccessLineReaderTest.java
                          • IndexPerformanceTest.java
                          • BinarySearchIndexTest.java
                        • fileFormat
                          • ChromosomeNameUnnormaliserTest.java
                    • VisualiserTest.java
                  • operation
                    • ParameterTest.java
                  • session
                    • SessionTest.java
                • databeans
                  • DataManagerTest.java
                  • fs
                    • FSDataEventTest.java
                  • LinkTest.java
                  • biobeans
                    • PhenodataTest.java
                  • features
                    • FeatureTest.java
                • util
                  • StringsTest.java
                  • LookaheadLineReaderTest.java
                  • BitTwiddlingTest.java
                  • GetLatestVersionTest.java
                  • FloatArrayListTest.java
                  • SecureSessionPoolTest.java
                  • rest
                    • FileServerTest.java
                  • FilesTest.java
                  • FileCleanUpTest.java
                • filebroker
                  • FileBrokerClientMock.java
                  • MockJettyFileServer.java
                  • FileBrokerClientTest.java
                  • ParallelDownloadTest.java
                  • ChecksumInputStreamTest.java
                  • encryption
                    • TestServer.java
                    • TestClient.java
                • ClientContextUtil.java
                • auth
                  • LoginTest.java
                • cluster
                  • ClusterParserTest.java
                • messaging
                  • MessagingTestBase.java
                  • AuthenticationTest.java
                  • JobStateTest.java
                  • message
                    • CommandMessageTest.java
                  • AdminAPITest.java
                  • DirectMessagingEndpointTest.java
                • gbrowser
                  • intervals
                    • RegionOperationsTest.java
              • chipster
                • web
                  • adminweb
                    • StandaloneAdminWeb.java
    • build.xml
    • dist
      • for-dist-files.txt
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        • main
          • resources
            • log4j2.xml
          • java
            • fi
              • csc
                • chipster
                  • toolbox
                    • resource
                      • ModuleResource.java
                      • ToolResource.java
                    • ToolboxClient.java
                    • ToolboxServer.java
                    • Toolbox.java
                    • rest
                      • IndentingModifier.java
                      • RestUtils.java
                      • JsonPrettyPrintQueryParamContainerResponseFilter.java
                    • ToolboxService.java
                    • SADLReplacements.java
                    • ToolboxModule.java
                    • toolpartsparser
                      • ToolPartsParser.java
                      • HeaderAsCommentParser.java
                      • JavaParser.java
      • gradle
        • wrapper
          • gradle-wrapper.properties
          • gradle-wrapper.jar
      • gradlew
      • .settings
        • org.eclipse.buildship.core.prefs
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      • .gitignore
      • .project
      • .classpath
    • ext
      • lib-src
        • note.txt
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      • applications
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            • README_de.txt
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              • wrapper.conf
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              • wrapper.conf
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        • apache-activemq-5.10.0
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              • js
                • common.js
                • prototype.js
                • standardista-table-sorting.js
                • amq_jquery_adapter.js
                • css.js
                • dojo.js
                • amq_dojo_adapter.js
                • mochi
                  • __package__.js
                  • MochiKit.js
                • prettify.js
                • amq.js
                • jquery-1.4.2.min.js
                • plotkit
                  • dummy.svg
                  • SweetCanvas.js
                  • Layout.js
                  • Canvas.js
                  • SVG.js
                  • Base.js
                  • iecanvas.htc
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                • amq_prototype_adapter.js
                • chat.js
              • chat.css
              • index.html
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          • examples
            • amqp
              • python
                • listener.py
                • publisher.py
              • java
                • src
                  • main
                    • java
                      • example
                        • Listener.java
                        • Publisher.java
                • pom.xml
                • readme.md
            • mqtt
              • websocket
                • img
