All Classes and Interfaces
Class
Description
This class provides a "Field based" implementation of a Plugin documents.
May be supplied by a
DocumentViewer
to support standard actions (such as copy and paste) or any additional custom actions.Interface implemented by a document which has text stored in places other than the document fields and want that
text available for search.
Searchable content for a single category.
Small helpers for extracting searchable content from XML data.
Various filterng options on element text.
Provide directions on how to handle element
Basic term in a Geneious advanced search query.
An alert panel which can seamlessly switch between displaying a loading spinner, or different types of alerts.
Levels are:
A rounded border with a solid fill at the left edge.
Defines where in the AlertPanel to place the text if the text does not
fill the component entirely.
An alias document created using 'Edit->Paste Alias' or programmatically using
AliasDocument.createAlias(AnnotatedPluginDocument).Provides information about how to layout of sequences (excluding the reference sequence) for rendering in an alignment or contig.
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.Represents the properties of the input to an AlignmentOperation
An interface for an Amino Acid sequence.
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.Gives an action to take when
AnnotatedPluginDocument.saveDocument(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument.ActiveLinkSaveBehaviour, jebl.util.ProgressListener) is called.Provides access to all the
DocumentNotes on an AnnotatedPluginDocumentAllows the implementation of a read mapper, reference assembler or de novo assembler.
Used for assembly algorithms to provide results back to Geneious.
Used for indicating whether an assembly algorithm outputs contigs, consensus sequences, or both.
Used for indicating whether an assembly algorithm supports no reference sequence, a single reference sequence, or multiple reference sequences.
Represents the input to an assembly algorithm.
The sequencing technology that a sequencing library was generated from.
Represents the type of paired read or mate pair data.
Some properties that briefly summarise what the input will look like.
Represents a single read or input contig.
Represents a reference sequence in an assembly.
A class holding one author name.
An enum representing the available badges that can be displayed in supported dropdowns.
Implement this to indicate that the object can supply a
Badge to the UI.A Base64 Encoder/Decoder.
A simple, text only search query.
A wrapper for
JScrollPane that has no viewport border.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).
A CharSequence whose data is stored as bytes (instead of a String) to reduce memory usage.
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.Provides a method for specifying whether something is enabled
Provides static utility methods for creating and manipulating CharSequences
(not necessarily Strings).
A boolean extended search option, displayed as a check-box.
Deprecated.
A Cml molecular structure document.
A document storing a table of codon usage frequencies.
Provides utility methods for dealing with colors
See documentation at
CombinedAlignmentAndSequenceDocumentSee documentation at
CombinedAlignmentAndSequenceDocumentSee documentation at
CombinedAlignmentAndSequenceDocumentA wrapper to both an alignment and a stand-alone sequence that appears as a single EditableSequenceDocument.
A multi choice extended search option, displayed as a combo-box.
A memory efficient nucleotide graph that only supports quality values in the range 0->256 and does not support traces.
A
RetrieveCallback that is suitable for a task that consists of several subtasks.A compound query is a set of queries combined by a logical operator.
Ways to connect the terms of a compound query.
Provides methods for reading from compressed files.
A wrapper class for a compressed file.
Represents a type of compression
A list made by joining multiple sublists of Ts together.
Available types of conditions.
The idea of a Constraint is very simple.
A wrapper around Constructor that improved performance.
An importer for folders containing files that must be imported as a set, and cannot be handled by the normal
DocumentFileImporter framework.A Geneious service providing documents in response to a search query.
The type of query for a sequence search
Most database service methods may throw this exception.
Represents a
DatabaseService operation that has failed because it has been canceled.Code using a
DatabaseService can get notified of special events by registering this listener
via addDatabaseServiceListener.Provides methods for reading and writing objects from
DataInputStream and DataOutputStreamAn implementation of a
SequenceAlignmentDocument.A plugin document holding one amino acid sequence.
