Uses of Class
com.biomatters.geneious.publicapi.plugin.Options
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Packages that use Options Package Description com.biomatters.geneious.publicapi.components Provides useful GUI (graphical user interface) components, none of which are necessary for creating a plugin, but many plugin implentations will find these components useful.com.biomatters.geneious.publicapi.databaseservice Provides the interface and associated classes for defining a database service which is a service that appears on the left-hand side of the main Geneious window and provides the user with access to a database, for example NCBI or the local database for storing the user's documents.com.biomatters.geneious.publicapi.plugin Provides theGeneiousPlugin
interface and plugin related interfaces. -
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Uses of Options in com.biomatters.geneious.publicapi.components
Methods in com.biomatters.geneious.publicapi.components with parameters of type Options Modifier and Type Method Description static void
Dialogs. showNonModalOptionsDialog(Options options, java.lang.String dialogTitle, boolean restoreAndSavePreferences, java.lang.Runnable applyAction, java.lang.Runnable closeAction, javax.swing.JComponent owner)
Display a non-modal options dialog with "Apply & Close", "Apply", and "Cancel" buttons based on anOptions
object.static boolean
Dialogs. showOptionsDialog(Options options, java.lang.String dialogTitle, boolean restoreAndSavePreferences)
Display an options dialog based on anOptions
object.static boolean
Dialogs. showOptionsDialog(Options options, java.lang.String dialogTitle, boolean restoreAndSavePreferences, javax.swing.JComponent owner)
Display an options dialog based on anOptions
object. -
Uses of Options in com.biomatters.geneious.publicapi.databaseservice
Methods in com.biomatters.geneious.publicapi.databaseservice that return Options Modifier and Type Method Description Options
SequenceDatabaseSuperService. getAddDatabaseOptions(DatabaseService.SequenceSearchQueryType databaseType)
Optionally override to returnOptions
which will be displayed to the user (in addition to the standard options) before adding a sequence database.Options
DatabaseService. getSequenceSearchOptions(java.lang.String program)
Optionally override to provide options which will be displayed at the bottom of the options in the Sequence Search interface when this database is selected and the given program is selected.Options
SequenceDatabaseSuperService. getSetupOptions()
Optionally override to returnOptions
which will be displayed to the user in a services set up section of the interface.Methods in com.biomatters.geneious.publicapi.databaseservice with parameters of type Options Modifier and Type Method Description void
SequenceDatabaseSuperService. addDatabase(AnnotatedPluginDocument[] annotatedDocuments, java.lang.String name, Options options, jebl.util.ProgressListener progressListener)
Add a new sequence database to the service from a selection of documents in Geneious.void
SequenceDatabaseSuperService. addDatabase(java.io.File file, java.lang.String name, Options options, jebl.util.ProgressListener progressListener, DatabaseService.SequenceSearchQueryType expectedDatabaseType)
Add a new sequence database to the service from a file on disk.void
SequenceDatabaseSuperService. applySetupOptions(Options setupOptions, jebl.util.ProgressListener progressListener)
Apply and save the specified setup options to the service.void
DatabaseService. batchSequenceSearch(java.util.List<AnnotatedPluginDocument> querySequences, java.lang.String program, Options options, RetrieveCallback callback)
If this is a Sequence Database (ie.DocumentSelectionSignature[]
DatabaseService. getDocumentTypesForSequenceSearch(DatabaseService.SequenceSearchQueryType queryType, java.lang.String program, Options searchOptions, boolean summaryDocumentTypes)
ReturnDocumentSelectionSignature
s describing all possible types of documents that can be returned from a sequence search on this service.void
DatabaseService. sequenceSearch(AnnotatedPluginDocument querySequence, java.lang.String program, Options options, RetrieveCallback callback)
If this is a Sequence Database (ie. -
Uses of Options in com.biomatters.geneious.publicapi.plugin
Classes in com.biomatters.geneious.publicapi.plugin with type parameters of type Options Modifier and Type Class Description class
PluginPreferences<T extends Options>
Allows a plugin to provideOptions
