Hierarchy For All Packages

Package Hierarchies:

• com.biomatters.geneious.publicapi.components,
• com.biomatters.geneious.publicapi.databaseservice,
• com.biomatters.geneious.publicapi.documents,
• com.biomatters.geneious.publicapi.documents.sequence,
• com.biomatters.geneious.publicapi.documents.types,
• com.biomatters.geneious.publicapi.implementations,
• com.biomatters.geneious.publicapi.implementations.sequence,
• com.biomatters.geneious.publicapi.implementations.structure,
• com.biomatters.geneious.publicapi.plugin,
• com.biomatters.geneious.publicapi.utilities,
• com.biomatters.geneious.publicapi.utilities.xml

Class Hierarchy

• java.lang.Object
  • javax.swing.AbstractAction (implements javax.swing.Action, java.lang.Cloneable, java.io.Serializable)
    • com.biomatters.geneious.publicapi.plugin.GeneiousAction
      • com.biomatters.geneious.publicapi.plugin.GeneiousAction.Divider
      • com.biomatters.geneious.publicapi.plugin.GeneiousAction.SubMenu
      • com.biomatters.geneious.publicapi.plugin.GeneiousAction.ToggleAction
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • java.util.AbstractList<E> (implements java.util.List<E>)
      • com.biomatters.geneious.publicapi.utilities.ConcatenatedList<T>
      • com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResultsOnSingleSequence
      • com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk<T> (implements com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.Provider, com.biomatters.geneious.publicapi.documents.XMLSerializable, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • com.biomatters.geneious.publicapi.documents.AbstractPluginDocument (implements com.biomatters.geneious.publicapi.documents.PluginDocument, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
    • com.biomatters.geneious.publicapi.implementations.structure.DefaultMolecularStructureDocument (implements com.biomatters.geneious.publicapi.documents.types.MolecularStructureDocument)
      • com.biomatters.geneious.publicapi.implementations.structure.CmlDocument
      • com.biomatters.geneious.publicapi.implementations.structure.GprDocument
      • com.biomatters.geneious.publicapi.implementations.structure.HinDocument
      • com.biomatters.geneious.publicapi.implementations.structure.MolDocument
      • com.biomatters.geneious.publicapi.implementations.structure.NwoDocument
      • com.biomatters.geneious.publicapi.implementations.structure.PdbDocument (implements com.biomatters.geneious.publicapi.documents.sequence.SequenceListDocument, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
      • com.biomatters.geneious.publicapi.implementations.structure.XyzDocument
    • com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument (implements com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument, com.biomatters.geneious.publicapi.documents.Renamable, com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument, com.biomatters.geneious.publicapi.implementations.SequenceGapInformation.Provider, com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack.Manager.Provider, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
      • com.biomatters.geneious.publicapi.implementations.sequence.DefaultAminoAcidSequence (implements com.biomatters.geneious.publicapi.documents.sequence.AminoAcidSequenceDocument)
      • com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideSequence (implements com.biomatters.geneious.publicapi.documents.sequence.NucleotideSequenceDocument)
        • com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideGraphSequence (implements com.biomatters.geneious.publicapi.documents.sequence.ChromatogramDocument, com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument, com.biomatters.geneious.publicapi.documents.sequence.ExtendedNucleotideGraph, com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph.ImmutableGraphProvider)
        • com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument
    • com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument (implements com.biomatters.geneious.publicapi.documents.sequence.ExtendedEditableSequenceListDocument, com.biomatters.geneious.publicapi.documents.sequence.PairedReads, com.biomatters.geneious.publicapi.documents.PluginDocument.SizeRequiredToLoadIntoMemoryProvider, com.biomatters.geneious.publicapi.documents.Renamable, com.biomatters.geneious.publicapi.documents.sequence.SequenceListDocument, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible, com.biomatters.geneious.publicapi.documents.XMLSerializableWithProgress)
    • com.biomatters.geneious.publicapi.documents.DocumentCollection (implements com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • javax.swing.AbstractSpinnerModel (implements java.io.Serializable, javax.swing.SpinnerModel)
    • javax.swing.SpinnerNumberModel (implements java.io.Serializable)
      • com.biomatters.geneious.publicapi.components.GSpinnerNumberModel (implements java.io.Serializable)
  • com.biomatters.geneious.publicapi.plugin.ActionProvider
  • com.biomatters.geneious.publicapi.documents.AdditionalSearchContent.Result
  • com.biomatters.geneious.publicapi.documents.AdditionalSearchContent.Utilities
  • com.biomatters.geneious.publicapi.documents.sequence.AlignmentLayout (implements com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • com.biomatters.geneious.publicapi.plugin.AlignmentOperation
  • com.biomatters.geneious.publicapi.plugin.AlignmentOperation.InputProperties
  • com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument (implements com.biomatters.geneious.publicapi.documents.XMLSerializable)
  • com.biomatters.geneious.publicapi.plugin.Assembler
  • com.biomatters.geneious.publicapi.plugin.Assembler.Callback
  • com.biomatters.geneious.publicapi.plugin.AssemblerInput
  • com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties
  • com.biomatters.geneious.publicapi.plugin.AssemblerInput.Read
  • com.biomatters.geneious.publicapi.plugin.AssemblerInput.Reads
  • com.biomatters.geneious.publicapi.plugin.AssemblerInput.ReferenceSequence
  • com.biomatters.geneious.publicapi.documents.Author (implements java.lang.Comparable<T>, com.biomatters.geneious.publicapi.documents.XMLSerializable)
