java.lang.Object
- com.biomatters.geneious.publicapi.plugin.DocumentType<T>

```
public final class DocumentType<T>
extends java.lang.Object
```
Declares one Geneious plugin document type used for associating icons and human readable names with PluginDocument classes. You can use either one of the static instances:
- OLIGO_DOC_TYPE
Or DocumentTypes may be generated a plugin via GeneiousPlugin.getDocumentTypes()

Field Summary

Fields
Modifier and Type	Field	Description
`static DocumentType<AliasDocument>`	`ALIAS_DOCUMENT_TYPE`	Document type for `AliasDocument`
`static DocumentType<SequenceAlignmentDocument>`	`ALIGNMENT_TYPE`	SequenceAlignmentDocument document type
`static DocumentType<AminoAcidSequenceDocument>`	`AMINO_ACID_SEQUENCE_TYPE`	AminoAcidSequenceDocument document type
`static DocumentType<JournalArticleDocument>`	`ARTICLE_TYPE`	JournalArticleDocument document type
`java.lang.Class<T>`	`classOfDocument`	Java class of document.
`static DocumentType<CodonUsageTableDocument>`	`CODON_USAGE_TABLE_DOCUMENT_TYPE`	Document type for `CodonUsageTableDocument`
`static DocumentType<SequenceAlignmentDocument>`	`CONTIG_TYPE`	Contig document type
`static DocumentField`	`DOCUMENT_TYPE_FIELD`	A field used for searching databases based on the document type.
`Icons`	`documentIcon`	An icon associated with documents of that type.
`java.lang.String`	`humanReadableName`	Human readable name of document type.
`static DocumentType<MolecularStructureDocument>`	`MOLECULAR_STRUCTURE_TYPE`	MolecularStructureDocument document type
`static DocumentType<?>`	`NUCLEOTIDE_SEQUENCE_LIST_TYPE`	Nucleotide Sequence List document type
`static DocumentType<NucleotideSequenceDocument>`	`NUCLEOTIDE_SEQUENCE_TYPE`	NucleotideSequenceDocument document type
`static DocumentType<OligoSequenceDocument>`	`OLIGO_DOC_TYPE`	Primer/Oligo sequence document type
`static java.lang.String`	`OVERRIDE_DOCUMENT_TYPE_KEY`	A `PluginDocument` may return a value from `PluginDocument.getFieldValue(String)` with this `fieldCodeName` to change the class used to get the document type of the document.
`java.lang.Class`	`overrideClass`	an alternative class that can be set on a document using `OVERRIDE_DOCUMENT_TYPE_KEY` to change its icon etc.
`static DocumentType<?>`	`PROTEIN_SEQUENCE_LIST_TYPE`	Protein Sequence List document type
`static DocumentType<PublicationDocument>`	`PUBLICATION_TYPE`	PublicationDocument document type
`static DocumentType<SequenceListDocument>`	`SEQUENCE_LIST_TYPE`	Sequence list document type which matches either nucleotide or protein sequence lists.
`static DocumentType<CombinedAlignmentAndAminoAcidSequenceDocument>`	`SEQUENCE_SEARCH_AMINO_ACID_HIT`	CombinedAlignmentAndAminoAcidSequenceDocument document type
`static DocumentType<CombinedAlignmentAndNucleotideSequenceDocument>`	`SEQUENCE_SEARCH_NUCLEOTIDE_HIT`	CombinedAlignmentAndNucleotideSequenceDocument document type
`static DocumentType<SequenceDocument>`	`SEQUENCE_TYPE`	SequenceDocument document type
`static DocumentType<TaxonomyDocument>`	`TAXONOMY_TYPE`	TaxonomyDocument document type
`static DocumentType<TextDocument>`	`TEXT_DOCUMENT_TYPE`	Document type for `TextDocument`
`static DocumentType<TreeDocument>`	`TREE_TYPE`	TreeDocument document type

