use of org.baderlab.csplugins.enrichmentmap.model.EnrichmentResultFilterParams.NESFilter in project EnrichmentMapApp by BaderLab.
the class MasterDetailDialogPage method finish.
@Override
public void finish() {
if (!validateInput())
return;
String prefix = legacySupport.getNextAttributePrefix();
SimilarityMetric similarityMetric = cutoffPanel.getSimilarityMetric();
double pvalue = cutoffPanel.getPValue();
double qvalue = cutoffPanel.getQValue();
NESFilter nesFilter = cutoffPanel.getNESFilter();
double cutoff = cutoffPanel.getCutoff();
double combined = cutoffPanel.getCombinedConstant();
Optional<Integer> minExperiments = cutoffPanel.getMinimumExperiments();
EMCreationParameters params = new EMCreationParameters(prefix, pvalue, qvalue, nesFilter, minExperiments, similarityMetric, cutoff, combined);
params.setCreateDistinctEdges(distinctEdgesCheckbox.isSelected());
List<DataSetParameters> dataSets = dataSetListModel.toList().stream().map(DataSetListItem::getDetailPanel).map(DetailPanel::createDataSetParameters).filter(x -> x != null).collect(Collectors.toList());
// Overwrite all the expression files if the common file has been provided
String exprPath = commonPanel.getExpressionFile();
if (!isNullOrEmpty(exprPath)) {
for (DataSetParameters dsp : dataSets) {
dsp.getFiles().setExpressionFileName(exprPath);
}
}
// Overwrite all the gmt files if a common file has been provided
String gmtPath = commonPanel.getGmtFile();
if (!isNullOrEmpty(gmtPath)) {
for (DataSetParameters dsp : dataSets) {
dsp.getFiles().setGMTFileName(gmtPath);
}
}
CreateEnrichmentMapTaskFactory taskFactory = taskFactoryFactory.create(params, dataSets);
TaskIterator tasks = taskFactory.createTaskIterator();
// Close this dialog after the progress dialog finishes normally
tasks.append(new AbstractTask() {
public void run(TaskMonitor taskMonitor) {
callback.close();
}
});
dialogTaskManager.execute(tasks);
}
use of org.baderlab.csplugins.enrichmentmap.model.EnrichmentResultFilterParams.NESFilter in project EnrichmentMapApp by BaderLab.
the class ResolverCommandTask method run.
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
logger.info("Running EnrichmentMap Data Set Resolver Task");
// Scan root folder (note: throws exception if no data sets were found)
ResolverTask resolverTask = new ResolverTask(rootFolder);
// blocks
taskManager.execute(new TaskIterator(resolverTask));
List<DataSetParameters> dataSets = resolverTask.getDataSetResults();
logger.info("resolved " + dataSets.size() + " data sets");
dataSets.forEach(params -> logger.info(params.toString()));
// Overwrite all the expression files if the common file has been provided
if (commonExpressionFile != null) {
if (!commonExpressionFile.canRead()) {
throw new IllegalArgumentException("Cannot read commonExpressionFile: " + commonExpressionFile);
}
for (DataSetParameters dsp : dataSets) {
dsp.getFiles().setExpressionFileName(commonExpressionFile.getAbsolutePath());
}
}
// Overwrite all the gmt files if a common file has been provided
if (commonGMTFile != null) {
if (!commonGMTFile.canRead()) {
throw new IllegalArgumentException("Cannot read commonGMTFile: " + commonGMTFile);
}
for (DataSetParameters dsp : dataSets) {
dsp.getFiles().setGMTFileName(commonGMTFile.getAbsolutePath());
}
}
// Create Enrichment Map
String prefix = legacySupport.getNextAttributePrefix();
SimilarityMetric sm = SimilarityMetric.valueOf(similarityMetric.getSelectedValue());
NESFilter nesf = NESFilter.valueOf(nesFilter.getSelectedValue());
String info = String.format("prefix:%s, pvalue:%f, qvalue:%f, nesFilter:%s, minExperiments:%d, similarityMetric:%s, similarityCutoff:%f, combinedConstant:%f", prefix, pvalue, qvalue, nesf, minExperiments, sm, similarityCutoff, combinedConstant);
logger.info(info);
EMCreationParameters params = new EMCreationParameters(prefix, pvalue, qvalue, nesf, Optional.ofNullable(minExperiments), sm, similarityCutoff, combinedConstant);
params.setCreateDistinctEdges(distinctEdges);
CreateEnrichmentMapTaskFactory taskFactory = taskFactoryFactory.create(params, dataSets);
TaskIterator tasks = taskFactory.createTaskIterator();
taskManager.execute(tasks);
logger.info("Done.");
}
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