Class DefaultTreeDocument
- java.lang.Object
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- com.biomatters.geneious.publicapi.implementations.DefaultTreeDocument
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- All Implemented Interfaces:
ExportableDocument
,PluginDocument
,EditableSameTaxaTreesDocument
,RootedTreeDocument
,SameTaxaTreesDocument
,TreeDocument
,XMLSerializable
,XMLSerializable.OldVersionCompatible
public class DefaultTreeDocument extends java.lang.Object implements RootedTreeDocument, ExportableDocument, EditableSameTaxaTreesDocument, XMLSerializable.OldVersionCompatible
A default implementation of a plugin document holding a tree.
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Nested Class Summary
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Nested classes/interfaces inherited from interface com.biomatters.geneious.publicapi.documents.ExportableDocument
ExportableDocument.Format
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Nested classes/interfaces inherited from interface com.biomatters.geneious.publicapi.documents.PluginDocument
PluginDocument.ReferencedDocumentsAlwaysLoaded, PluginDocument.ReferencedDocumentsNotLoaded, PluginDocument.SizeRequiredToLoadIntoMemoryProvider
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Nested classes/interfaces inherited from interface com.biomatters.geneious.publicapi.documents.XMLSerializable
XMLSerializable.OldVersionCompatible, XMLSerializable.VersionSupportType
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Field Summary
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Fields inherited from interface com.biomatters.geneious.publicapi.documents.PluginDocument
FILE_DATA_ATTRIBUTE_NAME, MAXIMUM_HTML_LENGTH, MODIFIED_DATE_FIELD
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Fields inherited from interface com.biomatters.geneious.publicapi.documents.XMLSerializable
ROOT_ELEMENT_NAME
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Constructor Summary
Constructors Constructor Description DefaultTreeDocument()
XML deserialization constructor.DefaultTreeDocument(jebl.evolution.trees.RootedTree tree, java.lang.String treeName, java.lang.String description, java.util.Date created)
Construct tree with explicit parametersDefaultTreeDocument(jebl.evolution.trees.Tree tree, java.lang.String treeName, java.lang.String summary, java.util.Date created)
DefaultTreeDocument(org.jdom.Element element)
XML deserialization constructor.
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Method Summary
All Methods Instance Methods Concrete Methods Deprecated Methods Modifier and Type Method Description boolean
canExport(ExportableDocument.Format format)
Check if a format is supported by document.boolean
export(ExportableDocument.Format format, java.io.OutputStream to)
Export a document.void
fromXML(org.jdom.Element doc)
Restore the object from the JDOM Element returned byXMLSerializable.toXML()
.java.util.Date
getCreationDate()
Get the date this document was created.java.lang.String
getDescription()
A human readable single line of text describing this document, to appear in the description field in the document table.java.util.List<DocumentField>
getDisplayableFields()
A list of columns for display in the main document panel.java.lang.Object
getFieldValue(java.lang.String fieldCodeName)
Get the value of a particular field.java.lang.String
getName()
A short name (preferably one or two words) for the document.jebl.evolution.trees.RootedTree
getTree()
Get the tree.java.util.List<? extends jebl.evolution.trees.Tree>
getTrees()
Get tree set.URN
getURN()
A Universal Resource Name.Geneious.MajorVersion
getVersionSupport(XMLSerializable.VersionSupportType versionType)
Gets either the latest version this class can serialize to viaXMLSerializable.OldVersionCompatible.toXML(Geneious.MajorVersion, ProgressListener)
or the most recent version in which the XML returned fromXMLSerializable.OldVersionCompatible.toXML(Geneious.MajorVersion, ProgressListener)
last changed.void
setSource(java.lang.String format, java.lang.String fileText)
Deprecated.Geneious tree documents no longer store the original source, so this method does nothing.void
setTrees(java.util.List<? extends jebl.evolution.trees.Tree> trees)
Set some trees.java.lang.String
toHTML()
Provide a textual view of document.org.jdom.Element
toXML()
Convert object to a JDOM element.org.jdom.Element
toXML(Geneious.MajorVersion majorVersion, jebl.util.ProgressListener progressListener)
Serializes this class to XML format, potentially to a format readable by an earlier version of Geneious.
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Constructor Detail
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DefaultTreeDocument
public DefaultTreeDocument()
XML deserialization constructor. SeeXMLSerializable
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DefaultTreeDocument
public DefaultTreeDocument(jebl.evolution.trees.RootedTree tree, java.lang.String treeName, java.lang.String description, java.util.Date created)
Construct tree with explicit parameters- Parameters:
tree
- as a jebl objecttreeName
- default name of documentdescription
- tree description. May be null.created
- date of creation
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DefaultTreeDocument
public DefaultTreeDocument(jebl.evolution.trees.Tree tree, java.lang.String treeName, java.lang.String summary, java.util.Date created)
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DefaultTreeDocument
public DefaultTreeDocument(org.jdom.Element element) throws XMLSerializationException
XML deserialization constructor. SeeXMLSerializable
- Parameters:
element
- the previously serialized element returned fromtoXML()
.- Throws:
XMLSerializationException
- if deserialization fails
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Method Detail
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setSource
@Deprecated public void setSource(java.lang.String format, java.lang.String fileText)
Deprecated.Geneious tree documents no longer store the original source, so this method does nothing.Save original text used when tree was imported.- Parameters:
format
- tree text formatfileText
- text in file- Throws:
org.jdom.IllegalDataException
- if fileText is not legal XML character data, as determined byVerifier.checkCharacterData(String)
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canExport
public boolean canExport(ExportableDocument.Format format)
Description copied from interface:ExportableDocument
Check if a format is supported by document.- Specified by:
canExport
in interfaceExportableDocument
- Parameters:
format
- export format- Returns:
- true if format is supported.
