Uses of Package
com.biomatters.geneious.publicapi.documents
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Packages that use com.biomatters.geneious.publicapi.documents Package Description 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.documents Provides interfaces and classes for defining documents in Geneious and related interfaces and classes for dealing with XMLSerialization.com.biomatters.geneious.publicapi.documents.sequence Provides interfaces specifying the types ofsequence
andalignment
documents in Geneious, together with concrete classes used by sequence documents such asSequenceAnnotation
andSequenceCharSequence
.com.biomatters.geneious.publicapi.documents.types Provides interfaces specifying the types of documents available in Geneious.com.biomatters.geneious.publicapi.implementations Provides implementations for many of the document interfaces defined in the package com.biomatters.geneious.publicapi.documents.types together with some utility classes for dealing with some of these document types.com.biomatters.geneious.publicapi.implementations.sequence ProvidesSequenceDocument
implementations for nucelotide, amino acid, and nucleotide graph (chromatogram) sequences.com.biomatters.geneious.publicapi.implementations.structure ProvidesMolecularStructureDocument
implementations for many commonly used 3D structure documents.com.biomatters.geneious.publicapi.plugin Provides theGeneiousPlugin
interface and plugin related interfaces.com.biomatters.geneious.publicapi.utilities Provides various utility methods and classes, none of which are necessary for creating a plugin, but many plugins implentations will find these methods useful.com.biomatters.geneious.publicapi.utilities.xml -
Classes in com.biomatters.geneious.publicapi.documents used by com.biomatters.geneious.publicapi.databaseservice Class Description AnnotatedPluginDocument An AnnotatedPluginDocument is a wrapper document that wraps anyPluginDocument
(such as aSequenceDocument
orSequenceAlignmentDocument
orTreeDocument
) 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.Condition Available types of conditions.DocumentField A Document Field describes the properties (but not value) of one data item of a plugin document or one field in a search query.DocumentFieldAndValue Wraps aDocumentField
together with its value.ElementProvider Provides a method to load an XML element with progress information and the ability to cancel it.PluginDocument PluginDocument defines the interface for a Document created by a plugin.URN An unmodifiable uniform resource name (URN), intended to serve as persistent, location-independent, resource identifiers.XMLSerializable Interface for handling persistent objects.XMLSerializable.OldVersionCompatible XMLSerializable classes are recommended implement this to indicate they support serializing to older version formats and potentially deserializing from newer version formats.XMLSerializable.VersionSupportType Used for specifying the type of version support when used withXMLSerializable.OldVersionCompatible.getVersionSupport(com.biomatters.geneious.publicapi.documents.XMLSerializable.VersionSupportType)
XMLSerializationException Represents a problem with XML serialization or deserialization. -
Classes in com.biomatters.geneious.publicapi.documents used by com.biomatters.geneious.publicapi.documents Class Description AbstractPluginDocument This class provides a "Field based" implementation of a Plugin documents.AdditionalSearchContent.Result Searchable content for a single category.AdditionalSearchContent.Utilities.Filter Various filterng options on element text.AdditionalSearchContent.Utilities.FilterElement Provide directions on how to handle elementAnnotatedPluginDocument An AnnotatedPluginDocument is a wrapper document that wraps anyPluginDocument
(such as aSequenceDocument
orSequenceAlignmentDocument
orTreeDocument
) 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.AnnotatedPluginDocument.ActiveLinkSaveBehaviour Gives an action to take whenAnnotatedPluginDocument.saveDocument(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument.ActiveLinkSaveBehaviour, jebl.util.ProgressListener)
is called.AnnotatedPluginDocument.DocumentNotes Provides access to all theDocumentNote
s on anAnnotatedPluginDocument
Condition Available types of conditions.Constraint The idea of a Constraint is very simple.DocumentField A Document Field describes the properties (but not value) of one data item of a plugin document or one field in a search query.DocumentField.SequenceType Possible values for theDocumentField.SEQUENCE_TYPE
field.DocumentHistory The document history for an AnnotatedPluginDocument is made up of a list ofentries
.DocumentHistoryEntry Represents a single 'edit' of a document in the document history.DocumentHistoryEntryField A document history field is basically a name-value pair that describes one aspect of aDocumentHistoryEntry
.DocumentListener Used for notifying when anAnnotatedPluginDocument
has changed.DocumentNote Represents an instance of aDocumentNoteType
that exists on a document.DocumentNoteField Describes the properties of a single value in a note.DocumentNoteField.Types All of the available note field types.DocumentNoteType This represents a "Note Type" in the program.DocumentSearchCache 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.ElementProvider Provides a method to load an XML element with progress information and the ability to cancel it.ExportableDocument.Format Current exportable formats.FieldWithName Interface implemented by fields that have a name.MalformedURNException Exception indicating an incorrectly formatted URN.PluginDocument PluginDocument defines the interface for a Document created by a plugin.URN An unmodifiable uniform resource name (URN), intended to serve as persistent, location-independent, resource identifiers.UrnWithRevisionNumber Represents an AnnotatedPluginDocument at a particular revision, via its URN (AnnotatedPluginDocument.getURN()
