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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