All Classes

Class	Description
AbstractPluginDocument	This class provides a "Field based" implementation of a Plugin documents.
ActionProvider	May be supplied by a DocumentViewer to support standard actions (such as copy and paste) or any additional custom actions.
AdditionalSearchContent	Interface implemented by a document which has text stored in places other than the document fields and want that text available for search.
AdditionalSearchContent.Result	Searchable content for a single category.
AdditionalSearchContent.Utilities	Small helpers for extracting searchable content from XML data.
AdditionalSearchContent.Utilities.Filter	Various filterng options on element text.
AdditionalSearchContent.Utilities.FilterElement	Provide directions on how to handle element
AdditionalXmlForDocument
AdvancedSearchQueryTerm	Basic term in a Geneious advanced search query.
AlertPanel	An alert panel which can seamlessly switch between displaying a loading spinner, or different types of alerts.
AlertPanel.AlertLevel	Levels are:
AlertPanel.RoundedAlertBorder	A rounded border with a solid fill at the left edge.
AlertPanel.TextAlign	Defines where in the AlertPanel to place the text if the text does not fill the component entirely.
AliasDocument	An alias document created using 'Edit->Paste Alias' or programmatically using AliasDocument.createAlias(AnnotatedPluginDocument).
AlignmentLayout	Provides information about how to layout of sequences (excluding the reference sequence) for rendering in an alignment or contig.
AlignmentOperation	A convenience class to enable plugins to contain alignment operations which do not need to concern themselves with: The type of documents that have been selected (sequence documents, sequence list documents, or alignment documents) Reordering and reversing of the sequences Whether the alignment is local or global Referenced documents Bases/residues unsupported by the underlying algorithm If a plugin wants to handle these itself, it could implement itself as a DocumentOperation instead, but that is not recommended.
AlignmentOperation.InputProperties	Represents the properties of the input to an AlignmentOperation
AminoAcidSequenceDocument	An interface for an Amino Acid sequence.
AnnotatedPluginDocument	An AnnotatedPluginDocument is a wrapper document that wraps any PluginDocument (such as a SequenceDocument or SequenceAlignmentDocument or TreeDocument) and adds extra information and provides extra functionality that the underlying PluginDocument need not concern itself with, such as allowing the user to rename the document or edit any fields displayed in the document table.
AnnotatedPluginDocument.ActiveLinkSaveBehaviour	Gives an action to take when AnnotatedPluginDocument.saveDocument(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument.ActiveLinkSaveBehaviour, jebl.util.ProgressListener) is called.
AnnotatedPluginDocument.DocumentNotes	Provides access to all the DocumentNotes on an AnnotatedPluginDocument
Assembler	Allows the implementation of a read mapper, reference assembler or de novo assembler.
Assembler.Callback	Used for assembly algorithms to provide results back to Geneious.
Assembler.ContigOutputSupport	Used for indicating whether an assembly algorithm outputs contigs, consensus sequences, or both.
Assembler.ReferenceSequenceSupport	Used for indicating whether an assembly algorithm supports no reference sequence, a single reference sequence, or multiple reference sequences.
AssemblerInput	Represents the input to an assembly algorithm.
AssemblerInput.DataType	The sequencing technology that a sequencing library was generated from.
AssemblerInput.PairedDataType	Represents the type of paired read or mate pair data.
AssemblerInput.Properties	Some properties that briefly summarise what the input will look like.
AssemblerInput.Read	Represents a single read or input contig.
AssemblerInput.ReferenceSequence	Represents a reference sequence in an assembly.
Author	A class holding one author name.
Badge	An enum representing the available badges that can be displayed in supported dropdowns.
BadgeSupplier	Implement this to indicate that the object can supply a Badge to the UI.
Base64Coder	A Base64 Encoder/Decoder.
BasicSearchQuery	A simple, text only search query.
BorderlessScrollPane	A wrapper for JScrollPane that has no viewport border.
BubbleToolTip	A tooltip component in the shape of a speech bubble (a rectangle on Mac because they ruin it by painting a rectangular shadow around everything).
ByteBackedCharSequence	A CharSequence whose data is stored as bytes (instead of a String) to reduce memory usage.
CallSoon	Provides a system for invoking a Runnable shortly in the Swing thread with optional coalescing of multiple calls and an optional delay until the runnable is invoked.
CallSoon.EnabledProvider	Provides a method for specifying whether something is enabled
CharSequenceUtilities	Provides static utility methods for creating and manipulating CharSequences (not necessarily Strings).
CheckboxSearchOption	A boolean extended search option, displayed as a check-box.
ChromatogramDocument	Deprecated. Check for instanceof NucleotideGraphSequenceDocument instead.
CmlDocument	A Cml molecular structure document.
CodonUsageTableDocument	A document storing a table of codon usage frequencies.
ColorUtilities	Provides utility methods for dealing with colors
CombinedAlignmentAndAminoAcidSequenceDocument	See documentation at CombinedAlignmentAndSequenceDocument
CombinedAlignmentAndNucleotideGraphSequenceDocument	See documentation at CombinedAlignmentAndSequenceDocument
CombinedAlignmentAndNucleotideSequenceDocument	See documentation at CombinedAlignmentAndSequenceDocument
CombinedAlignmentAndSequenceDocument	A wrapper to both an alignment and a stand-alone sequence that appears as a single EditableSequenceDocument.
ComboboxSearchOption	A multi choice extended search option, displayed as a combo-box.
CompactQualityOnlyGraph	A memory efficient nucleotide graph that only supports quality values in the range 0->256 and does not support traces.
CompositeRetrieveCallback	A RetrieveCallback that is suitable for a task that consists of several subtasks.
CompoundSearchQuery	A compound query is a set of queries combined by a logical operator.
CompoundSearchQuery.Operator	Ways to connect the terms of a compound query.
CompressionUtilities	Provides methods for reading from compressed files.
CompressionUtilities.CompressedFileWrapper	A wrapper class for a compressed file.
CompressionUtilities.CompressionMethod	Represents a type of compression
ConcatenatedList<T>	A list made by joining multiple sublists of Ts together.
Condition	Available types of conditions.
Constraint	The idea of a Constraint is very simple.
