@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;
}
@Override
public List<AnnotatedPluginDocument> performOperation(
AnnotatedPluginDocument[] annotatedDocuments,
ProgressListener progressListener,
Options options)
throws DocumentOperationException {
int PAGE_SIZE = 2;
try {
String query = options.getValueAsString("query");
int count = 0;
InputStream countInput = queryServer("query count " + query);
// Get the response
BufferedReader rd = new BufferedReader(new InputStreamReader(countInput));
String line;
while ((line = rd.readLine()) != null) {
count = Integer.parseInt(line.trim());
}
rd.close();
int numberOfPages = (int) Math.ceil(count / PAGE_SIZE);
CompositeProgressListener composite =
new CompositeProgressListener(progressListener, numberOfPages);
for (int page = 0; page < numberOfPages; page++) {
InputStream inputStream =
queryServer("query page_size " + PAGE_SIZE + " page_number " + page + " text " + query);
File outputFile =
new File(
System.getProperty("user.home")
+ File.separator
+ "traceData"
+ File.separator
+ "part"
+ page
+ ".tgz");
BufferedReader in = new BufferedReader(new InputStreamReader(inputStream));
BufferedOutputStream out = new BufferedOutputStream(new FileOutputStream(outputFile));
List<String> ids = new ArrayList<String>();
String line2 = null;
while ((line2 = in.readLine()) != null) {
if (composite.isCanceled()) {
break;
}
System.out.println(line2);
// out.write(n);
ids.add(line2);
}
if (composite.isCanceled()) {
break;
}
in.close();
InputStream tgzIn = queryServer("retrieve_gz all " + StringUtilities.join(", ", ids));
int n;
int byteCount = 0;
while ((n = tgzIn.read()) >= 0) {
byteCount++;
composite.setMessage("Downloaded " + byteCount + " bytes");
if (composite.isCanceled()) {
break;
}
// out.write(n);
}
tgzIn.close();
out.close();
if (composite.isCanceled()) {
break;
}
composite.beginNextSubtask();
break;
// out.close();
}
} catch (IOException ex) {
ex.toString();
ex.printStackTrace();
throw new DocumentOperationException(ex.getMessage(), ex);
}
return Collections.emptyList();
}
