this isn't nice for the users. Don't use it.
Geneious no longer supports resuming searches
Geneious no longer supports resuming searches
use #duplicateDocumentAndDealWithReferencedDocuments
use getUniqueNameForDocument(String, WritableDatabaseService, Collection)
use getUniqueNameForDocument(String, WritableDatabaseService, Collection)
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.
all cloud document URNs (as of Geneious 2022.2) return true from
URN.isLocal() and false from isCloud()
Geneious tree documents no longer store the original source, so this method does nothing.
this method no longer works and there is no replacement in the API. Sorry!
this functionality is now supplied by operation history
Importers and exporters should not be restricted, all though this method still functions.
Geneious no longer respects this as extensions are generally not case sensitive
Importers and exporters should not be restricted, all though this method still functions.
As the callback parameter is not fully supported anymore.
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.
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)
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)
there never was and there will never be a premium version of Geneious. Deprecated in API 4.600 (Geneious 6.0.0)
there never was and there will never be a premium version of Geneious. Deprecated in API 4.600 (Geneious 6.0.0)
there is no "Pro" version anymore, Geneious is Geneious. Consider using
Geneious.getName() instead. Deprecated in API 4.600 (Geneious 6.0.0)
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.
(Please use initializeAllPluginsInClasspath to only load plugins on the classpath)
(Please use initializeAllPluginsInClasspath to only load plugins on the classpath)
As of Geneious 2021.0.0, Geneious applies the custom CSS formatting
from this method across all HTML-formatted content to avoid formatting discrepancies.
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.
always returns true as of Geneious 2020 and later. See https://help.geneious.com/hc/en-us/articles/360044627452-Windows-Users-Geneious-Prime-2020-and-above-will-not-support-32-bit-Windows
As of version 2025.0.0 Geneious is Java 11 or later only, this will always return true
As of version 2025.0.0 Geneious is Java 11 or later only, this will always return true
As of version 6.0.0 Geneious is Java 6 or later only, this will always return true
As of version 10.0.0 Geneious is Java 8 or later only, this will always return true
As of version 10.0.0 Geneious is Java 8 or later only, this will always return true
As of version 2025.0.0 Geneious is Java 11 or later only, this will always return true
Geneious is no longer supported on Solaris
Geneious is no longer supported on Solaris
Geneious is no longer supported on Solaris