Constructor Summary

Constructors
Constructor	Description
`DocumentType(java.lang.String name, java.lang.Class<T> classOfDocument, Icons icon)`	constructor.
`DocumentType(java.lang.String name, java.lang.Class<T> classOfDocument, java.lang.Class overrideClass, Icons icon)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`boolean`	`equals(java.lang.Object o)`
`int`	`hashCode()`
`static boolean`	`isAlignment(AnnotatedPluginDocument annotatedPluginDocument)`
`static boolean`	`isAlignment(PluginDocument document)`
`static boolean`	`isAlignmentAndNotSequence(AnnotatedPluginDocument document)`
`static boolean`	`isAlignmentAndNotSequence(PluginDocument document)`
`static boolean`	`isAminoAcidSequence(AnnotatedPluginDocument annotatedPluginDocument)`
`static boolean`	`isAminoAcidSequence(PluginDocument document)`
`static boolean`	`isNucleotideSequence(AnnotatedPluginDocument annotatedPluginDocument)`
`static boolean`	`isNucleotideSequence(PluginDocument document)`
`static boolean`	`isSequence(AnnotatedPluginDocument annotatedPluginDocument)`
`static boolean`	`isSequence(PluginDocument document)`
`static boolean`	`isSequenceList(AnnotatedPluginDocument annotatedPluginDocument)`
`static boolean`	`isSequenceList(PluginDocument document)`
`boolean`	`matches(AnnotatedPluginDocument document)`	Checks if the given document matches this DocumentType
`static boolean`	`matches(java.util.Set<DocumentType> documentTypes, AnnotatedPluginDocument document)`	Returns true if the given document is at least one of the given document types.
`java.lang.String`	`toString()`

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

- Field Detail
  - OLIGO_DOC_TYPE
```
public static DocumentType<OligoSequenceDocument> OLIGO_DOC_TYPE
```
    Primer/Oligo sequence document type
  - MOLECULAR_STRUCTURE_TYPE
```
public static final DocumentType<MolecularStructureDocument> MOLECULAR_STRUCTURE_TYPE
```
    MolecularStructureDocument document type
    
    Since:
    
    API 4.50 (Geneious 5.5.0)
  - SEQUENCE_TYPE
```
public static final DocumentType<SequenceDocument> SEQUENCE_TYPE
```
    SequenceDocument document type
    
    Since:
    
    API 4.50 (Geneious 5.5.0)
  - NUCLEOTIDE_SEQUENCE_TYPE
```
public static final DocumentType<NucleotideSequenceDocument> NUCLEOTIDE_SEQUENCE_TYPE
```
    NucleotideSequenceDocument document type
    
    Since:
    
    API 4.50 (Geneious 5.5.0)
  - AMINO_ACID_SEQUENCE_TYPE
```
public static final DocumentType<AminoAcidSequenceDocument> AMINO_ACID_SEQUENCE_TYPE
```
    AminoAcidSequenceDocument document type
    
    Since:
    
    API 4.50 (Geneious 5.5.0)
  - ALIGNMENT_TYPE
```
public static final DocumentType<SequenceAlignmentDocument> ALIGNMENT_TYPE
```
    SequenceAlignmentDocument document type
    
    Since:
    
    API 4.50 (Geneious 5.5.0)
  - TAXONOMY_TYPE
```
public static final DocumentType<TaxonomyDocument> TAXONOMY_TYPE
```
    TaxonomyDocument document type
    
    Since:
    
    API 4.50 (Geneious 5.5.0)
  - ARTICLE_TYPE
```
public static final DocumentType<JournalArticleDocument> ARTICLE_TYPE
```
    JournalArticleDocument document type
    
    Since:
    
    API 4.50 (Geneious 5.5.0)
  - PUBLICATION_TYPE
```
public static final DocumentType<PublicationDocument> PUBLICATION_TYPE
```
    PublicationDocument document type
    
