All Classes
- AbstractPluginDocument
- ActionProvider
- AdditionalSearchContent
- AdditionalSearchContent.Result
- AdditionalSearchContent.Utilities
- AdditionalSearchContent.Utilities.Filter
- AdditionalSearchContent.Utilities.FilterElement
- AdditionalXmlForDocument
- AdvancedSearchQueryTerm
- AlertPanel
- AlertPanel.AlertLevel
- AlertPanel.RoundedAlertBorder
- AlertPanel.TextAlign
- AliasDocument
- AlignmentLayout
- AlignmentOperation
- AlignmentOperation.InputProperties
- AminoAcidSequenceDocument
- AnnotatedPluginDocument
- AnnotatedPluginDocument.ActiveLinkSaveBehaviour
- AnnotatedPluginDocument.DocumentNotes
- Assembler
- Assembler.Callback
- Assembler.ContigOutputSupport
- Assembler.ReferenceSequenceSupport
- AssemblerInput
- AssemblerInput.DataType
- AssemblerInput.PairedDataType
- AssemblerInput.Properties
- AssemblerInput.Read
- AssemblerInput.ReferenceSequence
- Author
- Badge
- BadgeSupplier
- Base64Coder
- BasicSearchQuery
- BorderlessScrollPane
- BubbleToolTip
- ByteBackedCharSequence
- CallSoon
- CallSoon.EnabledProvider
- CharSequenceUtilities
- CheckboxSearchOption
- ChromatogramDocument
- CmlDocument
- CodonUsageTableDocument
- ColorUtilities
- CombinedAlignmentAndAminoAcidSequenceDocument
- CombinedAlignmentAndNucleotideGraphSequenceDocument
- CombinedAlignmentAndNucleotideSequenceDocument
- CombinedAlignmentAndSequenceDocument
- ComboboxSearchOption
- CompactQualityOnlyGraph
- CompositeRetrieveCallback
- CompoundSearchQuery
- CompoundSearchQuery.Operator
- CompressionUtilities
- CompressionUtilities.CompressedFileWrapper
- CompressionUtilities.CompressionMethod
- ConcatenatedList
- Condition
- Constraint
- ConstructorWrapper
- DatabaseFolderImporter
- DatabaseService
- DatabaseService.SequenceSearchQueryType
- DatabaseServiceException
- DatabaseServiceException.Canceled
- DatabaseServiceListener
- DataInputOutputUtilities
- DefaultAlignmentDocument
- DefaultAminoAcidSequence
- DefaultHyperlinkListener
- DefaultHyperlinkListener.SerializableRunnable
- DefaultMolecularStructureDocument
- DefaultNucleotideGraph
- DefaultNucleotideGraphSequence
- DefaultNucleotideSequence
- DefaultPhylogenyDocument
- DefaultSameTaxaTreesDocument
- DefaultSequenceDocument
- DefaultSequenceDocument.Cache
- DefaultSequenceGraphFactories
- DefaultSequenceGraphFactories.SequenceAlignmentScorer
- DefaultSequenceGraphFactories.SingleSequenceScorer
- DefaultSequenceListDocument
- DefaultTreeDocument
- DependentComboboxSearchOption
- DialogButtonPanel
- Dialogs
- Dialogs.DialogAction
- Dialogs.DialogClosedListener
- Dialogs.DialogIcon
- Dialogs.DialogOptions
- Dialogs.Result
- Dialogs.SaveChanges
- DocumentAction
- DocumentCollection
- DocumentField
- DocumentField.SequenceType
- DocumentFieldAndValue
- DocumentFileExporter
- DocumentFileExporterAndExternalViewer
- DocumentFileImporter
- DocumentFileImporter.AutoDetectStatus
- DocumentFileImporter.ImportCallback
- DocumentFilter
- DocumentHistory
- DocumentHistoryEntry
- DocumentHistoryEntryField
- DocumentImportException
- DocumentImportException.Canceled
- DocumentListener
- DocumentNote
- DocumentNoteField
- DocumentNoteField.Types
- DocumentNoteType
- DocumentNoteUtilities
