Deprecated List (Geneious Public API)

Interfaces
Interface	Description
com.biomatters.geneious.publicapi.documents.sequence.ChromatogramDocument	Check for instanceof `NucleotideGraphSequenceDocument` instead.
com.biomatters.geneious.publicapi.plugin.GeneiousPreferences	Use `PluginPreferences` and `GeneiousPlugin.getPluginPreferences()` instead

Classes
Class Description

com.biomatters.geneious.publicapi.plugin.URLStreamHandlerManager
Do not call the methods in this class

Classes
Class	Description
com.biomatters.geneious.publicapi.plugin.URLStreamHandlerManager	Do not call the methods in this class

Exceptions
Exceptions	Description
com.biomatters.geneious.publicapi.plugin.SequenceSelection.SequenceIndex.SelectionWrongForDocumentsException	use `SequenceSelectionWithDocuments.SelectedDocumentsModifiedException` instead

Fields
Field	Description
com.biomatters.geneious.publicapi.documents.DocumentField.SEQUENCE_DIRECTION	no longer used by binning, replaced by `DocumentField.BINNING_FRAME`
com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation.TYPE_CONCATENATED_SEQUENCE	use `SequenceAnnotation.TYPE_CLONING_FRAGMENT` instead.
com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation.TYPE_LOW_QUALITY	replaced with `SequenceAnnotation.TYPE_TRIMMED`.
com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation.TYPE_PRIMER_BIND_REVERSE	Should only be used to check for legacy primers. To create new primers, instead use `SequenceAnnotation.TYPE_PRIMER_BIND` with `SequenceAnnotationInterval.Direction.rightToLeft`
com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier.TRANSLATED_REGION_INTERVALS_NAME	these are no longer created
com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument.SOURCE_QUALIFIER_NAME	from 7.0.0, this field is not added to new primer annotations