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                  • mqttws31.js
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                • css
                  • bootstrap.min.css
                  • bootstrap.min.responsive.css
              • java
                • src
                  • main
                    • java
                      • example
                        • Listener.java
                        • Publisher.java
                • pom.xml
                • readme.md
            • openwire
              • cpp
                • Listener.cpp
                • Publisher.cpp
                • readme.md
              • swissarmy
                • src
                  • ConsumerTool.java
                  • TopicPublisher.java
                  • CommandLineSupport.java
                  • StompExample.java
                  • ProducerTool.java
                  • EmbeddedBroker.java
                  • TopicListener.java
                  • RequesterTool.java
                  • Log4jJMSAppenderExample.java
                  • log4j-jms.properties
                  • jndi.properties
                  • ProducerAndConsumerTool.java
                • build.xml
                • readme.md
              • advanced-scenarios
                • jms-example-queue
                  • src
                    • main
                      • resources
                        • log4j.properties
                      • java
                        • example
                          • queue
                            • Producer.java
                            • Consumer.java
                  • pom.xml
                  • readme.md
                • jms-example-wildcard-consumer
                  • src
                    • main
                      • java
                        • example
                          • wildcard
                            • Client.java
                  • pom.xml
                  • readme.md
                • jms-example-exclusive-consumer
                  • src
                    • main
                      • java
                        • example
                          • queue
                            • exclusive
                              • Producer.java
                              • Consumer.java
                  • pom.xml
                  • readme.md
                • jms-example-topic
                  • src
                    • main
                      • resources
                        • log4j.properties
                      • java
                        • example
                          • topic
                            • Publisher.java
                            • Subscriber.java
                  • pom.xml
                  • readme.md
                • pom.xml
                • jms-example-queue-selector
                  • src
                    • main
                      • java
                        • example
                          • queue
                            • selector
                              • Producer.java
                              • Consumer.java
                  • pom.xml
                  • readme.md
                • jms-example-message-browser
                  • src
                    • main
                      • java
                        • example
                          • browser
                            • Producer.java
                            • Browser.java
                  • pom.xml
                  • readme.md
                • readme.md
                • jms-example-composite-destinations
                  • src
                    • main
                      • java
                        • example
                          • composite
                            • dest
                              • Producer.java
                              • Consumer.java
                  • pom.xml
                  • readme.md
                • jms-example-transaction
                  • src
                    • main
                      • java
                        • example
                          • transaction
                            • Client.java
                  • pom.xml
                  • readme.md
                • jms-example-durable-sub
                  • src
                    • main
                      • java
                        • example
                          • topic
                            • durable
                              • Publisher.java
                              • Subscriber.java
                  • pom.xml
                  • readme.md
                • jms-example-temp-destinations
                  • src
                    • main
                      • java
                        • example
                          • tempdest
                            • Consumer.java
                            • ProducerRequestReply.java
                  • pom.xml
                  • readme.md
              • ecommerce
                • src
                  • Vendor.java
                  • Retailer.java
                  • Supplier.java
                  • TransactionsDemo.java
                • build.xml
                • README.txt
              • java
                • src
                  • main
                    • java
                      • example
                        • Listener.java