  • com.biomatters.geneious.publicapi.utilities.Base64Coder
  • com.biomatters.geneious.publicapi.components.BubbleToolTip
  • com.biomatters.geneious.publicapi.documents.sequence.ByteBackedCharSequence (implements java.lang.CharSequence)
  • com.biomatters.geneious.publicapi.utilities.CallSoon
  • com.biomatters.geneious.publicapi.utilities.CharSequenceUtilities
  • com.biomatters.geneious.publicapi.documents.sequence.CompactQualityOnlyGraph (implements com.biomatters.geneious.publicapi.documents.sequence.ExtendedNucleotideGraph)
  • java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    • java.awt.Container
      • javax.swing.JComponent (implements java.io.Serializable)
        • javax.swing.AbstractButton (implements java.awt.ItemSelectable, javax.swing.SwingConstants)
          • javax.swing.JButton (implements javax.accessibility.Accessible)
            • com.biomatters.geneious.publicapi.components.GButton
              • com.biomatters.geneious.publicapi.components.MoreOptionsButton
              • com.biomatters.geneious.publicapi.components.ProOnlyComponents.Button
          • javax.swing.JMenuItem (implements javax.accessibility.Accessible, javax.swing.MenuElement)
            • javax.swing.JCheckBoxMenuItem (implements javax.accessibility.Accessible, javax.swing.SwingConstants)
              • com.biomatters.geneious.publicapi.components.ProOnlyComponents.CheckBoxMenuItem
            • javax.swing.JMenu (implements javax.accessibility.Accessible, javax.swing.MenuElement)
              • com.biomatters.geneious.publicapi.components.ProOnlyComponents.Menu
            • com.biomatters.geneious.publicapi.components.ProOnlyComponents.MenuItem
          • javax.swing.JToggleButton (implements javax.accessibility.Accessible)
            • javax.swing.JCheckBox (implements javax.accessibility.Accessible)
              • com.biomatters.geneious.publicapi.components.ProOnlyComponents.CheckBox
            • com.biomatters.geneious.publicapi.components.ProOnlyComponents.ToggleButton
        • javax.swing.JComboBox<E> (implements javax.accessibility.Accessible, java.awt.event.ActionListener, java.awt.ItemSelectable, javax.swing.event.ListDataListener)
          • com.biomatters.geneious.publicapi.components.GComboBox
            • com.biomatters.geneious.publicapi.components.ProOnlyComponents.ComboBox
        • javax.swing.JLabel (implements javax.accessibility.Accessible, javax.swing.SwingConstants)
          • com.biomatters.geneious.publicapi.components.GLabel
          • com.biomatters.geneious.publicapi.components.ProOnlyComponents.Label
        • javax.swing.JPanel (implements javax.accessibility.Accessible)
          • com.biomatters.geneious.publicapi.components.GPanel
            • com.biomatters.geneious.publicapi.components.DialogButtonPanel
            • com.biomatters.geneious.publicapi.components.GeneiousActionToolbar
          • com.biomatters.geneious.publicapi.components.OptionsPanel
          • com.biomatters.geneious.publicapi.components.ProOnlyComponents.Panel
          • com.biomatters.geneious.publicapi.components.ZoomPanel
        • javax.swing.JPopupMenu (implements javax.accessibility.Accessible, javax.swing.MenuElement)
          • com.biomatters.geneious.publicapi.components.GPopupMenu
        • javax.swing.JTable (implements javax.accessibility.Accessible, javax.swing.event.CellEditorListener, javax.swing.event.ListSelectionListener, javax.swing.event.RowSorterListener, javax.swing.Scrollable, javax.swing.event.TableColumnModelListener, javax.swing.event.TableModelListener)
          • com.biomatters.geneious.publicapi.components.GTable
        • javax.swing.text.JTextComponent (implements javax.accessibility.Accessible, javax.swing.Scrollable)
          • javax.swing.JEditorPane
            • com.biomatters.geneious.publicapi.components.GEditorPane
            • javax.swing.JTextPane
              • com.biomatters.geneious.publicapi.components.GTextPane
          • javax.swing.JTextArea
            • com.biomatters.geneious.publicapi.components.GTextArea
          • javax.swing.JTextField (implements javax.swing.SwingConstants)
            • com.biomatters.geneious.publicapi.components.GTextField
      • java.awt.Window (implements javax.accessibility.Accessible)
        • java.awt.Dialog
          • javax.swing.JDialog (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • com.biomatters.geneious.publicapi.components.GDialog
  • com.biomatters.geneious.publicapi.utilities.CompressionUtilities
  • com.biomatters.geneious.publicapi.utilities.CompressionUtilities.CompressedFileWrapper
  • com.biomatters.geneious.publicapi.documents.Constraint
  • com.biomatters.geneious.publicapi.databaseservice.DatabaseServiceListener
  • com.biomatters.geneious.publicapi.utilities.DataInputOutputUtilities
  • org.xml.sax.helpers.DefaultHandler (implements org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler)
    • org.jdom.input.SAXHandler (implements org.xml.sax.ext.DeclHandler, org.xml.sax.DTDHandler, org.xml.sax.ext.LexicalHandler)
      • com.biomatters.geneious.publicapi.utilities.xml.FilteredSaxHandler
  • com.biomatters.geneious.publicapi.components.DefaultHyperlinkListener (implements javax.swing.event.HyperlinkListener)
  • com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph (implements com.biomatters.geneious.publicapi.documents.sequence.ExtendedNucleotideGraph)
  • com.biomatters.geneious.publicapi.implementations.DefaultSameTaxaTreesDocument (implements com.biomatters.geneious.publicapi.documents.types.EditableSameTaxaTreesDocument, com.biomatters.geneious.publicapi.documents.ExportableDocument, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument.Cache
  • com.biomatters.geneious.publicapi.implementations.DefaultSequenceGraphFactories
  • com.biomatters.geneious.publicapi.implementations.DefaultSequenceGraphFactories.SequenceAlignmentScorer
  • com.biomatters.geneious.publicapi.implementations.DefaultSequenceGraphFactories.SingleSequenceScorer