A simple implementation of
HyperlinkListener which invokes the system's default browser.An interface intended for use with
DefaultHyperlinkListener.getUrlForMethod(SerializableRunnable)An implementation of a MolecularStructureDocument.
A
NucleotideGraph that stores its values in int[] arrays internally,
and allows getting and setting those arrays.An implementation of an editable chromatogram.
A plugin document holding one nucleotide sequence.
An implementation of a Phylogeny document.
A default implementation of a plugin document holding a list of trees.
A default implementation of a sequence document.
Used for controlling caching of the char sequence and annotations controlled from this class.
Provides convenience functionality to create a SequenceGraphFactory which
draws a bar graph from some simpler
interfaces.
Provides methods to supply a score for a given set of sequence residues and provide
a color for a given score.
Provides methods to supply a score for a given sequence residue and provide a color for a given score.
A default implementation of a
SequenceListDocument.A default implementation of a plugin document holding a tree.
Allows one combo box to have a set of possible values depending on the selected value
of another combo box option.
A panel used to lay out buttons at the bottom of a dialog.
A utility class for displaying dialogs, similar to
JOptionPane but with added functionality.Used to specify the properties of a button in a dialog.
A listener to be notified when a dialog is closed.
Specifies the icon to display on the left hand side of a dialog.
A class that specifies all the options for displaying a dialog.
The result of showing an "apply to all" dialog.
The options that the user can click on in the dialog shown by
Dialogs.showSaveChangesDialog(String, java.awt.Component).A
DocumentAction performs some operation to modify a document, without creating new documents.This class provides a field based document that stores a collection of other documents.
A Document Field describes the properties (but not value) of one data item of a plugin document or one field in a
search query.
Possible values for the
DocumentField.SEQUENCE_TYPE field.Wraps a
DocumentField together with its value.An exporter writes Geneious documents into external files.
A file exporter with an associated external viewer.
An importer reads external files and converts the contents to Geneious documents.
Possible results of file type auto detection.
Provides a system for filtering documents
The document history for an AnnotatedPluginDocument is made up of a list of
entries.Represents a single 'edit' of a document in the document history.
A document history field is basically a name-value pair that describes one aspect of a
DocumentHistoryEntry.An exception thrown when import of document fails due to improper format or unexpected data in file.
Represents a
DocumentFileImporter that has failed because it has been canceled.Used for notifying when an
AnnotatedPluginDocument has changed.Represents an instance of a
DocumentNoteType that exists on a document.Describes the properties of a single value in a note.
All of the available note field types.
This represents a "Note Type" in the program.
This gives access to the NoteTypes defined in the program.
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.
The DocumentOperation displays an optional OptionsPanel (a JPanel), and then performs an operation on the set of documents that the user has selected.
Provides a callback facility to DocumentOperations.
Creates a wrapper OperationCallback that delegates all methods to another OperationCallback
Provides a wrapper DocumentOperation that delegates all methods (except
DocumentOperation.getUniqueId()) to the wrapped operation.Represents input to a DocumentOperation.
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.
An option to allow the user to select a number of documents of a particular type from their local database.
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.
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.
Several plugin components (Viewers, Exporters, Operations, Actions) operate on one (or a set of) Geneious documents.
A signature is a set of Atoms.
Declares one Geneious plugin document type used for associating icons and
human readable names with
PluginDocument classes.Some core functionality provided by Geneious for adding and managing documents.
A viewer displays one (or more) Geneious documents to the user.
Information about the location of a viewer eg.
A DocumentViewerFactory creates a DocumentViewer which displays one or more Geneious documents
to the user.
Viewer precedence level.
DocumentViewers occasionally wish to interact with each other.
A mutable nucleotide sequence with residue graph.
A mutable tree set.
An extensions of a
SequenceDocument that can be edited.A
SequenceListDocument that can have its
internal lists of nucleotide and amino acid sequences reordered, added to, or removed from.Provides a method to load an XML element with progress information and
the ability to cancel it.
Calculates, and provides a method to determine whether residues in a
set of sequences are end gaps.