ConstructorWrapper	A wrapper around Constructor that improved performance.
DatabaseFolderImporter	An importer for folders containing files that must be imported as a set, and cannot be handled by the normal DocumentFileImporter framework.
DatabaseService	A Geneious service providing documents in response to a search query.
DatabaseService.SequenceSearchQueryType	The type of query for a sequence search
DatabaseServiceException	Most database service methods may throw this exception.
DatabaseServiceException.Canceled	Represents a DatabaseService operation that has failed because it has been canceled.
DatabaseServiceListener	Code using a DatabaseService can get notified of special events by registering this listener via addDatabaseServiceListener.
DataInputOutputUtilities	Provides methods for reading and writing objects from DataInputStream and DataOutputStream
DefaultAlignmentDocument	An implementation of a SequenceAlignmentDocument.
DefaultAminoAcidSequence	A plugin document holding one amino acid sequence.
DefaultHyperlinkListener	A simple implementation of HyperlinkListener which invokes the system's default browser.
DefaultHyperlinkListener.SerializableRunnable	An interface intended for use with DefaultHyperlinkListener.getUrlForMethod(SerializableRunnable)
DefaultMolecularStructureDocument	An implementation of a MolecularStructureDocument.
DefaultNucleotideGraph	A NucleotideGraph that stores its values in int[] arrays internally, and allows getting and setting those arrays.
DefaultNucleotideGraphSequence	An implementation of an editable chromatogram.
DefaultNucleotideSequence	A plugin document holding one nucleotide sequence.
DefaultPhylogenyDocument	An implementation of a Phylogeny document.
DefaultSameTaxaTreesDocument	A default implementation of a plugin document holding a list of trees.
DefaultSequenceDocument	A default implementation of a sequence document.
DefaultSequenceDocument.Cache	Used for controlling caching of the char sequence and annotations controlled from this class.
DefaultSequenceGraphFactories	Provides convenience functionality to create a SequenceGraphFactory which draws a bar graph from some simpler interfaces.
DefaultSequenceGraphFactories.SequenceAlignmentScorer	Provides methods to supply a score for a given set of sequence residues and provide a color for a given score.
DefaultSequenceGraphFactories.SingleSequenceScorer	Provides methods to supply a score for a given sequence residue and provide a color for a given score.
DefaultSequenceListDocument	A default implementation of a SequenceListDocument.
DefaultTreeDocument	A default implementation of a plugin document holding a tree.
DependentComboboxSearchOption	Allows one combo box to have a set of possible values depending on the selected value of another combo box option.
DialogButtonPanel	A panel used to lay out buttons at the bottom of a dialog.
Dialogs	A utility class for displaying dialogs, similar to JOptionPane but with added functionality.
Dialogs.DialogAction	Used to specify the properties of a button in a dialog.
Dialogs.DialogClosedListener	A listener to be notified when a dialog is closed.
Dialogs.DialogIcon	Specifies the icon to display on the left hand side of a dialog.
Dialogs.DialogOptions	A class that specifies all the options for displaying a dialog.
Dialogs.Result	The result of showing an "apply to all" dialog.
Dialogs.SaveChanges	The options that the user can click on in the dialog shown by Dialogs.showSaveChangesDialog(String, java.awt.Component).
DocumentAction	A DocumentAction performs some operation to modify a document, without creating new documents.
DocumentCollection	This class provides a field based document that stores a collection of other documents.
DocumentField	A Document Field describes the properties (but not value) of one data item of a plugin document or one field in a search query.
DocumentField.SequenceType	Possible values for the DocumentField.SEQUENCE_TYPE field.
DocumentFieldAndValue	Wraps a DocumentField together with its value.
DocumentFileExporter	An exporter writes Geneious documents into external files.
DocumentFileExporterAndExternalViewer	A file exporter with an associated external viewer.
DocumentFileImporter	An importer reads external files and converts the contents to Geneious documents.
DocumentFileImporter.AutoDetectStatus	Possible results of file type auto detection.
DocumentFileImporter.ImportCallback
DocumentFilter	Provides a system for filtering documents
DocumentHistory	The document history for an AnnotatedPluginDocument is made up of a list of entries.
DocumentHistoryEntry	Represents a single 'edit' of a document in the document history.
DocumentHistoryEntryField	A document history field is basically a name-value pair that describes one aspect of a DocumentHistoryEntry.
DocumentImportException	An exception thrown when import of document fails due to improper format or unexpected data in file.
DocumentImportException.Canceled	Represents a DocumentFileImporter that has failed because it has been canceled.
DocumentListener	Used for notifying when an AnnotatedPluginDocument has changed.
DocumentNote	Represents an instance of a DocumentNoteType that exists on a document.
DocumentNoteField	Describes the properties of a single value in a note.
DocumentNoteField.Types	All of the available note field types.
DocumentNoteType	This represents a "Note Type" in the program.
DocumentNoteUtilities	This gives access to the NoteTypes defined in the program.
DocumentOperation	A DocumentOperation creates a new document from a set of existing documents (or from no documents). The DocumentOperation displays an optional OptionsPanel (a JPanel), and then performs an operation on the set of documents that the user has selected.
DocumentOperation.OperationCallback	Provides a callback facility to DocumentOperations.
DocumentOperation.OperationCallback.Wrapper	Creates a wrapper OperationCallback that delegates all methods to another OperationCallback
DocumentOperation.Wrapper	Provides a wrapper DocumentOperation that delegates all methods (except DocumentOperation.getUniqueId()) to the wrapped operation.
DocumentOperationInput	Represents input to a DocumentOperation.
DocumentSearchCache<T extends PluginDocument>	Class which caches the results of a search for a particular type of document and automatically updates to include newly added documents of the particular type when they are added to the user's database.
DocumentSelectionOption	An option to allow the user to select a number of documents of a particular type from their local database.
DocumentSelectionOption.DoNotRememberInPreferences	An interface that documents used in a DocumentSelectionOption may implement so that the option doesn't cache their instance and reuse it on future instances of these options.
DocumentSelectionOption.FolderOrDocuments	The value type for DocumentSelectionOption which represents either a list of selected documents or a single selected folder which contains some documents of the correct type.
