private void doYourAnnotationsTest(
FeatureData rankedList, FeatureList<AnnotationItem> annotations, Method method)
throws IOException, SQLException, IllegalAccessException, ClassNotFoundException,
InstantiationException, InvalidParameterException, InvalidIndexException {
// db attributes
FunctionalDbDescriptor filterInfo =
new FunctionalDbDescriptor(
"your_annotation", "Your annotations", "your_annotations", "Your annotations");
// get term sizes
Map<String, Integer> termSizes = getYourAnnotationsTermSizes();
logger.info(filterInfo.getTitle() + "...\n");
GeneSetAnalysis gsea;
if (method == Method.Logistic) {
gsea = new LogisticScan(rankedList, annotations, order);
} else {
gsea =
new FatiScan(
rankedList,
annotations,
numberOfPartitions,
testMode,
outputFormat,
order,
duplicatesMode);
}
// run
try {
gsea.setLogger(logger);
// set term sizes
gsea.setTermSizes(termSizes);
gsea.run();
// save results
saveGeneSetAnalysisResults(gsea, filterInfo);
} catch (EmptyAnnotationException ene) {
result.addOutputItem(
new Item(
"annot_" + filterInfo.getName(),
"No annotation was found for " + filterInfo.getTitle() + " ids",
"Annotations for " + filterInfo.getTitle(),
Item.TYPE.MESSAGE,
Arrays.asList("WARNING"),
new HashMap<String, String>(),
"Annotation files"));
} catch (Exception ene) {
result.addOutputItem(
new Item(
"annot_" + filterInfo.getName(),
"Unexpected error was found while running analysis for "
+ filterInfo.getTitle()
+ " ids",
filterInfo.getTitle(),
Item.TYPE.MESSAGE,
Arrays.asList("ERROR"),
new HashMap<String, String>(),
"All results"));
ene.printStackTrace();
}
logger.info("...end of " + filterInfo.getTitle());
}
private void doTest(FeatureData rankedList, FunctionalFilter filter, Method method)
throws SQLException, IllegalAccessException, ClassNotFoundException, InstantiationException {
// db attributes
FunctionalDbDescriptor filterInfo = new FunctionalDbDescriptor(filter);
// get term sizes
// AnnotationDBManager adbm = new AnnotationDBManager(dbConnector);
// Map<String, Integer> termSizes = adbm.getAnnotationTermsSize(filterInfo.getPrefix());
logger.info(filterInfo.getTitle() + "...\n");
GeneSetAnalysis gsea;
if (method == Method.Logistic) {
gsea = new LogisticScan(rankedList, filter, species, order);
((LogisticScan) gsea).setWorkingDirectory(outdir);
} else {
gsea =
new FatiScan(
rankedList,
filter,
null,
numberOfPartitions,
testMode,
outputFormat,
order,
duplicatesMode);
}
// run
try {
gsea.setLogger(logger);
// set term sizes
// gsea.setTermSizes(termSizes);
gsea.run();
logger.print("saving results...");
// save results
saveGeneSetAnalysisResults(gsea, filterInfo);
logger.println("OK");
} catch (EmptyAnnotationException ene) {
result.addOutputItem(
new Item(
"annot_" + filterInfo.getName(),
"No annotation was found for " + filterInfo.getTitle() + " ids",
"Annotations for " + filterInfo.getTitle(),
Item.TYPE.MESSAGE,
Arrays.asList("WARNING"),
new HashMap<String, String>(),
"Annotation files"));
} catch (Exception ene) {
ene.printStackTrace();
result.addOutputItem(
new Item(
"annot_" + filterInfo.getName(),
"Unexpected error was found while running analysis for "
+ filterInfo.getTitle()
+ " ids",
filterInfo.getTitle(),
Item.TYPE.MESSAGE,
Arrays.asList("ERROR"),
new HashMap<String, String>(),
"All results"));
}
logger.info("...end of " + filterInfo.getTitle());
}