- DocumentOperation
- DocumentOperation.OperationCallback
- DocumentOperation.OperationCallback.Wrapper
- DocumentOperation.Wrapper
- DocumentOperationInput
- DocumentSearchCache
- DocumentSelectionOption
- DocumentSelectionOption.DoNotRememberInPreferences
- DocumentSelectionOption.FolderOrDocuments
- DocumentSelectionOption.OptionValueCreator
- DocumentSelectionSignature
- DocumentSelectionSignature.DocumentSelectionSignatureAtom
- DocumentType
- DocumentUtilities
- DocumentViewer
- DocumentViewer.ViewerLocation
- DocumentViewerFactory
- DocumentViewerFactory.ViewPrecedence
- DocumentViewerMessageHandler
- EditableNucleotideGraphSequenceDocument
- EditableSameTaxaTreesDocument
- EditableSequenceDocument
- EditableSequenceListDocument
- ElementProvider
- EndGapsHelper
- EndGapsManager
- EndGapsManager.Builder
- EValue
- Execution
- Execution.OutputListener
- ExportableDocument
- ExportableDocument.Format
- ExtendedEditableSequenceListDocument
- ExtendedNucleotideGraph
- ExtendedPrintable
- ExtendedPrintable.Factory
- ExtendedPrintable.Wrapper
- ExtendedSearchOption
- ExternalSort
- ExternalSort.Serializer
- FastSaxBuilder
- FieldWithName
- FileUtilities
- FileUtilities.RetryPolicy
- FileUtilities.TargetExistsAction
- Filterable
- FilteredSaxHandler
- FilteredSaxHandler.ElementHandler
- Findable
- Findable.FindAllCallback
- Findable.FindOptions
- Findable.FindResult
- FolderView
- FolderViewDocument
- GarbageCollectionNotifier
- GButton
- GCheckBox
- GComboBox
- GComboBox.AlternativeDropDownTextProvider
- GComboBox.DefaultModelWhereSetSelectedItemDoesntFireContentsChanged
- GComboBox.DescriptionProvider
- GComboBox.EnabledStateProvider
- GComboBox.IconsProvider
- GDefaultTreeCellRenderer
- GDialog
- GEditorPane
- Geneious
- Geneious.MajorVersion
- GeneiousAction
- GeneiousAction.Divider
- GeneiousAction.SubMenu
- GeneiousAction.ToggleAction
- GeneiousActionOptions
- GeneiousActionOptions.Category
- GeneiousActionOptions.MainMenu
- GeneiousActionOptions.ShortcutChangeListener
- GeneiousActionToolbar
- GeneiousActionToolbar.CustomToolbarComponent
- GeneiousGraphics2D
- GeneiousGridDocumentOperation
- GeneiousGridDocumentOperation.GridInput
- GeneiousGridDocumentOperation.LocationChangedListenerProvider
- GeneiousGridImporter
- GeneiousObjectInputStream
- GeneiousObjectOutputStream
- GeneiousPlugin
- GeneiousPreferences
- GeneiousPreferences.GeneiousCheckBoxPreference
- GeneiousPreferences.GeneiousComboBoxPreference
- GeneiousPreferences.GeneiousDependentPreference
- GeneiousPreferences.GeneiousPreference
- GeneiousPreferences.GeneiousRadioButtonPreference
- GeneiousPreferences.GeneiousStringPreference
- GeneiousService
- GeneiousService.ServiceStatus
- GeneiousServiceListener
- GeneiousServiceWithPanel
- GeneiousSoftReference
- GeneralUtilities
- GLabel
- GMenuItem
- GPanel
- GPopupMenu
- GprDocument
- GScrollPane
- GSpinnerNumberModel
- GTable
- GTextArea
- GTextField
- GTextPane
- GuiUtilities
- HinDocument
- HyperlinkButton
- Icons
- IconUtilities
- ImmutableSequence
- ImmutableSequence.Builder
- ImmutableSequenceImplementation
- ImportUtilities
- ImportUtilities.ActionWhenInvalid
- ImportUtilities.ImportDocumentType