  • com.biomatters.geneious.publicapi.implementations.DefaultTreeDocument (implements com.biomatters.geneious.publicapi.documents.types.EditableSameTaxaTreesDocument, com.biomatters.geneious.publicapi.documents.ExportableDocument, com.biomatters.geneious.publicapi.documents.types.RootedTreeDocument, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • com.biomatters.geneious.publicapi.components.Dialogs
  • com.biomatters.geneious.publicapi.components.Dialogs.DialogAction
  • com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions
  • com.biomatters.geneious.publicapi.components.Dialogs.Result
  • com.biomatters.geneious.publicapi.plugin.DocumentAction
  • com.biomatters.geneious.publicapi.documents.DocumentField (implements com.biomatters.geneious.publicapi.components.GComboBox.DescriptionProvider, com.biomatters.geneious.publicapi.documents.XMLSerializable, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • com.biomatters.geneious.publicapi.documents.DocumentFieldAndValue
  • com.biomatters.geneious.publicapi.plugin.DocumentFileExporter
    • com.biomatters.geneious.publicapi.plugin.DocumentFileExporterAndExternalViewer
  • com.biomatters.geneious.publicapi.plugin.DocumentFileImporter
  • com.biomatters.geneious.publicapi.plugin.DocumentFileImporter.ImportCallback
  • com.biomatters.geneious.publicapi.documents.DocumentHistory
  • com.biomatters.geneious.publicapi.documents.DocumentHistoryEntry (implements com.biomatters.geneious.publicapi.documents.XMLSerializable)
  • com.biomatters.geneious.publicapi.documents.DocumentHistoryEntryField (implements com.biomatters.geneious.publicapi.documents.XMLSerializable)
  • com.biomatters.geneious.publicapi.documents.DocumentNoteField
  • com.biomatters.geneious.publicapi.documents.DocumentNoteUtilities
  • com.biomatters.geneious.publicapi.plugin.DocumentOperation
    • com.biomatters.geneious.publicapi.plugin.DocumentOperation.Wrapper
    • com.biomatters.geneious.publicapi.plugin.GeneiousGridDocumentOperation
  • com.biomatters.geneious.publicapi.plugin.DocumentOperation.OperationCallback
    • com.biomatters.geneious.publicapi.plugin.DocumentOperation.OperationCallback.Wrapper
  • com.biomatters.geneious.publicapi.plugin.DocumentOperationInput
  • com.biomatters.geneious.publicapi.documents.DocumentSearchCache<T>
  • com.biomatters.geneious.publicapi.plugin.DocumentSelectionOption.FolderOrDocuments
  • com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature (implements com.biomatters.geneious.publicapi.documents.XMLSerializable)
  • com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature.DocumentSelectionSignatureAtom
  • com.biomatters.geneious.publicapi.plugin.DocumentType<T>
  • com.biomatters.geneious.publicapi.documents.DocumentUtilities
  • com.biomatters.geneious.publicapi.plugin.DocumentViewer
  • com.biomatters.geneious.publicapi.plugin.DocumentViewer.ViewerLocation
  • com.biomatters.geneious.publicapi.plugin.DocumentViewerFactory
  • com.biomatters.geneious.publicapi.plugin.DocumentViewerMessageHandler
  • javax.swing.text.EditorKit (implements java.lang.Cloneable, java.io.Serializable)
    • javax.swing.text.DefaultEditorKit
      • javax.swing.text.StyledEditorKit
        • javax.swing.text.html.HTMLEditorKit (implements javax.accessibility.Accessible)
          • com.biomatters.geneious.publicapi.components.GTextPane.MemoryFixedHTMLEditorKit
  • com.biomatters.geneious.publicapi.implementations.EndGapsHelper
  • com.biomatters.geneious.publicapi.implementations.EndGapsManager
  • com.biomatters.geneious.publicapi.implementations.EndGapsManager.Builder
  • com.biomatters.geneious.publicapi.utilities.Execution
  • com.biomatters.geneious.publicapi.utilities.Execution.OutputListener
  • com.biomatters.geneious.publicapi.plugin.ExtendedPrintable
    • com.biomatters.geneious.publicapi.plugin.ExtendedPrintable.Wrapper
  • com.biomatters.geneious.publicapi.plugin.ExtendedPrintable.Factory
  • com.biomatters.geneious.publicapi.databaseservice.ExtendedSearchOption
    • com.biomatters.geneious.publicapi.databaseservice.CheckboxSearchOption
    • com.biomatters.geneious.publicapi.databaseservice.ComboboxSearchOption
    • com.biomatters.geneious.publicapi.databaseservice.DependentComboboxSearchOption
    • com.biomatters.geneious.publicapi.databaseservice.TextFieldSearchOption
    • com.biomatters.geneious.publicapi.databaseservice.TextOrSimilaritySearchOption
  • com.biomatters.geneious.publicapi.documents.sequence.ExternalSort<T>
  • com.biomatters.geneious.publicapi.utilities.FileUtilities
  • com.biomatters.geneious.publicapi.plugin.Findable
  • com.biomatters.geneious.publicapi.plugin.Findable.FindOptions
  • com.biomatters.geneious.publicapi.databaseservice.FolderView (implements com.biomatters.geneious.publicapi.documents.XMLSerializable, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • com.biomatters.geneious.publicapi.utilities.GarbageCollectionNotifier
  • com.biomatters.geneious.publicapi.plugin.Geneious
  • com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions
  • com.biomatters.geneious.publicapi.components.GeneiousActionToolbar.CustomToolbarComponent
  • com.biomatters.geneious.publicapi.plugin.GeneiousGridDocumentOperation.GridInput
  • com.biomatters.geneious.publicapi.plugin.GeneiousGridImporter
  • com.biomatters.geneious.publicapi.plugin.GeneiousPlugin
  • com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousPreference
    • com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousCheckBoxPreference
    • com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousComboBoxPreference
    • com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousDependentPreference
    • com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousRadioButtonPreference
    • com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousStringPreference
  • com.biomatters.geneious.publicapi.plugin.GeneiousService
    • com.biomatters.geneious.publicapi.databaseservice.DatabaseService
      • com.biomatters.geneious.publicapi.databaseservice.PartiallyWritableDatabaseService
      • com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService
    • com.biomatters.geneious.publicapi.plugin.GeneiousServiceWithPanel
