// public PeptideCollection getCutoffCollection(double omssa, double mascot, double xtandem) {
// return getCutoffCollection(omssa, mascot, xtandem, false);
// }
public PeptideCollection getCutoffCollection(FilterSettings fs) {
PeptideCollection pc = new PeptideCollection();
for (PeptideHit p : peptideHits) {
if (fs.getUsePepProphet() && p.isPepXML()) {
if (p.getPepProphet() >= fs.getPeptideProphetCutoff()) {
pc.addPeptideHit(p);
}
} else {
switch (p.getSourceType()) {
case MASCOT:
if (fs.getUseIonIdent()) {
if (p.getIonScore() >= p.getIdent()) {
pc.addPeptideHit(p);
}
} else if (p.getExpect() <= fs.getMascotCutoff()) {
pc.addPeptideHit(p);
}
break;
case OMSSA:
if (p.getExpect() <= fs.getOmssaCutoff()) {
pc.addPeptideHit(p);
}
break;
case XTANDEM:
if (p.getExpect() <= fs.getXtandemCutoff()) {
pc.addPeptideHit(p);
}
break;
case SEQUEST:
if (p.getExpect() <= fs.getSequestCutoff()) {
pc.addPeptideHit(p);
}
break;
case PEPXML:
if (!p.CanGetPepProphet() || (p.getPepProphet() >= fs.getPeptideProphetCutoff())) {
pc.addPeptideHit(p);
}
break;
}
}
}
return pc;
}
@Deprecated
// since its questionable whether this
// is important enough to live in WordprocessingMLPackage,
// and in any case probably should be replaced with a TraversalUtil
// approach (which wouldn't involve marshal/unmarshall, and
// so should be more efficient).
public void filter(FilterSettings filterSettings) throws Exception {
if (filterTemplate == null) { // first use
Source xsltSource =
new StreamSource(
org.docx4j.utils.ResourceUtils.getResource(
"org/docx4j/openpackaging/packages/filter.xslt"));
filterTemplate = XmlUtils.getTransformerTemplate(xsltSource);
}
transform(filterTemplate, filterSettings.getSettings());
}
@Override
public void accept(AisPacket packet) {
if (out == null) {
// Open new output stream
out = getNextOutputStram();
}
end = System.currentTimeMillis();
if (start == 0) {
start = end;
}
for (IPacketFilter filter : filters) {
if (filter.rejectedByFilter(packet)) {
return;
}
}
Integer baseMMSI = -1;
String country = "";
String region = "";
Vdm vdm = packet.getVdm();
if (vdm == null) {
return;
}
// Get source tag properties
IProprietarySourceTag sourceTag = vdm.getSourceTag();
if (sourceTag != null) {
baseMMSI = sourceTag.getBaseMmsi();
if (sourceTag.getCountry() != null) {
country = sourceTag.getCountry().getTwoLetter();
}
if (sourceTag.getRegion() != null) {
region = sourceTag.getRegion();
}
}
if (region.equals("")) {
region = "0";
}
// Maybe check for start date
Date timestamp = vdm.getTimestamp();
if (filter.getStartDate() != null && timestamp != null) {
if (timestamp.before(filter.getStartDate())) {
return;
}
}
// Maybe check for end date
if (filter.getEndDate() != null && timestamp != null) {
if (timestamp.after(filter.getEndDate())) {
System.exit(0);
}
}
// Maybe check for base station MMSI
if (filter.getBaseStations().size() > 0) {
if (!filter.getBaseStations().contains(baseMMSI)) {
return;
}
}
// Maybe check for country
if (filter.getCountries().size() > 0) {
if (!filter.getCountries().contains(country)) {
return;
}
}
// Maybe check for region
if (filter.getRegions().size() > 0) {
if (!filter.getRegions().contains(region)) {
return;
}
}
if (stop) {
return;
}
// Count message
msgCount++;
// Print tag line packet
out.print(packet.getStringMessage() + "\r\n");
// Count bytes
bytes += packet.getStringMessage().length() + 2;
currentFileBytes += packet.getStringMessage().length() + 2;
// Maybe print parsed
if (dumpParsed) {
if (timestamp != null) {
out.println("+ timetamp " + timestampFormat.format(timestamp));
}
if (vdm.getTags() != null) {
for (IProprietaryTag tag : vdm.getTags()) {
out.println("+ " + tag.toString());
}
}
AisMessage aisMessage = packet.tryGetAisMessage();
if (aisMessage != null) {
out.println("+ " + aisMessage.toString());
} else {
out.println("+ AIS message could not be parsed");
}
// Check for binary message
if (aisMessage instanceof AisBinaryMessage) {
AisBinaryMessage binaryMessage = (AisBinaryMessage) aisMessage;
try {
AisApplicationMessage appMessage = binaryMessage.getApplicationMessage();
out.println(appMessage);
} catch (SixbitException e) {
}
}
out.println("---------------------------");
}
// Maybe time for new outfile
if (splitSize != null && currentFileBytes >= splitSize) {
out.close();
out = null;
currentFileBytes = 0;
}
}
@Override
protected void run(Injector injector) throws Exception {
if (filename == null && hostPort == null && (dir == null || name == null)) {
usage();
System.exit(-1);
}
// Create reader
AisReader aisReader;
if (filename != null) {
aisReader = AisReaders.createReaderFromFile(filename);
} else if (hostPort != null) {
AisTcpReader rrAisReader = AisReaders.createReader(hostPort);
rrAisReader.setTimeout(timeout);
aisReader = rrAisReader;
} else {
aisReader = AisReaders.createDirectoryReader(dir, name, recursive);
}
runtime *= 1000;
// Add times
filter.parseStartAndEnd(starttimeStr, endtimeStr);
// Add base stations
filter.parseBaseStations(baseStations);
// Add countries
filter.parseCountries(countries);
// Add regions
filter.parseRegions(regions);
// Output stream
if (outFile == null) {
out = System.out;
}
// Message handler
// Add filters
// Maybe insert downsampling filter
if (downsampleRate > 0) {
filters.add(new ReplayDownSampleFilter(downsampleRate));
}
if (doubletFiltering) {
filters.add(new ReplayDuplicateFilter());
}
if (expression != null) {
filters.add(new ExpressionFilter(expression));
}
if (geometry != null) {
LocationFilter locationFilter = new LocationFilter();
Area a = getGeometry(geometry);
locationFilter.addFilterGeometry(e -> a.contains(e));
filters.add(locationFilter);
}
// Register handler
aisReader.registerPacketHandler(this);
// Start reader thread
long start = System.currentTimeMillis();
aisReader.start();
while (true) {
Thread.sleep(500);
if (aisReader.getStatus() == Status.DISCONNECTED) {
break;
}
if (runtime > 0 && System.currentTimeMillis() - start > runtime) {
stop = true;
aisReader.stopReader();
break;
}
}
}