- ImportUtilities.ImportSource
- InputStreamFromRandomAccessFile
- Intern
- Interval
- IntList
- IntList.Array
- InvalidZipEntryException
- JournalArticleDocument
- JournalArticleDocument.Utils
- License
- License.PluginLicense
- Logs
- MalformedURNException
- MayReturnSlowly
- MessageDigestUtilities
- MolDocument
- MolecularStructureDocument
- MoreOptionsButton
- MultiThreadedProcessingSystem
- MultiThreadedTask
- MustReturnPromptly
- NoLongerViewedListener
- NucleotideCounter
- NucleotideGraph
- NucleotideGraph.ImmutableGraphProvider
- NucleotideGraphSequenceDocument
- NucleotideSequenceDocument
- NwoDocument
- OligoSequenceDocument
- OligoSequenceDocument.OligoType
- OperationLocationOptions
- OperationLocationOptions.LocationChangedListener
- OperationRecordDocument
- Options
- Options.Alignment
- Options.BooleanOption
- Options.ButtonOption
- Options.ComboBoxOption
- Options.ComponentCreator
- Options.DateOption
- Options.DoubleOption
- Options.EditableComboBoxOption
- Options.ExecutableFileSelectionOption
- Options.FileSelectionOption
- Options.IntegerOption
- Options.LabelOption
- Options.MultipleLineStringOption
- Options.MultipleOptions
- Options.Option
- Options.OptionValue
- Options.PageChooserType
- Options.RadioOption
- Options.RadioOption.DependentPosition
- Options.StringOption
- OptionsPanel
- OptionsPanel.RoundedLineBorder
- OutputStreamThatCountsBytesWritten
- OutputStreamToRandomAccessFile
- OverlayIcons
- PairedReadManager
- PairedReadManager.Builder
- PairedReadManager.Orientation
- PairedReads
- PartiallyWritableDatabaseService
- PasswordOption
- PdbDocument
- Percentage
- PhylogenyDocument
- PluginDocument
- PluginDocument.ReferencedDocumentsAlwaysLoaded
- PluginDocument.ReferencedDocumentsNotLoaded
- PluginDocument.SizeRequiredToLoadIntoMemoryProvider
- PluginDocumentXmlCollection
- PluginDocumentXmlCollection.ElementHandler
- PluginPreferences
- PluginUtilities
- PluginUtilities.WritableDatabaseServicesListener
- ProgressFrame
- ProgressInputStream
- ProgressInputStream.ProgressInterruptedIOException
- ProOnlyComponents
- ProOnlyComponents.Button
- ProOnlyComponents.CheckBox
- ProOnlyComponents.CheckBox.ProOnlySuffix
- ProOnlyComponents.CheckBoxMenuItem
- ProOnlyComponents.ComboBox
- ProOnlyComponents.Label
- ProOnlyComponents.Menu
- ProOnlyComponents.MenuItem
- ProOnlyComponents.Panel
- ProOnlyComponents.ToggleButton
- PublicationDocument
- PublicationDocument.Utils
- Query
- Query.Factory
- QueryField
- Renamable
- RetrieveCallback
- RootedTreeDocument
- RunnableWithProgress
- RuntimeDocumentOperationException
- SameTaxaTreesDocument
- ScrollPaneLayoutThatCorrectlyAccountsForVerticalScrollbarWidth
- SearchIndexCorruptOrMissingException
- SequenceAlignmentDocument
- SequenceAlignmentDocument.ReferencedSequence
- SequenceAlignmentListDocument
- SequenceAnnotation
- SequenceAnnotationGenerator
- SequenceAnnotationGenerator.AnnotationGeneratorResult
- SequenceAnnotationGenerator.AnnotationGeneratorResult.ResidueAdjustment
- SequenceAnnotationGenerator.AnnotationGeneratorResultOnAlignment
- SequenceAnnotationGenerator.AnnotationGeneratorResultsOnSingleSequence