      • com.biomatters.geneious.publicapi.databaseservice.SequenceDatabaseSuperService
  • com.biomatters.geneious.publicapi.utilities.GeneralUtilities
  • com.biomatters.geneious.publicapi.utilities.GuiUtilities
  • com.biomatters.geneious.publicapi.plugin.Icons
    • com.biomatters.geneious.publicapi.components.OverlayIcons
  • com.biomatters.geneious.publicapi.utilities.IconUtilities
  • com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence.Builder
  • com.biomatters.geneious.publicapi.utilities.ImportUtilities
  • java.io.InputStream (implements java.io.Closeable)
    • java.io.FilterInputStream
      • com.biomatters.geneious.publicapi.utilities.ProgressInputStream
    • com.biomatters.geneious.publicapi.utilities.InputStreamFromRandomAccessFile
    • java.io.ObjectInputStream (implements java.io.ObjectInput, java.io.ObjectStreamConstants)
      • com.biomatters.geneious.publicapi.documents.sequence.GeneiousObjectInputStream
  • com.biomatters.geneious.publicapi.utilities.Intern<T>
  • com.biomatters.geneious.publicapi.utilities.Interval (implements java.lang.Iterable<T>, com.biomatters.geneious.publicapi.documents.XMLSerializable, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • com.biomatters.geneious.publicapi.utilities.IntList
    • com.biomatters.geneious.publicapi.utilities.IntList.Array
  • com.biomatters.geneious.publicapi.documents.types.JournalArticleDocument.Utils
  • com.biomatters.geneious.publicapi.plugin.License
  • com.biomatters.geneious.publicapi.plugin.License.PluginLicense
  • com.biomatters.geneious.publicapi.utilities.MultiThreadedProcessingSystem<T>
  • com.biomatters.geneious.publicapi.utilities.MultiThreadedTask<ResultType>
  • com.biomatters.geneious.publicapi.plugin.NoLongerViewedListener
  • java.lang.Number (implements java.io.Serializable)
    • com.biomatters.geneious.publicapi.implementations.EValue (implements java.lang.Comparable<T>, com.biomatters.geneious.publicapi.documents.XMLSerializable, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
    • com.biomatters.geneious.publicapi.implementations.Percentage (implements java.lang.Comparable<T>, com.biomatters.geneious.publicapi.documents.XMLSerializable, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • com.biomatters.geneious.publicapi.plugin.OperationLocationOptions.LocationChangedListener
  • com.biomatters.geneious.publicapi.documents.OperationRecordDocument (implements com.biomatters.geneious.publicapi.documents.PluginDocument, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • com.biomatters.geneious.publicapi.plugin.Options (implements com.biomatters.geneious.publicapi.documents.XMLSerializable)
    • com.biomatters.geneious.publicapi.plugin.OperationLocationOptions
  • com.biomatters.geneious.publicapi.plugin.Options.MultipleOptions (implements com.biomatters.geneious.publicapi.documents.XMLSerializable)
  • com.biomatters.geneious.publicapi.plugin.Options.Option<ValueType,ComponentType> (implements com.biomatters.geneious.publicapi.documents.XMLSerializable)
    • com.biomatters.geneious.publicapi.plugin.DocumentSelectionOption
    • com.biomatters.geneious.publicapi.plugin.Options.BooleanOption
    • com.biomatters.geneious.publicapi.plugin.Options.ButtonOption
    • com.biomatters.geneious.publicapi.plugin.Options.ComboBoxOption<ValueType>
    • com.biomatters.geneious.publicapi.plugin.Options.DateOption
    • com.biomatters.geneious.publicapi.plugin.Options.DoubleOption
    • com.biomatters.geneious.publicapi.plugin.Options.EditableComboBoxOption
    • com.biomatters.geneious.publicapi.plugin.Options.ExecutableFileSelectionOption
    • com.biomatters.geneious.publicapi.plugin.Options.FileSelectionOption
    • com.biomatters.geneious.publicapi.plugin.Options.IntegerOption
    • com.biomatters.geneious.publicapi.plugin.Options.LabelOption
    • com.biomatters.geneious.publicapi.plugin.Options.MultipleLineStringOption
    • com.biomatters.geneious.publicapi.plugin.Options.RadioOption<ValueType>
    • com.biomatters.geneious.publicapi.plugin.Options.StringOption
    • com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionGrabOption
  • com.biomatters.geneious.publicapi.plugin.Options.OptionValue (implements com.biomatters.geneious.publicapi.documents.XMLSerializable)
  • com.biomatters.geneious.publicapi.components.OptionsPanel.RoundedLineBorder (implements javax.swing.border.Border)
  • java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
    • java.io.ObjectOutputStream (implements java.io.ObjectOutput, java.io.ObjectStreamConstants)
      • com.biomatters.geneious.publicapi.documents.sequence.GeneiousObjectOutputStream
    • com.biomatters.geneious.publicapi.utilities.OutputStreamThatCountsBytesWritten
    • com.biomatters.geneious.publicapi.utilities.OutputStreamToRandomAccessFile
  • com.biomatters.geneious.publicapi.implementations.PairedReadManager (implements com.biomatters.geneious.publicapi.documents.sequence.PairedReads, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • com.biomatters.geneious.publicapi.implementations.PairedReadManager.Builder
  • com.biomatters.geneious.publicapi.utilities.xml.PluginDocumentXmlCollection
  • com.biomatters.geneious.publicapi.utilities.xml.PluginDocumentXmlCollection.ElementHandler
  • com.biomatters.geneious.publicapi.plugin.PluginPreferences<T>
  • com.biomatters.geneious.publicapi.plugin.PluginUtilities
  • com.biomatters.geneious.publicapi.plugin.PluginUtilities.WritableDatabaseServicesListener
  • jebl.util.ProgressListener (implements jebl.util.Cancelable)
    • com.biomatters.geneious.publicapi.components.ProgressFrame
    • com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback
      • com.biomatters.geneious.publicapi.databaseservice.CompositeRetrieveCallback
  • com.biomatters.geneious.publicapi.components.ProOnlyComponents
  • com.biomatters.geneious.publicapi.documents.types.PublicationDocument.Utils
  • com.biomatters.geneious.publicapi.databaseservice.Query.Factory
  • com.biomatters.geneious.publicapi.databaseservice.QueryField (implements com.biomatters.geneious.publicapi.documents.XMLSerializable)
  • org.jdom.input.SAXBuilder