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export
public boolean export(ExportableDocument.Format format, java.io.OutputStream to) throws java.io.IOException
Description copied from interface:ExportableDocument
Export a document.- Specified by:
export
in interfaceExportableDocument
- Parameters:
format
- format to exportto
- output document to this stream.- Returns:
- true when file exported successfully, false otherwise.
- Throws:
java.io.IOException
- if the OutputStream can't be written to for any reason
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toXML
public org.jdom.Element toXML()
Description copied from interface:XMLSerializable
Convert object to a JDOM element. The representation should be complete so thatXMLSerializable.fromXML(org.jdom.Element)
can completely restore the object's representation. It is recommended that the returned element useXMLSerializable.ROOT_ELEMENT_NAME
as its name, in which case it must not define an attribute called "type". In this case, fromXML, will be called with an element whose name may differ from the element return from this function. This recommendation allows a more compact representation of the XML can be stored. This method generally should not be called directly. Instead, you should usually callXMLSerializer.classToXML(String, XMLSerializable)
which calls this method internally. PluginDocument implementations of this method may choose to throw anXMLSerializationException
, enclosed in aRuntimeException
.- Specified by:
toXML
in interfaceXMLSerializable
- Returns:
- object encoded as a JDOM element
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getVersionSupport
public Geneious.MajorVersion getVersionSupport(XMLSerializable.VersionSupportType versionType)
Description copied from interface:XMLSerializable.OldVersionCompatible
Gets either the latest version this class can serialize to viaXMLSerializable.OldVersionCompatible.toXML(Geneious.MajorVersion, ProgressListener)
or the most recent version in which the XML returned fromXMLSerializable.OldVersionCompatible.toXML(Geneious.MajorVersion, ProgressListener)
last changed. Example implementation:switch (versionType) { case FormatLastExtended: //added a new tag to xml in 10.0 that can be safely ignored by older versions return Geneious.MajorVersion.Version10_0; case FormatLastChanged: //renamed a tag in 9.1 meaning that older versions can no longer read the xml from 9.1 return Geneious.MajorVersion.Version9_1; case OldestVersionSerializableTo: //this document class can export xml that is compatible with 9.0 return Geneious.MajorVersion.Version9_0; default: throw new IllegalArgumentException("Unrecognized VersionSupportType"); }
- Specified by:
getVersionSupport
in interfaceXMLSerializable.OldVersionCompatible
- Parameters:
versionType
- specifies which version property to return- Returns:
- the major version of Geneious corresponding to the versionType for this classes toXML method.
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toXML
public org.jdom.Element toXML(Geneious.MajorVersion majorVersion, jebl.util.ProgressListener progressListener)
Description copied from interface:XMLSerializable.OldVersionCompatible
Serializes this class to XML format, potentially to a format readable by an earlier version of Geneious. It is acceptable for the XML to include unnecessary tags that will be ignored by the earlier version. For example if the implementation has only extended the XML since the earlier version, then the XML returned may be identical to the XML returned for the current version. SeeXMLSerializable.toXML()
for a more detailed description of what it means to serialize to XML. All classes that implement this method must also implement XMLSerializable.toXML() and should delegate back to this method using Geneious.getMajorVersion() and ProgressListener.EMPTY as parameters.- Specified by:
toXML
in interfaceXMLSerializable.OldVersionCompatible
- Parameters:
majorVersion
- the major version of Geneious to serialize to XML for. For example "6.0" but not "6.0.0". This must be a version returned greater or equal to a version returned fromgetVersionSupport
(VersionSupportType.OldestVersionSerializableTo
) and must never be greater than the current version (Geneious.getMajorVersion())progressListener
- for reporting progress and cancelling- Returns:
- object encoded as a JDOM element
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fromXML
public void fromXML(org.jdom.Element doc) throws XMLSerializationException
Description copied from interface:XMLSerializable
Restore the object from the JDOM Element returned byXMLSerializable.toXML()
. This method generally should not be called directly. Instead, you should usually callXMLSerializer.classFromXML(org.jdom.Element)
orXMLSerializer.classFromXML(org.jdom.Element, Class)
which calls this method internally. It is optional to implement this method. Instead of implementing an empty constructor and implementing this method properly, the implementation may instead throw an UnsupportedOperationException and implement a constructor that takes a singleElement
as a parameter. This allows for cleaner code such as support for final fields in the XMLSerializable class. The element parameter should not be modified since it may be reused. If you need a modified version of it, take a copy withElement.clone()
.- Specified by:
fromXML
in interfaceXMLSerializable
- Parameters:
doc
- representation from a previous call toXMLSerializable.toXML()
- Throws:
XMLSerializationException
- if the Element can't be converted into this type of object
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getDisplayableFields
public java.util.List<DocumentField> getDisplayableFields()
Description copied from interface:PluginDocument