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.
Used for building an
EndGapsManager which is too large to fit in memoryJust like a double, but the toString() method displays it as a nicely formatted e value
Executes an external program.
Reports output received from an external process.
Interface implemented by plugin documents that wish to implemenet a specialized export.
Current exportable formats.
Similar to an
EditableSequenceListDocument but
also allows replacing sequences with new sequences or modifying the contents of individual sequencesProvides an extended interface to a
NucleotideGraph.An alternative to
Printable which provides additional information and options
which also provides useful information when saving to an image.Provides factory methods for creating ExtendedPrintables
Wrapper that delegates all methods to the source ExtendedPrintable.
Base interface for extended search options.
Sorts some objects, using temporary files on disk if necessary because the objects can't all fit in memory (e.g.
Specifies how to serialize the elements to disk and read them back in again.
A Sax Builder that is faster and uses less memory than the standard sax builder it extends
(
SAXBuilder).Interface implemented by fields that have a name.
Provides utility methods for dealing with files.
Specifies a policy about what to do if a file action (e.g.
The action to take when moving/copying files and the target already exists
UI components in Geneious may contain a value filter to help users locate data quicker.
A Sax Handler that provides full jdom Elements for specified element names.
May be supplied by a document viewer
(via
getFindable())
to support textual searching inside the viewer.A callback for use with
Findable.findAllResults(FindOptions, FindAllCallback, ProgressListener)User options for a search.
Represents a single search result feature or location
Stores information about documents in a folder.
A PluginDocument may implement this interface to indicate that it provides information about the results
of a search.
Provides a system for notifying when an object has been garbage collected.
Same as JButton except not opaque on Mac OS by default.
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
A JComboBox that provides edit menu support ( copy, paste, undo etc).
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.ComboBoxModel which extends
DefaultComboBoxModel but which fixes performance issues when
iterating through selected items.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.
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.
Any items in the GComboBox may implement this interface, in which case they may have an icon rendered next to
them.
A wrapper of
DefaultTreeCellRenderer which provides support for rendering
tree nodes that are drop targets for drag and drop.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.
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 APIGeneral information about the Geneious Prime application.
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.
Geneious action items.
A subclass of GeneiousAction which is placed in a toolbar/menu as a divider.
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.
A subclass of GeneiousAction which is placed in a toolbar/menu as a toggle button or check box menu item.
Specifies information (such as the name, description,icon, keyboard shortcut and location) of a menu item or button in Geneious.
The category (if any) which this action fits into.
All available menu locations.
A listener that can be notified when the shortcut changes for a
GeneiousActionOptionsA panel which contains a JToolbar and adds additional functionality.
Encapsulates the information necessary for adding a custom component to the toolbar.
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.A grid-aware version of
DocumentOperation, containing many
convenience features to simplify the task of creating a grid-aware DocumentOperation.A class describing all the elements needed to run a program on the grid.
Interface that allows
OperationLocationOptions.LocationChangedListeners provided by program options
to be registered in LocationOptions that are displayed to the userImports one or more documents into Geneious from the contents of the given folder.
An input stream to read from data previously written using a
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.The base class for all Geneious plugins.
Deprecated.
Use
PluginPreferences and GeneiousPlugin.getPluginPreferences() insteadA preference for specifying a yes/no (on/off) choice.
A preference for specifying one of a set of values.
A preference which itself contains a list of
GeneiousPreferences.GeneiousPreference.Super class for all
GeneiousPreferences.GeneiousPreference types.A preference for specifying one of a small set of possible values.
A preference for specifying a string.
A service provides a piece of functionality for the Geneious system.
Possible states of service.
Callback used in
GeneiousService::initialize to enable a service to report the addition invalid input: '&'
removal of sub/child-services, and report back a change of status or name.This is a GeneiousService that displays a custom panel in Geneious when the service is selected.