    • com.biomatters.geneious.publicapi.utilities.xml.FastSaxBuilder
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument (implements com.biomatters.geneious.publicapi.documents.sequence.PairedReads, com.biomatters.geneious.publicapi.documents.PluginDocument)
    • com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument (implements com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
      • com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndAminoAcidSequenceDocument (implements com.biomatters.geneious.publicapi.documents.sequence.AminoAcidSequenceDocument)
      • com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndNucleotideGraphSequenceDocument (implements com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument)
      • com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndNucleotideSequenceDocument (implements com.biomatters.geneious.publicapi.documents.sequence.NucleotideSequenceDocument)
    • com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument (implements com.biomatters.geneious.publicapi.documents.PluginDocument, com.biomatters.geneious.publicapi.documents.PluginDocument.SizeRequiredToLoadIntoMemoryProvider, com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.Provider, com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack.Manager.Provider, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible, com.biomatters.geneious.publicapi.documents.XMLSerializableWithProgress)
      • com.biomatters.geneious.publicapi.documents.types.PhylogenyDocument (implements com.biomatters.geneious.publicapi.documents.types.SameTaxaTreesDocument)
        • com.biomatters.geneious.publicapi.implementations.DefaultPhylogenyDocument (implements com.biomatters.geneious.publicapi.documents.types.EditableSameTaxaTreesDocument, com.biomatters.geneious.publicapi.documents.ExportableDocument, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument.ReferencedSequence
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation (implements com.biomatters.geneious.publicapi.documents.XMLSerializable, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator
  • com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult
  • com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult.ResidueAdjustment
  • com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResultOnAlignment
  • com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionRange
  • com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SingleSequenceResultGenerator
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationGroup
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceBuilder
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence (implements java.lang.CharSequence, java.lang.Comparable<T>, com.biomatters.geneious.publicapi.documents.XMLSerializable, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
    • com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence (implements com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument)
      • com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument.Transformer
  • com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities
  • com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions
  • com.biomatters.geneious.publicapi.implementations.SequenceGapInformation
  • com.biomatters.geneious.publicapi.plugin.SequenceGraph (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
  • com.biomatters.geneious.publicapi.plugin.SequenceGraph.SequencePropertyRetriever
    • com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor
  • com.biomatters.geneious.publicapi.plugin.SequenceGraphFactory
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.AlignmentData (implements com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.Builder<T>
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary (implements com.biomatters.geneious.publicapi.documents.XMLSerializable, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.Coverage
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.PairwiseSimilarity
  • com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage (implements com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph, com.biomatters.geneious.publicapi.documents.XMLSerializable, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • com.biomatters.geneious.publicapi.plugin.SequenceSelection (implements com.biomatters.geneious.publicapi.documents.XMLSerializable, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectionInterval (implements com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • com.biomatters.geneious.publicapi.plugin.SequenceSelection.SequenceIndex (implements com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments (implements com.biomatters.geneious.publicapi.documents.XMLSerializable, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments.ExtractionStrategy (implements com.biomatters.geneious.publicapi.documents.XMLSerializable, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack
  • com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack.Manager (implements com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • com.biomatters.geneious.publicapi.utilities.SequenceUtilities
  • com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension
  • com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.Factory
    • com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsFactory
  • com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.SequenceAnnotationWrapper
  • com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsSection
  • com.biomatters.geneious.publicapi.plugin.ServiceUtilities
  • org.virion.jam.util.SimpleListenerManager (implements org.virion.jam.util.SimpleListener)
    • com.biomatters.geneious.publicapi.utilities.WeakSimpleListenerManager
  • com.biomatters.geneious.publicapi.utilities.StringUtilities
  • com.biomatters.geneious.publicapi.utilities.SystemUtilities
  • com.biomatters.geneious.publicapi.documents.types.TaxonomyDocument.Taxon
  • com.biomatters.geneious.publicapi.plugin.TestGeneious
  • com.biomatters.geneious.publicapi.utilities.ThreadUtilities