A list of columns for display in the main document panel. This function only defines the columns available to display, not the particular values of these columns, which are returned byPluginDocument.getFieldValue(String)
. Each column is specified by a Field. The fields should be obtained from a call to the appropriate Field.createXXXXField, where XXXX is the appropriate type. While it is not required, it is recommended that a PluginDocument handle returning a complete list of its displayable fields before the document has been properly constructed via a call toXMLSerializable.fromXML(org.jdom.Element)
The returned list need not and should not be modifiable.- Specified by:
getDisplayableFields
in interfacePluginDocument
- Returns:
- a list of document fields (or null to indicate no displayable fields)
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getFieldValue
public java.lang.Object getFieldValue(java.lang.String fieldCodeName)
Description copied from interface:PluginDocument
Get the value of a particular field.- Specified by:
getFieldValue
in interfacePluginDocument
- Parameters:
fieldCodeName
- field code. This should be thecode
of one of the fields returned fromPluginDocument.getDisplayableFields()
.- Returns:
- value for a field or null if this document does not have a field with the given field code.
The class of the returned value must be the
DocumentField.getValueType()
(or a subclass) of the corresponding DocumentField returned fromPluginDocument.getDisplayableFields()
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getName
public java.lang.String getName()
Description copied from interface:PluginDocument
A short name (preferably one or two words) for the document. If this PluginDocument is wrapped inside anAnnotatedPluginDocument
then this method will be overridden and delegate back toAnnotatedPluginDocument.getName()
. One way to look at it is that when you call PluginDocument.getName() you will get the current name of the document. If you are implementing PluginDocument.getName() then you are returning the default name for the document.- Specified by:
getName
in interfacePluginDocument
- Returns:
- document name. Cannot be null but may be an empty string.
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getURN
public URN getURN()
Description copied from interface:PluginDocument
A Universal Resource Name. Documents from external sources should set this to a unique name inside that service. Documents generated locally (such as from operations) and documents that don't have a unique identifier should return null since Geneious handles URNs for these.- Specified by:
getURN
in interfacePluginDocument
- Returns:
- the urn, or null if this document doesn't have a unique identifier
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getCreationDate
public java.util.Date getCreationDate()
Description copied from interface:PluginDocument
Get the date this document was created. This method may return null. Generally clients should useAnnotatedPluginDocument.getCreationDate()
instead as that will return either the date returned fromPluginDocument.getCreationDate()
or if that returned null,AnnotatedPluginDocument.getCreationDate()
will return the date the document was first instantiated.- Specified by:
getCreationDate
in interfacePluginDocument
- Returns:
- the date this document was created or null to use the date the document was first instantiated.
- See Also:
PluginDocument.MODIFIED_DATE_FIELD
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getDescription
public java.lang.String getDescription()
Description copied from interface:PluginDocument
A human readable single line of text describing this document, to appear in the description field in the document table.- Specified by:
getDescription
in interfacePluginDocument
- Returns:
- a one line simple text description of the document, or null if no description is available.
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toHTML
public java.lang.String toHTML()
Description copied from interface:PluginDocument
Provide a textual view of document. The contents should be at most 30K-60K characters. One reason is that this text is rendered using JTextPane, which is horrendously slow when handling large text. The more fundamental reason is that large amounts of text are generally not useful for a user. The whole idea of using a tool such as Geneious is to provide specialized viewers which make the large amount of bioinformatics data perceivable and comprehensible to a human user. Return an HTML body fragment (i.e. a fragment which sits inside a <body></body> tag). (Header,stylesheet and annotations are automatically added by GENEious code). Can optionally return an entire html tag set, as long as the first six characters are<html>
- Specified by:
toHTML
in interfacePluginDocument
- Returns:
- an HTML fragment of tag set, or null to have no text view.
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getTree
public jebl.evolution.trees.RootedTree getTree()
Description copied from interface:RootedTreeDocument
Get the tree.- Specified by:
getTree
in interfaceRootedTreeDocument
- Returns:
- a tree
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setTrees
public void setTrees(java.util.List<? extends jebl.evolution.trees.Tree> trees)
Description copied from interface:EditableSameTaxaTreesDocument
Set some trees.- Specified by:
setTrees
in interfaceEditableSameTaxaTreesDocument
- Parameters:
trees
- A list of new trees. A null entry means no change and the existing tree is taken.
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getTrees
public java.util.List<? extends jebl.evolution.trees.Tree> getTrees()
Description copied from interface:SameTaxaTreesDocument
Get tree set.- Specified by:
getTrees
in interfaceSameTaxaTreesDocument
- Returns:
- the trees
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