@Override
protected Void doInBackground() throws Exception {
// protein identification id
Collection<Comparable> protIdentIds = controller.getIdentificationIds();
// protein identification id and accession buffer
Map<Comparable, String> accBuffer = new LinkedHashMap<Comparable, String>();
// protein map
Map<String, Protein> proteins = new HashMap<String, Protein>();
try {
// iterate over each protein
for (Comparable protIdentId : protIdentIds) {
// get mapped protein accession
String protAcc = controller.getProteinAccession(protIdentId);
String protAccVersion = controller.getProteinAccessionVersion(protIdentId);
String database = controller.getSearchDatabase(protIdentId);
AccessionResolver resolver = new AccessionResolver(protAcc, protAccVersion, database, true);
String mappedProtAcc = resolver.isValidAccession() ? resolver.getAccession() : null;
if (mappedProtAcc != null) {
// get existing protein details
Protein protDetails =
PrideInspectorCacheManager.getInstance().getProteinDetails(mappedProtAcc);
if (protDetails != null) {
proteins.put(mappedProtAcc, protDetails);
}
accBuffer.put(protIdentId, mappedProtAcc);
if (accBuffer.size() == MAX_BATCH_DOWNLOAD_SIZE) {
// fetch and publish protein details
fetchAndPublish(accBuffer, proteins);
// clear accession buffer
accBuffer.clear();
// clear protein map
proteins = new HashMap<String, Protein>();
}
}
}
// this is important for cancelling
if (Thread.interrupted()) {
throw new InterruptedException();
}
if (!accBuffer.isEmpty() || !proteins.isEmpty()) {
fetchAndPublish(accBuffer, proteins);
}
} catch (InterruptedException e) {
logger.warn("Protein name download has been cancelled");
}
return null;
}
public synchronized void removeDataAccessController(DataAccessController controller) {
List<DataAccessController> oldControllers, newControllers;
int index = controllers.indexOf(controller);
if (index >= 0) {
oldControllers = new ArrayList<DataAccessController>(controllers);
// get the next available controller's index
int nextIndex = controllers.size() - 1 > index ? index : index - 1;
controllers.remove(controller);
if (foregroundController != null && foregroundController.equals(controller)) {
setForegroundDataAccessController(nextIndex >= 0 ? controllers.get(nextIndex) : null);
}
controller.close();
newControllers = new ArrayList<DataAccessController>(controllers);
EventBus.publish(
new RemoveDataSourceEvent<DataAccessController>(this, oldControllers, newControllers));
}
}
/**
* Replace one data access controller with another, and retain the position in the
* DataAccessMonitor.
*
* @param original original data access controller
* @param replacement replacement data access controller
*/
public synchronized void replaceDataAccessController(
DataAccessController original, DataAccessController replacement) {
List<DataAccessController> oldControllers, newControllers;
int index = controllers.indexOf(original);
if (index >= 0) {
oldControllers = new ArrayList<DataAccessController>(controllers);
controllers.add(index, replacement);
controllers.remove(original);
if (foregroundController != null && foregroundController.equals(original)) {
setForegroundDataAccessController(replacement);
}
original.close();
newControllers = new ArrayList<DataAccessController>(controllers);
// notify others
EventBus.publish(
new AddDataSourceEvent<DataAccessController>(this, oldControllers, newControllers));
} else {
// add as a new data access controller
addDataAccessController(replacement);
}
}
private void updateComponents() {
try {
this.removeAll();
if (controller != null) {
Collection<Comparable> expIds = controller.getExperimentAccs();
if (expIds == null || expIds.isEmpty()) {
this.add(dataSourceTabPane, BorderLayout.CENTER);
} else {
JSplitPane splitPane =
new JSplitPane(JSplitPane.VERTICAL_SPLIT, dataSourceTabPane, expTreeTabPane);
splitPane.setOneTouchExpandable(false);
splitPane.setDividerSize(0);
splitPane.setResizeWeight(0.3);
this.add(splitPane, BorderLayout.CENTER);
}
}
this.revalidate();
this.repaint();
} catch (DataAccessException e) {
e.printStackTrace(); // To change body of catch statement use File | Settings | File
// Templates.