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • com.biomatters.geneious.publicapi.databaseservice.DatabaseServiceException
      • com.biomatters.geneious.publicapi.plugin.DocumentImportException
        • com.biomatters.geneious.publicapi.plugin.DocumentImportException.Canceled
      • com.biomatters.geneious.publicapi.plugin.DocumentOperationException
        • com.biomatters.geneious.publicapi.plugin.DocumentOperationException.Canceled
        • com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments.DocumentsInvalidException
      • java.io.IOException
        • java.io.InterruptedIOException
          • com.biomatters.geneious.publicapi.utilities.ProgressInputStream.ProgressInterruptedIOException
      • com.biomatters.geneious.publicapi.documents.MalformedURNException
      • java.lang.RuntimeException
        • java.lang.IllegalStateException
          • com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments.SelectedDocumentsModifiedException
            • com.biomatters.geneious.publicapi.plugin.SequenceSelection.SequenceIndex.SelectionWrongForDocumentsException
        • com.biomatters.geneious.publicapi.plugin.RuntimeDocumentOperationException
      • com.biomatters.geneious.publicapi.documents.XMLSerializationException
  • jebl.evolution.trees.TreeChangeListener
    • com.biomatters.geneious.publicapi.plugin.TreeViewerExtension
  • com.biomatters.geneious.publicapi.plugin.TreeViewerExtension.Factory
  • com.biomatters.geneious.publicapi.plugin.URLStreamHandlerManager
  • com.biomatters.geneious.publicapi.documents.URN
  • com.biomatters.geneious.publicapi.documents.UrnWithRevisionNumber
  • com.biomatters.geneious.publicapi.plugin.UserEditablePreferences
  • com.biomatters.geneious.publicapi.documents.sequence.ValueAndFrequencyDistribution (implements com.biomatters.geneious.publicapi.documents.XMLSerializable, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
  • com.biomatters.geneious.publicapi.documents.sequence.ValueAndFrequencyDistribution.ValueAndFrequency
  • com.biomatters.geneious.publicapi.utilities.WeakReferenceList<E> (implements java.lang.Iterable<T>)
  • com.biomatters.geneious.publicapi.documents.XMLSerializer

Interface Hierarchy

• com.biomatters.geneious.publicapi.documents.AdditionalSearchContent
• com.biomatters.geneious.publicapi.documents.AdditionalSearchContent.Utilities.FilterElement
• com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument.DocumentNotes
• com.biomatters.geneious.publicapi.utilities.CallSoon.EnabledProvider
• com.biomatters.geneious.publicapi.documents.DocumentListener
• com.biomatters.geneious.publicapi.documents.DocumentNote
• com.biomatters.geneious.publicapi.documents.DocumentNoteType
• com.biomatters.geneious.publicapi.documents.ElementProvider
• com.biomatters.geneious.publicapi.documents.ExportableDocument
• com.biomatters.geneious.publicapi.documents.sequence.ExternalSort.Serializer<T>
• com.biomatters.geneious.publicapi.utilities.xml.FilteredSaxHandler.ElementHandler
• com.biomatters.geneious.publicapi.components.GComboBox.DescriptionProvider
• com.biomatters.geneious.publicapi.components.GComboBox.EnabledStateProvider
• com.biomatters.geneious.publicapi.components.GComboBox.IconsProvider
• com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions.ShortcutChangeListener
• com.biomatters.geneious.publicapi.plugin.GeneiousGraphics2D
• com.biomatters.geneious.publicapi.plugin.GeneiousPreferences
• com.biomatters.geneious.publicapi.plugin.GeneiousServiceListener
• com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph
  • com.biomatters.geneious.publicapi.documents.sequence.ChromatogramDocument
  • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument, com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument)
  • com.biomatters.geneious.publicapi.documents.sequence.ExtendedNucleotideGraph
  • com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph.ImmutableGraphProvider
  • com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.NucleotideSequenceDocument)
    • com.biomatters.geneious.publicapi.documents.sequence.ChromatogramDocument
    • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument)
• com.biomatters.geneious.publicapi.plugin.Options.ComponentCreator
• com.biomatters.geneious.publicapi.documents.sequence.PairedReads
• com.biomatters.geneious.publicapi.documents.PluginDocument.ReferencedDocumentsAlwaysLoaded
• com.biomatters.geneious.publicapi.documents.PluginDocument.ReferencedDocumentsNotLoaded
• com.biomatters.geneious.publicapi.documents.PluginDocument.SizeRequiredToLoadIntoMemoryProvider
• com.biomatters.geneious.publicapi.documents.Renamable
• com.biomatters.geneious.publicapi.implementations.SequenceGapInformation.Provider
• com.biomatters.geneious.publicapi.documents.sequence.SequenceListDocument
  • com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceListDocument
    • com.biomatters.geneious.publicapi.documents.sequence.ExtendedEditableSequenceListDocument
  • com.biomatters.geneious.publicapi.documents.sequence.ExtendedEditableSequenceListDocument
• com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.Provider
• com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack.Manager.Provider
• com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor.DiscardReferencesCallback
• com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService.SearchResultPropertiesAdjuster
• com.biomatters.geneious.publicapi.documents.XMLSerializable
  • com.biomatters.geneious.publicapi.databaseservice.AdvancedSearchQueryTerm
  • com.biomatters.geneious.publicapi.documents.sequence.AminoAcidSequenceDocument
  • com.biomatters.geneious.publicapi.databaseservice.BasicSearchQuery
  • com.biomatters.geneious.publicapi.documents.sequence.ChromatogramDocument
  • com.biomatters.geneious.publicapi.databaseservice.CompoundSearchQuery
  • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument, com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument)
  • com.biomatters.geneious.publicapi.documents.types.EditableSameTaxaTreesDocument
  • com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument
    • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument)