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.Provides general utility methods that don't fall under any
of the other utility classes:
FileUtilities,
GuiUtilities,
StringUtilities,
SystemUtilities,
ThreadUtilitiesSame as JLabel except it has the option to use a smaller font and includes a work-around for a JDK bug under Java 9.
Has the same functionality as JMenuItem but records when it is clicked for usage tracking purposes
Same as JPanel except not opaque by default.
Has the same functionality as a JPopupMenu but will correctly hide when switching between windows on Mac OS.
A Gpr molecular structure document.
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
Just like SpinnerNumberModel but allow reaching the maximum/minimum using up/down controls,
rather than stopping at the value before the maximum/minimum
Same as
JTextArea but has undo/redo capability, a popup Edit menu and
is linked to the main Edit menu.Same as
JTextField but has undo/redo capability, a popup Edit menu and
is linked to the main Edit menu.Same as
JTextPane but has undo/redo capability, a popup Edit menu and
is linked to the main Edit menu.Provides utility methods for dealing with GUI (swing) components
A Hin molecular structure document.
A clickable button with the aesthetics of a web hyperlink text.
Stores a set of different sized versions of the same icon.
Utilities for loading and manipulating images and icons.
An implementation of a
SequenceDocument that is immutable
and has very low memory usage.Provides a system for building a list of ImmutableSequence which are even more compact than normal by analyzing patterns
in the names of sequences.
Despite this class being public, it is only public for implementation reasons.
Provides methods for importing documents into Geneious.
Specifies what to do when a sequence with invalid bases/residues is encountered during import
whether to import ambiguous files as alignments of sequence lists.
An enum representing the source of an import.
Provides an InputStream view into the current position in a RandomAccessFile.
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
invalid input: '<'ul
No automatic garbage collection of Objects.Represents a directional interval.
Similar to a java.util.List but uses primitive ints instead of Integers for
better performance.
An implementation of an IntList that is mutable and backed by an array
An InvalidZipEntryException is thrown when the zip file contains an invalid/malicious entry and Geneious should abort
extracting the file.
Interface for plugin documents containing a Journal Article.
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.
A “gated” feature is a feature that requires a certain plan code (e.g.
Represents the properties of a license which is used to activate a "pay-for" plugin or feature.
This is a convenience class for logging that is easier to use, but isn't as flexible or powerful
as
java.util.logging.Exception indicating an incorrectly formatted URN.
An annotation which indicates a method may take a while to return, so the method should
never be called from the Swing thread.
Provides methods for producing message digests such as MD5 or SHA
A Mol molecular structure document.
Interface representing 3D model data of a molecular structure.
A button which toggles between "More Options" and "Fewer Options" with a down and up arrow icon respectively
(the text can be changed).
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.
Manages a task that can be split over multiple threads.
Example 1: to split a task across multiple threads (1 per processor), use:
Example 1: to split a task across multiple threads (1 per processor), use:
An annotation which indicates a method should always return promptly (under 50 ms),
usually because it may be called from the Swing thread.
May be supplied by a
DocumentViewer (via getNoLongerViewedListener)
to be notified when they are no longer being viewed.Counts the frequency of AT and GC nucleotides, including counting S as GC and W as AT.
Optional phred-like
quality information on the residues of a
sequence, and an optional chromatogram graph.An interface a NucleotideGraph may implement to indicate it can provide an immutable instance of itself.
A nucleotide sequence with an underlying "graph".
An interface for a nucleotide sequence.
A Nwo molecular structure document.
A sequence document which represents an olgionucleotide such as a Primer or DNA probe.
The possible types of oligos
An
Options that provides the ability to pick between running an Operation on the local computer or on a
supported GeneiousService.Used to indicate that the value returned from
OperationLocationOptions.getSelectedLocation() has changed.Stores references to the input and output documents a from single
DocumentOperation.Used the specifying how other options for a
Options.RadioOption are layed out.An option that stores a Boolean and is represented graphically as a check box.