based preferences that are displayed in the Geneious Preferences dialog.Subclasses of Options in com.biomatters.geneious.publicapi.plugin Modifier and Type Class Description class
OperationLocationOptions
AnOptions
that provides the ability to pick between running an Operation on the local computer or on a supportedGeneiousService
.Methods in com.biomatters.geneious.publicapi.plugin that return Options Modifier and Type Method Description Options
Options. addChildOptions(java.lang.String name, java.lang.String label, java.lang.String description)
Creates, adds and returns some child options.Options
Options.MultipleOptions. addValue(boolean fireChangeListeners)
Clone and add a new copy of the master options to these multiple options.Options
Findable.FindOptions. getAdditionalOptions()
Get additional options originally provided usingFindable.getAdditionalOptions(java.util.concurrent.Callable)
Options
Findable. getAdditionalOptions(java.util.concurrent.Callable<java.lang.String> currentSearchTextGetter)
A sub-class can optionally override this to replace the standard isCaseSensitive with some custom options.Options
Options.ButtonOption. getDependentChildOptions()
Options
AlignmentOperation. getGeneralOptions()
Gets some Options that work for this operation when invoked on any type and number of input sequencesOptions
DocumentOperation. getGeneralOptions()
Gets some Options that work for this document operation when invoked on any set of input sequences.Options
DocumentOperation.Wrapper. getGeneralOptions()
Options
GeneiousGridDocumentOperation. getGeneralOptions()
Options
SequenceAnnotationGenerator. getGeneralOptions()
Gets some Options that work for this annotation generator when invoked on any set of input sequences.Options
Options.MultipleOptions. getMasterOptions()
Returns the options that were used to construct this MultipleOptions.Options
AlignmentOperation. getOptions(SequenceDocument.Alphabet alphabet, boolean pairwise, boolean isSingleAlignment)
Get the options appropriate for aligning these sequencesOptions
AlignmentOperation. getOptions(AlignmentOperation.InputProperties inputProperties)
A more powerful alternative toAlignmentOperation.getOptions(com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument.Alphabet, boolean, boolean)
that may provide the properties of the input to the operation.abstract Options
Assembler. getOptions(OperationLocationOptions locationOptions, AssemblerInput.Properties inputProperties)
Gets some options to display to the user before performing assembly.abstract Options
DatabaseFolderImporter. getOptions(java.io.File folder, WritableDatabaseService destination, jebl.util.ProgressListener progress)
Provides some options applicable to this database importer to the user, or null if no user-specified options are required.Options
DocumentFileExporter. getOptions()
Provides all possible options that can be displayed to the user when exporting.Options
DocumentFileExporter. getOptions(AnnotatedPluginDocument[] documentsToExport)
Provide some options to display to the user when exporting.Options
DocumentFileImporter. getOptions(java.util.List<java.io.File> filesToImport, jebl.util.ProgressListener progressListener)
Provides some options applicable to this importer to the user.Options
DocumentOperation. getOptions(AnnotatedPluginDocument... documents)
Provides some options applicable to this document operation to the user.Options
DocumentOperation. getOptions(DocumentOperationInput operationInput)
More powerful alternative toDocumentOperation.getOptions(AnnotatedPluginDocument[])
which may provide additional values such as the location the operation is run and the currently selected region of any sequence in the documents.Options
DocumentOperation. getOptions(SequenceSelection sequenceSelection, AnnotatedPluginDocument... documents)
More powerful alternative toDocumentOperation.getOptions(AnnotatedPluginDocument[])
which may provide the currently selected region of any sequence in the documents.Options
DocumentOperation. getOptions(java.util.List<AnnotatedPluginDocument> documents)
A convenience method for callingDocumentOperation.getOptions(AnnotatedPluginDocument[])
Options
DocumentOperation. getOptions(org.jdom.Element optionsElement, java.util.List<AnnotatedPluginDocument> inputDocuments, java.util.List<AnnotatedPluginDocument> additionalParentDocuments)
Recreates some options for rerunning an earlier operation to recreate descendant documents.Options
DocumentOperation.Wrapper. getOptions(AnnotatedPluginDocument... documents)
Options