Methods
Method	Description
com.biomatters.geneious.publicapi.components.GeneiousActionToolbar.addButton(AbstractButton, boolean)	use `GeneiousActionToolbar.addAction(com.biomatters.geneious.publicapi.plugin.GeneiousAction)` or `GeneiousActionToolbar.addAction(com.biomatters.geneious.publicapi.plugin.GeneiousAction, boolean)` instead.
com.biomatters.geneious.publicapi.components.OptionsPanel.setVerticalSpacing(int)	use `OptionsPanel.setVerticalSpacing(int, int)` instead
com.biomatters.geneious.publicapi.components.ProgressFrame.getFrame()	use `ProgressFrame.getWindow()`
com.biomatters.geneious.publicapi.components.ProgressFrame.setAutoMinimize(int)	this isn't nice for the users. Don't use it.
com.biomatters.geneious.publicapi.databaseservice.DatabaseService.resumeSearch(String, RetrieveCallback)	Geneious no longer supports resuming searches
com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback.setSearchResumptionIdentifier(String)	Geneious no longer supports resuming searches
com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService._addDocumentCopyWithProperties(AnnotatedPluginDocument, ProgressListener, Map<String, Object>)	use `WritableDatabaseService.addDocumentCopyWithProperties(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument, jebl.util.ProgressListener, java.util.Map, com.biomatters.geneious.publicapi.documents.URN)`
com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService.duplicateDocumentAndDealWithReferencedDocuments(AnnotatedPluginDocument, ElementProvider, AtomicReference<Element>)	use #duplicateDocumentAndDealWithReferencedDocuments
com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument.getPotentialAdditionalXmlKeys(boolean)	use `AnnotatedPluginDocument.getAdditionalXml(String, boolean)` or `WritableDatabaseService.getAdditionalPerDocumentXmlKeys(boolean, ProgressListener)`
com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument.getSummary()	use `AnnotatedPluginDocument.getFieldValue(DocumentField)` with `DocumentField.DESCRIPTION_FIELD` to get the Description for the document.
com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument.setSummary(String)	use `setFieldValue(DocumentField.DESCRIPTION_FIELD, description)` instead
com.biomatters.geneious.publicapi.documents.DocumentUtilities.createAnnotatedPluginDocument(Element, ElementProvider, boolean)	use `DocumentUtilities.createAnnotatedPluginDocument(org.jdom.Element, ElementProvider, boolean)` instead, where the final parameter of null is equivalent to assignNewURN==false or `URN.generateUniqueLocalURN()` for assignNewURN==true
com.biomatters.geneious.publicapi.documents.DocumentUtilities.getUniqueNameForDocument(String)	use getUniqueNameForDocument(String, WritableDatabaseService, Collection)
com.biomatters.geneious.publicapi.documents.DocumentUtilities.unloadDocuments(Predicate<URN>)	Under no circumstances should this method be used! Core Geneious is responsible for managing the strong references (and by extension, the lifespan) of all `AnnotatedPluginDocument` in memory, even in the event of document-supplying services being removed (i.e. a network database logout event). Unloading documents from plugin code can cause serious data integrity issues within Geneious. For an in-depth explanation of document lifespan behaviour, see `AnnotatedPluginDocument's javadoc`.
com.biomatters.geneious.publicapi.documents.DocumentUtilities.wouldDocumentNameBeUnique(String)
com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation.getAnnotationAdjustedForDeletion(int, int, boolean, int)	use `SequenceAnnotation.getAnnotationAdjustedForDeletion(int, CharSequence, int)`
com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval.getResidues(CharSequence, int, boolean)	New code should use `SequenceAnnotationInterval.getResidues(CharSequence, int, boolean, boolean, boolean)`
com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval.merge(List<SequenceAnnotationInterval>)	equivalent to calling `merge(intervals, true)`
com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval.reverse()	use `SequenceAnnotationInterval.getReverse()` instead.
com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.Builder.getSequenceList()	use `SequenceListOnDisk.Builder.toSequenceListOnDiskOrInMemoryIfNecessary(ProgressListener)` or `SequenceListOnDisk.Builder.toSequenceList(ProgressListener)`
com.biomatters.geneious.publicapi.documents.URN.isCloud()	all cloud document URNs (as of Geneious 2022.2) return true from `URN.isLocal()` and false from isCloud()
com.biomatters.geneious.publicapi.documents.XMLSerializer.forName(String)	use `PluginUtilities.getClass(String)` instead.
com.biomatters.geneious.publicapi.implementations.DefaultTreeDocument.setSource(String, String)	Geneious tree documents no longer store the original source, so this method does nothing.
com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument.createExtensionForPrimerAnnotation(SequenceAnnotation)	this method no longer works and there is no replacement in the API. Sorry!
com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage.fromXML(Element, NucleotideGraph)
com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.extractIntervals(SequenceDocument, String, GeneticCode, int, boolean, List<SequenceAnnotationInterval>, boolean, boolean)	use `SequenceExtractionUtilities.extractIntervals(com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument, com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions)` instead.
com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions.setTranslation(GeneticCode, int)	use `SequenceExtractionUtilities.ExtractionOptions.setTranslation(GeneticCode geneticCode, int translationFrame, boolean removeFinalStopCodon, boolean translateFirstCodonUsingFirstCodonTable)` instead.
com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.translate(SequenceDocument, SequenceAnnotation)	use `SequenceExtractionUtilities.extractIntervals(com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument, com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions)` instead.
