Package com.biomatters.geneious.publicapi.plugin

Class DocumentOperationInput

java.lang.Object
com.biomatters.geneious.publicapi.plugin.DocumentOperationInput
public class DocumentOperationInput extends Object
Represents input to a DocumentOperation. This is supplied to the DocumentOperation via DocumentOperation.getOptions(DocumentOperationInput)
Since:
API 4.14 (Geneious 5.1)

  • Constructor Details

    • DocumentOperationInput

      public DocumentOperationInput(List<AnnotatedPluginDocument> inputDocuments)
      Constructs new DocumentOperationInput. Generally only core Geneious code should be calling this method.
      Parameters:
      inputDocuments - the documents to be used as input to this operation. May not be null but may be empty

    • DocumentOperationInput

      public DocumentOperationInput(AnnotatedPluginDocument... inputDocuments)
      Constructs new DocumentOperationInput. Generally only core Geneious code should be calling this method.
      Parameters:
      inputDocuments - the documents to be used as input to this operation. May not be null but may be empty

  • Method Details

    • setLocationOptions

      public DocumentOperationInput setLocationOptions(OperationLocationOptions locationOptions)
      Sets the location options to be used for this operation. Generally only core Geneious code should be calling this method
      Parameters:
      locationOptions - the location options to be used for this operation. May be null if this operation can only be run locally.
      Returns:
      this (for convenience)
      Throws:
      IllegalStateException - if this method is called more than once.

    • setSequenceSelection

      public DocumentOperationInput setSequenceSelection(SequenceSelection sequenceSelection)
      Sets the sequence selection to be used for this operation. Generally only core Geneious code should be calling this method
      Parameters:
      sequenceSelection - the sequence selection to be used for this operation. Never null but may be an empty selection
      Returns:
      this (for convenience)
      Throws:
      IllegalStateException - if this method is called more than once.

    • setResultsLocation

      public DocumentOperationInput setResultsLocation(WritableDatabaseService resultsLocation)
      Sets the results location to be used for this operation. Generally only core Geneious code should be calling this method
      Parameters:
      resultsLocation - the folder that the results of the operation will be stored in. May be null if results are not being stored.
      Returns:
      this (for convenience)
      Throws:
      IllegalStateException - if this method is called more than once.

    • getInputDocumentsList

      public List<AnnotatedPluginDocument> getInputDocumentsList()
      Returns:
      the documents to be used as input to the operation. Will never be null but may be empty (if it matches the selection signature of the DocumentOperation)

    • getInputDocumentsArray

      public AnnotatedPluginDocument[] getInputDocumentsArray()
      Returns:
      the documents to be used as input to the operation. Will never be null but may be empty (if it matches the selection signature of the DocumentOperation)

    • getLocationOptions

      public OperationLocationOptions getLocationOptions()
      Gets the location options used to control where the operation is run. Operation location options are created and handled automatically by Geneious. DocumentOperations will probably only need to use this method if they want to know whether they are running locally or on Geneious server for the purposes of showing/hiding options. For example when running on Geneious server, there is no need for a wrapper to an external command line program to provide the user with an option to specify the command line exectuable.
      Returns:
      location options used to control where the operation is run. Will be null if the operation can only be run locally. See OperationLocationOptions for more details.

    • getSequenceSelection

      public SequenceSelection getSequenceSelection()
      Returns:
      the sequence selection for the input documents. Will never be null but may be an empty selection.

    • getResultsLocation

      public WritableDatabaseService getResultsLocation()
      Returns:
      resultsLocation folder that the results of the operation will be stored in. Can only be null if the operation doesn't produce any documents (DocumentOperation.isDocumentGenerator() is false for this operation).