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  • ClothoBiofabEdition-master
    • ClothoApps
      • BamBglUnrestricted
        • src
          • org
            • clothocad
              • format
                • bambglunrestricted
                  • connect.java
      • BglBrickiDigester
        • src
          • org
            • clothocad
              • tool
                • bglbrickdigester
                  • connect.java
                  • digestMultiple.java
      • BglBricks
        • src
          • org
            • clothocad
              • format
                • bglbricks
                  • connect.java
      • BullTrowell2
        • src
          • org
            • clothocad
              • tool
                • bulltrowell
                  • AePlayWave.java
                  • connect.java
                  • interpreters
                    • HTMLColors.java
                    • addComposite.java
                    • addFeature.java
                    • addOligos.java
                    • addPart.java
                    • addPlasmid.java
                    • addPlate.java
                    • addVector.java
                    • interpreter.java
                  • view
                    • ExcelAdapter.java
                    • hub.java
                    • spreadsheet.java
                    • trashy.java
      • CollectionViewTool
        • src
          • org
            • clothocad
              • tool
                • collectionview
                  • GlassMessage.java
                  • StartupMessage.java
                  • browser.java
                  • connectCollectionView.java
                  • viewer.java
      • CollectorBrowser
        • src
          • org
            • clothocad
              • tool
                • collectorbrowser
                  • connect.java
      • ConcatenateFormat
        • src
          • org
            • clothocad
              • format
                • concatenateformat
                  • connect.java
      • ConfigurableConnection
        • src
          • org
            • clothocad
              • connection
                • configurableconnection
                  • ConfigurableConnection.java
      • ConnectionConfigTool
        • src
          • org
            • clothocad
              • tool
                • connectconfigtool
                  • blueTextField.java
                  • frame.java
                  • tool.java
      • DashBoard2
        • src
          • org
            • clothocore
              • widget
                • dashboard2
                  • DashBoardWidgetConnection.java
                  • gui
                    • Application.java
                    • BackgroundPanel.java
                    • BlurPanel.java
                    • ButtonPanel.java
                    • CurvesPanel.java
                    • GraphicsUtilities.java
                    • ItemPanel.java
                    • StackLayout.java
                    • SuperSearch.java
                    • ToolPanel.java
                  • util
                    • AbstractFilter.java
                    • ColorTintFilter.java
                    • GaussianBlurFilter.java
                    • GraphicsUtilities.java
      • ErrorReporter
        • src
          • org
            • clothocad
              • widget
                • errorreporter
                  • connect.java
                  • errorgui.java
                  • sendmail.java
      • FormatEditor
        • src
          • org
            • clothocad
              • tool
                • formateditor
                  • blueTextField.java
                  • connect.java
                  • frame.java
      • Freeform
        • src
          • org
            • clothocad
              • format
                • freeform
                  • connect.java
      • GoldenGateFour
        • src
          • org
            • clothocad
              • format
                • goldengatefour
                  • connect.java
      • GoldenGateTwo
        • src
          • org
            • clothocad
              • format
                • goldengatetwo
                  • connect.java
      • Grapevine
        • src
          • org
            • clothocad
              • tool
                • grapevine
                  • BrowseNotes.java
                  • NoteEditor.java
                  • PDFGenerator.java
                  • ScrollablePanel.java
                  • blueTextField.java
                  • connect.java
                  • factoidEditor.java
                  • factoidPanel.java
                  • subNotePanel.java
      • GroovyConsoleTC
        • src
          • org
            • clothocad
              • tool
                • groovyconsoletc
                  • Connect.java
                  • LaunchMe.java
      • GroovyScripter
        • src
          • org
            • clothocad
              • tool
                • groovyscripter