com.biomatters.geneious.publicapi.plugin.AlignmentOperation.getAlignmentOptionsDescription(List<CharSequence>, Options)	this functionality is now supplied by operation history
com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties.setLengthOfReferenceSequences(long)	use `AssemblerInput.Properties.setLengthOfReferenceSequences(long, long)` instead
com.biomatters.geneious.publicapi.plugin.DocumentFileExporter.isProOnly()	Importers and exporters should not be restricted, all though this method still functions.
com.biomatters.geneious.publicapi.plugin.DocumentFileImporter.arePermissibleExtensionsCaseSensitive()	Geneious no longer respects this as extensions are generally not case sensitive
com.biomatters.geneious.publicapi.plugin.DocumentFileImporter.importDocumentsFromMultipleFiles(List<File>, DocumentFileImporter.ImportCallback, ProgressListener)	use `DocumentFileImporter.importDocumentsFromMultipleFilesReturningUnimported(Options, java.util.List, com.biomatters.geneious.publicapi.plugin.DocumentFileImporter.ImportCallback, jebl.util.ProgressListener)` instead
com.biomatters.geneious.publicapi.plugin.DocumentFileImporter.isProOnly()	Importers and exporters should not be restricted, all though this method still functions.
com.biomatters.geneious.publicapi.plugin.DocumentOperation.performOperation(AnnotatedPluginDocument[], ProgressListener, Options, SequenceSelection, DocumentOperation.OperationCallback)	As the callback parameter is not fully supported anymore.
com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature.matches(DocumentSelectionSignature[], Class[])	Use `DocumentSelectionSignature.matches(DocumentSelectionSignature[], java.util.List)` instead.
com.biomatters.geneious.publicapi.plugin.ExtendedPrintable.Factory.getExtendedPrintableForTextComponent(JTextComponent)	use `ExtendedPrintable.Factory.createExtendedPrintable(javax.swing.JComponent)` instead
com.biomatters.geneious.publicapi.plugin.ExtendedPrintable.getRequiredHeight(int, Options)	use `ExtendedPrintable.getMinimumWidth(Options)`, `ExtendedPrintable.getMaximumWidth(Options)` and `ExtendedPrintable.getDefaultWidth(Options)` instead.
com.biomatters.geneious.publicapi.plugin.ExtendedPrintable.getRequiredWidth(Options)	use `ExtendedPrintable.getMinimumWidth(Options)`, `ExtendedPrintable.getMaximumWidth(Options)` and `ExtendedPrintable.getDefaultWidth(Options)` instead.
com.biomatters.geneious.publicapi.plugin.GeneiousPlugin.getPreferences()	GeneiousPreferences are the old style way of providing preferences. Use `GeneiousPlugin.getPluginPreferences()` instead which is more powerful and more consistent with other areas of the Geneious API.
com.biomatters.geneious.publicapi.plugin.GeneiousService.getPreferences()	use `GeneiousPlugin.getPluginPreferences()` instead
com.biomatters.geneious.publicapi.plugin.Icons.getOriginalIconUnscaled()	since API 4.201910 (Geneious 2019.1.0) use `Icons.getOriginalIconForRetina()` or `Icons.getOriginalIcon()` ()}instead.
com.biomatters.geneious.publicapi.plugin.License.freeVersionName()	the "free" version of Geneious no longer has a name, features are simply restricted when no license is active. Deprecated in API 4.600 (Geneious 6.0.0)
com.biomatters.geneious.publicapi.plugin.License.freeVersionSuffix()	the "free" version of Geneious no longer has a name, features are simply restricted when no license is active. Deprecated in API 4.600 (Geneious 6.0.0)
com.biomatters.geneious.publicapi.plugin.License.premiumVersionName()	there never was and there will never be a premium version of Geneious. Deprecated in API 4.600 (Geneious 6.0.0)
com.biomatters.geneious.publicapi.plugin.License.premiumVersionPrefix()	there never was and there will never be a premium version of Geneious. Deprecated in API 4.600 (Geneious 6.0.0)
com.biomatters.geneious.publicapi.plugin.License.proVersionName()	there is no "Pro" version anymore, Geneious is Geneious. Consider using `Geneious.getName()` instead. Deprecated in API 4.600 (Geneious 6.0.0)
com.biomatters.geneious.publicapi.plugin.License.proVersionSuffix()	there is no "Pro" version anymore, Geneious is Geneious. Consider using `License.restrictedName(boolean)` instead. Deprecated in API 4.600 (Geneious 6.0.0)
com.biomatters.geneious.publicapi.plugin.Options.addCustomComponent(JComponent)	Please instead use `Options.addCustomComponent(ComponentCreator)` as Swing is not thread safe and Options are frequently constructed outside the Swing thread.
com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.generateAnnotations(AnnotatedPluginDocument[], SequenceAnnotationGenerator.SelectionRange, ProgressListener, Options)	use `generate` instead. Create annotations from a set of documents. Note: The operation will be run in a non AWT thread. If you need to perform user interface interaction in addition to the options provided in the Options (for example prompting for user input) then you need to place this inside a ThreadUtilities.invokeAndWait() function call. WARNING: Geneious may call this method multiple times simultaneously. Therefore, any implementation should not store its internal state within instance fields. WARNING: The default implementation of this method calls `SequenceAnnotationGenerator.generate(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[], com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionRange, jebl.util.ProgressListener, Options)` but returns only the list of annotations, so any tracks, residue additions or deletions, and annotation deletions, and generated documents will not be respected. If you are invoking a SequenceAnnotationGenerator in another plugin, call `SequenceAnnotationGenerator.generate(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[], com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionRange, jebl.util.ProgressListener, Options)` instead.