    Since:
    
    API 4.50 (Geneious 5.5.0)
  - TREE_TYPE
```
public static final DocumentType<TreeDocument> TREE_TYPE
```
    TreeDocument document type
    
    Since:
    
    API 4.50 (Geneious 5.5.0)
  - SEQUENCE_LIST_TYPE
```
public static final DocumentType<SequenceListDocument> SEQUENCE_LIST_TYPE
```
    Sequence list document type which matches either nucleotide or protein sequence lists. However, for icon purposes, PROTEIN_SEQUENCE_LIST_TYPE and NUCLEOTIDE_SEQUENCE_LIST_TYPE takes precedence over this.
    
    Since:
    
    API 4.700 (Geneious 7.0.0)
    
    See Also:
    
    PROTEIN_SEQUENCE_LIST_TYPE
  - PROTEIN_SEQUENCE_LIST_TYPE
```
public static final DocumentType<?> PROTEIN_SEQUENCE_LIST_TYPE
```
    Protein Sequence List document type
    
    Since:
    
    API 4.700 (Geneious 7.0.0)
    
    See Also:
    
    SEQUENCE_LIST_TYPE
  - NUCLEOTIDE_SEQUENCE_LIST_TYPE
```
public static final DocumentType<?> NUCLEOTIDE_SEQUENCE_LIST_TYPE
```
    Nucleotide Sequence List document type
    
    Since:
    
    API 4.810 (Geneious 8.1.0)
    
    See Also:
    
    SEQUENCE_LIST_TYPE
  - CONTIG_TYPE
```
public static final DocumentType<SequenceAlignmentDocument> CONTIG_TYPE
```
    Contig document type
    
    Since:
    
    API 4.700 (Geneious 7.0.0)
  - ALIAS_DOCUMENT_TYPE
```
public static final DocumentType<AliasDocument> ALIAS_DOCUMENT_TYPE
```
    Document type for AliasDocument
    
    Since:
    
    API 4.1000 (Geneious 10.0.0)
  - TEXT_DOCUMENT_TYPE
```
public static final DocumentType<TextDocument> TEXT_DOCUMENT_TYPE
```
    Document type for TextDocument
    
    Since:
    
    API 4.201900 (Geneious 2019.0.0)
  - CODON_USAGE_TABLE_DOCUMENT_TYPE
```
public static final DocumentType<CodonUsageTableDocument> CODON_USAGE_TABLE_DOCUMENT_TYPE
```
    Document type for CodonUsageTableDocument
    
    Since:
    
    API 4.201900 (Geneious 2019.0.0)
  - SEQUENCE_SEARCH_NUCLEOTIDE_HIT
```
public static final DocumentType<CombinedAlignmentAndNucleotideSequenceDocument> SEQUENCE_SEARCH_NUCLEOTIDE_HIT
```
    CombinedAlignmentAndNucleotideSequenceDocument document type
    
    Since:
    
    API 4.50 (Geneious 5.5.0)
  - SEQUENCE_SEARCH_AMINO_ACID_HIT
```
public static final DocumentType<CombinedAlignmentAndAminoAcidSequenceDocument> SEQUENCE_SEARCH_AMINO_ACID_HIT
```
    CombinedAlignmentAndAminoAcidSequenceDocument document type
    
    Since:
    
    API 4.50 (Geneious 5.5.0)
  - OVERRIDE_DOCUMENT_TYPE_KEY
```
public static final java.lang.String OVERRIDE_DOCUMENT_TYPE_KEY
```
    A PluginDocument may return a value from PluginDocument.getFieldValue(String) with this fieldCodeName to change the class used to get the document type of the document. The value must be the fully qualified class name. Eg. this can be used to change the icon of a document depending on its contents as opposed to just its class.
    