                  • gframe.java
                  • groovyFrame.java
      • GroovyTranslator
        • src
          • org
            • clothocad
              • library
                • groovytranslator
                  • groovyActor.java
                  • groovyCollator.java
                  • groovyCollection.java
                  • groovyCollector.java
                  • groovyFeature.java
                  • groovyFormat.java
                  • groovyInstitution.java
                  • groovyLab.java
                  • groovyObjBase.java
                  • groovyObjType.java
                  • groovyPart.java
                  • groovyPerson.java
                  • groovyPlasmid.java
                  • groovyPort.java
                  • groovyStrain.java
                  • groovyVector.java
      • HelloWorld
        • src
          • org
            • clothocad
              • tool
                • helloworld
                  • HelloWorldController.java
                  • HelloWorldGUI.java
                  • connect.java
      • HibernateConnectionLibrary
        • src
          • org
            • clothocad
              • hibernate
                • ExampleQueries.java
                • HibernateConnection.java
                • data
                  • AttachmentTable.java
                  • CollectionTable.java
                  • Collectionxref.java
                  • CollectionxrefId.java
                  • CompositeXref.java
                  • ContainerTable.java
                  • FactoidTable.java
                  • FamilyNoteXref.java
                  • FamilyNoteXrefId.java
                  • FamilyTable.java
                  • FeatureFamilyXref.java
                  • FeatureFamilyXrefId.java
                  • FeatureNoteXref.java
                  • FeatureNoteXrefId.java
                  • FeatureTable.java
                  • FeatureTraitXref.java
                  • FeatureTraitXrefId.java
                  • FlexfieldDataXref.java
                  • FlexfieldTable.java
                  • FormatTable.java
                  • GrammarTable.java
                  • InstitutionTable.java
                  • LabTable.java
                  • NoteFactoidXref.java
                  • NoteFactoidXrefId.java
                  • NoteNoteXref.java
                  • NoteNoteXrefId.java
                  • NoteTable.java
                  • NucseqAnnotation.java
                  • NucseqTable.java
                  • OligoTable.java
                  • PartGrammarXref.java
                  • PartGrammarXrefId.java
                  • PartTable.java
                  • PersonTable.java
                  • PlasmidTable.java
                  • PlateTable.java
                  • PlateTypeTable.java
                  • SampleDataTable.java
                  • SampleDataXref.java
                  • SampleDataXrefId.java
                  • SampleTable.java
                  • SearchtagTable.java
                  • StrainNoteXref.java
                  • StrainNoteXrefId.java
                  • StrainPlasmidXref.java
                  • StrainPlasmidXrefId.java
                  • StrainTable.java
                  • TraitFamilyXref.java
                  • TraitFamilyXrefId.java
                  • TraitTable.java
                  • VectorTable.java
                  • WikitextTable.java
                • hibernateDatum.java
      • InstitutionEditor
        • src
          • org
            • clothocad
              • tool
                • institutioneditor
                  • blueTextField.java
                  • connect.java
                  • frame.java
      • InventoryManager
        • src
          • org
            • clothocad
              • tool
                • inventorymanager
                  • InventoryManagerTool.java
                  • InventoryManagerTopComponent.java
      • Knuckleboom
        • src
          • org
            • clothocad
              • viewer
                • knuckleboom
                  • connect.java
                  • frame.java
      • LabEditor
        • src
          • org
            • clothocad
              • tool
                • labeditor
                  • blueTextArea.java
                  • blueTextField.java
                  • connect.java
                  • frame.java
      • LocalConnection
        • src
          • org
            • clothocad
              • connection
                • localconnection
                  • LocalConnection.java
      • OnStartuper
        • src
          • org
            • clothocad
              • widget
                • onstartup
                  • connect.java
      • PCRPredicter
        • src
          • org
            • clothocad
              • tool
                • pcrpredict
                  • Calculator.java
                  • connect.java
                  • predictor.java
      • PersonEditor
        • src
          • org
            • clothocad
