Class Hierarchy (Geneious Public API)

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
- javax.swing.border.AbstractBorder (implements javax.swing.border.Border, java.io.Serializable)
  - com.biomatters.geneious.publicapi.components.AlertPanel.RoundedAlertBorder
- 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)
- javax.swing.AbstractListModel<E> (implements javax.swing.ListModel<E>, java.io.Serializable)
  - javax.swing.DefaultComboBoxModel<E> (implements javax.swing.MutableComboBoxModel<E>, java.io.Serializable)
    - com.biomatters.geneious.publicapi.components.GComboBox.DefaultModelWhereSetSelectedItemDoesntFireContentsChanged<E>
- 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.databaseservice.AdditionalXmlForDocument
- com.biomatters.geneious.publicapi.documents.AliasDocument (implements com.biomatters.geneious.publicapi.documents.PluginDocument, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
- 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 (implements com.biomatters.geneious.publicapi.components.BadgeSupplier)
- com.biomatters.geneious.publicapi.plugin.Assembler.Callback
- com.biomatters.geneious.publicapi.plugin.AssemblerInput
- com.biomatters.geneious.publicapi.plugin.AssemblerInput.Library
- 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.implementations.CodonUsageTableDocument (implements com.biomatters.geneious.publicapi.documents.PluginDocument, com.biomatters.geneious.publicapi.documents.XMLSerializable, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
- java.awt.Color (implements java.awt.Paint, java.io.Serializable)
  - com.biomatters.geneious.publicapi.laf.UI.ThemeInvertedColor
- com.biomatters.geneious.publicapi.utilities.ColorUtilities
- 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.HyperlinkButton
        
        com.biomatters.geneious.publicapi.components.MoreOptionsButton
        
        com.biomatters.geneious.publicapi.components.ProOnlyComponents.Button
        
        javax.swing.JMenuItem (implements javax.accessibility.Accessible, javax.swing.MenuElement)
        
        com.biomatters.geneious.publicapi.components.GMenuItem
        
        com.biomatters.geneious.publicapi.components.ProOnlyComponents.MenuItem
        
        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
        
        javax.swing.JToggleButton (implements javax.accessibility.Accessible)
        
        javax.swing.JCheckBox (implements javax.accessibility.Accessible)
        
        com.biomatters.geneious.publicapi.components.GCheckBox
        
        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<E>
        
        com.biomatters.geneious.publicapi.components.ProOnlyComponents.ComboBox
      - javax.swing.JLabel (implements javax.accessibility.Accessible, javax.swing.SwingConstants)
        
        javax.swing.tree.DefaultTreeCellRenderer (implements javax.swing.tree.TreeCellRenderer)
        
        com.biomatters.geneious.publicapi.components.GDefaultTreeCellRenderer
        
        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.AlertPanel
        
        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.JScrollPane (implements javax.accessibility.Accessible, javax.swing.ScrollPaneConstants)
        
        com.biomatters.geneious.publicapi.components.BorderlessScrollPane
        
        com.biomatters.geneious.publicapi.components.GScrollPane
      - 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
      - javax.swing.JTree (implements javax.accessibility.Accessible, javax.swing.Scrollable)
        
        com.biomatters.geneious.publicapi.plugin.WritableDatabaseServiceTree
    - java.awt.Window (implements javax.accessibility.Accessible)
      - java.awt.Dialog
        
        javax.swing.JDialog (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
        
        org.virion.jam.framework.JeblDialog
        
        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.documents.sequence.ConstructorWrapper
- com.biomatters.geneious.publicapi.plugin.DatabaseFolderImporter
- 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.documents.FieldWithName, 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.plugin.DocumentFilter
- 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.DocumentSelectionOption.OptionValueCreator
- 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
- com.biomatters.geneious.publicapi.implementations.EndGapsHelper
- com.biomatters.geneious.publicapi.implementations.EndGapsManager
- com.biomatters.geneious.publicapi.implementations.EndGapsManager.Builder
- java.util.EventObject (implements java.io.Serializable)
  - javax.swing.event.ChangeEvent
    - com.biomatters.geneious.publicapi.components.ZoomChangeEvent
- 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.FindAllCallback
- com.biomatters.geneious.publicapi.plugin.Findable.FindOptions
- com.biomatters.geneious.publicapi.plugin.Findable.FindResult
- 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.databaseservice.WritableDatabaseService.DummyService
  - 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.Logs
- com.biomatters.geneious.publicapi.utilities.MessageDigestUtilities
- com.biomatters.geneious.publicapi.utilities.MultiThreadedProcessingSystem<T>
- com.biomatters.geneious.publicapi.utilities.MultiThreadedTask<ResultType>
- com.biomatters.geneious.publicapi.plugin.NoLongerViewedListener
- com.biomatters.geneious.publicapi.implementations.sequence.NucleotideCounter
- 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.PasswordOption
  - com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionGrabOption
- com.biomatters.geneious.publicapi.plugin.Options.OptionValue (implements com.biomatters.geneious.publicapi.components.BadgeSupplier, com.biomatters.geneious.publicapi.components.Filterable, 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)
- java.lang.ref.Reference<T>
  - java.lang.ref.SoftReference<T>
    - com.biomatters.geneious.publicapi.GeneiousSoftReference<T>
- org.jdom.input.SAXBuilder
  - com.biomatters.geneious.publicapi.utilities.xml.FastSaxBuilder
- javax.swing.ScrollPaneLayout (implements java.awt.LayoutManager, javax.swing.ScrollPaneConstants, java.io.Serializable)
  - com.biomatters.geneious.publicapi.components.ScrollPaneLayoutThatCorrectlyAccountsForVerticalScrollbarWidth
- 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.Renamable, 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 (implements com.biomatters.geneious.publicapi.documents.sequence.PairedReads)
  - 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.implementations.sequence.SequenceTrack.Manager.Provider, 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.SelectedAnnotation
- 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.StateFrequencies<T>
- com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsSection
- com.biomatters.geneious.publicapi.plugin.ServiceUtilities
- com.biomatters.geneious.publicapi.plugin.SharingSummary
- 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.utilities.SystemUtilities.LowMemoryChecker
- com.biomatters.geneious.publicapi.documents.types.TaxonomyDocument.Taxon
- com.biomatters.geneious.publicapi.plugin.TestGeneious
- com.biomatters.geneious.publicapi.implementations.TextDocument (implements com.biomatters.geneious.publicapi.documents.PluginDocument, com.biomatters.geneious.publicapi.documents.XMLSerializable, com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible)
- 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.databaseservice.DatabaseServiceException.Canceled
      - com.biomatters.geneious.publicapi.databaseservice.SearchIndexCorruptOrMissingException
    - com.biomatters.geneious.publicapi.plugin.DocumentImportException
      - com.biomatters.geneious.publicapi.plugin.DocumentImportException.Canceled
    - com.biomatters.geneious.publicapi.plugin.DocumentOperationException
      - com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments.DocumentsInvalidException
    - java.io.IOException
      - java.io.InterruptedIOException
        
