List of usage examples for java.util TreeSet addAll
public boolean addAll(Collection<? extends E> c)
From source file:net.spfbl.data.Generic.java
public static TreeSet<String> getGenericAll() throws ProcessException { TreeSet<String> set = MAP.getGenericAll(); set.addAll(REGEX.getAll()); return set;//from www. j av a 2s . c om }
From source file:com.genentech.application.calcProps.SDFCalcProps.java
private static String calculate(String[] props, boolean predictTautomer, boolean dontFilter, boolean verbose, boolean debug, boolean printOnly, boolean addMolIndex, Set<Calculator> availCALCS, String inFile, String outFile) throws IOException, InterruptedException { String counterTag = "___sdfCalcProps_counter___"; String savedTitleTag = "___sdfCalcProps_saved_title___"; String tempFileRoot = "/tmp/sdfCalcProps.$$." + System.currentTimeMillis(); String tempOrigFileName = tempFileRoot + ".orig.sdf"; String filteredFileName = tempFileRoot + ".filtered.sdf"; Set<Calculator> calculators = new LinkedHashSet<Calculator>(); //Properties that depend on ionization state of the molecule ex. charge Set<Calculator> ionizedCalculators = new LinkedHashSet<Calculator>(); //Properties that depend on the neutral molecule. ex. MW Set<Calculator> neutralCalculators = new LinkedHashSet<Calculator>(); for (String prop : props) { //getCalculators takes care of getting all dependent calculators, recursively Set<Calculator> myCalcs = getCalculators(prop, availCALCS); //adding to a set, does not contain duplicates calculators calculators.addAll(myCalcs);//from w w w. ja v a 2 s . c o m } //divide calculators into those that require ionization and those that don't for (Calculator calc : calculators) { if (calc.requiresIonization()) { ionizedCalculators.add(calc); } else { neutralCalculators.add(calc); } } //get the set of SD tags that will be produced, each property produces a set of SD tags //using TreeSet to keep the SD tags in alphabetical order TreeSet<String> ionizedOutputTags = new TreeSet<String>(); for (Calculator p : ionizedCalculators) { ionizedOutputTags.addAll(getOutputFields(p.getName(), ionizedCalculators, verbose)); } TreeSet<String> neutralOutputTags = new TreeSet<String>(); for (Calculator p : neutralCalculators) { neutralOutputTags.addAll(getOutputFields(p.getName(), neutralCalculators, verbose)); } // The list of SD tags that will be produced // this set should be a union of tags from ionized and neutral tags // I guess I could just merge the treesets from ionized and neutral tags TreeSet<String> allOutputTags = new TreeSet<String>(String.CASE_INSENSITIVE_ORDER); for (String prop : props) { allOutputTags.addAll(getOutputFields(prop, calculators, verbose)); } if (debug) { System.err.println("============================================="); System.err.println("The following properties will be calculated."); printProperties(calculators, true); System.err.println("The following tags will be produced."); for (String t : allOutputTags) { System.err.print(t + " "); } System.err.println(); } //The following tags will be produced, exit after printing if (printOnly) { StringBuilder outputTags = assembleTags(allOutputTags); System.out.println("echo '" + outputTags + "'"); System.exit(0); } // special properties that dictate how molecules are preprocessed Calculator tautomerCalculator = null; Calculator filterCalculator = null; Calculator ionizeCalculator = null; for (Calculator calc : availCALCS) { if (calc.getName().equals("predictTautomer")) { tautomerCalculator = calc; } if (calc.getName().equals("filter")) { filterCalculator = calc; } if (calc.getName().equals("ionize")) { ionizeCalculator = calc; } } // assemble the command line base on the properties that were requested, // this is the most complicated part of this program "assembleCommands" //get a string of piped commands for calculating properties that depend on ionization state ionizedCalculators = consolidateByAggregationId(ionizedCalculators); String ionizedCommand = assembleCommands(ionizedCalculators, verbose, debug, counterTag, ionizedOutputTags); if (ionizedCommand != null) { //prepend command to generated ionized molecules ionizedCommand = ionizeCalculator.getProgName() + " " + ionizeCalculator.getProgOps() + " | " + ionizedCommand; } //get a string of piped commands for calculating