              • tool
                • personeditor
                  • GlassMessage.java
                  • blueTextArea.java
                  • blueTextField.java
                  • connect.java
                  • frame.java
      • PluginManager
        • src
          • org
            • clothocore
              • tool
                • pluginmanager
                  • gui
                    • ApplicationFrame.java
                    • ChooseDefaultConnection.java
                    • ChoosePreferredViewers.java
                    • CurvesPanel.java
                    • FancyPanel.java
                    • GradientPanel.java
                    • OpeningScreenChooser.java
                    • RightClickPopup.java
                    • ShowAndHideWidgets.java
                    • StackLayout.java
                    • UninstallPlugins.java
                  • io
                    • FileTreeWalk.java
                    • FileTreeWalker.java
                    • UnixGlobFileFilter.java
                    • connectPMToClotho.java
      • PrimerDesigner
        • src
          • org
            • clothocad
              • tool
                • primerdesigner
                  • Aligner.java
                  • DesignFrame.java
                  • PrimerDesignController.java
                  • PrimerDesignerListener.java
                  • PrimerResultFrame.java
                  • SaveFrame.java
                  • connect.java
      • RFC10
        • src
          • org
            • clothocad
              • format
                • rfc10
                  • connect.java
      • RFC10cds
        • src
          • org
            • clothocad
              • format
                • rfctencds
                  • connect.java
      • RegistryImport
        • src
          • org
            • clothocad
              • tool
                • registryimporter
                  • connect.java
                  • gui
                    • allParts.java
                    • frame.java
                    • parserGrabber.java
                    • registryPart.java
                    • registryPartold.java
      • SearchAlgorithms
        • src
          • org
            • clothocad
              • algorithm
                • searchalgorithm
                  • connect.java
                  • searchActor.java
      • SeqAnalyzer
        • src
          • org
            • clothocad
              • algorithm
                • seqanalyzer
                  • SequenceChecker.java
                  • SequenceCheckerActor.java
                  • sequencing
                    • ABIClassification.java
                    • ABITrace.java
                    • AlignedAbi.java
                    • BaseResult.java
                    • LinkedButton.java
                    • Nmapper.java
                    • jcatest.java
                    • newSeqAnalysis.java
                    • seqAnalysis.java
                    • seqReport.java
                    • sequencingPanel.java
                    • test.java
      • SequenceAnalysisTool
        • src
          • org
            • clothocad
              • tool
                • sequenceanalysistool
                  • connect.java
                  • gui
                    • SeqFrame.java
      • SequenceChecker
        • src
          • gui
            • Tester.java
          • jaligner
            • Alignment.java
            • Cell.java
            • Directions.java
            • Markups.java
            • NeedlemanWunsch.java
            • NeedlemanWunschGotoh.java
            • Sequence.java
            • SmithWatermanGotoh.java
            • TracebackNode.java
            • example
              • NeedlemanWunschExample.java
              • NeedlemanWunschGotohExample.java
              • SmithWatermanGotohExample.java
            • formats
              • CLUSTAL.java
              • FASTA.java
              • Format.java
              • FormatFactory.java
              • Pair.java
            • matrix
              • MatricesCompartor.java
              • Matrix.java
              • MatrixGenerator.java
              • MatrixLoader.java
              • MatrixLoaderException.java
            • test
              • NeedlemanWunschGotohTester.java
              • NeedlemanWunschTester.java
              • RandomSequenceGenerator.java
              • SmithWatermanGotohTester.java
            • ui
              • AlignCommandLine.java
              • AlignWindow.java
              • clipboard
                • ClipboardHandler.java
                • ClipboardHandlerAWT.java
                • ClipboardHandlerFactory.java
                • ClipboardListener.java
                • ClipboardPoller.java
              • filechooser
                • FileChooser.java
                • FileChooserException.java
                • FileChooserFactory.java
                • FileChooserTrusted.java
                • NamedInputStream.java
              • images