}
}
/**
* Fetch then publish
*
* @param accs protein accessions
* @param proteins protein map
* @throws Exception exception while fetching the protein
*/
private void fetchAndPublish(Map<Comparable, String> accs, Map<String, Protein> proteins)
throws Exception {
Collection<String> accsToFetch = new HashSet<String>(accs.values());
accsToFetch.removeAll(proteins.keySet());
// fetch protein details
Map<String, Protein> results = fetcher.getProteinDetails(accsToFetch);
// add results to cache
PrideInspectorCacheManager.getInstance().addProteinDetails(results.values());
// add results to protein map
proteins.putAll(results);
// public results
publish(new Tuple<TableContentType, Object>(TableContentType.PROTEIN_DETAILS, proteins));
// protein sequence coverage
Map<Comparable, Double> coverageMap = new HashMap<Comparable, Double>();
// peptide fits
Map<Tuple<Comparable, Comparable>, Integer> peptideFits =
new HashMap<Tuple<Comparable, Comparable>, Integer>();
for (Comparable protIdentId : accs.keySet()) {
// protein sequence coverage
Double coverage =
PrideInspectorCacheManager.getInstance()
.getSequenceCoverage(controller.getUid(), protIdentId);
if (coverage == null) {
String mappedProtAcc = accs.get(protIdentId);
// get protein details
Protein protein = proteins.get(mappedProtAcc);
if (protein != null) {
AnnotatedProtein annotatedProtein = new AnnotatedProtein(protein);
Collection<Comparable> peptideIds = controller.getPeptideIds(protIdentId);
for (Comparable peptideId : peptideIds) {
PeptideAnnotation peptide = new PeptideAnnotation();
peptide.setSequence(controller.getPeptideSequence(protIdentId, peptideId));
peptide.setStart(controller.getPeptideSequenceStart(protIdentId, peptideId));
peptide.setEnd(controller.getPeptideSequenceEnd(protIdentId, peptideId));
annotatedProtein.addAnnotation(peptide);
}
coverage = annotatedProtein.getSequenceCoverage();
coverageMap.put(protIdentId, coverage);
// cache the sequence coverage
PrideInspectorCacheManager.getInstance()
.addSequenceCoverage(controller.getUid(), protIdentId, coverage);
}
} else {
coverageMap.put(protIdentId, coverage);
}
// peptide fits
Collection<Comparable> peptideIdentIds = controller.getPeptideIds(protIdentId);
for (Comparable peptideIdentId : peptideIdentIds) {
Integer state =
PrideInspectorCacheManager.getInstance()
.getPeptideFitState(controller.getUid(), protIdentId, peptideIdentId);
if (state == null) {
String mappedProtAcc = accs.get(protIdentId);
// get protein details
Protein protein = proteins.get(mappedProtAcc);
if (protein != null) {
protein = new AnnotatedProtein(protein);
}
// get peptide sequence
String sequence = controller.getPeptideSequence(protIdentId, peptideIdentId);
// start and end position
int start = controller.getPeptideSequenceStart(protIdentId, peptideIdentId);
int end = controller.getPeptideSequenceEnd(protIdentId, peptideIdentId);
// peptide present
if (protein == null || sequence == null || protein.getSequenceString() == null) {
state = PeptideFitState.UNKNOWN;
} else {
if (protein.hasSubSequenceString(sequence, start, end)) {
state = PeptideFitState.STRICT_FIT;
} else if (protein.hasSubSequenceString(sequence)) {
state = PeptideFitState.FIT;
} else {
state = PeptideFitState.NOT_FIT;
}
}
PrideInspectorCacheManager.getInstance()
.addPeptideFitState(controller.getUid(), protIdentId, peptideIdentId, state);
}
peptideFits.put(new Tuple<Comparable, Comparable>(protIdentId, peptideIdentId), state);
}
}
// publish sequence coverage results
publish(
new Tuple<TableContentType, Object>(
TableContentType.PROTEIN_SEQUENCE_COVERAGE, coverageMap));
// publish peptide fit result
publish(new Tuple<TableContentType, Object>(TableContentType.PEPTIDE_FIT, peptideFits));
}
public synchronized void close() {
// ToDo: Exception handling
for (DataAccessController controller : controllers) {
controller.close();
}
}
/**
* Check whether the given data access controller is foreground data access controller
*
* @param controller data access controller
* @return boolean true if it is foreground data access controller
*/
public synchronized boolean isForegroundDataAccessController(DataAccessController controller) {
return foregroundController != null && foregroundController.equals(controller);
}
