Deprecated API

Contents

• Deprecated Interfaces
• Deprecated Classes
• Deprecated Exceptions
• Deprecated Fields
• Deprecated Methods
• Deprecated Constructors
• Deprecated Enum Constants

Deprecated Interfaces

Interface and 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

Deprecated Classes

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

Deprecated Exceptions

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

Deprecated Fields

Field and Description
com.biomatters.geneious.publicapi.documents.DocumentField.SEQUENCE_DIRECTION no longer used by binning, replaced by DocumentField.BINNING_FRAME
com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument.SOURCE_QUALIFIER_NAME from 7.0.0, this field is not added to new primer annotations
com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation.TYPE_LOW_QUALITY replaced with SequenceAnnotation.TYPE_TRIMMED.

Deprecated Methods

Method and Description
com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService._addDocumentCopyWithProperties(AnnotatedPluginDocument, ProgressListener, Map) 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.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.plugin.URLStreamHandlerManager.addStreamHandler(String, URLStreamHandler) Do not call
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.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.createAnnotatedPluginDocument(Element, ElementProvider, String) use DocumentUtilities.createAnnotatedPluginDocument(org.jdom.Element, ElementProvider, URN) 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.implementations.sequence.OligoSequenceDocument.createExtensionForPrimerAnnotation(SequenceAnnotation) this method no longer works and there is no replacement in the API. Sorry!
com.biomatters.geneious.publicapi.utilities.FileUtilities.createTempFile(String, String) use FileUtilities.createTempFile(String, String, boolean) 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.databaseservice.WritableDatabaseService.duplicateDocumentAndDealWithReferencedDocuments(AnnotatedPluginDocument, ElementProvider, AtomicReference) use #duplicateDocumentAndDealWithReferencedDocuments
com.biomatters.geneious.publicapi.plugin.SequenceSelection.extractIntervals()
com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.extractIntervals(SequenceDocument, String, GeneticCode, int, boolean, List, boolean, boolean) use SequenceExtractionUtilities.extractIntervals(com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument, com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions) instead.
com.biomatters.geneious.publicapi.documents.XMLSerializer.forName(String) use PluginUtilities.getClass(String) 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.implementations.sequence.SequencePropertiesStorage.fromXML(Element, NucleotideGraph)
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 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.utilities.SequenceUtilities.generateConsensusSequence(SequenceAlignmentDocument, ProgressListener) use SequenceUtilities.generateConsensus(com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument, jebl.util.ProgressListener) instead
com.biomatters.geneious.publicapi.plugin.AlignmentOperation.getAlignmentOptionsDescription(List, Options) this functionality is now supplied by operation history
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.plugin.ExtendedPrintable.Factory.getExtendedPrintableForTextComponent(JTextComponent) use ExtendedPrintable.Factory.createExtendedPrintable(javax.swing.JComponent) 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.components.ProgressFrame.getFrame() use ProgressFrame.getWindow()
com.biomatters.geneious.publicapi.plugin.SequenceSelection.getIntervals() use SequenceSelection.getIntervals(boolean) instead
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.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.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.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.documents.AnnotatedPluginDocument.getSummary() use AnnotatedPluginDocument.getFieldValue(DocumentField) with DocumentField.DESCRIPTION_FIELD to get the Description for the docment.
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.documents.DocumentUtilities.getUniqueNameForDocument(String) use getUniqueNameForDocument(String, WritableDatabaseService, Collection)
com.biomatters.geneious.publicapi.documents.DocumentUtilities.getUniqueNameForDocument(String, boolean) use getUniqueNameForDocument(String, WritableDatabaseService, Collection)
com.biomatters.geneious.publicapi.plugin.DocumentFileImporter.importDocumentsFromMultipleFiles(List, 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.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.plugin.DocumentFileExporter.isProOnly() Importers and exporters should not be restricted, all though this method still functions.
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.TestGeneious.isRunningApplication() Use Geneious.isClient() 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
com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature.matches(DocumentSelectionSignature[], Class[]) Use DocumentSelectionSignature.matches(DocumentSelectionSignature[], java.util.List) instead.
com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval.merge(List) equivalent to calling merge(intervals, true)
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.URLStreamHandlerManager.removeStreamHandler(String, URLStreamHandler) Do not call
com.biomatters.geneious.publicapi.databaseservice.DatabaseService.resumeSearch(String, RetrieveCallback) Geneious no longer supports resuming searches
com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval.reverse() use SequenceAnnotationInterval.getReverse() instead.
com.biomatters.geneious.publicapi.components.ProgressFrame.setAutoMinimize(int) this isn't nice for the users. Don't use it.
com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties.setLengthOfReferenceSequences(long) use AssemblerInput.Properties.setLengthOfReferenceSequences(long, long) instead
com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback.setSearchResumptionIdentifier(String) Geneious no longer supports resuming searches
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.documents.AnnotatedPluginDocument.setSummary(String) use setFieldValue(DocumentField.DESCRIPTION_FIELD, description) 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.components.OptionsPanel.setVerticalSpacing(int) use OptionsPanel.setVerticalSpacing(int, int) 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.documents.DocumentUtilities.wouldDocumentNameBeUnique(String)

Deprecated Constructors

Constructor and Description
com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument(SequenceDocument[], String, Double, String) use DefaultAlignmentDocument.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.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.components.ProgressFrame(String, String, long, boolean) use ProgressFrame.ProgressFrame(String, String) instead
com.biomatters.geneious.publicapi.components.ProgressFrame(String, String, long, boolean, Window) use ProgressFrame.ProgressFrame(String, String, java.awt.Window) instead
com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectionInterval(Interval, SequenceDocument) use #SelectionInterval(SequenceIndex, com.biomatters.geneious.publicapi.utilities.Interval) instead
com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectionInterval(int, int, SequenceDocument) use #SelectionInterval(SequenceIndex, int, int) instead
com.biomatters.geneious.publicapi.plugin.SequenceSelection(SequenceDocument, SequenceAnnotation) use SequenceSelection.SequenceSelection(com.biomatters.geneious.publicapi.plugin.SequenceSelection.SequenceIndex, com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation) instead

Deprecated Enum Constants

Enum Constant and Description
com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions.MainMenu.Pro the pro menu no longer exists, do not use.