DocumentSelectionOption.OptionValueCreator	For use with DocumentSelectionOption.setOptionValueCreator(com.biomatters.geneious.publicapi.plugin.DocumentSelectionOption.OptionValueCreator)
DocumentSelectionSignature	Several plugin components (Viewers, Exporters, Operations, Actions) operate on one (or a set of) Geneious documents.
DocumentSelectionSignature.DocumentSelectionSignatureAtom	A signature is a set of Atoms.
DocumentType<T>	Declares one Geneious plugin document type used for associating icons and human readable names with PluginDocument classes.
DocumentUtilities	Some core functionality provided by Geneious for adding and managing documents.
DocumentViewer	A viewer displays one (or more) Geneious documents to the user.
DocumentViewer.ViewerLocation	Information about the location of a viewer eg.
DocumentViewerFactory	A DocumentViewerFactory creates a DocumentViewer which displays one or more Geneious documents to the user.
DocumentViewerFactory.ViewPrecedence	Viewer precedence level.
DocumentViewerMessageHandler	DocumentViewers occasionally wish to interact with each other.
EditableNucleotideGraphSequenceDocument	A mutable nucleotide sequence with residue graph.
EditableSameTaxaTreesDocument	A mutable tree set.
EditableSequenceDocument	An extensions of a SequenceDocument that can be edited.
EditableSequenceListDocument	A SequenceListDocument that can have its internal lists of nucleotide and amino acid sequences reordered, added to, or removed from.
ElementProvider	Provides a method to load an XML element with progress information and the ability to cancel it.
EndGapsHelper	Calculates, and provides a method to determine whether residues in a set of sequences are end gaps.
EndGapsManager	Given a set of aligned sequences, provides methods for quickly finding all sequences that intersect a given base number, ignoring those sequences in end gap regions.
EndGapsManager.Builder	Used for building an EndGapsManager which is too large to fit in memory
EValue	Just like a double, but the toString() method displays it as a nicely formatted e value
Execution	Executes an external program.
Execution.OutputListener	Reports output received from an external process.
ExportableDocument	Interface implemented by plugin documents that wish to implemenet a specialized export.
ExportableDocument.Format	Current exportable formats.
ExtendedEditableSequenceListDocument	Similar to an EditableSequenceListDocument but also allows replacing sequences with new sequences or modifying the contents of individual sequences
ExtendedNucleotideGraph	Provides an extended interface to a NucleotideGraph.
ExtendedPrintable	An alternative to Printable which provides additional information and options which also provides useful information when saving to an image.
ExtendedPrintable.Factory	Provides factory methods for creating ExtendedPrintables
ExtendedPrintable.Wrapper	Wrapper that delegates all methods to the source ExtendedPrintable.
ExtendedSearchOption	Base interface for extended search options.
ExternalSort<T>	Sorts some objects, using temporary files on disk if necessary because the objects can't all fit in memory (e.g.
ExternalSort.Serializer<T>	Specifies how to serialize the elements to disk and read them back in again.
FastSaxBuilder	A Sax Builder that is faster and uses less memory than the standard sax builder it extends (SAXBuilder).
FieldWithName	Interface implemented by fields that have a name.
FileUtilities	Provides utility methods for dealing with files.
FileUtilities.RetryPolicy	Specifies a policy about what to do if a file action (e.g.
FileUtilities.TargetExistsAction	The action to take when moving/copying files and the target already exists
Filterable	UI components in Geneious may contain a value filter to help users locate data quicker.
FilteredSaxHandler	A Sax Handler that provides full jdom Elements for specified element names.
FilteredSaxHandler.ElementHandler
Findable	May be supplied by a document viewer (via getFindable()) to support textual searching inside the viewer.
Findable.FindAllCallback	A callback for use with Findable.findAllResults(FindOptions, FindAllCallback, ProgressListener)
Findable.FindOptions	User options for a search.
Findable.FindResult	Represents a single search result feature or location
FolderView	Stores information about documents in a folder.
FolderViewDocument	A PluginDocument may implement this interface to indicate that it provides information about the results of a search.
GarbageCollectionNotifier	Provides a system for notifying when an object has been garbage collected.
GButton	Same as JButton except not opaque on Mac OS by default.
GCheckBox	Like a JCheckBox except Is not opaque (calls setOpaque(false) in the constructor) Adds GCheckBox.setSmall(boolean) Works around a preferred size bug on High DPI displays under Java 9
GComboBox<E>	A JComboBox that provides edit menu support ( copy, paste, undo etc).
GComboBox.AlternativeDropDownTextProvider	Any items in the GComboBox may implement this interface, in which case, when the drop-down list is being displayed, GComboBox.AlternativeDropDownTextProvider.getDropDownText(boolean) will be called to obtain the displayed text instead of Component.toString() Note: A GComboBox which has items implementing this interface is not mutable.
GComboBox.DefaultModelWhereSetSelectedItemDoesntFireContentsChanged<E>	ComboBoxModel which extends DefaultComboBoxModel but which fixes performance issues when iterating through selected items.
GComboBox.DescriptionProvider	Any items in the GComboBox may implement this interface, in which case, when the drop-down list is being displayed, this description is displayed in grey text after the standard toString() representation of the item.
GComboBox.EnabledStateProvider	Any items in the GComboBox may implement this interface, in which case, when the drop-down list is being displayed, disabled items will not be selectable.
GComboBox.IconsProvider	Any items in the GComboBox may implement this interface, in which case they may have an icon rendered next to them.
GDefaultTreeCellRenderer	A wrapper of DefaultTreeCellRenderer which provides support for rendering tree nodes that are drop targets for drag and drop.
GDialog	Same as JDialog except when pack() is called, the dialog is resized to ensure that it is no bigger than the max height and width specified by the maxDimensions and no smaller than 300 by 125 pixels.
GEditorPane	An implementation of JEditorPane which was written to works around Java bug 6406218 That bug no longer exists, but tbis class is being left in as a simple proxy to JEditorPane so as not change the public API
Geneious	General information about the Geneious Prime application.
Geneious.MajorVersion	Represents a major version number of Geneious (the first 2 numbers of the 3 number version number) for versions of Geneious from 6.0 onwards.