                        • Publisher.java
                • pom.xml
                • readme.md
              • exploring-jms
                • build.xml
                • QueuePTPSamples
                  • RequestReply
                    • Replier.java
                    • Requestor.java
                  • TransactedTalk
                    • TransactedTalk.java
                  • SelectorTalk
                    • SelectorTalk.java
                  • QueueRoundTrip
                    • QueueRoundTrip.java
                  • Talk
                    • Talk.java
                  • QueueMonitor
                    • QueueMonitor.properties
                    • QueueMonitor.java
                • readme.txt
                • TopicPubSubSamples
                  • DurableChat
                    • DurableChat.java
                  • RequestReply
                    • TopicReplier.java
                    • TopicRequestor.java
                  • MessageMonitor
                    • MessageMonitor.java
                    • MessageMonitor.properties
                  • Chat
                    • Chat.java
                  • SelectorChat
                    • SelectorChat.java
                  • HierarchicalChat
                    • HierarchicalChat.java
                  • TransactedChat
                    • TransactedChat.java
                • conf
                  • log4j.properties
              • csharp
                • ActiveMQExamples
                  • Listener
                    • Listener.cs
                    • AssemblyInfo.cs
                    • NMSTracer.cs
                    • Listener.csproj
                  • ActiveMQExamples.userprefs
                  • Publisher
                    • Publisher.csproj
                    • AssemblyInfo.cs
                    • Publisher.cs
                    • NMSTracer.cs
                  • ActiveMQExamples.sln
                • readme.md
            • stomp
              • cpp
                • Listener.cpp
                • Publisher.cpp
                • readme.md
              • perl
                • publisher
                • readme.md
                • listener
              • php
                • publisher.php
                • listener.php
                • readme.md
              • ruby
                • catstomp.rb
                • stompcat.rb
                • listener.rb
                • readme.md
                • publisher.rb
              • websocket
                • img
                • readme.md
                • js
                  • stomp.js
                  • jquery-1.7.2.min.js
                • index.html
                • css
                  • bootstrap.min.css
                  • bootstrap.min.responsive.css
              • python
                • stompest
                  • sync
                    • listener.py
                    • publisher.py
                    • __init__.py
                  • readme.md
                  • async
                    • listener.py
                    • publisher.py
                    • __init__.py
                • stomppy
                  • listener.py
                  • publisher.py
                  • readme.md
                • readme.md
              • java
                • src
                  • main
                    • java
                      • example
                        • Listener.java
                        • Publisher.java
                • pom.xml
                • readme.md
              • csharp
                • ActiveMQExamples
                  • Listener
                    • Listener.cs
                    • AssemblyInfo.cs
                    • NMSTracer.cs
                    • Listener.csproj
                  • ActiveMQExamples.userprefs
                  • Publisher
                    • Publisher.csproj
                    • AssemblyInfo.cs
                    • Publisher.cs
                    • NMSTracer.cs
                  • ActiveMQExamples.sln
                • readme.md
            • conf
              • activemq-jdbc.xml
              • activemq-security.xml
              • activemq-specjms.xml
              • log4j.properties
              • camel.xml
              • activemq-leveldb-replicating.xml
              • activemq-static-network-broker2.xml
              • activemq-demo.xml
              • jetty-demo.xml
              • activemq-scalability.xml
              • activemq-throughput.xml
              • activemq-static-network-broker1.xml
              • activemq-stomp.xml
              • activemq.xml
              • activemq-jdbc-performance.xml
              • activemq-dynamic-network-broker1.xml
              • activemq-dynamic-network-broker2.xml
              • resin-web.xml
              • web.xml
            • other
              • perfharness
                • perfharness-activemq.sh
          • LICENSE
          • lib
            • activemq-protobuf-1.1.jar
            • geronimo-jms_1.1_spec-1.1.1.jar
            • activemq-web-5.10.0.jar
            • activemq-jaas-5.10.0.jar
            • web
              • json-simple-1.1.jar
              • jetty-websocket-7.6.9.v20130131.jar
              • jsp-api-2.1-glassfish-2.1.v20100127.jar
              • jdom-1.0.jar
              • geronimo-servlet_2.5_spec-1.2.jar
            • camel
              • camel-jms-2.13.1.jar