                • ToolbarIcons.java
              • logging
                • DocumentHandler.java
                • RecordFormatter.java
              • util
                • PrintJobMointor.java
                • TextComponentUtil.java
                • TextComponentUtilException.java
            • util
              • Commons.java
              • SequenceParser.java
              • SequenceParserException.java
          • org
            • clothocad
              • tool
                • sequencechecker
                  • Clone.java
                  • Construct.java
                  • SeqCheckController.java
                  • SeqCheckerTopComponent.java
                  • SequencingResult.java
          • sequencing
            • ABITrace.java
            • Analyzer.java
            • InteractiveReport.java
            • SeqReport.java
            • Tester.java
            • TraceExtract.java
            • sbbseq.java
            • temprunner.java
      • SequenceLight
        • src
          • org
            • clothocad
              • library
                • sequencelight
                  • ScrollablePanel.java
                  • colorPopup.java
                  • dnaKeymap.java
                  • findReplace.java
                  • iconPanel.java
                  • nucSeqEditor.java
                  • seqPanel.java
                  • util.java
      • SequenceView
        • src
          • org
            • clothocad
              • tool
                • sequenceview
                  • BasicPreferences.java
                  • ClothoSearchUtil.java
                  • ImportFeaturesWindow.java
                  • SequenceView.java
                  • SequenceViewAdjustmentListener.java
                  • SequenceViewDocumentListener.java
                  • SequenceViewGUI.java
                  • SequenceViewManager.java
                  • SequenceViewOutputWindow.java
                  • SequenceViewPartExport.java
                  • SequenceViewSearchTools.java
                  • SequenceViewTopComponent.java
      • Sledrunner
        • src
          • org
            • clothocad
              • tool
                • sledrunner
                  • connection.java
                  • hub.java
      • SpeXba
        • src
          • org
            • clothocad
              • format
                • spexba
                  • connect.java
      • SpreaditFeatures
        • src
          • org
            • clothocad
              • tool
                • spreaditfeatures
                  • ColorColumn.java
                  • ExcelAdapter.java
                  • colors
                    • ChooseColor.java
                    • ColorPicker.java
                  • connect.java
                  • featureEnterer.java
                  • helpers
                    • ButtonEditor.java
                    • ColorRenderer.java
                    • HTMLColors.java
                  • spreaditFeatures.java
      • SpreaditOligos
        • src
          • org
            • clothocad
              • tool
                • spreaditoligos
                  • ExcelAdapter.java
                  • connect.java
                  • oligoEnterer.java
                  • spreaditOligos.java
      • SpreaditParts
        • src
          • org
            • clothocad
              • tool
                • spreaditparts
                  • AvailabilityColorRenderer.java
                  • ExcelAdapter.java
                  • basicEnterer.java
                  • compositeEnterer.java
                  • connect.java
                  • plasmidDigester.java
                  • spreaditParts.java
                  • temporary.java
      • SpreaditVectors
        • src
          • org
            • clothocad
              • tool
                • spreaditvectors
                  • ExcelAdapter.java
                  • connect.java
                  • spreaditVectors.java
                  • vectorEnterer.java
      • StartupWizardTool
        • src
          • org
            • clothocad
              • tool
                • startupwizard
                  • connect.java
                  • localFrame.java
                  • mySqlFrame.java
      • StrainEditor
        • src
          • org
            • clothocad
              • tool
                • straineditor
                  • blueTextArea.java
                  • blueTextField.java
                  • connect.java
                  • frame.java
                  • genomicField.java
      • StringAppendAlgorithm
        • src
          • org
            • clothocad
              • algorithm
                • stringappend
                  • StringAppendAlgorithm.java
                  • StringAppendAlgorithmFactory.java
      • TutorialWizard
        • src
          • org
            • clothocad
              • tool
                • tutorialwizard
                  • Hub.java
                  • ImportedTutorialFrame.java