    See Also:
    
    Constant Field Values
  - humanReadableName
```
public final java.lang.String humanReadableName
```
    Human readable name of document type.
  - classOfDocument
```
public final java.lang.Class<T> classOfDocument
```
    Java class of document.
  - overrideClass
```
public final java.lang.Class overrideClass
```
    an alternative class that can be set on a document using OVERRIDE_DOCUMENT_TYPE_KEY to change its icon etc. Doesn't need to be a subclass of PluginDocument. Never null but may be the same as classOfDocument.
    
    Since:
    
    API 4.700 (Geneious 7.0.0)
  - documentIcon
```
public final Icons documentIcon
```
    An icon associated with documents of that type.
  - DOCUMENT_TYPE_FIELD
```
public static final DocumentField DOCUMENT_TYPE_FIELD
```
    A field used for searching databases based on the document type.
- Constructor Detail
  - DocumentType
```
public DocumentType(java.lang.String name,
                    java.lang.Class<T> classOfDocument,
                    Icons icon)
```
    constructor.
    
    Parameters:
    
    name - human readable name of document type
    
    classOfDocument - Java class of document, should extend PluginDocument
    
    icon - icon for documents of that type. May be null.
  - DocumentType
```
public DocumentType(java.lang.String name,
                    java.lang.Class<T> classOfDocument,
                    java.lang.Class overrideClass,
                    Icons icon)
```
    Parameters:
    
    name - human readable name of document type
    
    classOfDocument - Java class of document, should extend PluginDocument
    
    overrideClass - an optional alternative class that can be set on a document using OVERRIDE_DOCUMENT_TYPE_KEY to change its icon etc (may be null). Doesn't need to be a subclass of PluginDocument
    
    icon - icon for documents of that type. May be null.
    
    Since:
    
    API 4.700 (Geneious 7.0.0)
- Method Detail
  - isSequenceList
```
public static boolean isSequenceList(PluginDocument document)
```
    Parameters:
    
    document - the document (may be null in which case this will return false)
    
    Returns:
    
    true iff this document is a SequenceListDocument
  - isSequenceList
```
public static boolean isSequenceList(AnnotatedPluginDocument annotatedPluginDocument)
```
    Parameters:
    
    annotatedPluginDocument - the document (may be null in which case this will return false)
    
    Returns:
    
    true iff this document is a SequenceListDocument
  - isSequence
```
public static boolean isSequence(PluginDocument document)
```
    Parameters:
    
    document - the document (may be null in which case this will return false)
    
    Returns:
    
    true iff this document is a SequenceDocument
  - isNucleotideSequence
```
public static boolean isNucleotideSequence(PluginDocument document)
```
    Parameters:
    
    document - the document (may be null in which case this will return false)
    
    Returns:
    
    true iff this document is a NucleotideSequenceDocument
    
    Since:
    
    API 4.40 (Geneious 5.4.0)
  - isAminoAcidSequence
```
public static boolean isAminoAcidSequence(PluginDocument document)
```
    Parameters:
    
    document - the document (may be null in which case this will return false)
    
    Returns:
    
    true iff this document is a AminoAcidSequenceDocument
    
    Since:
    
    API 4.40 (Geneious 5.4.0)
  - isSequence
```
public static boolean isSequence(AnnotatedPluginDocument annotatedPluginDocument)
```
    Parameters:
    
    annotatedPluginDocument - the document (may be null in which case this will return false)
    
    Returns:
    
    true iff this document is a SequenceDocument
  - isNucleotideSequence
```
public static boolean isNucleotideSequence(AnnotatedPluginDocument annotatedPluginDocument)
```
    Parameters:
    
    annotatedPluginDocument - the document (may be null in which case this will return false)
    
    Returns:
    
    true iff this document is a NucleotideSequenceDocument
    
    Since:
    
    API 4.40 (Geneious 5.4.0)
  - isAminoAcidSequence
```
public static boolean isAminoAcidSequence(AnnotatedPluginDocument annotatedPluginDocument)
```
    Parameters:
    
    annotatedPluginDocument - the document (may be null in which case this will return false)
    