              • activemq-camel-5.10.0.jar
            • optional
              • spring-expression-3.2.8.RELEASE.jar
              • jaxb2-basics-runtime-0.6.4.jar
              • jasypt-spring3-1.9.1.jar
              • leveldb-api-0.6.jar
              • activemq-mqtt-5.10.0.jar
              • activemq-jms-pool-5.10.0.jar
              • spring-oxm-3.2.8.RELEASE.jar
              • activeio-core-3.1.4.jar
              • org.linkedin.zookeeper-impl-1.4.0.jar
              • org.linkedin.util-core-1.4.0.jar
              • activemq-amqp-5.10.0.jar
              • activemq-jdbc-store-5.10.0.jar
              • jasypt-1.9.1.jar
              • activemq-log4j-appender-5.10.0.jar
              • leveldbjni-1.8.jar
              • activemq-shiro-5.10.0.jar
              • commons-pool-1.6.jar
              • geronimo-j2ee-connector_1.5_spec-2.0.0.jar
              • xbean-spring-3.16.jar
              • hawtdispatch-scala-2.11-1.21.jar
              • activemq-http-5.10.0.jar
              • activemq-stomp-5.10.0.jar
              • commons-dbcp-1.4.jar
              • proton-jms-0.7.jar
              • hawtdispatch-transport-1.21.jar
              • hawtjni-runtime-1.9.jar
              • slf4j-log4j12-1.7.5.jar
              • xpp3-1.1.4c.jar
              • activemq-partition-5.10.0.jar
              • jettison-1.3.5.jar
              • hawtdispatch-1.21.jar
              • activemq-pool-5.10.0.jar
              • snappy-0.2.jar
              • hawtbuf-proto-1.10.jar
              • shiro-spring-1.2.2.jar
            • extra
              • mqtt-client-1.10.jar
            • activemq-spring-5.10.0.jar
            • insight-log4j-7.2.0.redhat-024-patched.jar
            • geronimo-j2ee-management_1.1_spec-1.0.1.jar
            • activemq-rar.txt
            • insight-log-core-7.2.0.redhat-024.jar
            • hawtbuf-1.10.jar
            • jcl-over-slf4j-1.7.5.jar
            • geronimo-jta_1.0.1B_spec-1.0.1.jar
            • slf4j-api-1.7.5.jar
            • activemq-console-5.10.0.jar
          • webapps
            • images
              • spacer.gif
            • admin
              • queues.jsp
              • xml
                • queues.jsp
                • topics.jsp
                • subscribers.jsp
              • slave.jsp
              • decorators
                • footer.jsp
                • header.jsp
                • head.jsp
              • queueGraph.jsp
              • queueConsumers.jsp
              • images
                • spacer.gif
              • topicProducers.jsp
              • connections.jsp
              • graph.jsp
              • browse.jsp
              • connection.jsp
              • test
                • systemProperties.jsp
                • dummy.jsp
                • index.jsp
              • message.jsp
              • 404.html
              • topics.jsp
              • topicSubscribers.jsp
              • index.jsp
              • META-INF
                • LICENSE
                • NOTICE
              • queueProducers.jsp
              • WEB-INF
                • tags
                  • form
                    • checkbox.tag
                    • short.tag
                    • tooltip.tag
                    • text.tag
                    • option.tag
                    • escape.tag
                    • forEachMapEntry.tag
                    • uri.tag
                  • jms
                    • forEachMessage.tag
                    • forEachConnection.tag
                    • formatTimestamp.tag
                    • persistent.tag
                • webconsole-jndi.xml
                • classes
                  • org
                    • apache
                      • activemq
                        • web
                          • WebConsoleStarter$OsgiUtil.class
                          • config
                            • OsgiConfiguration.class
                          • WebConsoleStarter.class
                          • handler
                            • BindingBeanNameUrlHandlerMapping.class
                          • filter
                            • ApplicationContextFilter$1.class
                            • ApplicationContextFilter$2.class
                            • ApplicationContextFilter.class
                          • controller
                            • DeleteMessage.class
                            • PurgeDestination.class
                            • CreateDestination.class
                            • DeleteJob.class
                            • DeleteDestination.class
                            • SendMessage.class
                            • CopyMessage.class
                            • CreateSubscriber.class
                            • DeleteSubscriber.class
                            • MoveMessage.class
                • dispatcher-servlet.xml
                • webconsole-properties.xml
                • webconsole-default.xml
                • jspf
                  • headertags.jspf
                  • old.jspf
                • webconsole-osgi.xml
                • webconsole-embedded.xml
                • webconsole-invm.xml
                • webconsole-query.xml
                • web.xml
              • 403.html
              • styles
                • type-settings.css
                • sorttable.css
                • prettify.css
                • site.css