properties on the neutral molecule neutralCalculators = consolidateByAggregationId(neutralCalculators); String neutralCommand = assembleCommands(neutralCalculators, verbose, debug, counterTag, allOutputTags); //save a temp file that contains a unique identifier //run filter to get rid of "bad" molecules String command = "sdfTagTool.csh -copy TITLE=" + savedTitleTag + " -addCounter -counterTag " + counterTag + " -title " + counterTag + " -in " + inFile + " -out .sdf | tee " + tempOrigFileName + " | " + filterCalculator.getProgName() + " " + filterCalculator.getProgOps() + " | sdfTagTool.csh -in .sdf -out .sdf -keep " + counterTag; //different command if not filtering if (dontFilter) { command = "sdfTagTool.csh -copy TITLE=" + savedTitleTag + " -addCounter -counterTag " + counterTag + " -title " + counterTag + " -in " + inFile + " -out .sdf | tee " + tempOrigFileName + " | sdfTagTool.csh -in .sdf -out .sdf -keep " + counterTag; } String cleanUpCommand = "sdfTagTool.csh -in .sdf -title " + savedTitleTag + " -out .sdf " + " | sdfTagTool.csh -in .sdf -remove \"" + counterTag + "|" + savedTitleTag + "\" -out " + outFile; //command to create a Mol_Index tag for each molecule if (addMolIndex) { cleanUpCommand = "sdfTagTool.csh -in .sdf -title " + savedTitleTag + " -out .sdf " + " -format 'Mol_Index=Mol_{" + counterTag + "}'" + " | sdfTagTool.csh -in .sdf -remove \"" + counterTag + "|" + savedTitleTag + "\" -out " + outFile; } //predict tautomer if (predictTautomer) { command = command + " | " + tautomerCalculator.getProgName() + " " + tautomerCalculator.getProgOps() + " > " + filteredFileName; } else { command = command + " > " + filteredFileName; } // command = command + "; cat " + filteredFileName; command = command + "; echo NCCO | babel -in .smi -out .sdf >> " + filteredFileName + "; cat " + filteredFileName; if (ionizedCommand != null && neutralCommand != null) { // merge temp file with the two tab files String mergeCommand = "sdfTabMerger.csh -sdf " + tempOrigFileName + " -tab - -mergeTag " + counterTag + " -mergeCol " + counterTag + " -out .sdf | " + cleanUpCommand; command = command + " | " + ionizedCommand + " | sdfTabMerger.csh -tab - -sdf " + filteredFileName + " -mergeTag " + counterTag + " -mergeCol " + counterTag + " -out .sdf | " + neutralCommand + " | " + mergeCommand; } else if (ionizedCommand == null && neutralCommand != null) { String mergeCommand = "sdfTabMerger.csh -sdf " + tempOrigFileName + " -tab - -mergeTag " + counterTag + " -mergeCol " + counterTag + " -out .sdf | " + cleanUpCommand; command = command + " | " + neutralCommand + " | " + mergeCommand; } else if (ionizedCommand != null && neutralCommand == null) { String mergeCommand = "sdfTabMerger.csh -sdf " + tempOrigFileName + " -tab - -mergeTag " + counterTag + " -mergeCol " + counterTag + " -out .sdf | " + cleanUpCommand; command = command + " | " + ionizedCommand + " | " + mergeCommand; } if (debug) { System.err.println("ionized command:\n" + ionizedCommand); System.err.println("neutral command:\n" + neutralCommand); System.err.println("Command to be executed:\n" + command); } return (command); }
From source file:uk.ac.ebi.intact.util.protein.utils.XrefUpdaterUtils.java
public static XrefUpdaterReport updateAllXrefs(Protein protein, UniprotProtein uniprotProtein, Map<String, String> databaseName2mi, DataContext context, ProteinUpdateProcessor processor, TreeSet<InteractorXref> sortedXrefs, TreeSet<UniprotXref> sortedUniprotXrefs) { sortedXrefs.clear();//from w ww . j a v a 2 s. co m sortedXrefs.addAll(protein.getXrefs()); Iterator<InteractorXref> intactIterator = sortedXrefs.iterator(); sortedUniprotXrefs.clear(); sortedUniprotXrefs.addAll(uniprotProtein.getCrossReferences()); Iterator<UniprotXref> uniprotIterator = sortedUniprotXrefs.iterator(); List<Xref> createdXrefs = new ArrayList<Xref>(uniprotProtein.getCrossReferences().size()); List<Xref> deletedXrefs = new ArrayList<Xref>(protein.getXrefs().size()); DaoFactory daoFactory = context.getDaoFactory(); CvObjectDao<CvDatabase> dbDao = daoFactory.getCvObjectDao(CvDatabase.class); XrefDao<InteractorXref> refDao = daoFactory.getXrefDao(InteractorXref.class); InteractorXref currentIntact = null; UniprotXref currentUniprot = null; String db = null; CvDatabase cvDatabase = null; if (intactIterator.hasNext() && uniprotIterator.hasNext()) { currentIntact = intactIterator.next(); currentUniprot = uniprotIterator.next(); db = databaseName2mi.get(currentUniprot.getDatabase().toLowerCase()); cvDatabase = currentIntact.getCvDatabase(); if (db != null && cvDatabase != null) { do { int dbComparator = cvDatabase.getIdentifier().compareTo(db); if (dbComparator == 0) { int acComparator = currentIntact.getPrimaryId().compareTo(currentUniprot.getAccession()); if (acComparator == 0) { if (intactIterator.hasNext() && uniprotIterator.hasNext()) { currentIntact = intactIterator.next(); currentUniprot = uniprotIterator.next(); db = databaseName2mi.get(currentUniprot.getDatabase().toLowerCase()); cvDatabase = currentIntact.getCvDatabase(); } else { currentIntact = null; currentUniprot = null; db = null; cvDatabase = null; } } else if (acComparator < 0) { //intact has no match in uniprot if (!CvDatabase.UNIPROT_MI_REF.equalsIgnoreCase(cvDatabase.getIdentifier()) && !CvDatabase.INTACT_MI_REF .equalsIgnoreCase(currentIntact.getCvDatabase().getIdentifier()) && !(currentIntact.getCvXrefQualifier() != null && ("intact-secondary" .equalsIgnoreCase(currentIntact.getCvXrefQualifier().getShortLabel()) || CvXrefQualifier.SECONDARY_AC.equalsIgnoreCase( currentIntact.getCvXrefQualifier().getShortLabel())))) { deletedXrefs.add(currentIntact); protein.removeXref(currentIntact); refDao.delete(currentIntact); } if (intactIterator.hasNext()) { currentIntact = intactIterator.next(); cvDatabase = currentIntact.getCvDatabase(); } else { currentIntact = null; cvDatabase = null; } } else { //uniprot has no match in intact CvDatabase cvDb = cvDatabase; InteractorXref newXref = new InteractorXref( IntactContext.getCurrentInstance().getInstitution(), cvDb, currentUniprot.getAccession(), null); protein.addXref(newXref); refDao.persist(newXref); createdXrefs.add(newXref); if (uniprotIterator.hasNext()) { currentUniprot = uniprotIterator.next(); db = databaseName2mi.get(currentUniprot.getDatabase().toLowerCase()); } else { currentUniprot = null; db = null; } } } else if (dbComparator < 0) { //intact has no match in uniprot if (!CvDatabase.UNIPROT_MI_REF .equalsIgnoreCase(currentIntact.getCvDatabase().getIdentifier()) && !CvDatabase.INTACT_MI_REF .equalsIgnoreCase(currentIntact.getCvDatabase().getIdentifier()) && !(currentIntact.getCvXrefQualifier() != null && ("intact-secondary" .equalsIgnoreCase(currentIntact.getCvXrefQualifier().getShortLabel()) || CvXrefQualifier.SECONDARY_AC.equalsIgnoreCase( currentIntact.getCvXrefQualifier().getShortLabel())))) { deletedXrefs.add(currentIntact); protein.removeXref(currentIntact); refDao.delete(currentIntact); } if (intactIterator.hasNext()) { currentIntact = intactIterator.next(); cvDatabase = currentIntact.getCvDatabase(); } else { currentIntact = null; cvDatabase = null; } } else { //uniprot has no match in intact CvDatabase cvDb = dbDao.getByIdentifier(db); if (cvDb != null) { InteractorXref newXref = new InteractorXref( IntactContext.getCurrentInstance().getInstitution(), cvDb, currentUniprot.getAccession(), null); protein.addXref(newXref); refDao.persist(newXref); createdXrefs.add(newXref); } else { log.debug("We are not copying across xref to " + db); } if (uniprotIterator.hasNext()) { currentUniprot = uniprotIterator.next(); db = databaseName2mi.get(currentUniprot.getDatabase().toLowerCase()); } else { currentUniprot = null; db = null; } } } while (currentIntact != null && currentUniprot != null && db != null && cvDatabase != null); } } if (currentIntact != null || intactIterator.hasNext()) { if (currentIntact == null) { currentIntact = intactIterator.next(); cvDatabase = currentIntact.getCvDatabase(); } do { //intact has no match in uniprot if (cvDatabase == null || (cvDatabase != null && !CvDatabase.UNIPROT_MI_REF.equalsIgnoreCase(cvDatabase.getIdentifier()) && !CvDatabase.INTACT_MI_REF.equalsIgnoreCase(cvDatabase.getIdentifier()) && !