  • com.biomatters.geneious.publicapi.databaseservice.FolderViewDocument
  • com.biomatters.geneious.publicapi.documents.types.JournalArticleDocument
  • com.biomatters.geneious.publicapi.documents.types.MolecularStructureDocument
  • com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph, com.biomatters.geneious.publicapi.documents.sequence.NucleotideSequenceDocument)
    • com.biomatters.geneious.publicapi.documents.sequence.ChromatogramDocument
    • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument)
  • com.biomatters.geneious.publicapi.documents.sequence.NucleotideSequenceDocument
    • com.biomatters.geneious.publicapi.documents.sequence.ChromatogramDocument
    • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument, com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument)
    • com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph)
      • com.biomatters.geneious.publicapi.documents.sequence.ChromatogramDocument
      • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument)
  • com.biomatters.geneious.publicapi.documents.PluginDocument
    • com.biomatters.geneious.publicapi.documents.sequence.AminoAcidSequenceDocument
    • com.biomatters.geneious.publicapi.documents.sequence.ChromatogramDocument
    • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument, com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument)
    • com.biomatters.geneious.publicapi.documents.types.EditableSameTaxaTreesDocument
    • com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument
      • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument)
    • com.biomatters.geneious.publicapi.databaseservice.FolderViewDocument
    • com.biomatters.geneious.publicapi.documents.types.JournalArticleDocument
    • com.biomatters.geneious.publicapi.documents.types.MolecularStructureDocument
    • com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph, com.biomatters.geneious.publicapi.documents.sequence.NucleotideSequenceDocument)
      • com.biomatters.geneious.publicapi.documents.sequence.ChromatogramDocument
      • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument)
    • com.biomatters.geneious.publicapi.documents.sequence.NucleotideSequenceDocument
      • com.biomatters.geneious.publicapi.documents.sequence.ChromatogramDocument
      • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument, com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument)
      • com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph)
        • com.biomatters.geneious.publicapi.documents.sequence.ChromatogramDocument
        • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument)
    • com.biomatters.geneious.publicapi.documents.types.PublicationDocument
      • com.biomatters.geneious.publicapi.documents.types.JournalArticleDocument
    • com.biomatters.geneious.publicapi.documents.types.RootedTreeDocument
    • com.biomatters.geneious.publicapi.documents.types.SameTaxaTreesDocument
      • com.biomatters.geneious.publicapi.documents.types.EditableSameTaxaTreesDocument
    • com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentListDocument
    • com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument
      • com.biomatters.geneious.publicapi.documents.sequence.AminoAcidSequenceDocument
      • com.biomatters.geneious.publicapi.documents.sequence.ChromatogramDocument
      • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument, com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument)
      • com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument
        • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument)
      • com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph, com.biomatters.geneious.publicapi.documents.sequence.NucleotideSequenceDocument)
        • com.biomatters.geneious.publicapi.documents.sequence.ChromatogramDocument
        • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument)
      • com.biomatters.geneious.publicapi.documents.sequence.NucleotideSequenceDocument
        • com.biomatters.geneious.publicapi.documents.sequence.ChromatogramDocument
        • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument, com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument)
        • com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph)
          • com.biomatters.geneious.publicapi.documents.sequence.ChromatogramDocument
          • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument)
      • com.biomatters.geneious.publicapi.documents.sequence.SequenceDocumentWithEditableAnnotations
        • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument, com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument)
        • com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument
          • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument)
    • com.biomatters.geneious.publicapi.documents.sequence.SequenceDocumentWithEditableAnnotations
      • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument, com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument)
      • com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument
        • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument)
    • com.biomatters.geneious.publicapi.documents.SummaryDocument
    • com.biomatters.geneious.publicapi.documents.types.TaxonomyDocument
    • com.biomatters.geneious.publicapi.documents.types.TreeDocument
      • com.biomatters.geneious.publicapi.documents.types.EditableSameTaxaTreesDocument
      • com.biomatters.geneious.publicapi.documents.types.RootedTreeDocument
      • com.biomatters.geneious.publicapi.documents.types.SameTaxaTreesDocument
        • com.biomatters.geneious.publicapi.documents.types.EditableSameTaxaTreesDocument
  • com.biomatters.geneious.publicapi.documents.types.PublicationDocument
    • com.biomatters.geneious.publicapi.documents.types.JournalArticleDocument
  • com.biomatters.geneious.publicapi.databaseservice.Query
    • com.biomatters.geneious.publicapi.databaseservice.AdvancedSearchQueryTerm
    • com.biomatters.geneious.publicapi.databaseservice.BasicSearchQuery