) and revision number (AnnotatedPluginDocument.getRevisionNumber()
)XMLSerializable Interface for handling persistent objects.XMLSerializable.OldVersionCompatible XMLSerializable classes are recommended implement this to indicate they support serializing to older version formats and potentially deserializing from newer version formats.XMLSerializable.VersionSupportType Used for specifying the type of version support when used withXMLSerializable.OldVersionCompatible.getVersionSupport(com.biomatters.geneious.publicapi.documents.XMLSerializable.VersionSupportType)
XMLSerializationException Represents a problem with XML serialization or deserialization. -
Classes in com.biomatters.geneious.publicapi.documents used by com.biomatters.geneious.publicapi.documents.sequence Class Description AbstractPluginDocument This class provides a "Field based" implementation of a Plugin documents.AnnotatedPluginDocument An AnnotatedPluginDocument is a wrapper document that wraps anyPluginDocument
(such as aSequenceDocument
orSequenceAlignmentDocument
orTreeDocument
) 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.DocumentField A Document Field describes the properties (but not value) of one data item of a plugin document or one field in a search query.PluginDocument PluginDocument defines the interface for a Document created by a plugin.PluginDocument.SizeRequiredToLoadIntoMemoryProvider A PluginDocument may implement this interface to indicate to Geneious the amount of memory it will probably require in order to load the document.Renamable Provides that ability to rename something.URN An unmodifiable uniform resource name (URN), intended to serve as persistent, location-independent, resource identifiers.XMLSerializable Interface for handling persistent objects.XMLSerializable.OldVersionCompatible XMLSerializable classes are recommended implement this to indicate they support serializing to older version formats and potentially deserializing from newer version formats.XMLSerializable.VersionSupportType Used for specifying the type of version support when used withXMLSerializable.OldVersionCompatible.getVersionSupport(com.biomatters.geneious.publicapi.documents.XMLSerializable.VersionSupportType)
XMLSerializableWithProgress An extended interface toXMLSerializable
to support providing progress (and the ability to cancel) when serializing and deserialing.XMLSerializationException Represents a problem with XML serialization or deserialization. -
Classes in com.biomatters.geneious.publicapi.documents used by com.biomatters.geneious.publicapi.documents.types Class Description Author A class holding one author name.PluginDocument PluginDocument defines the interface for a Document created by a plugin.PluginDocument.SizeRequiredToLoadIntoMemoryProvider A PluginDocument may implement this interface to indicate to Geneious the amount of memory it will probably require in order to load the document.Renamable Provides that ability to rename something.XMLSerializable Interface for handling persistent objects.XMLSerializable.OldVersionCompatible XMLSerializable classes are recommended implement this to indicate they support serializing to older version formats and potentially deserializing from newer version formats.XMLSerializableWithProgress An extended interface toXMLSerializable
to support providing progress (and the ability to cancel) when serializing and deserialing. -
Classes in com.biomatters.geneious.publicapi.documents used by com.biomatters.geneious.publicapi.implementations Class Description AbstractPluginDocument This class provides a "Field based" implementation of a Plugin documents.AnnotatedPluginDocument An AnnotatedPluginDocument is a wrapper document that wraps anyPluginDocument
(such as aSequenceDocument
orSequenceAlignmentDocument
orTreeDocument
) 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.DocumentField A Document Field describes the properties (but not value) of one data item of a plugin document or one field in a search query.ExportableDocument Interface implemented by plugin documents that wish to implemenet a specialized export.ExportableDocument.Format Current exportable formats.PluginDocument PluginDocument defines the interface for a Document created by a plugin.PluginDocument.SizeRequiredToLoadIntoMemoryProvider A PluginDocument may implement this interface to indicate to Geneious the amount of memory it will probably require in order to load the document.Renamable Provides that ability to rename something.URN An unmodifiable uniform resource name (URN), intended to serve as persistent, location-independent, resource identifiers.XMLSerializable Interface for handling persistent objects.XMLSerializable.OldVersionCompatible XMLSerializable classes are recommended implement this to indicate they support serializing to older version formats and potentially deserializing from newer version formats.XMLSerializable.VersionSupportType Used for specifying the type of version support when used withXMLSerializable.OldVersionCompatible.getVersionSupport(com.biomatters.geneious.publicapi.documents.XMLSerializable.VersionSupportType)
XMLSerializableWithProgress An extended interface toXMLSerializable