        com.biomatters.geneious.publicapi.utilities.ProgressInputStream.ProgressInterruptedIOException
      - com.biomatters.geneious.publicapi.utilities.InvalidZipEntryException
    - 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.laf.UI
- com.biomatters.geneious.publicapi.laf.UI.ClientProperties
- com.biomatters.geneious.publicapi.laf.UI.General
- com.biomatters.geneious.publicapi.laf.UI.Misc
- com.biomatters.geneious.publicapi.laf.UI.Symbols
- com.biomatters.geneious.publicapi.laf.UI.TabPane
- com.biomatters.geneious.publicapi.laf.UI.Tree
- com.biomatters.geneious.publicapi.plugin.URLStreamHandlerManager
- com.biomatters.geneious.publicapi.documents.URN
- com.biomatters.geneious.publicapi.documents.UrnWithRevisionNumber
- com.biomatters.geneious.publicapi.documents.UrnWithSequenceRegions
- 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.databaseservice.WritableDatabaseService.DocumentsToAdd
- com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService.DocumentToAdd
- 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.components.BadgeSupplier
com.biomatters.geneious.publicapi.utilities.CallSoon.EnabledProvider
com.biomatters.geneious.publicapi.components.Dialogs.DialogClosedListener
com.biomatters.geneious.publicapi.documents.DocumentListener
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.documents.FieldWithName
- com.biomatters.geneious.publicapi.documents.DocumentNote
com.biomatters.geneious.publicapi.components.Filterable
com.biomatters.geneious.publicapi.utilities.xml.FilteredSaxHandler.ElementHandler
com.biomatters.geneious.publicapi.components.GComboBox.AlternativeDropDownTextProvider
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.GeneiousGridDocumentOperation.LocationChangedListenerProvider
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.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
java.lang.Runnable
- com.biomatters.geneious.publicapi.components.DefaultHyperlinkListener.SerializableRunnable (also extends java.io.Serializable)
com.biomatters.geneious.publicapi.components.RunnableWithProgress<T>
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.SequenceListSummary.Provider
com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack.Manager.Provider
com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor.DiscardReferencesCallback
java.io.Serializable
- com.biomatters.geneious.publicapi.components.DefaultHyperlinkListener.SerializableRunnable (also extends java.lang.Runnable)
com.biomatters.geneious.publicapi.plugin.WorkflowSharingManager<O>
com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService.SearchResultPropertiesAdjuster
com.biomatters.geneious.publicapi.documents.XMLSerializable
- com.biomatters.geneious.publicapi.documents.PluginDocument
  - com.biomatters.geneious.publicapi.plugin.DocumentSelectionOption.DoNotRememberInPreferences
  - com.biomatters.geneious.publicapi.databaseservice.FolderViewDocument
  - com.biomatters.geneious.publicapi.documents.types.MolecularStructureDocument
  - com.biomatters.geneious.publicapi.documents.types.PublicationDocument
    - com.biomatters.geneious.publicapi.documents.types.JournalArticleDocument
  - 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.NucleotideSequenceDocument
      - 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.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.RootedTreeDocument
    - com.biomatters.geneious.publicapi.documents.types.SameTaxaTreesDocument
      - com.biomatters.geneious.publicapi.documents.types.EditableSameTaxaTreesDocument
- 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.XMLSerializableWithProgress
com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible

Annotation Type Hierarchy

com.biomatters.geneious.publicapi.plugin.MayReturnSlowly (implements java.lang.annotation.Annotation)
com.biomatters.geneious.publicapi.plugin.MustReturnPromptly (implements java.lang.annotation.Annotation)

Enum Hierarchy

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

Hierarchy For All Packages

Class Hierarchy

Interface Hierarchy

Annotation Type Hierarchy

Enum Hierarchy