DocumentOperation.Wrapper. getOptions(DocumentOperationInput operationInput)
Options
DocumentOperation.Wrapper. getOptions(SequenceSelection sequenceSelection, AnnotatedPluginDocument... documents)
Options
DocumentOperation.Wrapper. getOptions(org.jdom.Element optionsElement, java.util.List<AnnotatedPluginDocument> inputDocuments, java.util.List<AnnotatedPluginDocument> additionalParentDocuments)
Options
ExtendedPrintable. getOptions(boolean isSavingToFile)
Optionally provide additional printing and/or saving image to file options.Options
ExtendedPrintable.Wrapper. getOptions(boolean isSavingToFile)
Options
GeneiousGridDocumentOperation. getOptions(DocumentOperationInput operationInput)
Returns options for running the full grid operation (an almagimation of the options given byGeneiousGridDocumentOperation.getProgramOptions(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[])
, and some extra options describing where the job will run.Options
SequenceAnnotationGenerator. getOptions(AnnotatedPluginDocument[] documents, SequenceAnnotationGenerator.SelectionRange selectionRange)
Provides some options applicable to this annotation generator to the user.Options
SequenceAnnotationGenerator. getOptions(AnnotatedPluginDocument[] documents, SequenceAnnotationGenerator.SelectionRange selectionRange, boolean compactOptions)
Similar toSequenceAnnotationGenerator.getOptions(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[], com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionRange)
except that ifcompactOptions==true
then options returned may be more visually compact for rendering in a smaller region, such as in the sequence viewer controls in the case whereSequenceAnnotationGenerator.getNameInSequenceViewer()
is not null.Options
SequenceAnnotationGenerator. getOptions(SequenceAnnotationGenerator.SelectionRange selectionRange, AnnotatedPluginDocument... documents)
Options
SequenceAnnotationGenerator. getOptions(SequenceAnnotationGenerator.SelectionRange selectionRange, java.util.List<AnnotatedPluginDocument> documents)
Options
SequenceGraph. getOptions()
Provides options associated with this graph.Options
DocumentFileExporter. getOptionsForBatchExport(AnnotatedPluginDocument[] documentsToExport)
Provide some options to display to the user when batch exporting.Options
Options. getParentOptions()
Options
Options.Option. getParentOptions()
Returns the Options in which this option is containedOptions
DocumentFileExporter. getProgrammaticOptions()
Provides all possible options that are available when exporting.abstract Options
GeneiousGridDocumentOperation. getProgramOptions(AnnotatedPluginDocument... documents)
This method returns options for running the programstatic Options
GeneiousGridDocumentOperation. getProgramOptions(Options options)
A utility method to get the program options (equivalent to options taken fromGeneiousGridDocumentOperation.getProgramOptions(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[])
, given options taken fromDocumentOperation.getOptions(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[])
static Options
GeneiousGridDocumentOperation. getSelectedServiceOptions(Options options)
A utility method to get the configuration options for the service this operation has been chosen to run on.Methods in com.biomatters.geneious.publicapi.plugin that return types with arguments of type Options Modifier and Type Method Description java.util.Map<java.lang.String,Options>
Options. getChildOptions()
Get all child options added usingaddChildOptions(String, String, String, Options)
.java.util.List<Options>
Options.MultipleOptions. getValues()
Get all the current values for a set of multiple options.Methods in com.biomatters.geneious.publicapi.plugin with parameters of type Options Modifier and Type Method Description void
Options. addChildOptions(java.lang.String name, java.lang.String label, java.lang.String description, Options childOptions)
void
Options. addChildOptions(java.lang.String name, java.lang.String label, java.lang.String description, Options childOptions, boolean useParentPreferences)
Adds a set of existing Options as child options of this Options.void
Options. addChildOptions(java.lang.String name, java.lang.String label, java.lang.String description, Options childOptions, double weightY, boolean useParentPreferences)
Adds a set of existing Options as child options of this Options with the specified vertical weight.void
Options.Option. addChildOptionsDependent(Options childOptions, ValueType valueRequiredForDependentToBeEnabled, boolean displayThisOptionInChildOptionsHeading)