- SequenceAnnotationGenerator.SelectionGrabOption
- SequenceAnnotationGenerator.SelectionRange
- SequenceAnnotationGenerator.SingleSequenceResultGenerator
- SequenceAnnotationGroup
- SequenceAnnotationInterval
- SequenceAnnotationInterval.Direction
- SequenceAnnotationQualifier
- SequenceBuilder
- SequenceCharSequence
- SequenceDatabaseSuperService
- SequenceDocument
- SequenceDocument.Alphabet
- SequenceDocument.Transformer
- SequenceDocumentWithEditableAnnotations
- SequenceExtractionUtilities
- SequenceExtractionUtilities.ExtractionOptions
- SequenceGapInformation
- SequenceGapInformation.Provider
- SequenceGraph
- SequenceGraph.Location
- SequenceGraph.SequencePropertyRetriever
- SequenceGraphFactory
- SequenceListDocument
- SequenceListOnDisk
- SequenceListOnDisk.AlignmentData
- SequenceListOnDisk.Builder
- SequenceListSummary
- SequenceListSummary.Coverage
- SequenceListSummary.PairwiseSimilarity
- SequenceListSummary.Provider
- SequencePropertiesStorage
- SequenceSelection
- SequenceSelection.SelectedAnnotation
- SequenceSelection.SelectionInterval
- SequenceSelection.SequenceDocumentType
- SequenceSelection.SequenceIndex
- SequenceSelectionWithDocuments
- SequenceSelectionWithDocuments.DocumentsInvalidException
- SequenceSelectionWithDocuments.ExtractionStrategy
- SequenceSelectionWithDocuments.SelectedDocumentsModifiedException
- SequenceTrack
- SequenceTrack.Manager
- SequenceTrack.Manager.Provider
- SequenceUtilities
- SequenceViewerExtension
- SequenceViewerExtension.ComponentLocation
- SequenceViewerExtension.Factory
- SequenceViewerExtension.PropertyRetrieverAndEditor
- SequenceViewerExtension.PropertyRetrieverAndEditor.DiscardReferencesCallback
- SequenceViewerExtension.SequenceAnnotationWrapper
- SequenceViewerExtension.StateFrequencies
- SequenceViewerExtension.StatisticsFactory
- SequenceViewerExtension.StatisticsMethod
- SequenceViewerExtension.StatisticsSection
- ServiceUtilities
- SharingSummary
- StandardIcons
- StringUtilities
- SummaryDocument
- SystemUtilities
- SystemUtilities.LowMemoryChecker
- TaxonomyDocument
- TaxonomyDocument.Taxon
- TaxonomyDocument.TaxonomicLevel
- TestGeneious
- TextDocument
- TextDocument.Format
- TextFieldSearchOption
- TextOrSimilaritySearchOption
- ThreadUtilities
- TreeDocument
- TreeViewerExtension
- TreeViewerExtension.Factory
- UI
- UI.ClientProperties
- UI.General
- UI.Misc
- UI.Symbols
- UI.TabPane
- UI.ThemeInvertedColor
- UI.Tree
- URLStreamHandlerManager
- URN
- UrnWithRevisionNumber
- UrnWithSequenceRegions
- UserEditablePreferences
- ValueAndFrequencyDistribution
- ValueAndFrequencyDistribution.ValueAndFrequency
- WeakReferenceList
- WeakSimpleListenerManager
- WorkflowSharingManager
- WritableDatabaseService
- WritableDatabaseService.DeletedItemsType
- WritableDatabaseService.DocumentsToAdd
- WritableDatabaseService.DocumentToAdd
- WritableDatabaseService.DummyService
- WritableDatabaseService.SearchResultPropertiesAdjuster
- WritableDatabaseServiceTree
- XMLSerializable
- XMLSerializable.OldVersionCompatible
- XMLSerializable.VersionSupportType
- XMLSerializableWithProgress
- XMLSerializationException
- XMLSerializer
- XyzDocument
- ZoomChangeEvent
- ZoomPanel