(currentIntact.getCvXrefQualifier() != null && ("intact-secondary" .equalsIgnoreCase(currentIntact.getCvXrefQualifier().getShortLabel()) || CvXrefQualifier.SECONDARY_AC .equalsIgnoreCase(currentIntact.getCvXrefQualifier().getShortLabel()))))) { deletedXrefs.add(currentIntact); protein.removeXref(currentIntact); refDao.delete(currentIntact); } if (intactIterator.hasNext()) { currentIntact = intactIterator.next(); cvDatabase = currentIntact.getCvDatabase(); } else { currentIntact = null; cvDatabase = null; } } while (currentIntact != null); } if (currentUniprot != null || uniprotIterator.hasNext()) { if (currentUniprot == null) { currentUniprot = uniprotIterator.next(); db = databaseName2mi.get(currentUniprot.getDatabase().toLowerCase()); } if (db != null) { do { //uniprot has no match in intact CvDatabase cvDb = dbDao.getByIdentifier(db); if (cvDb != null) { InteractorXref newXref = new InteractorXref( IntactContext.getCurrentInstance().getInstitution(), cvDb, currentUniprot.getAccession(), null); protein.addXref(newXref); refDao.persist(newXref); createdXrefs.add(newXref); } else { log.debug("We are not copying across xref to " + db); } if (uniprotIterator.hasNext()) { currentUniprot = uniprotIterator.next(); db = databaseName2mi.get(currentUniprot.getDatabase().toLowerCase()); } else { currentUniprot = null; db = null; } } while (currentUniprot != null && db != null); } } // update uniprot xrefs XrefUpdaterReport report = updateUniprotXrefs(protein, uniprotProtein, context, processor); if (report == null && (!createdXrefs.isEmpty() || !deletedXrefs.isEmpty())) { report = new XrefUpdaterReport(protein, createdXrefs, deletedXrefs); } else if (report != null && (!createdXrefs.isEmpty() || !deletedXrefs.isEmpty())) { report.getAddedXrefs().addAll(createdXrefs); report.getRemovedXrefs().addAll(deletedXrefs); } sortedXrefs.clear(); sortedUniprotXrefs.clear(); return report; }
From source file:org.apache.ambari.eventdb.webservice.WorkflowJsonService.java
private static Set<Long> getXPoints(List<TaskAttempt> taskAttempts, long submitTimeX, long finishTimeX) { TreeSet<Long> xPoints = new TreeSet<Long>(); TreeSet<TaskAttempt> sortedAttempts = new TreeSet<TaskAttempt>(new Comparator<TaskAttempt>() { @Override/*from ww w .j a v a 2s .c om*/ public int compare(TaskAttempt t1, TaskAttempt t2) { if (t1.getStartTime() < t2.getStartTime()) return -1; else if (t1.getStartTime() > t2.getStartTime()) return 1; return t1.getTaskAttemptId().compareTo(t2.getTaskAttemptId()); } }); sortedAttempts.addAll(taskAttempts); getXPoints(sortedAttempts, xPoints); xPoints.add(submitTimeX); xPoints.add(finishTimeX); return xPoints; }
From source file:net.spfbl.whois.SubnetIPv4.java
protected static synchronized TreeSet<Subnet> getSubnetSet() { TreeSet<Subnet> subnetSet = new TreeSet<Subnet>(); subnetSet.addAll(MAP.values()); return subnetSet; }
From source file:net.spfbl.core.Client.java
public synchronized static TreeSet<Client> getSet() { TreeSet<Client> clientSet = new TreeSet<Client>(); clientSet.addAll(MAP.values()); return clientSet; }
From source file:net.spfbl.dns.QueryDNS.java
public static synchronized TreeSet<Zone> getValues() { TreeSet<Zone> serverSet = new TreeSet<Zone>(); serverSet.addAll(MAP.values()); return serverSet; }
From source file:jetbrains.exodus.env.Reflect.java
private static void dumpCounts(@NotNull final String message, @NotNull final IntHashMap<Integer> counts) { System.out.println();//from ww w . ja va 2 s.c o m System.out.println(message); final TreeSet<Integer> sortedKeys = new TreeSet<>(new Comparator<Integer>() { @Override public int compare(Integer o1, Integer o2) { final Integer count1 = counts.get(o1); final Integer count2 = counts.get(o2); if (count1 < count2) { return 1; } if (count2 < count1) { return -1; } return 0; } }); sortedKeys.addAll(counts.keySet()); for (final Integer key : sortedKeys) { System.out.print(key + ":" + counts.get(key) + ' '); } System.out.println(); }
From source file:org.marketcetera.util.ws.types.TypeTest.java
private static <V> TreeSet<V> toTreeSet(List<V> in, Comparator<? super V> comparator) { TreeSet<V> out; if (comparator == null) { out = new TreeSet<V>(); } else {//ww w. java2s .c o m out = new TreeSet<V>(comparator); } out.addAll(in); return out; }
From source file:com.ery.hadoop.mrddx.client.MRJOBClient.java
/** * ?//from w w w . j a v a 2 s . c o m * * @param paraMap ?? */ private void printParameter(Map<String, String> paraMap) { MRLog.systemOut("??:"); TreeSet<String> ts = new TreeSet<String>(); ts.addAll(paraMap.keySet()); Iterator<String> i = ts.iterator(); while (i.hasNext()) { String key = i.next(); System.out.println(key + ":" + paraMap.get(key)); } }