GeneiousAction	Geneious action items.
GeneiousAction.Divider	A subclass of GeneiousAction which is placed in a toolbar/menu as a divider.
GeneiousAction.SubMenu	A subclass of GeneiousAction which is placed in the menu as a submenu which opens to the right; In the toolbar, it will appear as a drop-down menu that opens downwards.
GeneiousAction.ToggleAction	A subclass of GeneiousAction which is placed in a toolbar/menu as a toggle button or check box menu item.
GeneiousActionOptions	Specifies information (such as the name, description,icon, keyboard shortcut and location) of a menu item or button in Geneious.
GeneiousActionOptions.Category	The category (if any) which this action fits into.
GeneiousActionOptions.MainMenu	All available menu locations.
GeneiousActionOptions.ShortcutChangeListener	A listener that can be notified when the shortcut changes for a GeneiousActionOptions
GeneiousActionToolbar	A panel which contains a JToolbar and adds additional functionality.
GeneiousActionToolbar.CustomToolbarComponent	Encapsulates the information necessary for adding a custom component to the toolbar.
GeneiousGraphics2D	Provides some (but not all) of the functionality of Graphics2D, but also provides some extra useful methods GeneiousGraphics2D.drawStringWithinBounds(String,int,int,int,int,boolean) GeneiousGraphics2D.drawStringCentred(String, int, int) The primary reason for the existence of this interface is so that SequenceGraphs can be rendered as a circular view in the SequenceViewer correctly.
GeneiousGridDocumentOperation	A grid-aware version of DocumentOperation, containing many convenience features to simplify the task of creating a grid-aware DocumentOperation.
GeneiousGridDocumentOperation.GridInput	A class describing all the elements needed to run a program on the grid.
GeneiousGridDocumentOperation.LocationChangedListenerProvider	Interface that allows OperationLocationOptions.LocationChangedListeners provided by program options to be registered in LocationOptions that are displayed to the user
GeneiousGridImporter	Imports one or more documents into Geneious from the contents of the given folder.
GeneiousObjectInputStream	An input stream to read from data previously written using a GeneiousObjectOutputStream.
GeneiousObjectOutputStream	An extension to ObjectOutputStream that tries to reduce disk space and also reduce memory usage when the stream is read back in again later.
GeneiousPlugin	The base class for all Geneious plugins.
GeneiousPreferences	Deprecated. Use PluginPreferences and GeneiousPlugin.getPluginPreferences() instead
GeneiousPreferences.GeneiousCheckBoxPreference	A preference for specifying a yes/no (on/off) choice.
GeneiousPreferences.GeneiousComboBoxPreference	A preference for specifying one of a set of values.
GeneiousPreferences.GeneiousDependentPreference	A preference which itself contains a list of GeneiousPreferences.GeneiousPreference.
GeneiousPreferences.GeneiousPreference	Super class for all GeneiousPreferences.GeneiousPreference types.
GeneiousPreferences.GeneiousRadioButtonPreference	A preference for specifying one of a small set of possible values.
GeneiousPreferences.GeneiousStringPreference	A preference for specifying a string.
GeneiousService	A service provides a piece of functionality for the Geneious system.
GeneiousService.ServiceStatus	Possible states of service.
GeneiousServiceListener	Callback used in GeneiousService::initialize to enable a service to report the addition & removal of sub/child-services, and report back a change of status or name.
GeneiousServiceWithPanel	This is a GeneiousService that displays a custom panel in Geneious when the service is selected.
GeneiousSoftReference<T>	A wrapper around a SoftReference so that Geneious can track all soft references to allow it to conditionally clear them all when it needs to evaluate if sufficient memory is available to run a task which requires a known amount of memory.
GeneralUtilities	Provides general utility methods that don't fall under any of the other utility classes: FileUtilities, GuiUtilities, StringUtilities, SystemUtilities, ThreadUtilities
GLabel	Same as JLabel except it has the option to use a smaller font and includes a work-around for a JDK bug under Java 9.
GMenuItem	Has the same functionality as JMenuItem but records when it is clicked for usage tracking purposes
GPanel	Same as JPanel except not opaque by default.
GPopupMenu	Has the same functionality as a JPopupMenu but will correctly hide when switching between windows on Mac OS.
GprDocument	A Gpr molecular structure document.
GScrollPane	Has the same functionality as JScrollPane but: Speeds up default scroll speed. Removes the border Sets the panel opaque property to false Sets the viewport opaque property to false
GSpinnerNumberModel	Just like SpinnerNumberModel but allow reaching the maximum/minimum using up/down controls, rather than stopping at the value before the maximum/minimum
GTable
GTextArea	Same as JTextArea but has undo/redo capability, a popup Edit menu and is linked to the main Edit menu.
GTextField	Same as JTextField but has undo/redo capability, a popup Edit menu and is linked to the main Edit menu.
GTextPane	Same as JTextPane but has undo/redo capability, a popup Edit menu and is linked to the main Edit menu.
GuiUtilities	Provides utility methods for dealing with GUI (swing) components
HinDocument	A Hin molecular structure document.
HyperlinkButton	A clickable button with the aesthetics of a web hyperlink text.
Icons	Stores a set of different sized versions of the same icon.
IconUtilities	Utilities for loading and manipulating images and icons.
ImmutableSequence	An implementation of a SequenceDocument that is immutable and has very low memory usage.
ImmutableSequence.Builder	Provides a system for building a list of ImmutableSequence which are even more compact than normal by analyzing patterns in the names of sequences.
ImmutableSequenceImplementation	Despite this class being public, it is only public for implementation reasons.
ImportUtilities	Provides methods for importing documents into Geneious.
ImportUtilities.ActionWhenInvalid	Specifies what to do when a sequence with invalid bases/residues is encountered during import
ImportUtilities.ImportDocumentType	whether to import ambiguous files as alignments of sequence lists.
ImportUtilities.ImportSource	An enum representing the source of an import.
InputStreamFromRandomAccessFile	Provides an InputStream view into the current position in a RandomAccessFile.