Provides the user with a button which may have actions associated with it by calling
Options.ButtonOption.addActionListener(java.awt.event.ActionListener).An option that provides the user with a list of options in a combo box
An interface for creating components on demand for use with
Options.addCustomComponent(com.biomatters.geneious.publicapi.plugin.Options.ComponentCreator)An option that stores a date.
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
Like a ComboBoxOption, but besides letting the user choose one of
the preconfigured default values, also allows arbitrary custom strings
to be entered.
Provides the user with an executable file name and provides assistance with finding
the location of it.
Provides functionality to let the user choose a file.
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.
An option that is only used for display purposes.
An option that stores a String and is displayed to the user as a multiple line text area
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).The base class of all types of options.
Possible values that a
Options.RadioOption or Options.ComboBoxOption can
take on.An enum listing the different types of child options choosers.
An option that provides the user with a list of radio buttons to select one of
An option that stores a String and is displayed graphically to the user as a single line text field.
A panel that lays out label/component pairs vertically.
The border used for boxes when
OptionsPanel.beginBorderedGroup(String, boolean).An OutputStream that counts the number of bytes written to it and forwards
write methods on to another output stream.
Provides an OutputStream view into the current position in a RandomAccessFile.
Keeps track of which sequences in a list of sequences are paired together and their paired distances.
Allows for the construction of a PairedReadManager where the data resides on disk instead of in memory.
Represents the relative orientation for a set of interlaced reads.
Provides data about whether nucleotide sequences are paired together and their expected paired distance.
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).
An option that stores a user entered password.
A PDB molecular structure document.
Just like a double, but the toString() method displays it as a percentage with the specified number of decimal places.
A document containing an alignment and one or more trees whose tips are the sequences
(i.e.
PluginDocument defines the interface for a Document created by a plugin.
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.
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.
A PluginDocument may implement this interface to indicate to Geneious the amount of memory it will probably require in order to load the document.
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.Allows a plugin to provide
Options based preferences
that are displayed in the Geneious Preferences dialog.Provides various functionality to access other installed plug-ins.
A listener used for notifying when root WritableDatabaseServices are added or removed in Geneious.
An implementation of
ProgressListener which displays progress using a progress bar and
a cancel button in a Frame.An InputStream that reports progress to a ProgressListener and queries the ProgressListener about when to cancel, throwing an ProgressInterruptedIOException when it should cancel.
An InterruptedIOException that was thrown by a ProgressInputStream
because its ProgressListener signaled that the operation was
aborted.
A set of components which automatically become disabled if the user does not have an active license.
Same as a
GButton but automatically becomes disabled if the user does not have an active license.Same as a
JCheckBox but automatically becomes disabled if the user does not have an active license.Same as a
JCheckBoxMenuItem but automatically becomes disabled if the user does not have an active license.Same as a
GComboBox but automatically becomes disabled if the user does not have an active license.Same as a
JLabel but automatically becomes disabled if the user does not have an active license.Same as a
JMenu but automatically becomes disabled if the user does not have an active license.Same as a
JMenuItem but automatically becomes disabled if the user does not have an active license.A Panel that wraps a component that is only available if the user has an active license.
Same as a
JToggleButton but automatically becomes disabled if the user does not have an active license.Interface for plugin documents containing a publication.
An interface that produces a common ancestor for various queries.
Provides methods for creating queries.
Basic block for building advanced search queries.
Provides that ability to rename something.
A callback that asynchronously reports back the documents resulting from a
DatabaseService search.A document containing one (rooted) tree.
A
RunnableWithProgress interface that works similar to
Runnable but has a generic return type and
can use a ProgressListener to show and cancel progress.Occasionally some methods that would like to throw a
DocumentOperationException are unable to do so because their API doesn't allow it.A document containing a list of trees.
This class can be used as a substitute for the default
ScrollPaneLayout used by a
JScrollPane.A wrapper exception around
DatabaseServiceException, primarily used to indicate that the search index is
corrupt or missing.An alignment or contig of sequences.
Represents a reference to the original document that a sequence in this alignment was aligned from.