    Returns:
    
    true iff this document is a AminoAcidSequenceDocument
    
    Since:
    
    API 4.40 (Geneious 5.4.0)
  - isAlignment
```
public static boolean isAlignment(PluginDocument document)
```
    Parameters:
    
    document - the document (may be null in which case this will return false)
    
    Returns:
    
    true iff this document is a SequenceAlignmentDocument
  - isAlignment
```
public static boolean isAlignment(AnnotatedPluginDocument annotatedPluginDocument)
```
    Parameters:
    
    annotatedPluginDocument - the document (may be null in which case this will return false)
    
    Returns:
    
    true iff this document is a SequenceAlignmentDocument
  - isAlignmentAndNotSequence
```
public static boolean isAlignmentAndNotSequence(PluginDocument document)
```
    Parameters:
    
    document - the document (may be null in which case this will return false)
    
    Returns:
    
    true iff this document is a SequenceAlignmentDocument and not a SequenceDocument (so it will return false on a CombinedAlignmentAndSequenceDocument
  - isAlignmentAndNotSequence
```
public static boolean isAlignmentAndNotSequence(AnnotatedPluginDocument document)
```
    Parameters:
    
    document - the document (may be null in which case this will return false)
    
    Returns:
    
    true iff this document is a SequenceAlignmentDocument and not a SequenceDocument (so it will return false on a CombinedAlignmentAndSequenceDocument
  - equals
```
public boolean equals(java.lang.Object o)
```
    Overrides:
    
    equals in class java.lang.Object
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class java.lang.Object
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object
  - matches
```
public boolean matches(AnnotatedPluginDocument document)
```
    Checks if the given document matches this DocumentType
    
    Parameters:
    
    document - the document to check if its type is this DocumentType
    
    Returns:
    
    true if this document matches this document type
    
    Since:
    
    API 4.810 (Geneious 8.1.0)
  - matches
```
public static boolean matches(java.util.Set<DocumentType> documentTypes,
                              AnnotatedPluginDocument document)
```
    Returns true if the given document is at least one of the given document types.
    
    Parameters:
    
    documentTypes - the document types to check if this document is at least one of
    
    document - the document to check
    
    Returns:
    
    true if the given document is at least one of the given document types.
    
    Since:
    
    API 4.810 (Geneious 8.1.0)

Class DocumentType<T>

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

OLIGO_DOC_TYPE

MOLECULAR_STRUCTURE_TYPE

SEQUENCE_TYPE

NUCLEOTIDE_SEQUENCE_TYPE

AMINO_ACID_SEQUENCE_TYPE

ALIGNMENT_TYPE

TAXONOMY_TYPE

ARTICLE_TYPE

PUBLICATION_TYPE

TREE_TYPE

SEQUENCE_LIST_TYPE

PROTEIN_SEQUENCE_LIST_TYPE

NUCLEOTIDE_SEQUENCE_LIST_TYPE

CONTIG_TYPE

ALIAS_DOCUMENT_TYPE

TEXT_DOCUMENT_TYPE

CODON_USAGE_TABLE_DOCUMENT_TYPE

SEQUENCE_SEARCH_NUCLEOTIDE_HIT

SEQUENCE_SEARCH_AMINO_ACID_HIT

OVERRIDE_DOCUMENT_TYPE_KEY

humanReadableName

classOfDocument

overrideClass

documentIcon

DOCUMENT_TYPE_FIELD

Constructor Detail

DocumentType

DocumentType

Method Detail

isSequenceList

isSequenceList

isSequence

isNucleotideSequence

isAminoAcidSequence

isSequence

isNucleotideSequence

isAminoAcidSequence

isAlignment

isAlignment

isAlignmentAndNotSequence

isAlignmentAndNotSequence

equals

hashCode

toString

matches

matches