Intern<T>	Manages manually interning Objects (like String.intern()) except this implemenation avoids the following pitfalls with String.intern() Objects are not interned into the permgen (the permgen is independent of the normal heap and limited to 64MB by default), so using String.intern too often can result in OutOfMemory errors when you have plently of free space This implemenation is faster than String.intern since it doesn't have to deal with garbage collecting weak references Disadvantages of this implemenation include
Interval	Represents a directional interval.
IntList	Similar to a java.util.List but uses primitive ints instead of Integers for better performance.
IntList.Array	An implementation of an IntList that is mutable and backed by an array
InvalidZipEntryException	An InvalidZipEntryException is thrown when the zip file contains an invalid/malicious entry and Geneious should abort extracting the file.
JournalArticleDocument	Interface for plugin documents containing a Journal Article.
JournalArticleDocument.Utils
License	Provides access to the current Geneious user license state, the names of various versions of Geneious, and support for being notified when the license key status changes.
License.PluginLicense	Represents the properties of a license which is used to activate a "pay-for" plugin or feature.
Logs	This is a convenience class for logging that is easier to use, but isn't as flexible or powerful as java.util.logging.
MalformedURNException	Exception indicating an incorrectly formatted URN.
MayReturnSlowly	An annotation which indicates a method may take a while to return, so the method should never be called from the Swing thread.
MessageDigestUtilities	Provides methods for producing message digests such as MD5 or SHA
MolDocument	A Mol molecular structure document.
MolecularStructureDocument	Interface representing 3D model data of a molecular structure.
MoreOptionsButton	A button which toggles between "More Options" and "Fewer Options" with a down and up arrow icon respectively (the text can be changed).
MultiThreadedProcessingSystem<T>	A utility class providing a system in which a number of elements are each independently processed in some way (in multiple threads) before calling finishedProcessing on each element in the same order as they originally came in.
MultiThreadedTask<ResultType>	Manages a task that can be split over multiple threads. Example 1: to split a task across multiple threads (1 per processor), use:
MustReturnPromptly	An annotation which indicates a method should always return promptly (under 50 ms), usually because it may be called from the Swing thread.
NoLongerViewedListener	May be supplied by a DocumentViewer (via getNoLongerViewedListener) to be notified when they are no longer being viewed.
NucleotideCounter	Counts the frequency of AT and GC nucleotides, including counting S as GC and W as AT.
NucleotideGraph	Optional phred-like quality information on the residues of a sequence, and an optional chromatogram graph.
NucleotideGraph.ImmutableGraphProvider	An interface a NucleotideGraph may implement to indicate it can provide an immutable instance of itself.
NucleotideGraphSequenceDocument	A nucleotide sequence with an underlying "graph".
NucleotideSequenceDocument	An interface for a nucleotide sequence.
NwoDocument	A Nwo molecular structure document.
OligoSequenceDocument	A sequence document which represents an olgionucleotide such as a Primer or DNA probe.
OligoSequenceDocument.OligoType	The possible types of oligos
OperationLocationOptions	An Options that provides the ability to pick between running an Operation on the local computer or on a supported GeneiousService.
OperationLocationOptions.LocationChangedListener	Used to indicate that the value returned from OperationLocationOptions.getSelectedLocation() has changed.
OperationRecordDocument	Stores references to the input and output documents a from single DocumentOperation.
Options	Provides options used by DocumentOperations, SequenceAnnotationGenerators and SequenceGraphs.
Options.Alignment	Used the specifying how other options for a Options.RadioOption are layed out.
Options.BooleanOption	An option that stores a Boolean and is represented graphically as a check box.
Options.ButtonOption	Provides the user with a button which may have actions associated with it by calling Options.ButtonOption.addActionListener(java.awt.event.ActionListener).
Options.ComboBoxOption<ValueType extends Options.OptionValue>	An option that provides the user with a list of options in a combo box
Options.ComponentCreator	An interface for creating components on demand for use with Options.addCustomComponent(com.biomatters.geneious.publicapi.plugin.Options.ComponentCreator)
Options.DateOption	An option that stores a date.
Options.DoubleOption	An option that stores an Double and is displayed graphically to the user as a single line text field with a spinner (up and down arrow) on the right-hand side
Options.EditableComboBoxOption	Like a ComboBoxOption, but besides letting the user choose one of the preconfigured default values, also allows arbitrary custom strings to be entered.
Options.ExecutableFileSelectionOption	Provides the user with an executable file name and provides assistance with finding the location of it.
Options.FileSelectionOption	Provides functionality to let the user choose a file.
Options.IntegerOption	An option that stores an Integer and is displayed graphically to the user as a single line text field with a spinner (up and down arrow) on the right-hand side.
Options.LabelOption	An option that is only used for display purposes.
Options.MultipleLineStringOption	An option that stores a String and is displayed to the user as a multiple line text area
Options.MultipleOptions	Stores the multiple options added using Options.addMultipleOptions(String, Options, boolean) and provides methods to access the current values (Options.MultipleOptions.getValues()) and to add change listeners (Options.MultipleOptions.addChangeListener(org.virion.jam.util.SimpleListener) and to change the enabled state Options.MultipleOptions.setEnabled(boolean).
Options.Option<ValueType,ComponentType extends javax.swing.JComponent>	The base class of all types of options.
Options.OptionValue	Possible values that a Options.RadioOption or Options.ComboBoxOption can take on.
Options.PageChooserType	An enum listing the different types of child options choosers.
Options.RadioOption<ValueType extends Options.OptionValue>	An option that provides the user with a list of radio buttons to select one of
Options.RadioOption.DependentPosition
Options.StringOption	An option that stores a String and is displayed graphically to the user as a single line text field.
OptionsPanel	A panel that lays out label/component pairs vertically.
OptionsPanel.RoundedLineBorder	The border used for boxes when OptionsPanel.beginBorderedGroup(String, boolean).
OutputStreamThatCountsBytesWritten	An OutputStream that counts the number of bytes written to it and forwards write methods on to another output stream.
OutputStreamToRandomAccessFile	Provides an OutputStream view into the current position in a RandomAccessFile.
OverlayIcons	An Icons wrapper that overlays one or more sets of Icons on top of a base set of Icons.
PairedReadManager	Keeps track of which sequences in a list of sequences are paired together and their paired distances.