Make the enabled state of some child options depend on the current value of this option.void
Options. addCollapsibleChildOptions(java.lang.String name, java.lang.String label, java.lang.String description, Options childOptions, boolean useParentPreferences, boolean defaultCollapsed)
Add child options that can be expanded and collapsed.void
Options.RadioOption. addDependent(ValueType optionValue, Options dependentOptions, boolean layoutDependentNearRadioButton)
Adds a dependent option that will be enabled when the radio button associated with the OptionValue is selected, and disabled when it is not.void
Options.ButtonOption. addDependentChildOptions(Options childOptions, java.lang.String dialogTitle)
The child options passed into this method will not be displayed inline in the options panel.Options.MultipleOptions
Options. addMultipleOptions(java.lang.String name, Options multipleOptions, boolean isAdvanced)
Adds a set of Options so that the user is able to choose to have one or more instances of these child options through the use of +/- buttons to the right of the options.abstract java.util.List<java.lang.CharSequence>
AlignmentOperation. align(SequenceDocument.Alphabet alphabet, java.util.List<java.lang.CharSequence> sequences, Options options, jebl.util.ProgressListener progressListener)
Align the given sequencesabstract void
Assembler. assemble(Options options, AssemblerInput assemblyInput, jebl.util.ProgressListener progressListener, Assembler.Callback callback)
Called to actually perform the assembly.void
DocumentFileExporter. export(java.io.File file, AnnotatedPluginDocument[] documents, jebl.util.ProgressListener progressListener, Options options)
Do the actual exporting.void
DocumentFileExporter. export(java.io.File file, PluginDocument[] documents, jebl.util.ProgressListener progressListener, Options options)
Do the actual exporting from PluginDocuments.java.util.List<SequenceAnnotationGenerator.AnnotationGeneratorResult>
SequenceAnnotationGenerator. generate(AnnotatedPluginDocument[] documents, SequenceAnnotationGenerator.SelectionRange selectionRange, jebl.util.ProgressListener progressListener, Options options)
Create annotations (and/or deletes annotations and/or modifies residues and/or modifies field values) on a set of documents.java.util.List<java.util.List<SequenceAnnotation>>
SequenceAnnotationGenerator. generateAnnotations(AnnotatedPluginDocument[] documents, SequenceAnnotationGenerator.SelectionRange selectionRange, jebl.util.ProgressListener progressListener, Options options)
Deprecated.usegenerate
instead.java.util.List<java.util.List<SequenceAnnotation>>
SequenceAnnotationGenerator. generateAnnotations(SequenceAnnotationGenerator.SelectionRange selectionRange, jebl.util.ProgressListener progressListener, Options options, AnnotatedPluginDocument... documents)
java.util.List<java.util.List<SequenceAnnotation>>
SequenceAnnotationGenerator. generateAnnotations(SequenceAnnotationGenerator.SelectionRange selectionRange, jebl.util.ProgressListener progressListener, Options options, java.util.List<AnnotatedPluginDocument> documents)
java.util.List<SequenceAnnotationGenerator.AnnotationGeneratorResultOnAlignment>
SequenceAnnotationGenerator. generateOnAlignments(AnnotatedPluginDocument[] documents, jebl.util.ProgressListener progressListener, Options options)
Create annotations (and/or deletes annotations and/or modifies residues and/or modifies field values) on a set of alignments.java.lang.String
AlignmentOperation. getAlignmentOptionsDescription(java.util.List<java.lang.CharSequence> alignedSequences, Options options)
Deprecated.this functionality is now supplied by operation historyjava.util.List<java.lang.String>
SequenceAnnotationGenerator. getAnnotationQualifiersToShowAfterNameForRealTimeAnnotations(Options options)
If this is a real time annotation generator (i.e.int
ExtendedPrintable. getDefaultHeight(int width, Options options)
If this component does not have a required height (i.e.int
ExtendedPrintable.Wrapper. getDefaultHeight(int width, Options options)
int
ExtendedPrintable. getDefaultWidth(Options options)
If this component does not have a required width (i.e.int
ExtendedPrintable.Wrapper. getDefaultWidth(Options options)
abstract GeneiousGridDocumentOperation.GridInput
GeneiousGridDocumentOperation. getGridInput(AnnotatedPluginDocument[] documents, Options programOptions, Options fullOptions)
Returns aGeneiousGridDocumentOperation.GridInput
object representing all the files and command-line inputs needed to run a job on the gridjava.lang.String