A document representing a list of alignments.
Provides information on a subset of the sequence.
A SequenceAnnotationGenerator generates annotations on a sequence, set of sequences, or an alignment.
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)An immutable class representing an insertion, deletion, or replacement of residues or bases in a sequence.
Represents the results of running a generator on a single alignment.
An implementation of a List of
SequenceAnnotationGenerator.AnnotationGeneratorResult where all elements except one are empty results.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.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().Provides a system for a SequenceAnnotationGenerator to generate results for just a single sequence.
An immutable class representing a collection of related
SequenceAnnotation types.Immutable pair of integers with a direction, representing a directed range in the sequence annotation.
The direction of a sequence annotation interval.
A named item of information (i.e.
Provides methods for creating
CharSequences for use as biological sequences.
A CharSequence that knows the length of its terminal gaps (sequences of '-') and
allows for efficient
insertions and
deletions of subsequences.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.
Interface representing one sequence.
Supported sequence types.
Provides a method for returning a new sequence which represents a transformation made to another sequence.
An extension of a
SequenceDocument that allows its annotations to be changed.Provides methods for extracting a portion of a sequence to a new sequence document.
Represents options controlling how sequence extraction works in
SequenceExtractionUtilities.extractIntervals(com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument, com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions).Precalculates information about the location of gaps ('-') in a CharSequence,
and can efficiently calculate translate between indices in the gapped and ungapped
sequence.
An interface that
SequenceDocuments can optionally to implement to indicate they may provide a (potentially) pre-built SequenceGapInformationA sequence graph is displayed in the SequenceViewer.
Provides additional information about the sequence(s) (e.g.
A sequence graph factory is used for creating instances of
SequenceGraphs every time a new document is viewed
in the sequence viewer.A document containing 0 or more nucleotide and 0 or more protein sequences.
A list of sequences which are loaded from disk on demand rather than all stored in memory.
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.
Used for building a SequenceListOnDisk.
Provides a summary of data in a list of sequences.
Represents the coverage (number of sequences covering a column in an alignment)
Immutable value class representing the number of identical and non-identical
pairs of bases/residues in an alignment column.
An interface that lists of sequences (e.g.
Provides supporting functionality for sequence classes that need to store
various sequence properties and serialise those to XML.
Specifies a selection of regions in a sequence, list of sequences, alignment or other sequence containing document.
Represents a single selected annotation
A contiguous selection of residues in a sequence.
Used for identifying the type of view the selection applies for identifying which list the index applies to in a
CombinedAlignmentAndSequenceDocumentRepresents the index of the selected sequence and the type (so that we can identify which list the index applies to in
SequenceListDocuments.This class associates a
SequenceSelection with the List of AnnotatedPluginDocument that it is
defined on.Thrown to indicate that a group of documents is not valid to have a SequenceSelectionWithDocuments upon.
Instances of this allow calling code to fine tune how
SequenceSelectionWithDocuments.getSequences() returns
SequenceDocuments from its selection and documents.Thrown when the selected documents are modified between the moment when the SequenceSelectionWithDocuments is constructed
and the documents within it are accessed.
A Sequence Track is a list of annotations that is associated with a sequence (in addition to those supplied by
SequenceDocument.getSequenceAnnotations()).Manages all the tracks on a single sequence, including allowing tracks to added or removed.
An interface implemented by
SequenceDocuments or SequenceAlignmentDocuments to indicate they provide sequence tracks.A noninstantiable class providing static methods for common tasks associated with nucleotide and
protein sequences.
An extension which provides extra functionality in the sequence/alignment/contig viewer.
A location in the sequence viewer for the component returned from
SequenceViewerExtension.createComponent() specified
by SequenceViewerExtension.getComponentLocation()A type of plugin for creating extensions to the sequence viewer returned from
GeneiousPlugin.getSequenceViewerExtensionFactories()Provides methods for querying the sequence viewer about the status of various things and
for requesting that the sequence viewer change its state.