PairedReadManager.Builder	Allows for the construction of a PairedReadManager where the data resides on disk instead of in memory.
PairedReadManager.Orientation	Represents the relative orientation for a set of interlaced reads.
PairedReads	Provides data about whether nucleotide sequences are paired together and their expected paired distance.
PartiallyWritableDatabaseService	A database service which allows partial editing of its contents (either the deleting or renaming or editing field values of some or all of its contents).
PasswordOption	An option that stores a user entered password.
PdbDocument	A PDB molecular structure document.
Percentage	Just like a double, but the toString() method displays it as a percentage with the specified number of decimal places.
PhylogenyDocument	A document containing an alignment and one or more trees whose tips are the sequences (i.e.
PluginDocument	PluginDocument defines the interface for a Document created by a plugin.
PluginDocument.ReferencedDocumentsAlwaysLoaded	PluginDocuments can optionally implement this empty interface to signify that they generally require their referenced documents when they are deserialized and for general use such as viewing the document, even if those referenced documents have not been modified since this PluginDocument was last saved.
PluginDocument.ReferencedDocumentsNotLoaded	PluginDocuments can optionally implement this empty interface to signify that they don't require their referenced documents when they are deserialized and for general use such as viewing the document.
PluginDocument.SizeRequiredToLoadIntoMemoryProvider	A PluginDocument may implement this interface to indicate to Geneious the amount of memory it will probably require in order to load the document.
PluginDocumentXmlCollection	Provides a system for serializing and deserializing a PluginDocument that contains a large number of sub-elements so that all the elements do not need to be in memory simultaneously.
PluginDocumentXmlCollection.ElementHandler
PluginPreferences<T extends Options>	Allows a plugin to provide Options based preferences that are displayed in the Geneious Preferences dialog.
PluginUtilities	Provides various functionality to access other installed plug-ins.
PluginUtilities.WritableDatabaseServicesListener	A listener used for notifying when root WritableDatabaseServices are added or removed in Geneious.
ProgressFrame	An implementation of ProgressListener which displays progress using a progress bar and a cancel button in a Frame.
ProgressInputStream	An InputStream that reports progress to a ProgressListener and queries the ProgressListener about when to cancel, throwing an ProgressInterruptedIOException when it should cancel.
ProgressInputStream.ProgressInterruptedIOException	An InterruptedIOException that was thrown by a ProgressInputStream because its ProgressListener signaled that the operation was aborted.
ProOnlyComponents	A set of components which automatically become disabled if the user does not have an active license.
ProOnlyComponents.Button	Same as a GButton but automatically becomes disabled if the user does not have an active license.
ProOnlyComponents.CheckBox	Same as a JCheckBox but automatically becomes disabled if the user does not have an active license.
ProOnlyComponents.CheckBox.ProOnlySuffix
ProOnlyComponents.CheckBoxMenuItem	Same as a JCheckBoxMenuItem but automatically becomes disabled if the user does not have an active license.
ProOnlyComponents.ComboBox	Same as a GComboBox but automatically becomes disabled if the user does not have an active license.
ProOnlyComponents.Label	Same as a JLabel but automatically becomes disabled if the user does not have an active license.
ProOnlyComponents.Menu	Same as a JMenu but automatically becomes disabled if the user does not have an active license.
ProOnlyComponents.MenuItem	Same as a JMenuItem but automatically becomes disabled if the user does not have an active license.
ProOnlyComponents.Panel	A Panel that wraps a component that is only available if the user has an active license.
ProOnlyComponents.ToggleButton	Same as a JToggleButton but automatically becomes disabled if the user does not have an active license.
PublicationDocument	Interface for plugin documents containing a publication.
PublicationDocument.Utils
Query	An interface that produces a common ancestor for various queries.
Query.Factory	Provides methods for creating queries.
QueryField	Basic block for building advanced search queries.
Renamable	Provides that ability to rename something.
RetrieveCallback	A callback that asynchronously reports back the documents resulting from a DatabaseService search.
RootedTreeDocument	A document containing one (rooted) tree.
RunnableWithProgress<T>	A RunnableWithProgress interface that works similar to Runnable but has a generic return type and can use a ProgressListener to show and cancel progress.
RuntimeDocumentOperationException	Occasionally some methods that would like to throw a DocumentOperationException are unable to do so because their API doesn't allow it.
SameTaxaTreesDocument	A document containing a list of trees.
ScrollPaneLayoutThatCorrectlyAccountsForVerticalScrollbarWidth	This class can be used as a substitute for the default ScrollPaneLayout used by a JScrollPane.
SearchIndexCorruptOrMissingException	A wrapper exception around DatabaseServiceException, primarily used to indicate that the search index is corrupt or missing.
SequenceAlignmentDocument	An alignment or contig of sequences.
SequenceAlignmentDocument.ReferencedSequence	Represents a reference to the original document that a sequence in this alignment was aligned from.
SequenceAlignmentListDocument	A document representing a list of alignments.
SequenceAnnotation	Provides information on a subset of the sequence.
SequenceAnnotationGenerator	A SequenceAnnotationGenerator generates annotations on a sequence, set of sequences, or an alignment.
SequenceAnnotationGenerator.AnnotationGeneratorResult	Represents the result of a single sequence from calling an annotation generator via SequenceAnnotationGenerator.generate(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[], com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionRange, jebl.util.ProgressListener, Options)
SequenceAnnotationGenerator.AnnotationGeneratorResult.ResidueAdjustment	An immutable class representing an insertion, deletion, or replacement of residues or bases in a sequence.
SequenceAnnotationGenerator.AnnotationGeneratorResultOnAlignment	Represents the results of running a generator on a single alignment.
SequenceAnnotationGenerator.AnnotationGeneratorResultsOnSingleSequence	An implementation of a List of SequenceAnnotationGenerator.AnnotationGeneratorResult where all elements except one are empty results.
SequenceAnnotationGenerator.SelectionGrabOption	If any option returned from SequenceAnnotationGenerator.getOptions(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[], com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionRange) is a SelectionGrabOption then the sequence viewer will interact with the option such that when the user clicks on the button representing this option, the current selection in the sequence viewer is copied to this option value.