                  • ScrollablePanel.java
                  • TutorialFrame.java
                  • TutorialParser.java
                  • Updater.java
                  • connect.java
      • WheelBarrow
        • src
          • org
            • clothocad
              • widget
                • wheelbarrow
                  • connect.java
                  • garbageBin.java
                  • objectItem.java
                  • wheelBarrowGui.java
      • WikiEditorPanel
        • src
          • org
            • clothocad
              • wikieditorpanel
                • WikiEditorPanel.java
      • moo
        • src
          • MooFrame.java
          • moo
            • Main.java
            • NoCopyPasteFrame.java
            • TestFrame.java
    • ClothoDevelopment
      • Cello
        • ANTLRVerilog
          • output
            • VerilogALexer.java
            • VerilogAParser.java
            • __Test__.java
        • src
          • org
            • clothocad
              • tool
                • cello
                  • CelloCircuit.java
                  • CelloFeature.java
                  • CelloFeatureType.java
                  • CelloGUI.java
                  • CelloGates.java
                  • CelloGene.java
                  • CelloGeneTable.java
                  • CelloIPromoter.java
                  • CelloIPromoterTable.java
                  • CelloInput1Motif.java
                  • CelloInput2Motif.java
                  • CelloNOR.java
                  • CelloNOR3.java
                  • CelloNot.java
                  • CelloPrimitive.java
                  • CelloPrimitiveType.java
                  • CelloRBS.java
                  • CelloRBSTable.java
                  • CelloRGenePromoterTable.java
                  • CelloRPromoter.java
                  • CelloRPromoterTable.java
                  • CelloTerminator.java
                  • CelloTerminatorTable.java
                  • CelloTool.java
                  • DAGEdge.java
                  • DAGVertex.java
                  • DAGraph.java
                  • Main.java
                  • VerilogALexer.java
                  • VerilogAParser.java
                  • VerilogLexer.java
                  • VerilogParser.java
      • EugeneScripter
        • src
          • org
            • clothocad
              • tool
                • eugenescripter
                  • EugeneLexer.java
                  • EugeneSyntaxKit.java
                  • eugeneFrame.java
                  • eugeneProcess.java
                  • eugeneTool.java
      • Spectacles
        • src
          • org
            • clothocad
              • tool
                • spectacles
                  • Spectacles.java
                  • eugeneimportexport
                    • DevicePartWrapper.java
                    • EugeneExporter.java
                    • EugeneImporter.java
                    • Manager.java
                  • snippets
                    • DeviceTracker.java
                    • GridLayout.java
                    • Snippets.java
                  • ui
                    • frames
                      • AboutDialog.java
                      • DeviceDialog.java
                      • NotepadWindow.java
                      • PreferencesDialog.java
                      • PropertiesDialog.java
                      • WorkspaceFrame.java
                    • scenes
                      • SpectaclesFactory.java
                      • ThumbnailScene.java
                      • WorkspaceScene.java
    • ClothoFabApps
      • FabDash
        • src
          • org
            • clothocore
              • widget
                • fabdash
                  • CollectionBrowser.java
                  • Connect.java
                  • InventoryTopComponent.java
                  • OutputHandler.java
                  • PopulateTools.java
                  • UserFrame.java
                  • browser
                    • ObjTypeChooser.java
                    • ScrollablePanel.java
                    • SearchBar.java
                    • SuperSearch.java
      • ToolAppBrowser
        • src
          • org
            • clothocad
              • tool
                • toolappbrowser
                  • Connect.java
                  • tc
                    • BrowsePanel.java
                    • BrowseTCTopComponent.java
                    • ScrollablePanel.java
    • ClothoProject
      • ClothoCore
        • src
          • org
            • clothocore
              • api
                • actor
                  • Actor.java
                  • RunStatus.java
                  • data
                    • BooleanToken.java
                    • CharacterToken.java
                    • DoubleToken.java
                    • IntegerToken.java
                    • ListToken.java
                    • MapToken.java
                    • ObjBaseToken.java
                    • StringToken.java