to support providing progress (and the ability to cancel) when serializing and deserialing.XMLSerializationException Represents a problem with XML serialization or deserialization. -
Classes in com.biomatters.geneious.publicapi.documents used by com.biomatters.geneious.publicapi.implementations.sequence Class Description AbstractPluginDocument This class provides a "Field based" implementation of a Plugin documents.AnnotatedPluginDocument An AnnotatedPluginDocument is a wrapper document that wraps anyPluginDocument
(such as aSequenceDocument
orSequenceAlignmentDocument
orTreeDocument
) 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.DocumentField A Document Field describes the properties (but not value) of one data item of a plugin document or one field in a search query.PluginDocument PluginDocument defines the interface for a Document created by a plugin.Renamable Provides that ability to rename something.URN An unmodifiable uniform resource name (URN), intended to serve as persistent, location-independent, resource identifiers.XMLSerializable Interface for handling persistent objects.XMLSerializable.OldVersionCompatible XMLSerializable classes are recommended implement this to indicate they support serializing to older version formats and potentially deserializing from newer version formats.XMLSerializable.VersionSupportType Used for specifying the type of version support when used withXMLSerializable.OldVersionCompatible.getVersionSupport(com.biomatters.geneious.publicapi.documents.XMLSerializable.VersionSupportType)
XMLSerializationException Represents a problem with XML serialization or deserialization. -
Classes in com.biomatters.geneious.publicapi.documents used by com.biomatters.geneious.publicapi.implementations.structure Class Description AbstractPluginDocument This class provides a "Field based" implementation of a Plugin documents.DocumentField A Document Field describes the properties (but not value) of one data item of a plugin document or one field in a search query.PluginDocument PluginDocument defines the interface for a Document created by a plugin.URN An unmodifiable uniform resource name (URN), intended to serve as persistent, location-independent, resource identifiers.XMLSerializable Interface for handling persistent objects.XMLSerializable.OldVersionCompatible XMLSerializable classes are recommended implement this to indicate they support serializing to older version formats and potentially deserializing from newer version formats.XMLSerializable.VersionSupportType Used for specifying the type of version support when used withXMLSerializable.OldVersionCompatible.getVersionSupport(com.biomatters.geneious.publicapi.documents.XMLSerializable.VersionSupportType)
XMLSerializationException Represents a problem with XML serialization or deserialization. -
Classes in com.biomatters.geneious.publicapi.documents used by com.biomatters.geneious.publicapi.plugin Class Description AliasDocument An alias document created using 'Edit->Paste Alias' or programmatically usingAliasDocument.createAlias(AnnotatedPluginDocument)
.AnnotatedPluginDocument An AnnotatedPluginDocument is a wrapper document that wraps anyPluginDocument
(such as aSequenceDocument
orSequenceAlignmentDocument
orTreeDocument
) 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.DocumentField A Document Field describes the properties (but not value) of one data item of a plugin document or one field in a search query.DocumentFieldAndValue Wraps aDocumentField
together with its value.DocumentNote Represents an instance of aDocumentNoteType
that exists on a document.DocumentSearchCache 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.PluginDocument PluginDocument defines the interface for a Document created by a plugin.URN An unmodifiable uniform resource name (URN), intended to serve as persistent, location-independent, resource identifiers.XMLSerializable Interface for handling persistent objects.XMLSerializable.OldVersionCompatible XMLSerializable classes are recommended implement this to indicate they support serializing to older version formats and potentially deserializing from newer version formats.XMLSerializable.VersionSupportType Used for specifying the type of version support when used withXMLSerializable.OldVersionCompatible.getVersionSupport(com.biomatters.geneious.publicapi.documents.XMLSerializable.VersionSupportType)
XMLSerializationException Represents a problem with XML serialization or deserialization. -
Classes in com.biomatters.geneious.publicapi.documents used by com.biomatters.geneious.publicapi.utilities Class Description AnnotatedPluginDocument An AnnotatedPluginDocument is a wrapper document that wraps anyPluginDocument
(such as aSequenceDocument
orSequenceAlignmentDocument
orTreeDocument
) 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.XMLSerializable Interface for handling persistent objects.XMLSerializable.OldVersionCompatible XMLSerializable classes are recommended implement this to indicate they support serializing to older version formats and potentially deserializing from newer version formats.XMLSerializable.VersionSupportType Used for specifying the type of version support when used withXMLSerializable.OldVersionCompatible.getVersionSupport(com.biomatters.geneious.publicapi.documents.XMLSerializable.VersionSupportType)
XMLSerializationException Represents a problem with XML serialization or deserialization. -
Classes in com.biomatters.geneious.publicapi.documents used by com.biomatters.geneious.publicapi.utilities.xml Class Description XMLSerializationException Represents a problem with XML serialization or deserialization.