SequenceAnnotationGenerator.SelectionRange	represents a rectangular selection range in a list of sequences, and also behaves like a Linked List in that it provides a link to the next SelectionRange in a chain of selections (see SequenceAnnotationGenerator.SelectionRange.getNext().
SequenceAnnotationGenerator.SingleSequenceResultGenerator	Provides a system for a SequenceAnnotationGenerator to generate results for just a single sequence.
SequenceAnnotationGroup	An immutable class representing a collection of related SequenceAnnotation types.
SequenceAnnotationInterval	Immutable pair of integers with a direction, representing a directed range in the sequence annotation.
SequenceAnnotationInterval.Direction	The direction of a sequence annotation interval.
SequenceAnnotationQualifier	A named item of information (i.e.
SequenceBuilder	Provides methods for creating CharSequences for use as biological sequences.
SequenceCharSequence	A CharSequence that knows the length of its terminal gaps (sequences of '-') and allows for efficient insertions and deletions of subsequences.
SequenceDatabaseSuperService	A plugin should return a service which extends this class if it wishes to provide a Sequence Search facility that can have databases added and removed by the user or if there are some general preferences that apply to the Sequence Datbases of the plugin.
SequenceDocument	Interface representing one sequence.
SequenceDocument.Alphabet	Supported sequence types.
SequenceDocument.Transformer	Provides a method for returning a new sequence which represents a transformation made to another sequence.
SequenceDocumentWithEditableAnnotations	An extension of a SequenceDocument that allows its annotations to be changed.
SequenceExtractionUtilities	Provides methods for extracting a portion of a sequence to a new sequence document.
SequenceExtractionUtilities.ExtractionOptions	Represents options controlling how sequence extraction works in SequenceExtractionUtilities.extractIntervals(com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument, com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions).
SequenceGapInformation	Precalculates information about the location of gaps ('-') in a CharSequence, and can efficiently calculate translate between indices in the gapped and ungapped sequence.
SequenceGapInformation.Provider	An interface that SequenceDocuments can optionally to implement to indicate they may provide a (potentially) pre-built SequenceGapInformation
SequenceGraph	A sequence graph is displayed in the SequenceViewer.
SequenceGraph.Location
SequenceGraph.SequencePropertyRetriever	Provides additional information about the sequence(s) (e.g.
SequenceGraphFactory	A sequence graph factory is used for creating instances of SequenceGraphs every time a new document is viewed in the sequence viewer.
SequenceListDocument	A document containing 0 or more nucleotide and 0 or more protein sequences.
SequenceListOnDisk<T extends SequenceDocument>	A list of sequences which are loaded from disk on demand rather than all stored in memory.
SequenceListOnDisk.AlignmentData	An immutable class (all of whose elements are immutable too) representing the sequences and data relevant to the sequences (excluding the reference sequence) in an alignment.
SequenceListOnDisk.Builder<T extends SequenceDocument>	Used for building a SequenceListOnDisk.
SequenceListSummary	Provides a summary of data in a list of sequences.
SequenceListSummary.Coverage	Represents the coverage (number of sequences covering a column in an alignment)
SequenceListSummary.PairwiseSimilarity	Immutable value class representing the number of identical and non-identical pairs of bases/residues in an alignment column.
SequenceListSummary.Provider	An interface that lists of sequences (e.g.
SequencePropertiesStorage	Provides supporting functionality for sequence classes that need to store various sequence properties and serialise those to XML.
SequenceSelection	Specifies a selection of regions in a sequence, list of sequences, alignment or other sequence containing document.
SequenceSelection.SelectedAnnotation	Represents a single selected annotation
SequenceSelection.SelectionInterval	A contiguous selection of residues in a sequence.
SequenceSelection.SequenceDocumentType	Used for identifying the type of view the selection applies for identifying which list the index applies to in a CombinedAlignmentAndSequenceDocument
SequenceSelection.SequenceIndex	Represents the index of the selected sequence and the type (so that we can identify which list the index applies to in SequenceListDocuments.
SequenceSelectionWithDocuments	This class associates a SequenceSelection with the List of AnnotatedPluginDocument that it is defined on.
SequenceSelectionWithDocuments.DocumentsInvalidException	Thrown to indicate that a group of documents is not valid to have a SequenceSelectionWithDocuments upon.
SequenceSelectionWithDocuments.ExtractionStrategy	Instances of this allow calling code to fine tune how SequenceSelectionWithDocuments.getSequences() returns SequenceDocuments from its selection and documents.
SequenceSelectionWithDocuments.SelectedDocumentsModifiedException	Thrown when the selected documents are modified between the moment when the SequenceSelectionWithDocuments is constructed and the documents within it are accessed.
SequenceTrack	A Sequence Track is a list of annotations that is associated with a sequence (in addition to those supplied by SequenceDocument.getSequenceAnnotations()).
SequenceTrack.Manager	Manages all the tracks on a single sequence, including allowing tracks to added or removed.
SequenceTrack.Manager.Provider	An interface implemented by SequenceDocuments or SequenceAlignmentDocuments to indicate they provide sequence tracks.
SequenceUtilities	A noninstantiable class providing static methods for common tasks associated with nucleotide and protein sequences.
SequenceViewerExtension	An extension which provides extra functionality in the sequence/alignment/contig viewer.
SequenceViewerExtension.ComponentLocation	A location in the sequence viewer for the component returned from SequenceViewerExtension.createComponent() specified by SequenceViewerExtension.getComponentLocation()
SequenceViewerExtension.Factory	A type of plugin for creating extensions to the sequence viewer returned from GeneiousPlugin.getSequenceViewerExtensionFactories()
SequenceViewerExtension.PropertyRetrieverAndEditor	Provides methods for querying the sequence viewer about the status of various things and for requesting that the sequence viewer change its state.
SequenceViewerExtension.PropertyRetrieverAndEditor.DiscardReferencesCallback	Used for indicating that references to values returned from SequenceViewerExtension.PropertyRetrieverAndEditor.getVisibleAnnotations(PropertyRetrieverAndEditor.DiscardReferencesCallback) must be discarded.
SequenceViewerExtension.SequenceAnnotationWrapper	Wraps a SequenceAnnotation and provides extra information about the location (sequence, track) of the annotation.