GeneiousGridDocumentOperation. getHTMLSummary(Options options)
Should return a summary of the operation that was run including all parameters sent to the command line application and any other options that the user entered.static OperationLocationOptions
GeneiousGridDocumentOperation. getLocationOptions(Options options)
A utility method to get the location options (the options visible at the top of the options taken fromDocumentOperation.getOptions(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[])
) ,int
ExtendedPrintable. getMaximumHeight(int width, Options options)
Get the maximum height (inclusive) of the component when saved as an image.int
ExtendedPrintable.Wrapper. getMaximumHeight(int width, Options options)
int
ExtendedPrintable. getMaximumWidth(Options options)
Get the maximum width (inclusive) of the component when saved as an image.int
ExtendedPrintable.Wrapper. getMaximumWidth(Options options)
int
ExtendedPrintable. getMinimumHeight(int width, Options options)
Get the minimum height (inclusive) of the component when saved as an image.int
ExtendedPrintable.Wrapper. getMinimumHeight(int width, Options options)
int
ExtendedPrintable. getMinimumWidth(Options options)
Get the minimum width (inclusive) of the component when saved as an image.int
ExtendedPrintable.Wrapper. getMinimumWidth(Options options)
abstract int
ExtendedPrintable. getPagesRequired(java.awt.Dimension dimensions, Options options)
int
ExtendedPrintable.Wrapper. getPagesRequired(java.awt.Dimension dimensions, Options options)
static Options
GeneiousGridDocumentOperation. getProgramOptions(Options options)
A utility method to get the program options (equivalent to options taken fromGeneiousGridDocumentOperation.getProgramOptions(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[])
, given options taken fromDocumentOperation.getOptions(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[])
int
ExtendedPrintable. getRequiredHeight(int width, Options options)
Deprecated.int
ExtendedPrintable.Wrapper. getRequiredHeight(int width, Options options)
int
ExtendedPrintable. getRequiredWidth(Options options)
Deprecated.int
ExtendedPrintable.Wrapper. getRequiredWidth(Options options)
java.lang.Double
AlignmentOperation. getScore(java.util.List<java.lang.CharSequence> alignedSequences, Options options)
Used as score parameter when constructing the result alignment, seeDefaultAlignmentDocument#DefaultAlignmentDocument(SequenceDocument[], List, String, Double, String)
static Options
GeneiousGridDocumentOperation. getSelectedServiceOptions(Options options)
A utility method to get the configuration options for the service this operation has been chosen to run on.SequenceAnnotationGenerator.SingleSequenceResultGenerator
SequenceAnnotationGenerator. getSingleSequenceGenerator(Options options)
Optionally provides an alternative way of generating annotations for large data sets to reduce memory usage.void
DocumentFileImporter. importDocuments(Options options, java.io.File file, DocumentFileImporter.ImportCallback callback, jebl.util.ProgressListener progressListener)
Import document(s) from file into a callback.java.util.List<java.io.File>
DocumentFileImporter. importDocumentsFromMultipleFilesReturningUnimported(Options options, java.util.List<java.io.File> filesToImport, DocumentFileImporter.ImportCallback callback, jebl.util.ProgressListener progressListener)
An alternative toDocumentFileImporter.importDocuments(java.io.File, com.biomatters.geneious.publicapi.plugin.DocumentFileImporter.ImportCallback, jebl.util.ProgressListener)
that importers which import multiple files may implement.abstract WritableDatabaseService
DatabaseFolderImporter. importFolder(java.io.File folder, WritableDatabaseService destination, Options options, jebl.util.ProgressListener progress)
Import the external database to a GeneiousWritableDatabaseService
and report back the containing the added documents.boolean
AlignmentOperation. isRefine(Options options)
static boolean
GeneiousGridDocumentOperation. isRemoteRun(Options options)
Returns true if the job represented by the given options (fromDocumentOperation.getOptions(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[])
) is a remote run.boolean
Options.BooleanOption. moveToOptions(Options newParentOptions, java.lang.String optionalNewLabel, java.lang.String optionalNewName)
boolean
Options.Option. moveToOptions(Options newParentOptions, java.lang.String optionalNewLabel, java.lang.String optionalNewName)