com.biomatters.geneious.publicapi.plugin.SequenceGraphFactory.createDocumentBasedGraph(AnnotatedPluginDocument)	This method causes ambiguity about whether the Alignment of Sequence aspect of a `CombinedAlignmentAndSequenceDocument` is required so is no longer used on CombinedAlignmentAndSequenceDocuments. All implementations should instead implement `SequenceGraphFactory.createDocumentBasedGraphForAlignment(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument)` or `SequenceGraphFactory.createDocumentBasedGraphForSequence(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument)`.
com.biomatters.geneious.publicapi.plugin.SequenceSelection.extractIntervals()
com.biomatters.geneious.publicapi.plugin.SequenceSelection.getIntervals()	use `SequenceSelection.getIntervals(boolean)` instead
com.biomatters.geneious.publicapi.plugin.SequenceSelection.getSelectedSequences()	use `SequenceSelection.getSelectedSequenceIndices()`
com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectionInterval.getSequence()	use `SequenceSelection.SelectionInterval.getSequenceIndex()` and `SequenceSelection.SequenceIndex.getSequence(java.util.List)` instead.
com.biomatters.geneious.publicapi.plugin.TestGeneious.isRunningApplication()	Use `Geneious.isClient()` instead
com.biomatters.geneious.publicapi.plugin.TreeViewerExtension.Factory.createTreeViewerExtension(AnnotatedPluginDocument)	Use `TreeViewerExtension.Factory.createTreeViewerExtension(DocumentViewer, com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument)` instead.
com.biomatters.geneious.publicapi.plugin.URLStreamHandlerManager.addStreamHandler(String, URLStreamHandler)	Do not call
com.biomatters.geneious.publicapi.plugin.URLStreamHandlerManager.removeStreamHandler(String, URLStreamHandler)	Do not call
com.biomatters.geneious.publicapi.utilities.FileUtilities.createTempFile(String, String)	use `FileUtilities.createTempFile(String, String, boolean)` instead.
com.biomatters.geneious.publicapi.utilities.GuiUtilities.createHelpButton(boolean)	As of Geneious 2021.0.0, all help buttons are created as non-small buttons. Use `GuiUtilities.createHelpButton()` instead.
com.biomatters.geneious.publicapi.utilities.GuiUtilities.getDialogHtmlHead()	As of Geneious 2021.0.0, Geneious applies the custom CSS formatting from this method across all HTML-formatted content to avoid formatting discrepancies.
com.biomatters.geneious.publicapi.utilities.GuiUtilities.getScaledValue(int)	On Java 9 or above, the scale factor is always 1. Geneious ships with a bundled JRE that is always higher than Java 9, rendering this method effectively obsolete.
com.biomatters.geneious.publicapi.utilities.Interval.getMax()	using `Interval.getMaxExclusive()` or `Interval.getMaxInclusive()` instead is recommended as the code is easier to understand and less likely to contain bugs.
com.biomatters.geneious.publicapi.utilities.Interval.getTo()	using `Interval.getToExclusive()` ()} or `Interval.getToInclusive()` ()} instead is recommended as the code is easier to understand and less likely to contain bugs.
com.biomatters.geneious.publicapi.utilities.SequenceUtilities.asJeblSequence(AnnotatedPluginDocument, SequenceDocument)	use `SequenceUtilities.asJeblSequence(SequenceAlignmentDocument.ReferencedSequence, SequenceDocument)`
com.biomatters.geneious.publicapi.utilities.SequenceUtilities.asTranslation(CharSequence, GeneticCode)	use `SequenceUtilities.asTranslation(CharSequence, jebl.evolution.sequences.GeneticCode, boolean)` instead.
com.biomatters.geneious.publicapi.utilities.SequenceUtilities.generateConsensusSequence(SequenceAlignmentDocument, ProgressListener)	use `SequenceUtilities.generateConsensus(com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument, jebl.util.ProgressListener)` instead
com.biomatters.geneious.publicapi.utilities.SequenceUtilities.getAnnotationsOfType(SequenceDocument, String)	use `SequenceUtilities.getAnnotationsOfType(com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument, String, boolean)` instead.
com.biomatters.geneious.publicapi.utilities.SequenceUtilities.getForwardRegexForSequence(CharSequence, SequenceType, boolean, boolean)	use `SequenceUtilities.getForwardRegexForSequence(CharSequence, jebl.evolution.sequences.SequenceType, boolean, boolean, boolean)` instead
com.biomatters.geneious.publicapi.utilities.SystemUtilities.isJava10OrLater()	As of version 2025.0.0 Geneious is Java 11 or later only, this will always return true
com.biomatters.geneious.publicapi.utilities.SystemUtilities.isJava11OrLater()	As of version 2025.0.0 Geneious is Java 11 or later only, this will always return true
com.biomatters.geneious.publicapi.utilities.SystemUtilities.isJava6OrLater()	As of version 6.0.0 Geneious is Java 6 or later only, this will always return true
com.biomatters.geneious.publicapi.utilities.SystemUtilities.isJava7OrLater()	As of version 10.0.0 Geneious is Java 8 or later only, this will always return true
com.biomatters.geneious.publicapi.utilities.SystemUtilities.isJava8OrLater()	As of version 10.0.0 Geneious is Java 8 or later only, this will always return true
com.biomatters.geneious.publicapi.utilities.SystemUtilities.isJava9OrLater()	As of version 2025.0.0 Geneious is Java 11 or later only, this will always return true
com.biomatters.geneious.publicapi.utilities.SystemUtilities.isRetinaDisplay()	doesn't work in open JDK. And a user could have multiple screens, one of which is retina, so doesn't always work correctly in other JDKs. Use `SystemUtilities.isRetinaDisplay(Graphics2D)` instead.
com.biomatters.geneious.publicapi.utilities.SystemUtilities.isSolaris()	Geneious is no longer supported on Solaris
com.biomatters.geneious.publicapi.utilities.SystemUtilities.isSolarisSparc()	Geneious is no longer supported on Solaris
com.biomatters.geneious.publicapi.utilities.SystemUtilities.isSolarisX86()	Geneious is no longer supported on Solaris