SequenceViewerExtension.StateFrequencies<T extends jebl.evolution.sequences.State>	Provides frequencies of nucleotides or amino acids
SequenceViewerExtension.StatisticsFactory	A convenience Factory for creating statistics.
SequenceViewerExtension.StatisticsMethod	Specifies the method used for calculating statistics when multiple sequences or regions are provided
SequenceViewerExtension.StatisticsSection	One or more lines of statistics that show up in the statistics section of the sequence viewer.
ServiceUtilities	Provides various utility functionality dealing with GeneiousServices.
SharingSummary	Represents a summary of the sharing configuration for a workflow.
StandardIcons	The set of standard icons used in Geneious.
StringUtilities	Provides utility methods for creating and manipulating Strings.
SummaryDocument	Any summary document should "implement" this empty interface to enable special handling of summary documents inside Geneious.
SystemUtilities	Provides utility methods for interacting with the operating system.
SystemUtilities.LowMemoryChecker	Used by code that loops and needs to check regularly if Geneious is running low on memory to know whether to abort the operation.
TaxonomyDocument	A plugin document containing one TaxonomyDocument.Taxon, which holds information (rank, scientific name and alternative names) about one taxon in a taxonomy, and a reference to its parent taxon (if any).
TaxonomyDocument.Taxon	A taxon (element of a taxonomy) consisting of its scientific name (e.g.
TaxonomyDocument.TaxonomicLevel	Represents a taxonomic level (AKA rank) that a Taxon can have in a Taxonomy, e.g.
TestGeneious	Provides methods to facilitate writing test cases for Geneious plugins
TextDocument	A document containing text that can be marked up in various formats such as html.
TextDocument.Format	Format of the text
TextFieldSearchOption	An extended search option which is displayed as a Text Field.
TextOrSimilaritySearchOption	A specialized option for local search.
ThreadUtilities	Provides utility methods for managing threads.
TreeDocument	The common base for all documents that hold one or several trees.
TreeViewerExtension	A tree viewer extension is used for creating a custom controls section in the tree viewer.
TreeViewerExtension.Factory	The factory class that plugins provide via GeneiousPlugin.getTreeViewerExtensionFactories() for creating TreeViewerExtensions
UI	This class provides a set of getter properties for various UI settings used by Geneious.
UI.ClientProperties	Component-based client properties defined and used by Geneious.
UI.General	Geneious application color palette and application-wide user interface constants.
UI.Misc	A collection of properties for specific Geneious main frame components.
UI.Symbols	A collection of standardised unicode symbol characters.
UI.TabPane	Properties related to the aesthetics of JTabbedPane.
UI.ThemeInvertedColor	This class extends java.awt.Color and provides colors which become inverted on dark based themes.
UI.Tree	Properties related to the aesthetics of JTree.
URLStreamHandlerManager	Deprecated. Do not call the methods in this class
URN	An unmodifiable uniform resource name (URN), intended to serve as persistent, location-independent, resource identifiers.
UrnWithRevisionNumber	Represents an AnnotatedPluginDocument at a particular revision, via its URN (AnnotatedPluginDocument.getURN()) and revision number (AnnotatedPluginDocument.getRevisionNumber())
UrnWithSequenceRegions	Stores the URN of an AnnotatedPluginDocument plus optionally AnnotatedPluginDocument.getRevisionNumber() AnnotatedPluginDocument.getInternalPluginDocumentRevisionNumber() A sequence index if the document is a SequenceListDocument or SequenceAlignmentDocument A list of residue Intervals within the sequence A hash of the residues corresponding to the regions in the sequence so we can detect if the sequence residues have changed since this reference was created
UserEditablePreferences	Provides a mechanism for plugins to store advanced user configurable settings as name/value pairs.
ValueAndFrequencyDistribution	Provides a sorted distribution of longs and the frequency of each of them.
ValueAndFrequencyDistribution.ValueAndFrequency	Represents a value and the number of occurrences of the value
WeakReferenceList<E>	Manages a list of WeakReferences, and providing an iterator over the objects which are still strongly referenced.
WeakSimpleListenerManager	Just like a SimpleListenerManager except the references to the listeners are WeakReferences.
WorkflowSharingManager<O extends Options>	Interface for managing sharing settings of workflows in the application.
WritableDatabaseService	Provides a DatabaseService that supports writing documents to it as well as providing a hierarchical folder representation of the database.
WritableDatabaseService.DeletedItemsType	Defines the way that a WritableDatabaseService implements its "Deleted Items" (also known as "soft delete" or "trash" or "recycle bin").
WritableDatabaseService.DocumentsToAdd	Holds information required for adding one or more documents to a database, potentially to different sub-folders.
WritableDatabaseService.DocumentToAdd	Holds information required for adding a single document to a database via WritableDatabaseService.addDocumentCopies(DocumentsToAdd, ProgressListener) and for databases implementing this via WritableDatabaseService.addDocumentsImplementation(List, ProgressListener).
WritableDatabaseService.DummyService	A dummy implementation of WritableDatabaseService that provides no functionality apart from a name and icons
WritableDatabaseService.SearchResultPropertiesAdjuster
WritableDatabaseServiceTree	A GUI component that lets the user choose a WritableDatabaseService from the root services supplied.
XMLSerializable	Interface for handling persistent objects.
XMLSerializable.OldVersionCompatible	XMLSerializable classes are recommended implement this to indicate they support serializing to older version formats and potentially deserializing from newer version formats.
XMLSerializable.VersionSupportType	Used for specifying the type of version support when used with XMLSerializable.OldVersionCompatible.getVersionSupport(com.biomatters.geneious.publicapi.documents.XMLSerializable.VersionSupportType)
XMLSerializableWithProgress	An extended interface to XMLSerializable to support providing progress (and the ability to cancel) when serializing and deserialing.
XMLSerializationException	Represents a problem with XML serialization or deserialization.
XMLSerializer	Serialization helper class.
XyzDocument	An XYZ molecular structure document.
ZoomChangeEvent	An event fired to listeners added via ZoomPanel.addChangeListener(ChangeListener)
ZoomPanel	A panel for displaying and setting a zoom level.