Moves this Option from its current parent Options to another parent Options.boolean
Options.RadioOption. moveToOptions(Options newParentOptions, java.lang.String optionalNewLabel, java.lang.String optionalNewName)
java.util.List<AnnotatedPluginDocument>
DocumentOperation. performOperation(AnnotatedPluginDocument[] annotatedDocuments, jebl.util.ProgressListener progressListener, Options options)
Create document(s) from a set of documents.java.util.List<AnnotatedPluginDocument>
DocumentOperation. performOperation(AnnotatedPluginDocument[] annotatedDocuments, jebl.util.ProgressListener progressListener, Options options, SequenceSelection sequenceSelection)
void
DocumentOperation. performOperation(AnnotatedPluginDocument[] annotatedDocuments, jebl.util.ProgressListener progressListener, Options options, SequenceSelection sequenceSelection, DocumentOperation.OperationCallback callback)
Do not use.java.util.List<AnnotatedPluginDocument>
DocumentOperation. performOperation(java.util.List<AnnotatedPluginDocument> documents, jebl.util.ProgressListener progressListener, Options options)
A convenience method for callingDocumentOperation.performOperation(AnnotatedPluginDocument[], ProgressListener, Options)
java.util.List<AnnotatedPluginDocument>
DocumentOperation. performOperation(jebl.util.ProgressListener progressListener, Options options, AnnotatedPluginDocument... documents)
A convenience method for callingDocumentOperation.performOperation(AnnotatedPluginDocument[], ProgressListener, Options)
java.util.List<AnnotatedPluginDocument>
DocumentOperation.Wrapper. performOperation(AnnotatedPluginDocument[] annotatedDocuments, jebl.util.ProgressListener progressListener, Options options)
java.util.List<AnnotatedPluginDocument>
DocumentOperation.Wrapper. performOperation(AnnotatedPluginDocument[] annotatedDocuments, jebl.util.ProgressListener progressListener, Options options, SequenceSelection sequenceSelection)
void
DocumentOperation.Wrapper. performOperation(AnnotatedPluginDocument[] annotatedDocuments, jebl.util.ProgressListener progressListener, Options options, SequenceSelection sequenceSelection, DocumentOperation.OperationCallback callback)
void
GeneiousGridDocumentOperation. performOperation(AnnotatedPluginDocument[] documents, jebl.util.ProgressListener progress, Options _options, SequenceSelection sequenceSelection, DocumentOperation.OperationCallback callback)
boolean
AlignmentOperation. preserveSequenceOrder(Options options)
abstract int
ExtendedPrintable. print(java.awt.Graphics2D graphics, java.awt.Dimension dimensions, int pageIndex, Options options)
print a single page of this component.int
ExtendedPrintable.Wrapper. print(java.awt.Graphics2D graphics, java.awt.Dimension dimensions, int pageIndex, Options options)
void
Options.MultipleOptions. removeValue(Options value)
Removes one of the multiple options terms.java.util.List<AnnotatedPluginDocument>
GeneiousGridDocumentOperation. runLocally(AnnotatedPluginDocument[] documents, jebl.util.ProgressListener progressListener, Options programOptions, Options fullOptions, java.lang.String executableLocation)
GeneiousGridDocumentOperations that support local runs must implement either this method orGeneiousGridDocumentOperation.runLocally(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[], jebl.util.ProgressListener, Options, Options, String, OperationCallback)
void
GeneiousGridDocumentOperation. runLocally(AnnotatedPluginDocument[] documents, jebl.util.ProgressListener progressListener, Options programOptions, Options fullOptions, java.lang.String executableLocation, DocumentOperation.OperationCallback callback)
GeneiousGridDocumentOperations that support local runs must implement either this method orGeneiousGridDocumentOperation.runLocally(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[], jebl.util.ProgressListener, Options, Options, String)
java.util.List<AnnotatedPluginDocument>
GeneiousGridDocumentOperation. runLocally(java.util.List<AnnotatedPluginDocument> documents, jebl.util.ProgressListener progressListener, Options programOptions, Options fullOptions, java.lang.String executableLocation)
GeneiousGridDocumentOperations that support local runs should implement this method.Constructors in com.biomatters.geneious.publicapi.plugin with parameters of type Options Constructor Description FindOptions(java.lang.String text, boolean caseSensitive, boolean isFromStart, boolean isForwards, Options additionalOptions)
This constructor must only be called by Geneious; do not call it from a plugin!
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