                    • Token.java
                  • io
                    • InputPort.java
                    • ListInputPort.java
                    • ListOutputPort.java
                    • MapInputPort.java
                    • MapOutputPort.java
                    • ObjBaseInputPort.java
                    • ObjBaseOutputPort.java
                    • OutputPort.java
                    • Port.java
                  • workflow
                    • CompositeActor.java
                    • IOLink.java
                    • IfElseAlgorithm.java
                    • LoopActor.java
                • core
                  • Collator.java
                  • Collector.java
                  • PluginManager.java
                  • PluginTypeEnum.java
                  • QuickStart.java
                  • wrapper
                    • AlgorithmWrapper.java
                    • ConnectionWrapper.java
                    • PluginWrapper.java
                    • ToolWrapper.java
                    • ViewerWrapper.java
                    • WidgetWrapper.java
                    • support
                      • ClothoDependency.java
                      • ClothoHelp.java
                • data
                  • Annotation.java
                  • Attachment.java
                  • Collection.java
                  • Comment.java
                  • ConflictResolution.java
                  • Container.java
                  • DataListener.java
                  • ExpData.java
                  • Factoid.java
                  • Family.java
                  • Feature.java
                  • FlexField.java
                  • Format.java
                  • Grammar.java
                  • Institution.java
                  • Lab.java
                  • Note.java
                  • NucSeq.java
                  • ObjBase.java
                  • ObjLink.java
                  • ObjType.java
                  • Oligo.java
                  • OligoSample.java
                  • Part.java
                  • Person.java
                  • Plasmid.java
                  • PlasmidSample.java
                  • Plate.java
                  • PlateType.java
                  • Reference.java
                  • Sample.java
                  • SampleData.java
                  • SequenceRead.java
                  • Strain.java
                  • StrainSample.java
                  • Vector.java
                  • WikiText.java
                  • XMLImporter.java
                • dnd
                  • CopyAndPaste.java
                  • DragHandler.java
                  • ObjBaseDropTargetListener.java
                  • ObjBaseObserver.java
                  • RefreshEvent.java
                  • TransferableObject.java
                • plugin
                  • ClothoAlgorithm.java
                  • ClothoConnection.java
                  • ClothoFormat.java
                  • ClothoGrammar.java
                  • ClothoPlugin.java
                  • ClothoTool.java
                  • ClothoViewer.java
                  • ClothoWidget.java
              • boot
                • Installer.java
              • core
                • Hub.java
              • util
                • basic
                  • FileUtils.java
                  • ImageSource.java
                  • ObjBasePopup.java
                  • ReaderInputStream.java
                  • UnknownKeywordException.java
                • blast
                  • BlastNCBIQuery.java
                  • BlastRequester.java
                • buttons
                  • GlassButton.java
                  • TransparentButton.java
                • chooser
                  • ClothoOpenChooser.java
                  • ClothoOpenChooserFrame.java
                  • ClothoSaveChooser.java
                  • ClothoSaveChooserFrame.java
                • def
                  • DefaultPluginManager.java
                  • DefaultViewer.java
                • dialog
                  • ClothoDialogBox.java
                  • DialogFrame.java
                  • WaitingDialog.java
                • elements
                  • AutoComboBox.java
                  • AutoTextField.java
                • frames
                  • GraphicFrame.java
                  • OptionFrame.java
                • misc
                  • BareBonesBrowserLaunch.java
                  • ClothoSearchUtil.java
                  • ClothoTxtUtil.java
                  • CommandHelp.java
                  • StackLayout.java
                  • WordGenerator.java
                • panels
                  • CardPanel.java
                  • ClothoJEditorPane.java
                  • ClothoSequenceJPanel.java
                • xml
                  • XMLParser.java
                  • XmlGenerator.java
      • MenuTasks
        • src
          • org
            • clothocad
              • library
                • menutasks
                  • ImportIDT.java