    • com.biomatters.geneious.publicapi.databaseservice.CompoundSearchQuery
  • com.biomatters.geneious.publicapi.documents.types.RootedTreeDocument
  • com.biomatters.geneious.publicapi.documents.types.SameTaxaTreesDocument
    • com.biomatters.geneious.publicapi.documents.types.EditableSameTaxaTreesDocument
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentListDocument
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument
    • com.biomatters.geneious.publicapi.documents.sequence.AminoAcidSequenceDocument
    • com.biomatters.geneious.publicapi.documents.sequence.ChromatogramDocument
    • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument, com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument)
    • com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument
      • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument)
    • com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph, com.biomatters.geneious.publicapi.documents.sequence.NucleotideSequenceDocument)
      • com.biomatters.geneious.publicapi.documents.sequence.ChromatogramDocument
      • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument)
    • com.biomatters.geneious.publicapi.documents.sequence.NucleotideSequenceDocument
      • com.biomatters.geneious.publicapi.documents.sequence.ChromatogramDocument
      • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument, com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument)
      • com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph)
        • com.biomatters.geneious.publicapi.documents.sequence.ChromatogramDocument
        • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument)
    • com.biomatters.geneious.publicapi.documents.sequence.SequenceDocumentWithEditableAnnotations
      • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument, com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument)
      • com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument
        • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument)
  • com.biomatters.geneious.publicapi.documents.sequence.SequenceDocumentWithEditableAnnotations
    • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument, com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument)
    • com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument
      • com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument (also extends com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument)
  • com.biomatters.geneious.publicapi.documents.SummaryDocument
  • com.biomatters.geneious.publicapi.documents.types.TaxonomyDocument
  • com.biomatters.geneious.publicapi.documents.types.TreeDocument
    • com.biomatters.geneious.publicapi.documents.types.EditableSameTaxaTreesDocument
    • com.biomatters.geneious.publicapi.documents.types.RootedTreeDocument
    • com.biomatters.geneious.publicapi.documents.types.SameTaxaTreesDocument
      • com.biomatters.geneious.publicapi.documents.types.EditableSameTaxaTreesDocument
  • com.biomatters.geneious.publicapi.documents.XMLSerializableWithProgress
• com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • com.biomatters.geneious.publicapi.components.Dialogs.SaveChanges
    • com.biomatters.geneious.publicapi.components.Dialogs.DialogIcon
    • com.biomatters.geneious.publicapi.components.ProOnlyComponents.CheckBox.ProOnlySuffix
    • com.biomatters.geneious.publicapi.databaseservice.CompoundSearchQuery.Operator
    • com.biomatters.geneious.publicapi.databaseservice.DatabaseService.SequenceSearchQueryType
    • com.biomatters.geneious.publicapi.documents.AdditionalSearchContent.Utilities.Filter
    • com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument.ActiveLinkSaveBehaviour
    • com.biomatters.geneious.publicapi.documents.Condition
    • com.biomatters.geneious.publicapi.documents.DocumentField.SequenceType
    • com.biomatters.geneious.publicapi.documents.DocumentNoteField.Types
    • com.biomatters.geneious.publicapi.documents.ExportableDocument.Format
    • com.biomatters.geneious.publicapi.documents.XMLSerializable.VersionSupportType
    • com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval.Direction
    • com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument.Alphabet
    • com.biomatters.geneious.publicapi.documents.types.TaxonomyDocument.TaxonomicLevel
    • com.biomatters.geneious.publicapi.implementations.PairedReadManager.Orientation
    • com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument.OligoType
    • com.biomatters.geneious.publicapi.plugin.Assembler.ReferenceSequenceSupport
    • com.biomatters.geneious.publicapi.plugin.Assembler.ContigOutputSupport
    • com.biomatters.geneious.publicapi.plugin.AssemblerInput.DataType
    • com.biomatters.geneious.publicapi.plugin.DocumentFileImporter.AutoDetectStatus
    • com.biomatters.geneious.publicapi.plugin.DocumentViewerFactory.ViewPrecedence
    • com.biomatters.geneious.publicapi.plugin.Geneious.MajorVersion
    • com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions.MainMenu
    • com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions.Category
    • com.biomatters.geneious.publicapi.plugin.GeneiousService.ServiceStatus
    • com.biomatters.geneious.publicapi.plugin.Options.PageChooserType
    • com.biomatters.geneious.publicapi.plugin.Options.Alignment
    • com.biomatters.geneious.publicapi.plugin.Options.RadioOption.DependentPosition
    • com.biomatters.geneious.publicapi.plugin.SequenceGraph.Location
    • com.biomatters.geneious.publicapi.plugin.SequenceSelection.SequenceDocumentType
    • com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.ComponentLocation
    • com.biomatters.geneious.publicapi.utilities.CompressionUtilities.CompressionMethod
    • com.biomatters.geneious.publicapi.utilities.FileUtilities.RetryPolicy
    • com.biomatters.geneious.publicapi.utilities.FileUtilities.TargetExistsAction
    • com.biomatters.geneious.publicapi.utilities.ImportUtilities.ImportDocumentType
    • com.biomatters.geneious.publicapi.utilities.ImportUtilities.ActionWhenInvalid
    • com.biomatters.geneious.publicapi.utilities.StandardIcons