Used for indicating that references to values returned from
SequenceViewerExtension.PropertyRetrieverAndEditor.getVisibleAnnotations(PropertyRetrieverAndEditor.DiscardReferencesCallback)
must be discarded.Wraps a
SequenceAnnotation and provides extra information about the location (sequence, track) of the annotation.Provides frequencies of nucleotides or amino acids
A convenience Factory for creating statistics.
Specifies the method used for calculating statistics when multiple sequences or regions are provided
One or more lines of statistics that show up in the statistics section of the sequence viewer.
Provides various utility functionality dealing with
GeneiousServices.Represents a summary of the sharing configuration for a workflow.
The set of standard icons used in Geneious.
Provides utility methods for creating and manipulating Strings.
Any summary document should "implement" this empty interface to enable special handling of summary documents inside
Geneious.
Provides utility methods for interacting with the operating system.
Used by code that loops and needs to check regularly if Geneious is running low on memory to know whether to abort the operation.
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).A taxon (element of a taxonomy) consisting of its scientific name
(e.g.
Represents a taxonomic level (AKA rank) that a Taxon can have in a Taxonomy,
e.g.
Provides methods to facilitate writing test cases for Geneious plugins
A document containing text that can be marked up in various formats such as html.
Format of the text
An extended search option which is displayed as a Text Field.
A specialized option for local search.
Provides utility methods for managing threads.
The common base for all documents that hold one or several trees.
A tree viewer extension is used for creating a custom controls section in the tree viewer.
The factory class that plugins provide via
GeneiousPlugin.getTreeViewerExtensionFactories()
for creating TreeViewerExtensionsThis class provides a set of getter properties for various UI settings used by Geneious.
Component-based client properties defined and used by Geneious.
Geneious application color palette and application-wide user interface constants.
A collection of properties for specific Geneious main frame components.
A collection of standardised unicode symbol characters.
Properties related to the aesthetics of
JTabbedPane.This class extends
java.awt.Color and provides colors which become inverted on dark based
themes.Properties related to the aesthetics of
JTree.Deprecated.
Do not call the methods in this class
An unmodifiable uniform resource name (URN), intended to serve as persistent, location-independent, resource identifiers.
Represents an AnnotatedPluginDocument at a particular revision, via its URN (
AnnotatedPluginDocument.getURN())
and revision number (AnnotatedPluginDocument.getRevisionNumber())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
Provides a mechanism for plugins to store advanced user configurable settings as name/value pairs.
Provides a sorted distribution of longs and the frequency of each of them.
Represents a value and the number of occurrences of the value
Manages a list of
WeakReferences, and providing
an iterator over the objects which are still strongly referenced.Just like a
SimpleListenerManager except the references to the listeners
are WeakReferences.Interface for managing sharing settings of workflows in the application.
Provides a DatabaseService that supports writing documents to it as
well as providing a hierarchical folder representation of the database.
Defines the way that a
WritableDatabaseService implements its "Deleted Items" (also known as "soft delete" or "trash" or "recycle bin").Holds information required for adding one or more documents to a database, potentially to different sub-folders.
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).A dummy implementation of WritableDatabaseService that provides no functionality apart from a name and icons
A GUI component that lets the user choose a WritableDatabaseService from the root services supplied.
Interface for handling persistent objects.
XMLSerializable classes are recommended implement this to indicate they support serializing to older version
formats and potentially deserializing from newer version formats.
Used for specifying the type of version support when used with
XMLSerializable.OldVersionCompatible.getVersionSupport(com.biomatters.geneious.publicapi.documents.XMLSerializable.VersionSupportType)An extended interface to
XMLSerializable to support providing progress (and the ability to cancel)
when serializing and deserialing.Represents a problem with XML serialization or deserialization.
Serialization helper class.
An XYZ molecular structure document.
An event fired to listeners added via
ZoomPanel.addChangeListener(ChangeListener)A panel for displaying and setting a zoom level.
NucleotideGraphSequenceDocumentinstead.