@Override
public List<AnnotatedPluginDocument> performOperation(
AnnotatedPluginDocument[] annotatedDocuments,
ProgressListener progressListener,
Options options)
throws DocumentOperationException {
String queryText = ((ExampleWorkflowOptions) options).getSearchQuery();
// First create a composite progress to represent the 3 components of this example
// 1) Getting the results from NCBI (80% of total time)
// 2) Building the alignment (15% of total time)
// 3) Building a tree (5% of total time)
CompositeProgressListener compositeProgress =
new CompositeProgressListener(progressListener, 0.8, 0.15, 0.05);
// First get the ncbi database and search it:
compositeProgress.beginSubtask("Searching NCBI");
DatabaseService ncbiNucleotideService =
(DatabaseService) PluginUtilities.getGeneiousService("NCBI_nucleotide_gbc");
// The various services available are found by running this commented out code:
// for (GeneiousService service : PluginUtilities.getGeneiousServices()) {
// System.out.println(service.getUniqueID());
// }
Query query = Query.Factory.createQuery(queryText);
List<AnnotatedPluginDocument> sequences;
try {
sequences = ncbiNucleotideService.retrieve(query, compositeProgress);
} catch (DatabaseServiceException e) {
throw new DocumentOperationException("Failed to search NCBI database", e);
}
if (compositeProgress.isCanceled()) throw new DocumentOperationException.Canceled();
if (sequences.size() < 3)
throw new DocumentOperationException(
"NCBI returned "
+ sequences.size()
+ " results, but we require at least 3 to build a tree");
// Now get the alignment operation and perform the alignment:
compositeProgress.beginSubtask("Build alignment");
final DocumentOperation alignmentOperation =
PluginUtilities.getCategoryOperation(GeneiousActionOptions.Category.Alignment);
Options alignmentOptions =
alignmentOperation.getOptions(
sequences); // Get the options provided by the alignment operation.
alignmentOptions.setValue(
"operation", "MUSCLE_NUCLEOTIDE_"); // Tell it to use muscle for alignment.
// To find out what options are available on the alignment do the following commented out line:
// System.out.println(alignmentOptions.getDescriptionAndState());
List<AnnotatedPluginDocument> alignment =
alignmentOperation.performOperation(sequences, compositeProgress, alignmentOptions);
if (compositeProgress.isCanceled()) throw new DocumentOperationException.Canceled();
// Now get the tree operation and build a tree:
compositeProgress.beginSubtask("Build tree");
final DocumentOperation treeOperation =
PluginUtilities.getCategoryOperation(GeneiousActionOptions.Category.TreeBuilding);
Options treeOptions = treeOperation.getOptions(alignment);
treeOptions.setValue("treeBuilding.buildMethod", "UPGMA");
// To find out what options are available on the tree builder, do the following commented out
// line:
// System.out.println(treeOptions.getDescriptionAndState());
final List<AnnotatedPluginDocument> treeResults =
treeOperation.performOperation(alignment, compositeProgress, treeOptions);
if (treeResults != null && treeResults.size() == 1) {
treeResults.get(0).setName("Tree of " + queryText);
}
return treeResults;
}
/**
* Used as an alternative to {@link #beginNextSubtask()}. Instead of calling {@link
* #beginNextSubtask()} once after each subtask (except the last), you can instead call
* beginSubTask at the beginning of every subtask including the first.
*
* @param message a message to be displayed to the user as a prefix in the progress message
*/
public void beginSubtask(String message) {
currentSubTaskMessage = message;
setMessage("");
beginSubtask();
currentSubTaskMessage = message;
}