Constructors
Constructor	Description
com.biomatters.geneious.publicapi.components.AlertPanel(FlowLayout)	To change the text alignment use `AlertPanel(TextAlign)`, changing gaps is no longer supported.
com.biomatters.geneious.publicapi.components.ProgressFrame(String, String, long, boolean)	use `ProgressFrame(String, String)` instead
com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument(SequenceDocument[], String, Double, String)	use `DefaultAlignmentDocument(String, com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument...)` instead.
com.biomatters.geneious.publicapi.plugin.GeneiousAction(String, String, Icons, GeneiousActionOptions.Category, GeneiousActionOptions.MainMenu, boolean, boolean, KeyStroke)	Construct `GeneiousActionOptions` first then use constructor `GeneiousAction(GeneiousActionOptions)` instead.
com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions(String, String, Icons, GeneiousActionOptions.Category, GeneiousActionOptions.MainMenu, boolean, boolean, KeyStroke, boolean)	Use other constructors in combination with setters instead
com.biomatters.geneious.publicapi.plugin.SequenceSelection(SequenceDocument, SequenceAnnotation)	use `SequenceSelection(com.biomatters.geneious.publicapi.plugin.SequenceSelection.SequenceIndex, com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation)` instead
com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectionInterval(int, int, SequenceDocument)	use `SelectionInterval(SequenceIndex, int, int)` instead

Enum Constants
Enum Constant	Description
com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions.MainMenu.Pro	the pro menu no longer exists, do not use.
com.biomatters.geneious.publicapi.utilities.StandardIcons.sortAscending
com.biomatters.geneious.publicapi.utilities.StandardIcons.sortDescending

Deprecated API

Contents