              • js
                • common.js
                • standardista-table-sorting.js
                • css.js
                • mochi
                  • __package__.js
                  • MochiKit.js
                • prettify.js
                • plotkit
                  • dummy.svg
                  • SweetCanvas.js
                  • Layout.js
                  • Canvas.js
                  • SVG.js
                  • Base.js
                  • iecanvas.htc
                  • SweetSVG.js
              • 500.html
              • subscribers.jsp
              • network.jsp
              • send.jsp
              • scheduled.jsp
            • api
              • WEB-INF
                • web.xml
            • favicon.ico
            • fileserver
              • META-INF
                • LICENSE
                • NOTICE
              • WEB-INF
                • classes
                  • org
                    • apache
                      • activemq
                        • util
                          • IOHelper.class
                          • RestFilter.class
                          • FilenameGuardFilter.class
                          • FilenameGuardFilter$GuardedHttpServletRequest.class
                • web.xml
              • index.html
            • styles
              • type-settings.css
              • sorttable.css
              • prettify.css
              • site.css
            • index.html
          • README.txt
          • data
            • activemq.log
          • bin
            • activemq.jar
            • linux-x86-64
              • wrapper
              • libwrapper.so
              • activemq
              • wrapper.conf
            • wrapper.jar
            • linux-x86-32
              • wrapper
              • libwrapper.so
              • activemq
              • wrapper.conf
            • activemq
            • diag
            • activemq-admin
          • NOTICE
          • docs
            • user-guide.html
            • WebConsole-README.txt
            • index.html
          • conf
            • jetty.xml
            • broker.ks
            • jetty-realm.properties
            • credentials.properties
            • jmx.access
            • log4j.properties
            • logging.properties
            • users.properties
            • groups.properties
            • broker.ts
            • client.ts
            • credentials-enc.properties
            • activemq.xml
            • jmx.password
            • client.ks
            • broker-localhost.cert
            • login.config
      • lib
        • cron4j-1.1.5.jar
        • jcommander-1.30.jar
        • hk2-api-2.4.0-b34.jar
        • jersey-media-json-jackson-2.22.2.jar
        • viski-chipster-1.0.1.jar
        • jackson-annotations-2.5.4.jar
        • jetty-schemas-3.1.jar
        • concurrent.jar
        • activation.jar
        • commons-logging-1.1.jar
        • batik-dom.jar
        • jetty-jaspi-9.2.10.v20150310.jar
        • batik-xml.jar
        • saaj-api.jar
        • jetty-continuation-9.2.10.v20150310.jar
        • jersey-media-jaxb-2.22.2.jar
        • jgraph-5.12.2.1.jar
        • jetty-servlet-9.2.10.v20150310.jar
        • jetty-io-9.2.10.v20150310.jar
        • jetty-annotations-9.2.10.v20150310.jar
        • jetty-jaas-9.2.10.v20150310.jar
        • commons-io-2.2.jar
        • miglayout-4.0-swing.jar
        • jetty-webapp-9.2.10.v20150310.jar
        • reactive-streams-1.0.2.jar
        • log4j-api-jar-2.2.jar
        • jetty-rewrite-9.2.10.v20150310.jar
        • hibernate-commons-annotations-jar-4.0.5.Final.jar
        • jetty-alpn-server-9.2.10.v20150310.jar
        • jetty-jmx-9.2.10.v20150310.jar
        • jandex-jar-1.1.0.Final.jar
        • jersey-container-grizzly2-http-2.22.2.jar
        • commons-daemon.jar
        • hk2-utils-2.4.0-b34.jar
        • jetty-deploy-9.2.10.v20150310.jar
        • jetty-cdi-9.2.10.v20150310.jar
        • jersey-entity-filtering-2.22.2.jar
        • javax.inject-2.4.0-b34.jar
        • batik-svggen.jar
        • jackson-jaxrs-json-provider-2.5.4.jar
        • jersey-client-2.22.2.jar
        • stringtemplate-3.0.jar
        • jakarta-regexp-1.5.jar
        • javax.annotation-api-1.2.jar
        • hamcrest-core-1.3.jar
        • jetty-xml-9.2.10.v20150310.jar
        • jboss-logging-jar-3.1.3.GA.jar
        • batik-util.jar
        • commons-pool-1.3.jar
        • jboss-transaction-api_1.2_spec-jar-1.0.0.Final.jar
        • jetty-jndi-9.2.10.v20150310.jar
        • argparse4j-0.4.3.jar
        • servlet-api-3.1.jar
        • jboss-logging-annotations-jar-1.2.0.Beta1.jar
        • jetty-servlets-9.2.10.v20150310.jar
        • jetty-http-9.2.10.v20150310.jar
        • javax.inject-1.jar
        • jackson-jaxrs-base-2.5.4.jar
        • jetty-plus-9.2.10.v20150310.jar
        • jetty-alpn-client-9.2.10.v20150310.jar
        • hibernate-jpa-2.1-api-jar-1.0.0.Final.jar
        • hk2-locator-2.4.0-b34.jar
        • jetty-quickstart-9.2.10.v20150310.jar
        • jetty-proxy-9.2.10.v20150310.jar
        • jackson-module-jaxb-annotations-2.5.4.jar
        • hibernate-c3p0-jar-4.3.8.Final.jar
        • javax.ws.rs-api-2.0.1.jar
        • eclipse-icons.jar
        • jetty-security-9.2.10.v20150310.jar
      • lib-ext
        • fatjar.jar
    • bin
      • .gitignore
    • .gitignore
    • LICENSE.txt
    • .project
    • .classpath